diff --git a/.clang-format b/.clang-format
index b684a9d53eb8568ec9dd9656cbeb954219932d55..455bf99fe1ea498f7868b65c0949ca1b9135754d 100644
--- a/.clang-format
+++ b/.clang-format
@@ -1,5 +1,7 @@
Language: Cpp
BasedOnStyle: LLVM
BreakBeforeBraces: Allman
-IndentCaseLabels: true
ConstructorInitializerIndentWidth: 0
+IndentWidth: 4
+ContinuationIndentWidth: 4
+AccessModifierOffset: -4
diff --git a/bindings/python/include/ADIOSPy.h b/bindings/python/include/ADIOSPy.h
index 925e7f24455ae4ef605447ed5d551c1778f7c104..f6d6ebb742ce1144a2c93dbf1f2db41ee504392b 100644
--- a/bindings/python/include/ADIOSPy.h
+++ b/bindings/python/include/ADIOSPy.h
@@ -48,25 +48,25 @@ class ADIOSPy : public ADIOS
{
public:
- ADIOSPy(MPI_Comm mpiComm, const bool debug);
- ~ADIOSPy();
+ ADIOSPy(MPI_Comm mpiComm, const bool debug);
+ ~ADIOSPy();
- void HelloMPI(); ///< says hello from rank/size for testing
+ void HelloMPI(); ///< says hello from rank/size for testing
- VariablePy DefineVariablePy(const std::string name,
- const pyList localDimensionsPy = pyList(),
- const pyList globalDimensionsPy = pyList(),
- const pyList globalOffsetsPy = pyList());
+ VariablePy DefineVariablePy(const std::string name,
+ const pyList localDimensionsPy = pyList(),
+ const pyList globalDimensionsPy = pyList(),
+ const pyList globalOffsetsPy = pyList());
- MethodPy &DeclareMethodPy(const std::string methodName);
+ MethodPy &DeclareMethodPy(const std::string methodName);
- EnginePy OpenPy(const std::string name, const std::string accessMode,
- const MethodPy &method, pyObject py_comm = pyObject());
+ EnginePy OpenPy(const std::string name, const std::string accessMode,
+ const MethodPy &method, pyObject py_comm = pyObject());
- void DefineVariableType(VariablePy &variablePy);
+ void DefineVariableType(VariablePy &variablePy);
private:
- std::set<std::string> m_VariablesPyNames;
+ std::set<std::string> m_VariablesPyNames;
};
} // end namespace
diff --git a/bindings/python/include/EnginePy.h b/bindings/python/include/EnginePy.h
index 8e4be5c15e44f4f4a2a100eb2f72042cb7b02dc4..437247f5be634fff88d27a9ffda705ed1a95bafe 100644
--- a/bindings/python/include/EnginePy.h
+++ b/bindings/python/include/EnginePy.h
@@ -42,39 +42,40 @@ class EnginePy
{
public:
- EnginePy(ADIOSPy &adiosPy);
+ EnginePy(ADIOSPy &adiosPy);
- ~EnginePy();
+ ~EnginePy();
- std::shared_ptr<Engine> m_Engine;
+ std::shared_ptr<Engine> m_Engine;
- void WritePy(VariablePy &variable, const pyArray &array);
+ void WritePy(VariablePy &variable, const pyArray &array);
- void Advance();
+ void Advance();
- void Close();
+ void Close();
- void GetEngineType() const;
+ void GetEngineType() const;
private:
- ADIOSPy &m_ADIOSPy;
- bool m_IsVariableTypeDefined = false;
-
- template <class T> void DefineVariableInADIOS(VariablePy &variable)
- {
- auto &var = m_ADIOSPy.DefineVariable<T>(
- variable.m_Name, variable.m_LocalDimensions,
- variable.m_GlobalDimensions, variable.m_GlobalOffsets);
- variable.m_VariablePtr = &var;
- variable.m_IsVariableDefined = true;
- }
-
- template <class T>
- void WriteVariableInADIOS(VariablePy &variable, const pyArray &array)
- {
- m_Engine->Write(*reinterpret_cast<Variable<T> *>(variable.m_VariablePtr),
- PyArrayToPointer<T>(array));
- }
+ ADIOSPy &m_ADIOSPy;
+ bool m_IsVariableTypeDefined = false;
+
+ template <class T> void DefineVariableInADIOS(VariablePy &variable)
+ {
+ auto &var = m_ADIOSPy.DefineVariable<T>(
+ variable.m_Name, variable.m_LocalDimensions,
+ variable.m_GlobalDimensions, variable.m_GlobalOffsets);
+ variable.m_VariablePtr = &var;
+ variable.m_IsVariableDefined = true;
+ }
+
+ template <class T>
+ void WriteVariableInADIOS(VariablePy &variable, const pyArray &array)
+ {
+ m_Engine->Write(
+ *reinterpret_cast<Variable<T> *>(variable.m_VariablePtr),
+ PyArrayToPointer<T>(array));
+ }
};
} // end namespace
diff --git a/bindings/python/include/MethodPy.h b/bindings/python/include/MethodPy.h
index 3ab8b003196b9443e0338ede51a25b34d4ddb3ed..5bdb9a3aa082aeccd2c5d254e0036e36e981066d 100644
--- a/bindings/python/include/MethodPy.h
+++ b/bindings/python/include/MethodPy.h
@@ -41,21 +41,21 @@ class MethodPy : public Method
{
public:
- MethodPy(const std::string type, const bool debugMode);
+ MethodPy(const std::string type, const bool debugMode);
- ~MethodPy();
+ ~MethodPy();
#ifdef HAVE_BOOSTPYTHON
- static pyObject SetParametersPy(pyTuple args, pyDict kwargs);
- static pyObject AddTransportPy(pyTuple args, pyDict kwargs);
+ static pyObject SetParametersPy(pyTuple args, pyDict kwargs);
+ static pyObject AddTransportPy(pyTuple args, pyDict kwargs);
#endif
#ifdef HAVE_PYBIND11
- void SetParametersPyBind11(pybind11::kwargs kwargs);
- void AddTransportPyBind11(const std::string type, pybind11::kwargs kwargs);
+ void SetParametersPyBind11(pybind11::kwargs kwargs);
+ void AddTransportPyBind11(const std::string type, pybind11::kwargs kwargs);
#endif
- void PrintAll() const;
+ void PrintAll() const;
};
}
diff --git a/bindings/python/include/VariablePy.h b/bindings/python/include/VariablePy.h
index 8d843bae20b5a0a2a4c36f230ebe38a809a8659b..91b71be593dac143c5505111ac525aa4e2f5cc69 100644
--- a/bindings/python/include/VariablePy.h
+++ b/bindings/python/include/VariablePy.h
@@ -29,25 +29,25 @@ class VariablePy
{
public:
- VariablePy(const std::string name, const pyList localDimensionsPy,
- const pyList globalDimensionsPy, const pyList globalOffsetsPy);
+ VariablePy(const std::string name, const pyList localDimensionsPy,
+ const pyList globalDimensionsPy, const pyList globalOffsetsPy);
- ~VariablePy();
+ ~VariablePy();
- void SetLocalDimensions(const pyList list);
+ void SetLocalDimensions(const pyList list);
- void SetGlobalDimensionsAndOffsets(const pyList globalDimensions,
- const pyList globalOffsets);
+ void SetGlobalDimensionsAndOffsets(const pyList globalDimensions,
+ const pyList globalOffsets);
- Dims GetLocalDimensions();
+ Dims GetLocalDimensions();
- void *m_VariablePtr = nullptr;
- bool m_IsVariableDefined = false;
+ void *m_VariablePtr = nullptr;
+ bool m_IsVariableDefined = false;
- const std::string m_Name;
- Dims m_LocalDimensions;
- Dims m_GlobalDimensions;
- Dims m_GlobalOffsets;
+ const std::string m_Name;
+ Dims m_LocalDimensions;
+ Dims m_GlobalDimensions;
+ Dims m_GlobalOffsets;
};
} // end namespace
diff --git a/bindings/python/include/adiosPyFunctions.h b/bindings/python/include/adiosPyFunctions.h
index e64a798b4a6513679b195437c053dc6cf4da3689..8ef0ff9f66c7e1c15f48fcfb627d87b3ee300f5b 100644
--- a/bindings/python/include/adiosPyFunctions.h
+++ b/bindings/python/include/adiosPyFunctions.h
@@ -67,37 +67,37 @@ KwargsToMap(const pybind11::kwargs &dictionary);
template <class T> const T *PyArrayToPointer(const pyArray &array)
{
#ifdef HAVE_BOOSTPYTHON
- return reinterpret_cast<const T *>(array.get_data());
+ return reinterpret_cast<const T *>(array.get_data());
#endif
#ifdef HAVE_PYBIND11
- return reinterpret_cast<const T *>(array.data());
+ return reinterpret_cast<const T *>(array.data());
#endif
}
template <class T> bool IsType(const pyArray &array)
{
#ifdef HAVE_BOOSTPYTHON
- if (array.get_dtype() == dtype::get_builtin<T>())
- return true;
+ if (array.get_dtype() == dtype::get_builtin<T>())
+ return true;
#endif
#ifdef HAVE_PYBIND11
- if (pybind11::isinstance<pybind11::array_t<T>>(array))
- return true;
+ if (pybind11::isinstance<pybind11::array_t<T>>(array))
+ return true;
#endif
- return false;
+ return false;
}
template <class T, class U> T PyCast(U object)
{
#ifdef HAVE_BOOSTPYTHON
- return boost::python::extract<T>(object);
+ return boost::python::extract<T>(object);
#endif
#ifdef HAVE_PYBIND11
- return pybind11::cast<T>(object);
+ return pybind11::cast<T>(object);
#endif
}
diff --git a/bindings/python/src/ADIOSPy.cpp b/bindings/python/src/ADIOSPy.cpp
index e8dd0e0a0f22df439ab850348156566717272649..6e45ce3970e59404c5b979b20418cd2f71e50141 100644
--- a/bindings/python/src/ADIOSPy.cpp
+++ b/bindings/python/src/ADIOSPy.cpp
@@ -27,14 +27,14 @@ ADIOSPy::~ADIOSPy() {}
void ADIOSPy::HelloMPI()
{
- std::cout << "Hello ADIOSPy from rank " << m_RankMPI << "/" << m_SizeMPI
- << "\n";
+ std::cout << "Hello ADIOSPy from rank " << m_RankMPI << "/" << m_SizeMPI
+ << "\n";
}
MethodPy &ADIOSPy::DeclareMethodPy(const std::string methodName)
{
- Method &method = DeclareMethod(methodName);
- return *reinterpret_cast<MethodPy *>(&method);
+ Method &method = DeclareMethod(methodName);
+ return *reinterpret_cast<MethodPy *>(&method);
}
VariablePy ADIOSPy::DefineVariablePy(const std::string name,
@@ -42,16 +42,16 @@ VariablePy ADIOSPy::DefineVariablePy(const std::string name,
const pyList globalDimensionsPy,
const pyList globalOffsetsPy)
{
- if (m_DebugMode == true)
- {
- if (m_VariablesPyNames.count(name) == 1)
- throw std::invalid_argument("ERROR: Variable " + name +
- " is already defined\n");
- }
-
- m_VariablesPyNames.insert(name);
- return VariablePy(name, localDimensionsPy, globalDimensionsPy,
- globalOffsetsPy);
+ if (m_DebugMode == true)
+ {
+ if (m_VariablesPyNames.count(name) == 1)
+ throw std::invalid_argument("ERROR: Variable " + name +
+ " is already defined\n");
+ }
+
+ m_VariablesPyNames.insert(name);
+ return VariablePy(name, localDimensionsPy, globalDimensionsPy,
+ globalOffsetsPy);
}
void ADIOSPy::DefineVariableType(VariablePy &variablePy) {}
@@ -59,28 +59,29 @@ void ADIOSPy::DefineVariableType(VariablePy &variablePy) {}
EnginePy ADIOSPy::OpenPy(const std::string name, const std::string accessMode,
const MethodPy &method, pyObject py_comm)
{
- EnginePy enginePy(*this);
-
- bool isEmpty = IsEmpty(py_comm);
-
- if (isEmpty == true) // None
- {
- enginePy.m_Engine = Open(name, accessMode, method);
- }
- else
- {
- if (import_mpi4py() < 0)
- throw std::logic_error(
- "ERROR: could not import mpi4py communicator in Open " + name + "\n");
- MPI_Comm *comm_p = PyMPIComm_Get(py_comm.ptr());
- if (comm_p == nullptr)
- throw std::invalid_argument(
- "ERROR: MPI communicator is nullptr in Open " + name + "\n");
-
- enginePy.m_Engine = Open(name, accessMode, *comm_p, method);
- }
-
- return enginePy;
+ EnginePy enginePy(*this);
+
+ bool isEmpty = IsEmpty(py_comm);
+
+ if (isEmpty == true) // None
+ {
+ enginePy.m_Engine = Open(name, accessMode, method);
+ }
+ else
+ {
+ if (import_mpi4py() < 0)
+ throw std::logic_error(
+ "ERROR: could not import mpi4py communicator in Open " + name +
+ "\n");
+ MPI_Comm *comm_p = PyMPIComm_Get(py_comm.ptr());
+ if (comm_p == nullptr)
+ throw std::invalid_argument(
+ "ERROR: MPI communicator is nullptr in Open " + name + "\n");
+
+ enginePy.m_Engine = Open(name, accessMode, *comm_p, method);
+ }
+
+ return enginePy;
}
} // end namespace
diff --git a/bindings/python/src/EnginePy.cpp b/bindings/python/src/EnginePy.cpp
index 581d0580d98c74700c908a30491d5f41b3272287..20826731f42d8916a8be02d01eadd123df6005dd 100644
--- a/bindings/python/src/EnginePy.cpp
+++ b/bindings/python/src/EnginePy.cpp
@@ -24,74 +24,74 @@ EnginePy::~EnginePy() {}
void EnginePy::WritePy(VariablePy &variable, const pyArray &array)
{
- if (variable.m_IsVariableDefined == false) // here define variable
- {
+ if (variable.m_IsVariableDefined == false) // here define variable
+ {
+ if (IsType<char>(array))
+ DefineVariableInADIOS<char>(variable);
+ else if (IsType<unsigned char>(array))
+ DefineVariableInADIOS<unsigned char>(variable);
+ else if (IsType<short>(array))
+ DefineVariableInADIOS<short>(variable);
+ else if (IsType<unsigned short>(array))
+ DefineVariableInADIOS<unsigned short>(variable);
+ else if (IsType<int>(array))
+ DefineVariableInADIOS<int>(variable);
+ else if (IsType<unsigned int>(array))
+ DefineVariableInADIOS<unsigned int>(variable);
+ else if (IsType<long int>(array))
+ DefineVariableInADIOS<long int>(variable);
+ else if (IsType<unsigned long int>(array))
+ DefineVariableInADIOS<unsigned long int>(variable);
+ else if (IsType<long long int>(array))
+ DefineVariableInADIOS<long long int>(variable);
+ else if (IsType<unsigned long long int>(array))
+ DefineVariableInADIOS<unsigned long long int>(variable);
+ else if (IsType<float>(array))
+ DefineVariableInADIOS<float>(variable);
+ else if (IsType<double>(array))
+ DefineVariableInADIOS<double>(variable);
+ else if (IsType<long double>(array))
+ DefineVariableInADIOS<long double>(variable);
+ else if (IsType<std::complex<float>>(array))
+ DefineVariableInADIOS<std::complex<float>>(variable);
+ else if (IsType<std::complex<double>>(array))
+ DefineVariableInADIOS<std::complex<double>>(variable);
+ else if (IsType<std::complex<long double>>(array))
+ DefineVariableInADIOS<std::complex<long double>>(variable);
+ }
+
if (IsType<char>(array))
- DefineVariableInADIOS<char>(variable);
+ WriteVariableInADIOS<char>(variable, array);
else if (IsType<unsigned char>(array))
- DefineVariableInADIOS<unsigned char>(variable);
+ WriteVariableInADIOS<unsigned char>(variable, array);
else if (IsType<short>(array))
- DefineVariableInADIOS<short>(variable);
+ WriteVariableInADIOS<short>(variable, array);
else if (IsType<unsigned short>(array))
- DefineVariableInADIOS<unsigned short>(variable);
+ WriteVariableInADIOS<unsigned short>(variable, array);
else if (IsType<int>(array))
- DefineVariableInADIOS<int>(variable);
+ WriteVariableInADIOS<int>(variable, array);
else if (IsType<unsigned int>(array))
- DefineVariableInADIOS<unsigned int>(variable);
+ WriteVariableInADIOS<unsigned int>(variable, array);
else if (IsType<long int>(array))
- DefineVariableInADIOS<long int>(variable);
+ WriteVariableInADIOS<long int>(variable, array);
else if (IsType<unsigned long int>(array))
- DefineVariableInADIOS<unsigned long int>(variable);
+ WriteVariableInADIOS<unsigned long int>(variable, array);
else if (IsType<long long int>(array))
- DefineVariableInADIOS<long long int>(variable);
+ WriteVariableInADIOS<long long int>(variable, array);
else if (IsType<unsigned long long int>(array))
- DefineVariableInADIOS<unsigned long long int>(variable);
+ WriteVariableInADIOS<unsigned long long int>(variable, array);
else if (IsType<float>(array))
- DefineVariableInADIOS<float>(variable);
+ WriteVariableInADIOS<float>(variable, array);
else if (IsType<double>(array))
- DefineVariableInADIOS<double>(variable);
+ WriteVariableInADIOS<double>(variable, array);
else if (IsType<long double>(array))
- DefineVariableInADIOS<long double>(variable);
+ WriteVariableInADIOS<long double>(variable, array);
else if (IsType<std::complex<float>>(array))
- DefineVariableInADIOS<std::complex<float>>(variable);
+ WriteVariableInADIOS<std::complex<float>>(variable, array);
else if (IsType<std::complex<double>>(array))
- DefineVariableInADIOS<std::complex<double>>(variable);
+ WriteVariableInADIOS<std::complex<double>>(variable, array);
else if (IsType<std::complex<long double>>(array))
- DefineVariableInADIOS<std::complex<long double>>(variable);
- }
-
- if (IsType<char>(array))
- WriteVariableInADIOS<char>(variable, array);
- else if (IsType<unsigned char>(array))
- WriteVariableInADIOS<unsigned char>(variable, array);
- else if (IsType<short>(array))
- WriteVariableInADIOS<short>(variable, array);
- else if (IsType<unsigned short>(array))
- WriteVariableInADIOS<unsigned short>(variable, array);
- else if (IsType<int>(array))
- WriteVariableInADIOS<int>(variable, array);
- else if (IsType<unsigned int>(array))
- WriteVariableInADIOS<unsigned int>(variable, array);
- else if (IsType<long int>(array))
- WriteVariableInADIOS<long int>(variable, array);
- else if (IsType<unsigned long int>(array))
- WriteVariableInADIOS<unsigned long int>(variable, array);
- else if (IsType<long long int>(array))
- WriteVariableInADIOS<long long int>(variable, array);
- else if (IsType<unsigned long long int>(array))
- WriteVariableInADIOS<unsigned long long int>(variable, array);
- else if (IsType<float>(array))
- WriteVariableInADIOS<float>(variable, array);
- else if (IsType<double>(array))
- WriteVariableInADIOS<double>(variable, array);
- else if (IsType<long double>(array))
- WriteVariableInADIOS<long double>(variable, array);
- else if (IsType<std::complex<float>>(array))
- WriteVariableInADIOS<std::complex<float>>(variable, array);
- else if (IsType<std::complex<double>>(array))
- WriteVariableInADIOS<std::complex<double>>(variable, array);
- else if (IsType<std::complex<long double>>(array))
- WriteVariableInADIOS<std::complex<long double>>(variable, array);
+ WriteVariableInADIOS<std::complex<long double>>(variable, array);
}
void EnginePy::Advance() { m_Engine->Advance(); }
@@ -100,7 +100,7 @@ void EnginePy::Close() { m_Engine->Close(-1); }
void EnginePy::GetEngineType() const
{
- std::cout << "Engine type " << m_Engine->m_EngineType << "\n";
+ std::cout << "Engine type " << m_Engine->m_EngineType << "\n";
}
} // end namespace
diff --git a/bindings/python/src/MethodPy.cpp b/bindings/python/src/MethodPy.cpp
index 4310de6739be79c1495574d36e54e0229af0fa34..937df58fb72a55456b0f65b6e0be0c0820994793 100644
--- a/bindings/python/src/MethodPy.cpp
+++ b/bindings/python/src/MethodPy.cpp
@@ -34,66 +34,68 @@ MethodPy::~MethodPy() {}
#ifdef HAVE_BOOSTPYTHON
pyObject MethodPy::SetParametersPy(pyTuple args, pyDict kwargs)
{
- if (py::len(args) > 1)
- throw std::invalid_argument("ERROR: syntax of Method SetParameters "
- "function is incorrect, only use dictionary\n");
-
- MethodPy &self = PyCast<MethodPy &>(args[0]);
- self.m_Parameters = DictToMap(kwargs);
- return args[0];
+ if (py::len(args) > 1)
+ throw std::invalid_argument(
+ "ERROR: syntax of Method SetParameters "
+ "function is incorrect, only use dictionary\n");
+
+ MethodPy &self = PyCast<MethodPy &>(args[0]);
+ self.m_Parameters = DictToMap(kwargs);
+ return args[0];
}
pyObject MethodPy::AddTransportPy(pyTuple args, pyDict kwargs)
{
- if (py::len(args) != 2)
- throw std::invalid_argument(
- "ERROR: syntax of Method AddTransport function is incorrect, only use "
- "one string for transport followed by a dictionary for parameters\n");
-
- MethodPy &self = PyCast<MethodPy &>(args[0]);
- const std::string type = PyCast<std::string>(args[1]);
-
- auto parameters = DictToMap(kwargs);
- parameters.insert(std::make_pair("transport", type));
- self.m_TransportParameters.push_back(parameters);
- return args[0];
+ if (py::len(args) != 2)
+ throw std::invalid_argument("ERROR: syntax of Method AddTransport "
+ "function is incorrect, only use "
+ "one string for transport followed by a "
+ "dictionary for parameters\n");
+
+ MethodPy &self = PyCast<MethodPy &>(args[0]);
+ const std::string type = PyCast<std::string>(args[1]);
+
+ auto parameters = DictToMap(kwargs);
+ parameters.insert(std::make_pair("transport", type));
+ self.m_TransportParameters.push_back(parameters);
+ return args[0];
}
#endif
#ifdef HAVE_PYBIND11
void MethodPy::SetParametersPyBind11(pybind11::kwargs kwargs)
{
- this->m_Parameters = KwargsToMap(kwargs);
+ this->m_Parameters = KwargsToMap(kwargs);
}
void MethodPy::AddTransportPyBind11(const std::string type,
pybind11::kwargs kwargs)
{
- auto parameters = KwargsToMap(kwargs);
- parameters.insert(std::make_pair("transport", type));
- this->m_TransportParameters.push_back(parameters);
+ auto parameters = KwargsToMap(kwargs);
+ parameters.insert(std::make_pair("transport", type));
+ this->m_TransportParameters.push_back(parameters);
}
#endif
void MethodPy::PrintAll() const
{
- std::cout << "Method parameters\n";
- for (const auto ¶m : m_Parameters)
- std::cout << "Parameter: " << param.first << "\t Value: " << param.second
- << "\n";
+ std::cout << "Method parameters\n";
+ for (const auto ¶m : m_Parameters)
+ std::cout << "Parameter: " << param.first
+ << "\t Value: " << param.second << "\n";
- std::cout << "\n";
- std::cout << "Transport Parameters\n";
+ std::cout << "\n";
+ std::cout << "Transport Parameters\n";
- for (const auto &transportParameters : m_TransportParameters)
- {
- std::cout << "Transport:\n";
- for (const auto ¶m : transportParameters)
- std::cout << "Parameter: " << param.first << "\t Value: " << param.second
- << "\n";
+ for (const auto &transportParameters : m_TransportParameters)
+ {
+ std::cout << "Transport:\n";
+ for (const auto ¶m : transportParameters)
+ std::cout << "Parameter: " << param.first
+ << "\t Value: " << param.second << "\n";
- std::cout << "\n";
- }
+ std::cout << "\n";
+ }
}
} // end namespace
diff --git a/bindings/python/src/VariablePy.cpp b/bindings/python/src/VariablePy.cpp
index 7d677d567e1f3a645490300d5bbf90a3fc744117..09d92899e844848a723284f2900b5c6f48ad7076 100644
--- a/bindings/python/src/VariablePy.cpp
+++ b/bindings/python/src/VariablePy.cpp
@@ -26,14 +26,14 @@ VariablePy::~VariablePy() {}
void VariablePy::SetLocalDimensions(const pyList list)
{
- // this->m_Dimensions = ListToVector( list );
+ // this->m_Dimensions = ListToVector( list );
}
void VariablePy::SetGlobalDimensionsAndOffsets(const pyList globalDimensions,
const pyList globalOffsets)
{
- // this->m_GlobalDimensions = ListToVector( globalDimensions );
- // this->m_GlobalOffsets = ListToVector( globalOffsets );
+ // this->m_GlobalDimensions = ListToVector( globalDimensions );
+ // this->m_GlobalOffsets = ListToVector( globalOffsets );
}
Dims VariablePy::GetLocalDimensions() { return this->m_LocalDimensions; }
diff --git a/bindings/python/src/adiosPyFunctions.cpp b/bindings/python/src/adiosPyFunctions.cpp
index 778134179a353f2ba64b2552c24866c8fd199170..92d18b4c0dfe0fe37e959fb4eccafc10632f869f 100644
--- a/bindings/python/src/adiosPyFunctions.cpp
+++ b/bindings/python/src/adiosPyFunctions.cpp
@@ -24,64 +24,64 @@ namespace py = pybind11;
Dims ListToVector(const pyList &list)
{
- const unsigned int length = py::len(list);
- Dims vec;
- vec.reserve(length);
+ const unsigned int length = py::len(list);
+ Dims vec;
+ vec.reserve(length);
- for (unsigned int i = 0; i < length; i++)
- vec.push_back(PyCast<std::size_t>(list[i]));
+ for (unsigned int i = 0; i < length; i++)
+ vec.push_back(PyCast<std::size_t>(list[i]));
- return vec;
+ return vec;
}
#ifdef HAVE_BOOSTPYTHON
std::map<std::string, std::string> DictToMap(const pyDict &dictionary)
{
- std::map<std::string, std::string> parameters;
+ std::map<std::string, std::string> parameters;
- pyList keys = dictionary.keys();
- const unsigned int length = py::len(keys);
+ pyList keys = dictionary.keys();
+ const unsigned int length = py::len(keys);
- for (unsigned int k = 0; k < length; ++k)
- {
- const std::string key(PyCast<std::string>(keys[k]));
- const std::string value(PyCast<std::string>(dictionary[keys[k]]));
- parameters.insert(std::make_pair(key, value));
- }
+ for (unsigned int k = 0; k < length; ++k)
+ {
+ const std::string key(PyCast<std::string>(keys[k]));
+ const std::string value(PyCast<std::string>(dictionary[keys[k]]));
+ parameters.insert(std::make_pair(key, value));
+ }
- return parameters;
+ return parameters;
}
#endif
#ifdef HAVE_PYBIND11
std::map<std::string, std::string> KwargsToMap(const pybind11::kwargs &kwargs)
{
- std::map<std::string, std::string> parameters;
-
- for (const auto &pair : kwargs)
- {
- const std::string key(PyCast<std::string>(pair.first));
- const std::string value(PyCast<std::string>(pair.second));
- parameters.insert(std::make_pair(key, value));
- }
- return parameters;
+ std::map<std::string, std::string> parameters;
+
+ for (const auto &pair : kwargs)
+ {
+ const std::string key(PyCast<std::string>(pair.first));
+ const std::string value(PyCast<std::string>(pair.second));
+ parameters.insert(std::make_pair(key, value));
+ }
+ return parameters;
}
#endif
bool IsEmpty(pyObject object)
{
- bool isEmpty = false;
+ bool isEmpty = false;
#ifdef HAVE_BOOSTPYTHON
- if (object == boost::python::object())
- isEmpty = true;
+ if (object == boost::python::object())
+ isEmpty = true;
#endif
#ifdef HAVE_PYBIND11
- if (object == pybind11::none())
- isEmpty = true;
+ if (object == pybind11::none())
+ isEmpty = true;
#endif
- return isEmpty;
+ return isEmpty;
}
} // end namespace
diff --git a/bindings/python/src/glueBoostPython.cpp b/bindings/python/src/glueBoostPython.cpp
index 532cec900ed71e7c16266e4974f5e36cf65c81c1..1718700b47dbcfa66a29524b7a437a6aae3eedb4 100644
--- a/bindings/python/src/glueBoostPython.cpp
+++ b/bindings/python/src/glueBoostPython.cpp
@@ -24,10 +24,10 @@ namespace np = boost::python::numpy;
adios::ADIOSPy ADIOSPy(py::object py_comm, const bool debug)
{
- MPI_Comm *comm_p = PyMPIComm_Get(py_comm.ptr());
- if (comm_p == NULL)
- py::throw_error_already_set();
- return adios::ADIOSPy(*comm_p, debug);
+ MPI_Comm *comm_p = PyMPIComm_Get(py_comm.ptr());
+ if (comm_p == NULL)
+ py::throw_error_already_set();
+ return adios::ADIOSPy(*comm_p, debug);
}
using ReturnInternalReference = py::return_internal_reference<>;
@@ -36,39 +36,39 @@ BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(open_overloads, adios::ADIOSPy::OpenPy,
BOOST_PYTHON_MODULE(ADIOSPy)
{
- if (import_mpi4py() < 0)
- return; /* Python 2.X */
+ if (import_mpi4py() < 0)
+ return; /* Python 2.X */
- Py_Initialize();
- np::initialize();
+ Py_Initialize();
+ np::initialize();
- py::class_<adios::Dims>("Dims").def(
- boost::python::vector_indexing_suite<adios::Dims>());
- // functions
- py::def("ADIOSPy", ADIOSPy);
+ py::class_<adios::Dims>("Dims").def(
+ boost::python::vector_indexing_suite<adios::Dims>());
+ // functions
+ py::def("ADIOSPy", ADIOSPy);
- // classes
- py::class_<adios::ADIOSPy>("ADIOS", py::no_init)
- .def("HelloMPI", &adios::ADIOSPy::HelloMPI)
- .def("DefineVariable", &adios::ADIOSPy::DefineVariablePy)
- .def("DeclareMethod", &adios::ADIOSPy::DeclareMethodPy,
- ReturnInternalReference())
- .def("Open", &adios::ADIOSPy::OpenPy, open_overloads());
+ // classes
+ py::class_<adios::ADIOSPy>("ADIOS", py::no_init)
+ .def("HelloMPI", &adios::ADIOSPy::HelloMPI)
+ .def("DefineVariable", &adios::ADIOSPy::DefineVariablePy)
+ .def("DeclareMethod", &adios::ADIOSPy::DeclareMethodPy,
+ ReturnInternalReference())
+ .def("Open", &adios::ADIOSPy::OpenPy, open_overloads());
- py::class_<adios::VariablePy>("Variable", py::no_init)
- .def("SetLocalDimensions", &adios::VariablePy::SetLocalDimensions)
- .def("GetLocalDimensions", &adios::VariablePy::GetLocalDimensions);
+ py::class_<adios::VariablePy>("Variable", py::no_init)
+ .def("SetLocalDimensions", &adios::VariablePy::SetLocalDimensions)
+ .def("GetLocalDimensions", &adios::VariablePy::GetLocalDimensions);
- py::class_<adios::MethodPy>("Method", py::no_init)
- .def("SetParameters",
- py::raw_function(&adios::MethodPy::SetParametersPy, 1))
- .def("AddTransport",
- py::raw_function(&adios::MethodPy::AddTransportPy, 1))
- .def("PrintAll", &adios::MethodPy::PrintAll);
+ py::class_<adios::MethodPy>("Method", py::no_init)
+ .def("SetParameters",
+ py::raw_function(&adios::MethodPy::SetParametersPy, 1))
+ .def("AddTransport",
+ py::raw_function(&adios::MethodPy::AddTransportPy, 1))
+ .def("PrintAll", &adios::MethodPy::PrintAll);
- // Engine
- py::class_<adios::EnginePy>("EnginePy", py::no_init)
- .def("Write", &adios::EnginePy::WritePy)
- .def("Advance", &adios::EnginePy::WritePy)
- .def("Close", &adios::EnginePy::Close);
+ // Engine
+ py::class_<adios::EnginePy>("EnginePy", py::no_init)
+ .def("Write", &adios::EnginePy::WritePy)
+ .def("Advance", &adios::EnginePy::WritePy)
+ .def("Close", &adios::EnginePy::Close);
}
diff --git a/bindings/python/src/gluePyBind11.cpp b/bindings/python/src/gluePyBind11.cpp
index cd3cc32f700a07d853eb479e53c21d4b10a4228c..dd76c295c061c1b7ae81d776612de46d8412b821 100644
--- a/bindings/python/src/gluePyBind11.cpp
+++ b/bindings/python/src/gluePyBind11.cpp
@@ -21,43 +21,43 @@ namespace py = pybind11;
adios::ADIOSPy ADIOSPy(py::object py_comm, const bool debug)
{
- MPI_Comm *comm_p = PyMPIComm_Get(py_comm.ptr());
- if (comm_p == NULL)
- py::error_already_set();
- return adios::ADIOSPy(*comm_p, debug);
+ MPI_Comm *comm_p = PyMPIComm_Get(py_comm.ptr());
+ if (comm_p == NULL)
+ py::error_already_set();
+ return adios::ADIOSPy(*comm_p, debug);
}
PYBIND11_PLUGIN(ADIOSPy)
{
- if (import_mpi4py() < 0)
- throw std::runtime_error(
- "ERROR: mpi4py not loaded correctly\n"); /* Python 2.X */
+ if (import_mpi4py() < 0)
+ throw std::runtime_error(
+ "ERROR: mpi4py not loaded correctly\n"); /* Python 2.X */
- py::module m("ADIOSPy", "ADIOS Python bindings using pybind11");
+ py::module m("ADIOSPy", "ADIOS Python bindings using pybind11");
- m.def("ADIOSPy", &ADIOSPy, "Function that creates an ADIOS object");
+ m.def("ADIOSPy", &ADIOSPy, "Function that creates an ADIOS object");
- py::class_<adios::ADIOSPy>(m, "ADIOS")
- .def("HelloMPI", &adios::ADIOSPy::HelloMPI)
- .def("DefineVariable", &adios::ADIOSPy::DefineVariablePy)
- .def("DeclareMethod", &adios::ADIOSPy::DeclareMethodPy,
- py::return_value_policy::reference_internal)
- .def("Open", &adios::ADIOSPy::OpenPy);
+ py::class_<adios::ADIOSPy>(m, "ADIOS")
+ .def("HelloMPI", &adios::ADIOSPy::HelloMPI)
+ .def("DefineVariable", &adios::ADIOSPy::DefineVariablePy)
+ .def("DeclareMethod", &adios::ADIOSPy::DeclareMethodPy,
+ py::return_value_policy::reference_internal)
+ .def("Open", &adios::ADIOSPy::OpenPy);
- py::class_<adios::VariablePy>(m, "Variable")
- .def("SetLocalDimensions", &adios::VariablePy::SetLocalDimensions)
- .def("GetLocalDimensions", &adios::VariablePy::GetLocalDimensions);
+ py::class_<adios::VariablePy>(m, "Variable")
+ .def("SetLocalDimensions", &adios::VariablePy::SetLocalDimensions)
+ .def("GetLocalDimensions", &adios::VariablePy::GetLocalDimensions);
- py::class_<adios::MethodPy>(m, "Method")
- .def("SetParameters", &adios::MethodPy::SetParametersPyBind11)
- .def("AddTransport", &adios::MethodPy::AddTransportPyBind11)
- .def("PrintAll", &adios::MethodPy::PrintAll);
+ py::class_<adios::MethodPy>(m, "Method")
+ .def("SetParameters", &adios::MethodPy::SetParametersPyBind11)
+ .def("AddTransport", &adios::MethodPy::AddTransportPyBind11)
+ .def("PrintAll", &adios::MethodPy::PrintAll);
- // Engine
- py::class_<adios::EnginePy>(m, "Engine")
- .def("Write", &adios::EnginePy::WritePy)
- .def("Advance", &adios::EnginePy::WritePy)
- .def("Close", &adios::EnginePy::Close);
+ // Engine
+ py::class_<adios::EnginePy>(m, "Engine")
+ .def("Write", &adios::EnginePy::WritePy)
+ .def("Advance", &adios::EnginePy::WritePy)
+ .def("Close", &adios::EnginePy::Close);
- return m.ptr();
+ return m.ptr();
}
diff --git a/doc/API_design/API_example_use.cpp b/doc/API_design/API_example_use.cpp
index af3fbdbdd7e5db586166bc696f40b3ac9df9cadd..a35146935cf564dea610accee6ad67efdfbe6ce6 100644
--- a/doc/API_design/API_example_use.cpp
+++ b/doc/API_design/API_example_use.cpp
@@ -6,428 +6,458 @@
void cb_AsyncWriteAdvanceCompleted(std::shared_ptr<adios::Engine> writer)
{
- std::cout
- << "AdvanceAsync() completed. We can modify our zero-copy variables\n";
+ std::cout << "AdvanceAsync() completed. We can modify our zero-copy "
+ "variables\n";
}
void cb_AsyncReadAdvanceCompleted(std::shared_ptr<adios::Engine> writer)
{
- std::cout << "AdvanceAsync() completed. We have new data to read and we have "
- "the lock on it\n";
+ std::cout
+ << "AdvanceAsync() completed. We have new data to read and we have "
+ "the lock on it\n";
}
int main(int argc, char *argv[])
{
- // Application variables
- MPI_Comm comm = MPI_COMM_WORLD;
- const unsigned int NX = 10;
- double Temperature[1][NX + 2]; // We will want to write only Nx elements,
- // skipping the first and last (think ghost
- // cells)
- std::vector<float> RaggedArray;
-
- int Nparts, nproc;
-
- // Global class/object that serves for init, finalize and provides ADIOS
- // functions
- adios::ADIOS adios("config.xml", comm, /*verbose=*/adios::INFO,
- /*debugflag=*/false);
-
- /*************
- * WRITE API
- *************/
-
- /* Method
- * We associate Engines and Transports and user settings into an object called
- * Method.
- * ADIOS checks if it is defined by the user in the config file, and fills it
- * out if it is.
- */
-
- adios::Method &wmethod = adios.DeclareMethod("WriteMethod");
- if (!wmethod.isUserDefined())
- {
- // if not defined by user, we can change the default settings
- wmethod.SetEngine("BP"); // BP is the default engine
- wmethod.AllowThreads(
- 1); // no threading for data processing (except for staging)
- wmethod.AddTransport(
- "File", "lucky=yes"); // ISO-POSIX file is the default transport
- wmethod.AddTransport("Staging"); //"The" staging method developed in ECP
- wmethod.SetParameters("have_metadata_file",
- "yes"); // Passing parameters to the engine
- wmethod.SetParameters("Aggregation",
- (nproc + 1) / 2); // number of aggregators
- wmethod.SetParameters("verbose", adios::Verbose::WARN); // Verbosity level
- // for this engine
- // and what it calls
- }
-
- // Define variables with transformations.
- adios::Variable<unsigned int> &varNX = adios.DefineVariable<unsigned int>(
- "NX"); // global single-value across processes
- auto &varNproc = adios.DefineVariable<int>(
- "nproc", adios::Dims{adios::GLOBAL_VALUE}); // same def for global value
- adios::Variable<int> &varNparts = adios.DefineVariable<int>(
- "Nparts",
- adios::Dims{
- adios::LOCAL_VALUE}); // a single-value different on every process
- adios::Variable<double> &var2D = adios.DefineVariable<double>(
- "Temperature",
- adios::Dims{nproc, NX}); // 2D global array, 1D decomposition
- adios::Variable<float> &varRagged = adios.DefineVariable<float>(
- "Ragged", adios::Dims{nproc, adios::VARYING_DIMENSION}); // ragged array
-
- // add transform to variable
- adios::Transform zfp = adios::transform::ZFP();
- var2D.AddTransform(zfp, "accuracy=0.001");
-
- // open...write.write.write...advance...write.write.write...advance...
- // ...close cycle
- // "w" create/overwrite on open, "a" append at open, "u" open for update (does
- // not increase step), "r" open for read.
- std::shared_ptr<adios::Engine> writer = adios.Open(
- "myNumbers.bp", "w", comm, wmethod, adios::IOMode::INDEPENDENT);
-
- if (writer == nullptr)
- throw std::ios_base::failure("ERROR: failed to open ADIOS writer\n");
-
- // Zero-Copy API: Define a variable with local dimensions now, and make ADIOS
- // allocate it inside its buffers
- // This requires an engine created. The variable will be deallocated in
- // writer->Close()
- // Calling varZeroCopy.SetSelection() later should throw an exception, i.e.
- // modification is not allowed
- // 2D global array, 1D decomposition
- adios::Variable<double> &varZeroCopy = adios.DefineVariable<double>(
- "ZC", adios::Dims{nproc, NX}, adios::Dims{1, NX}, adios::Dims{rank, 0});
- double fillValue = -1.0;
- double *const myVarZC =
- writer->AllocateVariable<double>(varZeroCopy, fillValue);
-
- for (int step = 0; step < 10; ++step)
- {
- // write scalar value
- writer->Write<int>(varNparts, Nparts);
-
- // Make a selection to describe the local dimensions of the variable we
- // write and
- // its offsets in the global spaces. This could have been done in
- // adios.DefineVariable()
- adios::Selection sel = adios.SelectionBoundingBox(
- {1, NX}, {rank, NX}); // local dims and offsets; both as list
- var2D.SetSelection(
- sel); // Shall we call it SetSpaceSelection, SetOutputSelection?
-
- // Select the area that we want to write from the data pointer we pass to
- // the writer
- // Think HDF5 memspace, just not hyperslabs yet, only a bounding box
- // selection
- // Engine will copy this bounding box from the data pointer into the buffer.
- // Size of the bounding box should match the
- // "space" selection which was given above. Default memspace is the full
- // selection.
- adios::Selection memspace = adios.SelectionBoundingBox(
- {1, NX}, {0, 1}); // local dims and offsets; both as list
- var2D.SetMemorySelection(memspace);
-
- writer->Write<double>(var2D, *Temperature);
-
- // Indicate we are done for this step.
- // N-to-M Aggregation, disk I/O will be performed during this call, unless
- // time aggregation postpones all of that to some later step.
- // When Advance() returns, user can overwrite its Zero Copy variables.
- // Internal buffer is freed only if there are no Zero Copy variables and
- // there is no time aggregation going on
- writer->Advance(); // same as AppendMode
- writer->Advance(adios::APPEND, 0.0); // append new step at next write
- writer->Advance(adios::UPDATE); // do not increase step;
-
- // When AdvanceAsync returns, user need to wait for notification that he can
- // overwrite the Zero Copy variables.
- writer->AdvanceAsync(adios::APPEND, cb_AsyncWriteAdvanceCompleted);
- }
-
- // Called once: indicate that we are done with this output for the run
- // Zero Copy variables will be deallocated
- writer->Close();
-
- /*************
- * READ API
- *************/
- adios::Method &rmethod = adios.DeclareMethod("ReadMethod");
- if (!rmethod.isUserDefined())
- {
- // if not defined by user, we can change the default settings
- rmethod.SetEngine("BP"); // BP is the default engine
- rmethod.AddTransport("Staging"); //"The" staging method developed in ECP
- rmethod.SetParameters("Aggregation",
- (nproc + 1) / 2); // number of aggregators
- rmethod.SetParameters("verbose", adios::Verbose::WARN); // Verbosity level
- // for this engine
- // and what it calls
- }
-
- // 1. Open a stream, where every reader can see everything in a stream (so
- // that they can read a global array)
- // Blocking read of a variable
- try
- {
- // These method settings are developer-only, not available to the user
- rmethod.SetReadMultiplexPattern(adios::GLOBAL_READERS); // Each reader
- // process sees
- // everything from
- // the stream
- rmethod.SetStreamOpenMode(adios::WAITFORSTREAM); // In Open(), wait for the
- // first step appear
- // (default)
-
- // Open a stream
- std::shared_ptr<adios::Engine> reader =
- adios.Open("filename.bp", "r", comm, rmethod, adios::IOMode::COLLECTIVE,
- /*timeout_sec=*/300.0); // wait this long for the stream,
- // return error afterwards
-
- /* Variable names are available as a vector of strings */
- std::cout << "List of variables in file: " << reader->VariableNames()
- << "\n";
- /* read a Global scalar which has a single value in a step */
- reader->Read<unsigned int>("NX", NX);
-
- // inquiry about a variable, whose name we know
- adios::Variable<double> var2D =
- reader->InquireVariableDouble("Temperature");
- std::vector<std::size_t> gdims = var2D.GetGlobalDimensions();
- int nsteps = var2D.GetSteps();
-
- struct adios::BlockInfo blocks = reader.InquiryVariableBlockInfo(
- reader, var2D); // get per-writer size info
- // this is adios1 ADIOS_VARBLOCK
- struct adios::Statistics stats = reader.InquiryVariableStat(
- reader, var2D, perstepstat, perblockstat); // get min/max statistics
- // this is adios1 ADIOS_VARSTAT
-
- while (true)
+ // Application variables
+ MPI_Comm comm = MPI_COMM_WORLD;
+ const unsigned int NX = 10;
+ double Temperature[1][NX + 2]; // We will want to write only Nx elements,
+ // skipping the first and last (think ghost
+ // cells)
+ std::vector<float> RaggedArray;
+
+ int Nparts, nproc;
+
+ // Global class/object that serves for init, finalize and provides ADIOS
+ // functions
+ adios::ADIOS adios("config.xml", comm, /*verbose=*/adios::INFO,
+ /*debugflag=*/false);
+
+ /*************
+ * WRITE API
+ *************/
+
+ /* Method
+ * We associate Engines and Transports and user settings into an object
+ * called
+ * Method.
+ * ADIOS checks if it is defined by the user in the config file, and fills
+ * it
+ * out if it is.
+ */
+
+ adios::Method &wmethod = adios.DeclareMethod("WriteMethod");
+ if (!wmethod.isUserDefined())
{
- // Make a selection to describe the local dimensions of the variable we
- // READ and
- // its offsets in the global spaces
- adios::Selection bbsel = adios.SelectionBoundingBox(
- {1, NX}, {0, 0}); // local dims and offsets; both as list
- var2D.SetSelection(bbsel);
- adios::Selection memspace = adios.SelectionBoundingBox(
- {1, NX}, {0, 1}); // local dims and offsets; both as list
- var2D.SetMemorySelection(memspace);
- reader->Read<double>(var2D, *Temperature);
- // var2D, Temperature );
-
- // Better for staging to schedule several reads at once
- reader->ScheduleRead<double>(var2D, *Temperature);
- reader->PerformReads(adios::BLOCKINGREAD);
-
- // promise to not read more from this step/item
- reader->Release();
-
- // want to move on to the next available step/item
- reader->Advance(adios::NEXT_AVAILABLE); // default
- reader->Advance(
- adios::LATEST_AVAILABLE); // interested only in the latest data
+ // if not defined by user, we can change the default settings
+ wmethod.SetEngine("BP"); // BP is the default engine
+ wmethod.AllowThreads(
+ 1); // no threading for data processing (except for staging)
+ wmethod.AddTransport(
+ "File", "lucky=yes"); // ISO-POSIX file is the default transport
+ wmethod.AddTransport("Staging"); //"The" staging method developed in ECP
+ wmethod.SetParameters("have_metadata_file",
+ "yes"); // Passing parameters to the engine
+ wmethod.SetParameters("Aggregation",
+ (nproc + 1) / 2); // number of aggregators
+ wmethod.SetParameters("verbose",
+ adios::Verbose::WARN); // Verbosity level
+ // for this engine
+ // and what it calls
}
- // Close file/stream
- reader->Close();
- }
- catch (adios::end_of_stream &e)
- {
- // Reached end of stream, end processing loop
- // Close file/stream
- reader->Close();
- }
- catch (adios::file_not_found &e)
- {
- // File/stream does not exist, quit
- }
-
- // 2. Open a stream, where each item from the writers will get to a single
- // reader only
- // If the writers are collective, that means a whole steps go to different
- // readers
- // If the writers are independent, that means each writer's output goes to
- // different readers
- // Also show here ScheduleRead/PerformRead
- // try
- {
- rmethod.SetReadMultiplexPattern(adios::FIFO_READERS); // Each reader process
- // sees everything
- // from the stream
- rmethod.SetStreamOpenMode(adios::WAITFORSTREAM); // In Open(), wait for the
- // first step appear
- // (default)
-
- // Open a stream
- std::shared_ptr<adios::Engine> reader = adios.Open(
- "filename.bp", "r", comm, rmethod, adios::IOMode::INDEPENDENT,
- /*timeout_sec=*/300.0); // wait this long for the stream, return error
- // afterwards
-
- while (true)
+
+ // Define variables with transformations.
+ adios::Variable<unsigned int> &varNX = adios.DefineVariable<unsigned int>(
+ "NX"); // global single-value across processes
+ auto &varNproc = adios.DefineVariable<int>(
+ "nproc", adios::Dims{adios::GLOBAL_VALUE}); // same def for global value
+ adios::Variable<int> &varNparts = adios.DefineVariable<int>(
+ "Nparts", adios::Dims{adios::LOCAL_VALUE}); // a single-value
+ // different on every
+ // process
+ adios::Variable<double> &var2D = adios.DefineVariable<double>(
+ "Temperature",
+ adios::Dims{nproc, NX}); // 2D global array, 1D decomposition
+ adios::Variable<float> &varRagged = adios.DefineVariable<float>(
+ "Ragged", adios::Dims{nproc, adios::VARYING_DIMENSION}); // ragged array
+
+ // add transform to variable
+ adios::Transform zfp = adios::transform::ZFP();
+ var2D.AddTransform(zfp, "accuracy=0.001");
+
+ // open...write.write.write...advance...write.write.write...advance...
+ // ...close cycle
+ // "w" create/overwrite on open, "a" append at open, "u" open for update
+ // (does
+ // not increase step), "r" open for read.
+ std::shared_ptr<adios::Engine> writer = adios.Open(
+ "myNumbers.bp", "w", comm, wmethod, adios::IOMode::INDEPENDENT);
+
+ if (writer == nullptr)
+ throw std::ios_base::failure("ERROR: failed to open ADIOS writer\n");
+
+ // Zero-Copy API: Define a variable with local dimensions now, and make
+ // ADIOS
+ // allocate it inside its buffers
+ // This requires an engine created. The variable will be deallocated in
+ // writer->Close()
+ // Calling varZeroCopy.SetSelection() later should throw an exception, i.e.
+ // modification is not allowed
+ // 2D global array, 1D decomposition
+ adios::Variable<double> &varZeroCopy = adios.DefineVariable<double>(
+ "ZC", adios::Dims{nproc, NX}, adios::Dims{1, NX}, adios::Dims{rank, 0});
+ double fillValue = -1.0;
+ double *const myVarZC =
+ writer->AllocateVariable<double>(varZeroCopy, fillValue);
+
+ for (int step = 0; step < 10; ++step)
{
- // Make a selection to describe the local dimensions of the variable we
- // READ and
- // its offsets in the global spaces if we know this somehow
- adios::Selection bbsel = adios.SelectionBoundingBox(
- {1, NX}, {0, 0}); // local dims and offsets; both as list
- var2D->SetSelection(bbsel);
- reader->Read<double>(var2D, *Temperature);
-
- // Let ADIOS allocate space for the incoming (per-writer) item
- double *data = reader->Read<double>(var2D);
-
- // promise to not read more from this step/item
- reader->Release();
-
- // want to move on to the next available step/item
- reader->Advance(); // default
- reader->Advance(adios::LATEST_AVAILABLE); // This should be an error, or
- // could it make sense?
+ // write scalar value
+ writer->Write<int>(varNparts, Nparts);
+
+ // Make a selection to describe the local dimensions of the variable we
+ // write and
+ // its offsets in the global spaces. This could have been done in
+ // adios.DefineVariable()
+ adios::Selection sel = adios.SelectionBoundingBox(
+ {1, NX}, {rank, NX}); // local dims and offsets; both as list
+ var2D.SetSelection(
+ sel); // Shall we call it SetSpaceSelection, SetOutputSelection?
+
+ // Select the area that we want to write from the data pointer we pass
+ // to
+ // the writer
+ // Think HDF5 memspace, just not hyperslabs yet, only a bounding box
+ // selection
+ // Engine will copy this bounding box from the data pointer into the
+ // buffer.
+ // Size of the bounding box should match the
+ // "space" selection which was given above. Default memspace is the full
+ // selection.
+ adios::Selection memspace = adios.SelectionBoundingBox(
+ {1, NX}, {0, 1}); // local dims and offsets; both as list
+ var2D.SetMemorySelection(memspace);
+
+ writer->Write<double>(var2D, *Temperature);
+
+ // Indicate we are done for this step.
+ // N-to-M Aggregation, disk I/O will be performed during this call,
+ // unless
+ // time aggregation postpones all of that to some later step.
+ // When Advance() returns, user can overwrite its Zero Copy variables.
+ // Internal buffer is freed only if there are no Zero Copy variables and
+ // there is no time aggregation going on
+ writer->Advance(); // same as AppendMode
+ writer->Advance(adios::APPEND, 0.0); // append new step at next write
+ writer->Advance(adios::UPDATE); // do not increase step;
+
+ // When AdvanceAsync returns, user need to wait for notification that he
+ // can
+ // overwrite the Zero Copy variables.
+ writer->AdvanceAsync(adios::APPEND, cb_AsyncWriteAdvanceCompleted);
}
- reader->Close();
- }
-
- // 3. Open a stream and return immediately, not waiting for data to appear
- // In this mode we cannot inquiry variables, but can schedule reads
- // try
- {
- rmethod.SetReadMultiplexPattern(adios::GLOBAL_READERS); // Each reader
- // process sees
- // everything from
- // the stream
- rmethod.SetStreamOpenMode(adios::NOWAITFORSTREAM); // In Open(), wait for
- // the first step appear
- // (default)
-
- // Open a stream
- std::shared_ptr<adios::Engine> reader = adios.Open(
- "filename.bp", "r", comm, rmethod, adios::IOMode::INDEPENDENT);
-
- while (true)
+
+ // Called once: indicate that we are done with this output for the run
+ // Zero Copy variables will be deallocated
+ writer->Close();
+
+ /*************
+ * READ API
+ *************/
+ adios::Method &rmethod = adios.DeclareMethod("ReadMethod");
+ if (!rmethod.isUserDefined())
{
+ // if not defined by user, we can change the default settings
+ rmethod.SetEngine("BP"); // BP is the default engine
+ rmethod.AddTransport("Staging"); //"The" staging method developed in ECP
+ rmethod.SetParameters("Aggregation",
+ (nproc + 1) / 2); // number of aggregators
+ rmethod.SetParameters("verbose",
+ adios::Verbose::WARN); // Verbosity level
+ // for this engine
+ // and what it calls
+ }
- // Let ADIOS allocate space for the incoming (per-writer) item
- reader->ScheduleRead(); // read whatever comes
-
- // One way is to handle the incoming data through a callback (which will
- // be called in a thread)
- // void cb( const void *data, std::string doid, std::string var,
- // std::string dtype, std::vector<std::size_t> varshape );
- // void cb( adios::VARCHUNK * chunk ); // see adios1 for VARCHUNK
- reader->SetReadCallback(cb);
- reader->PerformReads(adios::NONBLOCKINGREAD);
-
- // Another way is checking back manually like in adios1 and processing
- // chunks
- reader->PerformReads(adios::NONBLOCKINGREAD);
- int ck;
- adios::VARCHUNK *chunk;
- try
- {
- while ((ck = reader->CheckReads(&chunk)) > 0)
+ // 1. Open a stream, where every reader can see everything in a stream (so
+ // that they can read a global array)
+ // Blocking read of a variable
+ try
+ {
+ // These method settings are developer-only, not available to the user
+ rmethod.SetReadMultiplexPattern(adios::GLOBAL_READERS); // Each reader
+ // process sees
+ // everything from
+ // the stream
+ rmethod.SetStreamOpenMode(
+ adios::WAITFORSTREAM); // In Open(), wait for the
+ // first step appear
+ // (default)
+
+ // Open a stream
+ std::shared_ptr<adios::Engine> reader = adios.Open(
+ "filename.bp", "r", comm, rmethod, adios::IOMode::COLLECTIVE,
+ /*timeout_sec=*/300.0); // wait this long for the stream,
+ // return error afterwards
+
+ /* Variable names are available as a vector of strings */
+ std::cout << "List of variables in file: " << reader->VariableNames()
+ << "\n";
+ /* read a Global scalar which has a single value in a step */
+ reader->Read<unsigned int>("NX", NX);
+
+ // inquiry about a variable, whose name we know
+ adios::Variable<double> var2D =
+ reader->InquireVariableDouble("Temperature");
+ std::vector<std::size_t> gdims = var2D.GetGlobalDimensions();
+ int nsteps = var2D.GetSteps();
+
+ struct adios::BlockInfo blocks = reader.InquiryVariableBlockInfo(
+ reader, var2D); // get per-writer size info
+ // this is adios1 ADIOS_VARBLOCK
+ struct adios::Statistics stats =
+ reader.InquiryVariableStat(reader, var2D, perstepstat,
+ perblockstat); // get min/max statistics
+ // this is adios1 ADIOS_VARSTAT
+
+ while (true)
{
- if (chunk)
- {
- // process the chunk first
- // ...
- // free memory of chunk (not the data!)
- adios::FreeChunk(chunk);
- }
- else
- {
- // no chunk was returned, slow down a little
- sleep(1);
- }
+ // Make a selection to describe the local dimensions of the variable
+ // we
+ // READ and
+ // its offsets in the global spaces
+ adios::Selection bbsel = adios.SelectionBoundingBox(
+ {1, NX}, {0, 0}); // local dims and offsets; both as list
+ var2D.SetSelection(bbsel);
+ adios::Selection memspace = adios.SelectionBoundingBox(
+ {1, NX}, {0, 1}); // local dims and offsets; both as list
+ var2D.SetMemorySelection(memspace);
+ reader->Read<double>(var2D, *Temperature);
+ // var2D, Temperature );
+
+ // Better for staging to schedule several reads at once
+ reader->ScheduleRead<double>(var2D, *Temperature);
+ reader->PerformReads(adios::BLOCKINGREAD);
+
+ // promise to not read more from this step/item
+ reader->Release();
+
+ // want to move on to the next available step/item
+ reader->Advance(adios::NEXT_AVAILABLE); // default
+ reader->Advance(adios::LATEST_AVAILABLE); // interested only in the
+ // latest data
}
- }
- catch (std::exception &e)
- {
- // some error happened while getting a chunk
- }
-
- reader->Release();
-
- // When AdvanceAsync returns new data is not yet available.
- // A callback will tell us when we have the new data (and we have the lock
- // on it to read)
- writer->AdvanceAsync(adios::NEXT_AVAILABLE, cb_AsyncReadAdvanceCompleted);
- // Do we need more fine grained control? Like this function does not get
- // the lock and so
- // do we need to call Advance() to get the lock?
+ // Close file/stream
+ reader->Close();
}
- reader->Close();
- }
- // Note: chunk reading also works if scheduling reads for specific variables
-
- // 4. Open it as file and see all steps at once.
- // Allow for reading multiple steps of a variable into a contiguous array
- try
- {
- rmethod.AddTransport(
- "BP"); // Set a file engine here. Shall we have RemoveTransport() too?
-
- // Open a file with all steps immediately available
- std::shared_ptr<adios::Engine> reader = adios.OpenFileReader(
- "filename.bp", comm, rmethod, adios::COLLECTIVE_IO);
-
- /* NX */
- /* There is a single value for each step. We can read all into a 1D array
- * with a step selection.
- * Steps are not automatically presented as an array dimension and read does
- * not read it as array.
- */
- // We can also just conveniently get the first step with a simple read
- // statement.
- reader->Read<unsigned int>(
- "NX", &NX); // read a Global scalar which has a single value in a step
- reader->Read<unsigned int>(
- varNX, &NX); // read a Global scalar which has a single value in a step
-
- adios::Variable<void> varNXread = reader->InquireVariable("NX");
- adios::Variable<unsigned int> varNXreadint =
- reader->InquireVariableInt("NX");
- std::vector<unsigned int> Nxs(
- varNXread.GetSteps()); // number of steps available
- // make a StepSelection to select multiple steps. Args: From, #of
- // consecutive steps
- adios::StepSelection stepsNx(0, varNXread.GetSteps());
- // ? How do we make a selection for an arbitrary list of steps ?
- varNXread.SetStepSelection(stepsNx);
- reader->Read<unsigned int>(varNXreadint, Nxs.data());
- reader->Read<void>(varNXread, Nxs.data());
-
- auto itmax = std::max_element(std::begin(Nxs), std::end(Nxs));
- auto itmin = std::min_element(std::begin(Nxs), std::end(Nxs));
- if (*itmin != *itmax)
+ catch (adios::end_of_stream &e)
+ {
+ // Reached end of stream, end processing loop
+ // Close file/stream
+ reader->Close();
+ }
+ catch (adios::file_not_found &e)
+ {
+ // File/stream does not exist, quit
+ }
+
+ // 2. Open a stream, where each item from the writers will get to a single
+ // reader only
+ // If the writers are collective, that means a whole steps go to different
+ // readers
+ // If the writers are independent, that means each writer's output goes to
+ // different readers
+ // Also show here ScheduleRead/PerformRead
+ // try
+ {
+ rmethod.SetReadMultiplexPattern(
+ adios::FIFO_READERS); // Each reader process
+ // sees everything
+ // from the stream
+ rmethod.SetStreamOpenMode(
+ adios::WAITFORSTREAM); // In Open(), wait for the
+ // first step appear
+ // (default)
+
+ // Open a stream
+ std::shared_ptr<adios::Engine> reader = adios.Open(
+ "filename.bp", "r", comm, rmethod, adios::IOMode::INDEPENDENT,
+ /*timeout_sec=*/300.0); // wait this long for the stream, return
+ // error
+ // afterwards
+
+ while (true)
+ {
+ // Make a selection to describe the local dimensions of the variable
+ // we
+ // READ and
+ // its offsets in the global spaces if we know this somehow
+ adios::Selection bbsel = adios.SelectionBoundingBox(
+ {1, NX}, {0, 0}); // local dims and offsets; both as list
+ var2D->SetSelection(bbsel);
+ reader->Read<double>(var2D, *Temperature);
+
+ // Let ADIOS allocate space for the incoming (per-writer) item
+ double *data = reader->Read<double>(var2D);
+
+ // promise to not read more from this step/item
+ reader->Release();
+
+ // want to move on to the next available step/item
+ reader->Advance(); // default
+ reader->Advance(
+ adios::LATEST_AVAILABLE); // This should be an error, or
+ // could it make sense?
+ }
+ reader->Close();
+ }
+
+ // 3. Open a stream and return immediately, not waiting for data to appear
+ // In this mode we cannot inquiry variables, but can schedule reads
+ // try
+ {
+ rmethod.SetReadMultiplexPattern(adios::GLOBAL_READERS); // Each reader
+ // process sees
+ // everything from
+ // the stream
+ rmethod.SetStreamOpenMode(
+ adios::NOWAITFORSTREAM); // In Open(), wait for
+ // the first step appear
+ // (default)
+
+ // Open a stream
+ std::shared_ptr<adios::Engine> reader = adios.Open(
+ "filename.bp", "r", comm, rmethod, adios::IOMode::INDEPENDENT);
+
+ while (true)
+ {
+
+ // Let ADIOS allocate space for the incoming (per-writer) item
+ reader->ScheduleRead(); // read whatever comes
+
+ // One way is to handle the incoming data through a callback (which
+ // will
+ // be called in a thread)
+ // void cb( const void *data, std::string doid, std::string var,
+ // std::string dtype, std::vector<std::size_t> varshape );
+ // void cb( adios::VARCHUNK * chunk ); // see adios1 for VARCHUNK
+ reader->SetReadCallback(cb);
+ reader->PerformReads(adios::NONBLOCKINGREAD);
+
+ // Another way is checking back manually like in adios1 and
+ // processing
+ // chunks
+ reader->PerformReads(adios::NONBLOCKINGREAD);
+ int ck;
+ adios::VARCHUNK *chunk;
+ try
+ {
+ while ((ck = reader->CheckReads(&chunk)) > 0)
+ {
+ if (chunk)
+ {
+ // process the chunk first
+ // ...
+ // free memory of chunk (not the data!)
+ adios::FreeChunk(chunk);
+ }
+ else
+ {
+ // no chunk was returned, slow down a little
+ sleep(1);
+ }
+ }
+ }
+ catch (std::exception &e)
+ {
+ // some error happened while getting a chunk
+ }
+
+ reader->Release();
+
+ // When AdvanceAsync returns new data is not yet available.
+ // A callback will tell us when we have the new data (and we have
+ // the lock
+ // on it to read)
+ writer->AdvanceAsync(adios::NEXT_AVAILABLE,
+ cb_AsyncReadAdvanceCompleted);
+ // Do we need more fine grained control? Like this function does not
+ // get
+ // the lock and so
+ // do we need to call Advance() to get the lock?
+ }
+ reader->Close();
+ }
+ // Note: chunk reading also works if scheduling reads for specific variables
+
+ // 4. Open it as file and see all steps at once.
+ // Allow for reading multiple steps of a variable into a contiguous array
+ try
+ {
+ rmethod.AddTransport("BP"); // Set a file engine here. Shall we have
+ // RemoveTransport() too?
+
+ // Open a file with all steps immediately available
+ std::shared_ptr<adios::Engine> reader = adios.OpenFileReader(
+ "filename.bp", comm, rmethod, adios::COLLECTIVE_IO);
+
+ /* NX */
+ /* There is a single value for each step. We can read all into a 1D
+ * array
+ * with a step selection.
+ * Steps are not automatically presented as an array dimension and read
+ * does
+ * not read it as array.
+ */
+ // We can also just conveniently get the first step with a simple read
+ // statement.
+ reader->Read<unsigned int>(
+ "NX",
+ &NX); // read a Global scalar which has a single value in a step
+ reader->Read<unsigned int>(
+ varNX,
+ &NX); // read a Global scalar which has a single value in a step
+
+ adios::Variable<void> varNXread = reader->InquireVariable("NX");
+ adios::Variable<unsigned int> varNXreadint =
+ reader->InquireVariableInt("NX");
+ std::vector<unsigned int> Nxs(
+ varNXread.GetSteps()); // number of steps available
+ // make a StepSelection to select multiple steps. Args: From, #of
+ // consecutive steps
+ adios::StepSelection stepsNx(0, varNXread.GetSteps());
+ // ? How do we make a selection for an arbitrary list of steps ?
+ varNXread.SetStepSelection(stepsNx);
+ reader->Read<unsigned int>(varNXreadint, Nxs.data());
+ reader->Read<void>(varNXread, Nxs.data());
+
+ auto itmax = std::max_element(std::begin(Nxs), std::end(Nxs));
+ auto itmin = std::min_element(std::begin(Nxs), std::end(Nxs));
+ if (*itmin != *itmax)
+ {
+ throw std::ios_base::failure(
+ "ERROR: NX is not the same at all steps!\n");
+ }
+
+ /* Nparts */
+ // Nparts local scalar is presented as a 1D array of nproc elements.
+ // We can read all steps into a 2D array of nproc * nsteps
+ adios::Variable<void> varNpartsread = reader->InquireVariable("Nparts");
+ std::vector<int> partsV(Nproc * varNpartsread->GetSteps());
+ varNpartsread->SetStepSelection(
+ adios.StepSelection(0, varNpartsread.GetSteps()));
+ reader->Read<int>("Nparts", partsV.data());
+ reader->Read<void>(varNpartsread,
+ partsV.data()); // missing spatial selection = whole
+ // array at each step
+
+ // Close file/stream
+ reader->Close();
+ }
+ catch (adios::file_not_found &e)
{
- throw std::ios_base::failure("ERROR: NX is not the same at all steps!\n");
+ // File/stream does not exist, quit
}
- /* Nparts */
- // Nparts local scalar is presented as a 1D array of nproc elements.
- // We can read all steps into a 2D array of nproc * nsteps
- adios::Variable<void> varNpartsread = reader->InquireVariable("Nparts");
- std::vector<int> partsV(Nproc * varNpartsread->GetSteps());
- varNpartsread->SetStepSelection(
- adios.StepSelection(0, varNpartsread.GetSteps()));
- reader->Read<int>("Nparts", partsV.data());
- reader->Read<void>(
- varNpartsread,
- partsV.data()); // missing spatial selection = whole array at each step
-
- // Close file/stream
- reader->Close();
- }
- catch (adios::file_not_found &e)
- {
- // File/stream does not exist, quit
- }
-
- return 0;
+ return 0;
}
diff --git a/examples/globalArray/globalArrayNoXML.cpp b/examples/globalArray/globalArrayNoXML.cpp
index e8f96975ee3f22a19ec21cc8389edc2b967088bc..64f33e42dce0cf2e0b66427b17d6abf7661477d0 100644
--- a/examples/globalArray/globalArrayNoXML.cpp
+++ b/examples/globalArray/globalArrayNoXML.cpp
@@ -19,105 +19,108 @@
int main(int argc, char *argv[])
{
- int rank, size;
- const int NX = 10;
- double t[NX];
- std::vector<double> p(NX);
- MPI_Comm comm = MPI_COMM_WORLD;
+ int rank, size;
+ const int NX = 10;
+ double t[NX];
+ std::vector<double> p(NX);
+ MPI_Comm comm = MPI_COMM_WORLD;
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(comm, &rank);
- MPI_Comm_size(comm, &size);
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(comm, &rank);
+ MPI_Comm_size(comm, &size);
- try
- {
- // ADIOS manager object creation. MPI must be initialized
- adios::ADIOS adios("globalArrayNoXML.xml", comm, true);
-
- // set a maximum buffersize that ADIOS can use (for one group).
- // multiple groups may use each such buffersize if they are overlapped or
- // use time-aggregation or use zero-copy staging
-
- // Define Group and its variables
- // The group's transport can be defined at runtime in the input XML file
- adios.CreateGroup("arrays");
-
- // Set the maximum buffersize for this group. This must happen before
- // defining a zero copy variable, which will cause the group's internal
- // buffer
- // allocated (during the variable definition call)
- // adios.SetMaxBuffersize ("arrays", 10000000);
-
- adios.CreateVariable("arrays", "NX", "int"); // scalar variable
- adios.CreateVariable("arrays", "size", "int");
- adios.CreateVariable("arrays", "size", "rank");
-
- // define a 2D array with 1D decomposition
- adios.CreateVariable("arrays", "temperature", "double", "1,NX", "NONE",
- "size,NX", "rank,0");
-
- // // set a variable-level transformation for this variable
- // adios.SetVariableTransform ("arrays", "temperature", "none");
-
- adios.CreateVariable("arrays", "pressure", "std::vector<double>", "1,NX",
- "size,NX", "rank,0");
-
- // set a group-level transport
- adios.SetTransport("arrays", "time-aggregate"); // no options passed here
-
- // Get Monitor info
- std::ofstream logStream("info_" + std::to_string(rank) + ".log");
- adios.MonitorGroups(logStream);
-
- adios.Open("arrays", "globalArray.bp", "w", 100000000);
-
- for (int it = 1; it <= 13; it++)
+ try
{
-
- for (int i = 0; i < NX; i++)
- {
- t[i] = it * 100.0 + rank * NX + i;
- p[i] = it * 1000.0 + rank * NX + i;
- }
-
- // if (it==1)
- //
- // else
- // adios.Open("arrays", "globalArray.bp", "a", 100000000 );
-
- // uint64_t adios_groupsize, adios_totalsize;
- // adios_groupsize = 4 + 4 + 4 + 2*NX*sizeof(double);
- // adios_totalsize = adios.GroupSize("arrays", adios_groupsize);
-
- adios.Write("arrays", "NX", &NX);
- adios.Write("arrays", "size", &size);
- adios.Write("arrays", "rank", &rank);
- adios.Write("arrays", "temperature", t);
- adios.Write("arrays", "pressure", &p);
-
- MPI_Barrier(comm);
- if (rank == 0)
- printf("Timestep %d written\n", it);
+ // ADIOS manager object creation. MPI must be initialized
+ adios::ADIOS adios("globalArrayNoXML.xml", comm, true);
+
+ // set a maximum buffersize that ADIOS can use (for one group).
+ // multiple groups may use each such buffersize if they are overlapped
+ // or
+ // use time-aggregation or use zero-copy staging
+
+ // Define Group and its variables
+ // The group's transport can be defined at runtime in the input XML file
+ adios.CreateGroup("arrays");
+
+ // Set the maximum buffersize for this group. This must happen before
+ // defining a zero copy variable, which will cause the group's internal
+ // buffer
+ // allocated (during the variable definition call)
+ // adios.SetMaxBuffersize ("arrays", 10000000);
+
+ adios.CreateVariable("arrays", "NX", "int"); // scalar variable
+ adios.CreateVariable("arrays", "size", "int");
+ adios.CreateVariable("arrays", "size", "rank");
+
+ // define a 2D array with 1D decomposition
+ adios.CreateVariable("arrays", "temperature", "double", "1,NX", "NONE",
+ "size,NX", "rank,0");
+
+ // // set a variable-level transformation for this variable
+ // adios.SetVariableTransform ("arrays", "temperature", "none");
+
+ adios.CreateVariable("arrays", "pressure", "std::vector<double>",
+ "1,NX", "size,NX", "rank,0");
+
+ // set a group-level transport
+ adios.SetTransport("arrays",
+ "time-aggregate"); // no options passed here
+
+ // Get Monitor info
+ std::ofstream logStream("info_" + std::to_string(rank) + ".log");
+ adios.MonitorGroups(logStream);
+
+ adios.Open("arrays", "globalArray.bp", "w", 100000000);
+
+ for (int it = 1; it <= 13; it++)
+ {
+
+ for (int i = 0; i < NX; i++)
+ {
+ t[i] = it * 100.0 + rank * NX + i;
+ p[i] = it * 1000.0 + rank * NX + i;
+ }
+
+ // if (it==1)
+ //
+ // else
+ // adios.Open("arrays", "globalArray.bp", "a",
+ // 100000000 );
+
+ // uint64_t adios_groupsize, adios_totalsize;
+ // adios_groupsize = 4 + 4 + 4 + 2*NX*sizeof(double);
+ // adios_totalsize = adios.GroupSize("arrays", adios_groupsize);
+
+ adios.Write("arrays", "NX", &NX);
+ adios.Write("arrays", "size", &size);
+ adios.Write("arrays", "rank", &rank);
+ adios.Write("arrays", "temperature", t);
+ adios.Write("arrays", "pressure", &p);
+
+ MPI_Barrier(comm);
+ if (rank == 0)
+ printf("Timestep %d written\n", it);
+ }
+
+ adios.Close("arrays");
+
+ MPI_Barrier(comm);
+ // need barrier before we destroy the ADIOS object here automatically
+ if (rank == 0)
+ printf("Finalize adios\n");
}
-
- adios.Close("arrays");
-
- MPI_Barrier(comm);
- // need barrier before we destroy the ADIOS object here automatically
- if (rank == 0)
- printf("Finalize adios\n");
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
+ catch (std::exception &e) // need to think carefully how to handle C++
+ // exceptions with MPI to avoid deadlocking
{
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << e.what() << "\n";
+ }
}
- }
- if (rank == 0)
- printf("Finalize MPI\n");
- MPI_Finalize();
- return 0;
+ if (rank == 0)
+ printf("Finalize MPI\n");
+ MPI_Finalize();
+ return 0;
}
diff --git a/examples/globalArray/globalArrayXML.cpp b/examples/globalArray/globalArrayXML.cpp
index 9d3285df6295b0d6b605bcfc0f92b8d49872a779..c25d046e32cb1fcef4a77c8049d3ebef6444108b 100644
--- a/examples/globalArray/globalArrayXML.cpp
+++ b/examples/globalArray/globalArrayXML.cpp
@@ -19,80 +19,81 @@
int main(int argc, char *argv[])
{
- int rank, size;
- const int NX = 10;
- double t[NX];
- std::vector<double> p(NX);
- MPI_Comm comm = MPI_COMM_WORLD;
+ int rank, size;
+ const int NX = 10;
+ double t[NX];
+ std::vector<double> p(NX);
+ MPI_Comm comm = MPI_COMM_WORLD;
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(comm, &rank);
- MPI_Comm_size(comm, &size);
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(comm, &rank);
+ MPI_Comm_size(comm, &size);
- try
- {
- // ADIOS manager object creation. MPI must be initialized
- adios::ADIOS adios("globalArrayXML.xml", comm, true);
+ try
+ {
+ // ADIOS manager object creation. MPI must be initialized
+ adios::ADIOS adios("globalArrayXML.xml", comm, true);
- adios::ADIOS_OUTPUT &ckptfile =
- adios.Open("globalArray.bp", comm, "a", "POSIX");
+ adios::ADIOS_OUTPUT &ckptfile =
+ adios.Open("globalArray.bp", comm, "a", "POSIX");
- adios::ADIOS_OUTPUT ckptfile("globalArray.bp", subcomm, "a", "POSIX");
- // adios::ADIOS_OUTPUT *ckptfile = adios.Open( "globalArray.bp", "POSIX");
+ adios::ADIOS_OUTPUT ckptfile("globalArray.bp", subcomm, "a", "POSIX");
+ // adios::ADIOS_OUTPUT *ckptfile = adios.Open( "globalArray.bp",
+ // "POSIX");
- // Get Monitor info
- std::ofstream logStream("info_" + std::to_string(rank) + ".log");
- adios.MonitorGroups(logStream);
+ // Get Monitor info
+ std::ofstream logStream("info_" + std::to_string(rank) + ".log");
+ adios.MonitorGroups(logStream);
- for (int it = 1; it <= 13; it++)
- {
+ for (int it = 1; it <= 13; it++)
+ {
- for (int i = 0; i < NX; i++)
- {
- t[i] = it * 100.0 + rank * NX + i;
- p[i] = it * 1000.0 + rank * NX + i;
- }
+ for (int i = 0; i < NX; i++)
+ {
+ t[i] = it * 100.0 + rank * NX + i;
+ p[i] = it * 1000.0 + rank * NX + i;
+ }
- // if (it==1)
- // adios.Open("arrays", "globalArray.bp", "w");
- // else
- // adios.Open("arrays", "globalArray.bp", "a");
+ // if (it==1)
+ // adios.Open("arrays", "globalArray.bp", "w");
+ // else
+ // adios.Open("arrays", "globalArray.bp", "a");
- // uint64_t adios_groupsize, adios_totalsize;
- // adios_groupsize = 4 + 4 + 4 + 2*NX*sizeof(double);
- // adios_totalsize = adios.GroupSize("arrays", adios_groupsize);
+ // uint64_t adios_groupsize, adios_totalsize;
+ // adios_groupsize = 4 + 4 + 4 + 2*NX*sizeof(double);
+ // adios_totalsize = adios.GroupSize("arrays", adios_groupsize);
- ckptfile.Write("NX", &NX);
- ckptfile.Write("pressure", &p);
- // adios.Write ("arrays", "NX", &NX);
- // adios.Write ("arrays", "size", &size);
- // adios.Write ("arrays", "rank", &rank);
- // adios.Write ("arrays", "temperature", t);
- // adios.Write ("arrays", "pressure", &p);
+ ckptfile.Write("NX", &NX);
+ ckptfile.Write("pressure", &p);
+ // adios.Write ("arrays", "NX", &NX);
+ // adios.Write ("arrays", "size", &size);
+ // adios.Write ("arrays", "rank", &rank);
+ // adios.Write ("arrays", "temperature", t);
+ // adios.Write ("arrays", "pressure", &p);
- // adios.Close ("arrays");
- ckptfile.PerformIO();
- MPI_Barrier(comm);
- if (rank == 0)
- printf("Timestep %d written\n", it);
+ // adios.Close ("arrays");
+ ckptfile.PerformIO();
+ MPI_Barrier(comm);
+ if (rank == 0)
+ printf("Timestep %d written\n", it);
+ }
+ MPI_Barrier(comm);
+ ckptfile.Close();
+ // need barrier before we destroy the ADIOS object here automatically
+ if (rank == 0)
+ printf("Finalize adios\n");
}
- MPI_Barrier(comm);
- ckptfile.Close();
- // need barrier before we destroy the ADIOS object here automatically
- if (rank == 0)
- printf("Finalize adios\n");
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
+ catch (std::exception &e) // need to think carefully how to handle C++
+ // exceptions with MPI to avoid deadlocking
{
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << e.what() << "\n";
+ }
}
- }
- if (rank == 0)
- printf("Finalize MPI\n");
- MPI_Finalize();
- return 0;
+ if (rank == 0)
+ printf("Finalize MPI\n");
+ MPI_Finalize();
+ return 0;
}
diff --git a/examples/globalArray/globalArrayZeroCopy.cpp b/examples/globalArray/globalArrayZeroCopy.cpp
index 8206c131aa9388f39618f064c8b98ecdfacf2c42..a85b5dc56e77f55430e8c21920248cf196c22a2f 100644
--- a/examples/globalArray/globalArrayZeroCopy.cpp
+++ b/examples/globalArray/globalArrayZeroCopy.cpp
@@ -19,109 +19,111 @@
int main(int argc, char *argv[])
{
- int rank, size;
- const int NX = 10;
- MPI_Comm comm = MPI_COMM_WORLD;
-
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(comm, &rank);
- MPI_Comm_size(comm, &size);
-
- try
- {
- // ADIOS manager object creation. MPI must be initialized
- adios::ADIOS adios("globalArrayNoXML.xml", comm, true);
-
- // set a maximum buffersize that ADIOS can use (for one group).
- // multiple groups may use each such buffersize if they are overlapped or
- // use time-aggregation or use zero-copy staging
- adios.SetMaxBuffersize(100000000);
-
- // Define Group and its variables
- // The group's transport can be defined at runtime in the input XML file
- adios.CreateGroup("arrays", adios_stat_default);
-
- // Set the maximum buffersize for this group. This must happen before
- // defining a zero copy variable, which will cause the group's internal
- // buffer
- // allocated (during the variable definition call)
- adios.SetMaxBuffersize("arrays", 10000000);
-
- adios.DefineVariable("arrays", "NX", "int"); // scalar variable
- adios.DefineVariable("arrays", "size", "int");
- adios.DefineVariable("arrays", "size", "rank");
-
- // Define and allocate a 2D array with 1D decomposition and get back a
- // pre-allocated typed pointer.
- // The size of the array must be known at this point, so no scalar variables
- // can
- // be used for its dimensions.
- std::string ldim = "1," + std::to_string(NX); // == "1,10" if NX==10
- std::string gdim = std::to_string(size) + "," + std::to_string(NX);
- std::string offs = std::to_string(rank) + ",0";
-
- double *t = adios.DefineZeroCopyVariable("arrays", "temperature", "double",
- ldim, gdim, offs);
-
- // set a variable-level transformation for this variable
- adios.SetVariableTransform("arrays", "temperature", "none");
-
- std::vector<double> p = adios.DefineZeroCopyVariable(
- "arrays", "pressure", "std::vector<double>", ldim, gdim, offs);
-
- // set a group-level transformation
- adios.SetGroupTransform("arrays", "time-aggregate",
- ""); // no options passed here
-
- // Get Monitor info
- std::ofstream logStream("info_" + std::to_string(rank) + ".log");
- adios.MonitorGroups(logStream);
-
- for (int it = 1; it <= 13; it++)
- {
+ int rank, size;
+ const int NX = 10;
+ MPI_Comm comm = MPI_COMM_WORLD;
+
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(comm, &rank);
+ MPI_Comm_size(comm, &size);
- for (int i = 0; i < NX; i++)
- {
- t[i] = it * 100.0 + rank * NX + i;
- p[i] = it * 1000.0 + rank * NX + i;
- }
-
- if (it == 1)
- adios.Open("arrays", "globalArray.bp", "w");
- else
- adios.Open("arrays", "globalArray.bp", "a");
-
- // uint64_t adios_groupsize, adios_totalsize;
- // adios_groupsize = 4 + 4 + 4 + 2*NX*sizeof(double);
- // adios_totalsize = adios.GroupSize("arrays", adios_groupsize);
-
- adios.Write("arrays", "NX", &NX);
- adios.Write("arrays", "size", &size);
- adios.Write("arrays", "rank", &rank);
- adios.Write("arrays", "temperature", t);
- adios.Write("arrays", "pressure", &p);
-
- adios.Close("arrays");
- MPI_Barrier(comm);
- if (rank == 0)
- printf("Timestep %d written\n", it);
+ try
+ {
+ // ADIOS manager object creation. MPI must be initialized
+ adios::ADIOS adios("globalArrayNoXML.xml", comm, true);
+
+ // set a maximum buffersize that ADIOS can use (for one group).
+ // multiple groups may use each such buffersize if they are overlapped
+ // or
+ // use time-aggregation or use zero-copy staging
+ adios.SetMaxBuffersize(100000000);
+
+ // Define Group and its variables
+ // The group's transport can be defined at runtime in the input XML file
+ adios.CreateGroup("arrays", adios_stat_default);
+
+ // Set the maximum buffersize for this group. This must happen before
+ // defining a zero copy variable, which will cause the group's internal
+ // buffer
+ // allocated (during the variable definition call)
+ adios.SetMaxBuffersize("arrays", 10000000);
+
+ adios.DefineVariable("arrays", "NX", "int"); // scalar variable
+ adios.DefineVariable("arrays", "size", "int");
+ adios.DefineVariable("arrays", "size", "rank");
+
+ // Define and allocate a 2D array with 1D decomposition and get back a
+ // pre-allocated typed pointer.
+ // The size of the array must be known at this point, so no scalar
+ // variables
+ // can
+ // be used for its dimensions.
+ std::string ldim = "1," + std::to_string(NX); // == "1,10" if NX==10
+ std::string gdim = std::to_string(size) + "," + std::to_string(NX);
+ std::string offs = std::to_string(rank) + ",0";
+
+ double *t = adios.DefineZeroCopyVariable("arrays", "temperature",
+ "double", ldim, gdim, offs);
+
+ // set a variable-level transformation for this variable
+ adios.SetVariableTransform("arrays", "temperature", "none");
+
+ std::vector<double> p = adios.DefineZeroCopyVariable(
+ "arrays", "pressure", "std::vector<double>", ldim, gdim, offs);
+
+ // set a group-level transformation
+ adios.SetGroupTransform("arrays", "time-aggregate",
+ ""); // no options passed here
+
+ // Get Monitor info
+ std::ofstream logStream("info_" + std::to_string(rank) + ".log");
+ adios.MonitorGroups(logStream);
+
+ for (int it = 1; it <= 13; it++)
+ {
+
+ for (int i = 0; i < NX; i++)
+ {
+ t[i] = it * 100.0 + rank * NX + i;
+ p[i] = it * 1000.0 + rank * NX + i;
+ }
+
+ if (it == 1)
+ adios.Open("arrays", "globalArray.bp", "w");
+ else
+ adios.Open("arrays", "globalArray.bp", "a");
+
+ // uint64_t adios_groupsize, adios_totalsize;
+ // adios_groupsize = 4 + 4 + 4 + 2*NX*sizeof(double);
+ // adios_totalsize = adios.GroupSize("arrays", adios_groupsize);
+
+ adios.Write("arrays", "NX", &NX);
+ adios.Write("arrays", "size", &size);
+ adios.Write("arrays", "rank", &rank);
+ adios.Write("arrays", "temperature", t);
+ adios.Write("arrays", "pressure", &p);
+
+ adios.Close("arrays");
+ MPI_Barrier(comm);
+ if (rank == 0)
+ printf("Timestep %d written\n", it);
+ }
+ MPI_Barrier(comm);
+ // need barrier before we destroy the ADIOS object here automatically
+ if (rank == 0)
+ printf("Finalize adios\n");
}
- MPI_Barrier(comm);
- // need barrier before we destroy the ADIOS object here automatically
- if (rank == 0)
- printf("Finalize adios\n");
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
+ catch (std::exception &e) // need to think carefully how to handle C++
+ // exceptions with MPI to avoid deadlocking
{
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << e.what() << "\n";
+ }
}
- }
- if (rank == 0)
- printf("Finalize MPI\n");
- MPI_Finalize();
- return 0;
+ if (rank == 0)
+ printf("Finalize MPI\n");
+ MPI_Finalize();
+ return 0;
}
diff --git a/examples/groupless/basic/reader.cpp b/examples/groupless/basic/reader.cpp
index ea8832438a92fc97b1ceb5c78efe033079d18b4c..1e91476b27d48444819de5f303b1f1dcdf82f576 100644
--- a/examples/groupless/basic/reader.cpp
+++ b/examples/groupless/basic/reader.cpp
@@ -16,178 +16,183 @@
int main(int argc, char *argv[])
{
- int rank, nproc;
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- MPI_Comm_size(MPI_COMM_WORLD, &nproc);
- const bool adiosDebug = true;
-
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
-
- // Application variable
- std::vector<double> NiceArray;
- std::vector<float> RaggedArray;
- unsigned int Nx;
- int Nparts;
- int Nwriters;
-
- try
- {
- // Define method for engine creation
- // 1. Get method def from config file or define new one
- adios::Method &bpReaderSettings = adios.GetMethod("input");
- if (bpReaderSettings.undeclared())
+ int rank, nproc;
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &nproc);
+ const bool adiosDebug = true;
+
+ adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
+
+ // Application variable
+ std::vector<double> NiceArray;
+ std::vector<float> RaggedArray;
+ unsigned int Nx;
+ int Nparts;
+ int Nwriters;
+
+ try
{
- // if not defined by user, we can change the default settings
- bpReaderSettings.SetEngine("BP"); // BP is the default engine
- }
-
- // Create engine smart pointer due to polymorphism,
- // Default behavior
- // auto bpReader = adios.Open( "myNumbers.bp", "r" );
- // this would just open with a default transport, which is "BP"
- auto bpReader = adios.Open("myNumbers.bp", "r", bpReaderSettings);
-
- // All the above is same as default use:
- // auto bpReader = adios.Open( "myNumbers.bp", "r");
-
- if (bpReader == nullptr)
- throw std::ios_base::failure("ERROR: failed to open ADIOS bpReader\n");
-
- /* Variable names are available as a vector of strings */
- std::cout << "List of variables in file: " << bpReader->VariableNames
- << "\n";
-
- /* NX */
- bpReader->Read<unsigned int>(
- "NX", Nx); // read a Global scalar which has a single value in a step
-
- /* nproc */
- bpReader->Read<int>("nproc", Nwriters); // also a global scalar
-
- /* Nparts */
- // Nparts local scalar is presented as a 1D array of Nwriters elements.
- // We need to read a specific value the same way as reading from any 1D
- // array.
- // Make a single-value selection to describe our rank's position in the
- // 1D array of Nwriters values.
- if (rank < Nwriters)
- {
- std::shared_ptr<adios::Variable> varNparts =
- bpReader.InquiryVariable("Nparts");
- std::unique_ptr<adios::Selection> selNparts =
- adios.SelectionBoundingBox({1}, {rank});
- varNparts->SetSelection(selNparts);
- bpReader->Read<int>(varNparts, Nparts);
- }
- // or we could just read the whole array by every process
- std::vector<int> partsV(Nwriters);
- bpReader->Read<int>(
- "Nparts",
- partsV
- .data()); // read with string name, no selection => read whole array
-
- std::vector<int> partsV;
- bpReader->Read<int>(
- "Nparts",
- partsV); // read with string name, no selection => read whole array
- (Nwriters == partsV.size())
-
- /* Nice */
+ // Define method for engine creation
+ // 1. Get method def from config file or define new one
+ adios::Method &bpReaderSettings = adios.GetMethod("input");
+ if (bpReaderSettings.undeclared())
+ {
+ // if not defined by user, we can change the default settings
+ bpReaderSettings.SetEngine("BP"); // BP is the default engine
+ }
+
+ // Create engine smart pointer due to polymorphism,
+ // Default behavior
+ // auto bpReader = adios.Open( "myNumbers.bp", "r" );
+ // this would just open with a default transport, which is "BP"
+ auto bpReader = adios.Open("myNumbers.bp", "r", bpReaderSettings);
+
+ // All the above is same as default use:
+ // auto bpReader = adios.Open( "myNumbers.bp", "r");
+
+ if (bpReader == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: failed to open ADIOS bpReader\n");
+
+ /* Variable names are available as a vector of strings */
+ std::cout << "List of variables in file: " << bpReader->VariableNames
+ << "\n";
+
+ /* NX */
+ bpReader->Read<unsigned int>(
+ "NX",
+ Nx); // read a Global scalar which has a single value in a step
+
+ /* nproc */
+ bpReader->Read<int>("nproc", Nwriters); // also a global scalar
+
+ /* Nparts */
+ // Nparts local scalar is presented as a 1D array of Nwriters elements.
+ // We need to read a specific value the same way as reading from any 1D
+ // array.
+ // Make a single-value selection to describe our rank's position in the
+ // 1D array of Nwriters values.
+ if (rank < Nwriters)
+ {
+ std::shared_ptr<adios::Variable> varNparts =
+ bpReader.InquiryVariable("Nparts");
+ std::unique_ptr<adios::Selection> selNparts =
+ adios.SelectionBoundingBox({1}, {rank});
+ varNparts->SetSelection(selNparts);
+ bpReader->Read<int>(varNparts, Nparts);
+ }
+ // or we could just read the whole array by every process
+ std::vector<int> partsV(Nwriters);
+ bpReader->Read<int>("Nparts",
+ partsV.data()); // read with string name, no
+ // selection => read whole array
+
+ std::vector<int> partsV;
+ bpReader->Read<int>("Nparts",
+ partsV); // read with string name, no selection =>
+ // read whole array
+ (Nwriters == partsV.size())
+
+ /* Nice */
+ // inquiry about a variable, whose name we know
+ std::shared_ptr<adios::Variable>
+ varNice = bpReader.InquiryVariable("Nice");
+
+ if (varNice == nullptr)
+ throw std::ios_base::failure("ERROR: failed to find variable "
+ "'myDoubles' in input file\n");
+
+ // ? how do we know about the type? std::string varNice->m_Type
+ uint64_t gdim =
+ varNice->m_GlobalDimensions[0]; // ?member var or member func?
+ uint64_t ldim = gdim / nproc;
+ uint64_t offs = rank * ldim;
+ if (rank == nproc - 1)
+ {
+ ldim = gdim - (ldim * gdim);
+ }
+
+ NiceArray.reserve(ldim);
+
+ // Make a 1D selection to describe the local dimensions of the variable
+ // we
+ // READ and
+ // its offsets in the global spaces
+ std::unique_ptr<adios::Selection> bbsel = adios.SelectionBoundingBox(
+ {ldim}, {offs}); // local dims and offsets; both as list
+ varNice->SetSelection(bbsel);
+ bpReader->Read<double>(varNice, NiceArray.data());
+
+ /* Ragged */
// inquiry about a variable, whose name we know
- std::shared_ptr<adios::Variable>
- varNice = bpReader.InquiryVariable("Nice");
-
- if (varNice == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to find variable 'myDoubles' in input file\n");
-
- // ? how do we know about the type? std::string varNice->m_Type
- uint64_t gdim =
- varNice->m_GlobalDimensions[0]; // ?member var or member func?
- uint64_t ldim = gdim / nproc;
- uint64_t offs = rank * ldim;
- if (rank == nproc - 1)
- {
- ldim = gdim - (ldim * gdim);
- }
-
- NiceArray.reserve(ldim);
-
- // Make a 1D selection to describe the local dimensions of the variable we
- // READ and
- // its offsets in the global spaces
- std::unique_ptr<adios::Selection> bbsel = adios.SelectionBoundingBox(
- {ldim}, {offs}); // local dims and offsets; both as list
- varNice->SetSelection(bbsel);
- bpReader->Read<double>(varNice, NiceArray.data());
-
- /* Ragged */
- // inquiry about a variable, whose name we know
- std::shared_ptr<adios::Variable<void>> varRagged =
- bpReader.InquiryVariable("Ragged");
- if (varRagged->m_GlobalDimensions[1] != adios::VARYING_DIMENSION)
- {
- throw std::ios_base::failure(
- "Unexpected condition: Ragged array's fast dimension "
- "is supposed to be VARYING_DIMENSION\n");
- }
- // We have here varRagged->sum_nblocks, nsteps, nblocks[], global
- if (rank < varRagged->nblocks[0]) // same as rank < Nwriters in this example
- {
- // get per-writer size information
- varRagged->InquiryBlocks();
- // now we have the dimensions per block
-
- unsigned long long int ldim = varRagged->blockinfo[rank].m_Dimensions[1];
- RaggedArray.resize(ldim);
-
- std::unique_ptr<adios::Selection> wbsel = adios.SelectionWriteblock(rank);
- varRagged->SetSelection(wbsel);
- bpReader->Read<float>(varRagged, RaggedArray.data());
-
- // We can use bounding box selection as well
- std::unique_ptr<adios::Selection> rbbsel =
- adios.SelectionBoundingBox({1, ldim}, {rank, 0});
- varRagged->SetSelection(rbbsel);
- bpReader->Read<float>(varRagged, RaggedArray.data());
+ std::shared_ptr<adios::Variable<void>> varRagged =
+ bpReader.InquiryVariable("Ragged");
+ if (varRagged->m_GlobalDimensions[1] != adios::VARYING_DIMENSION)
+ {
+ throw std::ios_base::failure(
+ "Unexpected condition: Ragged array's fast dimension "
+ "is supposed to be VARYING_DIMENSION\n");
+ }
+ // We have here varRagged->sum_nblocks, nsteps, nblocks[], global
+ if (rank <
+ varRagged->nblocks[0]) // same as rank < Nwriters in this example
+ {
+ // get per-writer size information
+ varRagged->InquiryBlocks();
+ // now we have the dimensions per block
+
+ unsigned long long int ldim =
+ varRagged->blockinfo[rank].m_Dimensions[1];
+ RaggedArray.resize(ldim);
+
+ std::unique_ptr<adios::Selection> wbsel =
+ adios.SelectionWriteblock(rank);
+ varRagged->SetSelection(wbsel);
+ bpReader->Read<float>(varRagged, RaggedArray.data());
+
+ // We can use bounding box selection as well
+ std::unique_ptr<adios::Selection> rbbsel =
+ adios.SelectionBoundingBox({1, ldim}, {rank, 0});
+ varRagged->SetSelection(rbbsel);
+ bpReader->Read<float>(varRagged, RaggedArray.data());
+ }
+
+ /* Extra help to process Ragged */
+ int maxRaggedDim =
+ varRagged->GetMaxGlobalDimensions(1); // contains the largest
+ std::vector<int> raggedDims = varRagged->GetVaryingGlobalDimensions(
+ 1); // contains all individual sizes in that dimension
+
+ // Close file/stream
+ bpReader->Close();
}
-
- /* Extra help to process Ragged */
- int maxRaggedDim =
- varRagged->GetMaxGlobalDimensions(1); // contains the largest
- std::vector<int> raggedDims = varRagged->GetVaryingGlobalDimensions(
- 1); // contains all individual sizes in that dimension
-
- // Close file/stream
- bpReader->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
+ catch (std::invalid_argument &e)
{
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
+ catch (std::ios_base::failure &e)
{
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
+ catch (std::exception &e)
{
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- MPI_Finalize();
+ MPI_Finalize();
- return 0;
+ return 0;
}
diff --git a/examples/groupless/basic/writer.cpp b/examples/groupless/basic/writer.cpp
index 33debd164199378814b12c12af7c74462e65d057..cbd556ccc1cabf313b470b22fd84da2ca8ca9409 100644
--- a/examples/groupless/basic/writer.cpp
+++ b/examples/groupless/basic/writer.cpp
@@ -21,143 +21,158 @@ typedef enum { VARYING_DIMENSION = -1, LOCAL_VALUE = 0, GLOBAL_VALUE = 1 };
int main(int argc, char *argv[])
{
- int rank, nproc;
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- MPI_Comm_size(MPI_COMM_WORLD, &nproc);
- const bool adiosDebug = true;
-
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
-
- // Application variable
- const unsigned int Nx = 10;
- const int Nparts = rand() % 6 + 5; // random size per process, 5..10 each
-
- std::vector<double> NiceArray(Nx);
- for (int i = 0; i < Nx; i++)
- {
- NiceArray[i] = rank * Nx + (double)i;
- }
-
- std::vector<float> RaggedArray(Nparts);
- for (int i = 0; i < Nparts; i++)
- {
- RaggedArray[i] = rank * Nx + (float)i;
- }
-
- try
- {
- // Define group and variables with transforms, variables don't have
- // functions, only group can access variables
- adios::Variable<unsigned int> &varNX = adios.DefineVariable<unsigned int>(
- "NX"); // global single-value across processes
- adios::Variable<int> &varNproc = adios.DefineVariable<int>(
- "nproc", adios::GLOBAL_VALUE); // same def for global value
- adios::Variable<int> &varNparts = adios.DefineVariable<int>(
- "Nparts",
- adios::LOCAL_VALUE); // a single-value different on every process
- adios::Variable<double> &varNice =
- adios.DefineVariable<double>("Nice", {nproc * Nx}); // 1D global array
- adios::Variable<float> &varRagged = adios.DefineVariable<float>(
- "Ragged", {nproc, adios::VARYING_DIMENSION}); // ragged array
-
- // add transform to variable in group...not executed (just testing API)
- adios::Transform bzip2 = adios::transform::BZIP2();
- varNice->AddTransform(bzip2, 1);
-
- // Define method for engine creation
- // 1. Get method def from config file or define new one
- adios::Method &bpWriterSettings = adios.GetMethod("output");
- if (bpWriterSettings.undeclared())
+ int rank, nproc;
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &nproc);
+ const bool adiosDebug = true;
+
+ adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
+
+ // Application variable
+ const unsigned int Nx = 10;
+ const int Nparts = rand() % 6 + 5; // random size per process, 5..10 each
+
+ std::vector<double> NiceArray(Nx);
+ for (int i = 0; i < Nx; i++)
{
- // if not defined by user, we can change the default settings
- bpWriterSettings.SetEngine("BP"); // BP is the default engine
- bpWriterSettings.AddTransport(
- "File", "lucky=yes"); // ISO-POSIX file is the default transport
- // Passing parameters to the transport
- bpWriterSettings.SetParameters("have_metadata_file",
- "yes"); // Passing parameters to the engine
- bpWriterSettings.SetParameters("Aggregation",
- (nproc + 1) / 2); // number of aggregators
+ NiceArray[i] = rank * Nx + (double)i;
}
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- // "w" means we overwrite any existing file on disk, but AdvanceStep will
- // append steps later.
- auto bpWriter = adios.Open("myNumbers.bp", "w", bpWriterSettings);
-
- if (bpWriter == nullptr)
- throw std::ios_base::failure("ERROR: failed to open ADIOS bpWriter\n");
+ std::vector<float> RaggedArray(Nparts);
+ for (int i = 0; i < Nparts; i++)
+ {
+ RaggedArray[i] = rank * Nx + (float)i;
+ }
- if (rank == 0)
+ try
{
- // Writing a global scalar from only one process
- bpWriter->Write<unsigned int>(varNX, Nx);
+ // Define group and variables with transforms, variables don't have
+ // functions, only group can access variables
+ adios::Variable<unsigned int> &varNX =
+ adios.DefineVariable<unsigned int>(
+ "NX"); // global single-value across processes
+ adios::Variable<int> &varNproc = adios.DefineVariable<int>(
+ "nproc", adios::GLOBAL_VALUE); // same def for global value
+ adios::Variable<int> &varNparts =
+ adios.DefineVariable<int>("Nparts",
+ adios::LOCAL_VALUE); // a single-value
+ // different on
+ // every process
+ adios::Variable<double> &varNice = adios.DefineVariable<double>(
+ "Nice", {nproc * Nx}); // 1D global array
+ adios::Variable<float> &varRagged = adios.DefineVariable<float>(
+ "Ragged", {nproc, adios::VARYING_DIMENSION}); // ragged array
+
+ // add transform to variable in group...not executed (just testing API)
+ adios::Transform bzip2 = adios::transform::BZIP2();
+ varNice->AddTransform(bzip2, 1);
+
+ // Define method for engine creation
+ // 1. Get method def from config file or define new one
+ adios::Method &bpWriterSettings = adios.GetMethod("output");
+ if (bpWriterSettings.undeclared())
+ {
+ // if not defined by user, we can change the default settings
+ bpWriterSettings.SetEngine("BP"); // BP is the default engine
+ bpWriterSettings.AddTransport(
+ "File",
+ "lucky=yes"); // ISO-POSIX file is the default transport
+ // Passing parameters to the transport
+ bpWriterSettings.SetParameters(
+ "have_metadata_file",
+ "yes"); // Passing parameters to the engine
+ bpWriterSettings.SetParameters("Aggregation",
+ (nproc + 1) /
+ 2); // number of aggregators
+ }
+
+ // Open returns a smart pointer to Engine containing the Derived class
+ // Writer
+ // "w" means we overwrite any existing file on disk, but AdvanceStep
+ // will
+ // append steps later.
+ auto bpWriter = adios.Open("myNumbers.bp", "w", bpWriterSettings);
+
+ if (bpWriter == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: failed to open ADIOS bpWriter\n");
+
+ if (rank == 0)
+ {
+ // Writing a global scalar from only one process
+ bpWriter->Write<unsigned int>(varNX, Nx);
+ }
+ // Writing a local scalar on every process. Will be shown at reading as
+ // a 1D
+ // array
+ bpWriter->Write<int>(varNparts, Nparts);
+
+ // Writing a global scalar on every process is useless. Information will
+ // be
+ // thrown away
+ // and only rank 0's data will be in the output
+ bpWriter->Write<int>(varNproc, nproc);
+
+ // Make a 1D selection to describe the local dimensions of the variable
+ // we
+ // write and
+ // its offsets in the global spaces
+ adios::Selection &sel = adios.SelectionBoundingBox(
+ {Nx}, {rank * Nx}); // local dims and offsets; both as list
+ varNice.SetSelection(sel);
+ bpWriter->Write<double>(varNice,
+ NiceArray.data()); // Base class Engine own
+ // the Write<T> that
+ // will call overloaded
+ // Write from Derived
+
+ adios::Selection &lsel =
+ adios.SelectionBoundingBox({1, Nparts}, {rank, 0});
+ varRagged.SetSelection(sel);
+ bpWriter->Write<float>(varRagged,
+ RaggedArray.data()); // Base class Engine
+ // own the Write<T>
+ // that will call
+ // overloaded Write
+ // from Derived
+
+ // Indicate we are done for this step
+ // N-to-M Aggregation, disk I/O will be performed during this call,
+ // unless
+ // time aggregation postpones all of that to some later step
+ bpWriter->Advance();
+ bpWriter->AdvanceAsync(callback_func_to_notify_me);
+
+ // Called once: indicate that we are done with this output for the run
+ bpWriter->Close();
}
- // Writing a local scalar on every process. Will be shown at reading as a 1D
- // array
- bpWriter->Write<int>(varNparts, Nparts);
-
- // Writing a global scalar on every process is useless. Information will be
- // thrown away
- // and only rank 0's data will be in the output
- bpWriter->Write<int>(varNproc, nproc);
-
- // Make a 1D selection to describe the local dimensions of the variable we
- // write and
- // its offsets in the global spaces
- adios::Selection &sel = adios.SelectionBoundingBox(
- {Nx}, {rank * Nx}); // local dims and offsets; both as list
- varNice.SetSelection(sel);
- bpWriter->Write<double>(varNice, NiceArray.data()); // Base class Engine own
- // the Write<T> that
- // will call overloaded
- // Write from Derived
-
- adios::Selection &lsel = adios.SelectionBoundingBox({1, Nparts}, {rank, 0});
- varRagged.SetSelection(sel);
- bpWriter->Write<float>(varRagged, RaggedArray.data()); // Base class Engine
- // own the Write<T>
- // that will call
- // overloaded Write
- // from Derived
-
- // Indicate we are done for this step
- // N-to-M Aggregation, disk I/O will be performed during this call, unless
- // time aggregation postpones all of that to some later step
- bpWriter->Advance();
- bpWriter->AdvanceAsync(callback_func_to_notify_me);
-
- // Called once: indicate that we are done with this output for the run
- bpWriter->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
+ catch (std::invalid_argument &e)
{
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
+ catch (std::ios_base::failure &e)
{
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
+ catch (std::exception &e)
{
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- MPI_Finalize();
+ MPI_Finalize();
- return 0;
+ return 0;
}
diff --git a/examples/groupless/compound/reader.cpp b/examples/groupless/compound/reader.cpp
index 6dc89ad4bd512c915409c6f1902c76739234d641..58a0e1fd69bb18293f1445ab082d2631683132b1 100644
--- a/examples/groupless/compound/reader.cpp
+++ b/examples/groupless/compound/reader.cpp
@@ -16,201 +16,207 @@
int main(int argc, char *argv[])
{
- int rank, nproc;
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- MPI_Comm_size(MPI_COMM_WORLD, &nproc);
- const bool adiosDebug = true;
-
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
-
- // Application variable
- // GSE === user-defined structure
- //
- // Like HDF5 example, read with a subset of the structure that was written.
- // Easily handled by FFS and HDF5, but ambitious for ADIOS
- typedef struct s2_t
- {
- double c;
- int a;
- };
- unsigned int Nx;
- int Nparts;
- int Nwriters;
-
- try
- {
- // Define method for engine creation
- // 1. Get method def from config file or define new one
- adios::Method &bpReaderSettings = adios.GetMethod("input");
- if (bpReaderSettings.undeclared())
+ int rank, nproc;
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &nproc);
+ const bool adiosDebug = true;
+
+ adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
+
+ // Application variable
+ // GSE === user-defined structure
+ //
+ // Like HDF5 example, read with a subset of the structure that was written.
+ // Easily handled by FFS and HDF5, but ambitious for ADIOS
+ typedef struct s2_t
{
- // if not defined by user, we can change the default settings
- bpReaderSettings.SetEngine("BP"); // BP is the default engine
- }
-
- // Create engine smart pointer due to polymorphism,
- // Default behavior
- // auto bpReader = adios.Open( "myNumbers.bp", "r" );
- // this would just open with a default transport, which is "BP"
- auto bpReader = adios.Open("myNumbers.bp", "r", bpReaderSettings);
-
- // All the above is same as default use:
- // auto bpReader = adios.Open( "myNumbers.bp", "r");
-
- if (bpReader == nullptr)
- throw std::ios_base::failure("ERROR: failed to open ADIOS bpReader\n");
-
- /* Variable names are available as a vector of strings */
- std::cout << "List of variables in file: " << bpReader->VariableNames
- << "\n";
-
- /* NX */
- bpReader->Read<unsigned int>(
- "NX", Nx); // read a Global scalar which has a single value in a step
-
- /* nproc */
- bpReader->Read<int>("nproc", Nwriters); // also a global scalar
-
- /* Nparts */
- // Nparts local scalar is presented as a 1D array of Nwriters elements.
- // We need to read a specific value the same way as reading from any 1D
- // array.
- // Make a single-value selection to describe our rank's position in the
- // 1D array of Nwriters values.
- if (rank < Nwriters)
+ double c;
+ int a;
+ };
+ unsigned int Nx;
+ int Nparts;
+ int Nwriters;
+
+ try
{
- std::shared_ptr<adios::Variable> varNparts =
- bpReader.InquiryVariable("Nparts");
- std::unique_ptr<adios::Selection> selNparts =
- adios.SelectionBoundingBox({1}, {rank});
- varNparts->SetSelection(selNparts);
- bpReader->Read<int>(varNparts, Nparts);
- }
- // or we could just read the whole array by every process
- std::vector<int> partsV(Nwriters);
- bpReader->Read<int>(
- "Nparts",
- partsV
- .data()); // read with string name, no selection => read whole array
-
- std::vector<int> partsV;
- bpReader->Read<int>(
- "Nparts",
- partsV); // read with string name, no selection => read whole array
- (Nwriters == partsV.size())
-
- /* Nice */
+ // Define method for engine creation
+ // 1. Get method def from config file or define new one
+ adios::Method &bpReaderSettings = adios.GetMethod("input");
+ if (bpReaderSettings.undeclared())
+ {
+ // if not defined by user, we can change the default settings
+ bpReaderSettings.SetEngine("BP"); // BP is the default engine
+ }
+
+ // Create engine smart pointer due to polymorphism,
+ // Default behavior
+ // auto bpReader = adios.Open( "myNumbers.bp", "r" );
+ // this would just open with a default transport, which is "BP"
+ auto bpReader = adios.Open("myNumbers.bp", "r", bpReaderSettings);
+
+ // All the above is same as default use:
+ // auto bpReader = adios.Open( "myNumbers.bp", "r");
+
+ if (bpReader == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: failed to open ADIOS bpReader\n");
+
+ /* Variable names are available as a vector of strings */
+ std::cout << "List of variables in file: " << bpReader->VariableNames
+ << "\n";
+
+ /* NX */
+ bpReader->Read<unsigned int>(
+ "NX",
+ Nx); // read a Global scalar which has a single value in a step
+
+ /* nproc */
+ bpReader->Read<int>("nproc", Nwriters); // also a global scalar
+
+ /* Nparts */
+ // Nparts local scalar is presented as a 1D array of Nwriters elements.
+ // We need to read a specific value the same way as reading from any 1D
+ // array.
+ // Make a single-value selection to describe our rank's position in the
+ // 1D array of Nwriters values.
+ if (rank < Nwriters)
+ {
+ std::shared_ptr<adios::Variable> varNparts =
+ bpReader.InquiryVariable("Nparts");
+ std::unique_ptr<adios::Selection> selNparts =
+ adios.SelectionBoundingBox({1}, {rank});
+ varNparts->SetSelection(selNparts);
+ bpReader->Read<int>(varNparts, Nparts);
+ }
+ // or we could just read the whole array by every process
+ std::vector<int> partsV(Nwriters);
+ bpReader->Read<int>("Nparts",
+ partsV.data()); // read with string name, no
+ // selection => read whole array
+
+ std::vector<int> partsV;
+ bpReader->Read<int>("Nparts",
+ partsV); // read with string name, no selection =>
+ // read whole array
+ (Nwriters == partsV.size())
+
+ /* Nice */
+ // inquiry about a variable, whose name we know
+ /* GSE === compound type declaration borrowed heavily from HDF5
+ style */
+ adios::CompType mtype(sizeof(s2_t));
+ mtype.insertMember("c_name", OFFSET(s2_t, c), PredType::NATIVE_DOUBLE);
+ mtype.insertMember("a_name", OFFSET(s2_t, a), PredType::NATIVE_INT);
+
+ /*
+ * GSE === this is a bit conceptually different. There was no real
+ * check in the prior API that the variable in the file was in any way
+ * "compatible" with how we planned to read it. This could be done
+ * here, by providing the details of the structure that we are
+ * prepared to read in the inquiryVariable, or if we had an API that
+ * allowed more introspection, we could perhaps support a query on the
+ * adios::Variable and a later operation that informed it of the data
+ * type that we were prepared to extract from it.
+ */
+ std::shared_ptr<adios::Variable> varNice =
+ bpReader.InquiryVariable("Nice", mtype);
+
+ if (varNice == nullptr)
+ throw std::ios_base::failure("ERROR: failed to find variable "
+ "'myDoubles' in input file\n");
+
+ // ? how do we know about the type? std::string varNice->m_Type
+ uint64_t gdim =
+ varNice->m_GlobalDimensions[0]; // ?member var or member func?
+ uint64_t ldim = gdim / nproc;
+ uint64_t offs = rank * ldim;
+ if (rank == nproc - 1)
+ {
+ ldim = gdim - (ldim * gdim);
+ }
+
+ NiceArray.reserve(ldim);
+
+ // Make a 1D selection to describe the local dimensions of the variable
+ // we
+ // READ and
+ // its offsets in the global spaces
+ std::unique_ptr<adios::Selection> bbsel = adios.SelectionBoundingBox(
+ {ldim}, {offs}); // local dims and offsets; both as list
+ varNice->SetSelection(bbsel);
+ // GSE === Again, templated here?
+ bpReader->Read<s2_t>(varNice, NiceArray.data());
+
+ /* Ragged */
// inquiry about a variable, whose name we know
- /* GSE === compound type declaration borrowed heavily from HDF5 style */
- adios::CompType mtype(sizeof(s2_t));
- mtype.insertMember("c_name", OFFSET(s2_t, c), PredType::NATIVE_DOUBLE);
- mtype.insertMember("a_name", OFFSET(s2_t, a), PredType::NATIVE_INT);
-
- /*
- * GSE === this is a bit conceptually different. There was no real
- * check in the prior API that the variable in the file was in any way
- * "compatible" with how we planned to read it. This could be done
- * here, by providing the details of the structure that we are
- * prepared to read in the inquiryVariable, or if we had an API that
- * allowed more introspection, we could perhaps support a query on the
- * adios::Variable and a later operation that informed it of the data
- * type that we were prepared to extract from it.
- */
- std::shared_ptr<adios::Variable> varNice =
- bpReader.InquiryVariable("Nice", mtype);
-
- if (varNice == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to find variable 'myDoubles' in input file\n");
-
- // ? how do we know about the type? std::string varNice->m_Type
- uint64_t gdim =
- varNice->m_GlobalDimensions[0]; // ?member var or member func?
- uint64_t ldim = gdim / nproc;
- uint64_t offs = rank * ldim;
- if (rank == nproc - 1)
- {
- ldim = gdim - (ldim * gdim);
- }
-
- NiceArray.reserve(ldim);
-
- // Make a 1D selection to describe the local dimensions of the variable we
- // READ and
- // its offsets in the global spaces
- std::unique_ptr<adios::Selection> bbsel = adios.SelectionBoundingBox(
- {ldim}, {offs}); // local dims and offsets; both as list
- varNice->SetSelection(bbsel);
- // GSE === Again, templated here?
- bpReader->Read<s2_t>(varNice, NiceArray.data());
-
- /* Ragged */
- // inquiry about a variable, whose name we know
- std::shared_ptr<adios::Variable<void>> varRagged =
- bpReader.InquiryVariable("Ragged");
- if (varRagged->m_GlobalDimensions[1] != adios::VARYING_DIMENSION)
- {
- throw std::ios_base::failure(
- "Unexpected condition: Ragged array's fast dimension "
- "is supposed to be VARYING_DIMENSION\n");
- }
- // We have here varRagged->sum_nblocks, nsteps, nblocks[], global
- if (rank < varRagged->nblocks[0]) // same as rank < Nwriters in this example
- {
- // get per-writer size information
- varRagged->InquiryBlocks();
- // now we have the dimensions per block
-
- unsigned long long int ldim = varRagged->blockinfo[rank].m_Dimensions[1];
- RaggedArray.resize(ldim);
-
- std::unique_ptr<adios::Selection> wbsel = adios.SelectionWriteblock(rank);
- varRagged->SetSelection(wbsel);
- bpReader->Read<float>(varRagged, RaggedArray.data());
-
- // We can use bounding box selection as well
- std::unique_ptr<adios::Selection> rbbsel =
- adios.SelectionBoundingBox({1, ldim}, {rank, 0});
- varRagged->SetSelection(rbbsel);
- bpReader->Read<float>(varRagged, RaggedArray.data());
+ std::shared_ptr<adios::Variable<void>> varRagged =
+ bpReader.InquiryVariable("Ragged");
+ if (varRagged->m_GlobalDimensions[1] != adios::VARYING_DIMENSION)
+ {
+ throw std::ios_base::failure(
+ "Unexpected condition: Ragged array's fast dimension "
+ "is supposed to be VARYING_DIMENSION\n");
+ }
+ // We have here varRagged->sum_nblocks, nsteps, nblocks[], global
+ if (rank <
+ varRagged->nblocks[0]) // same as rank < Nwriters in this example
+ {
+ // get per-writer size information
+ varRagged->InquiryBlocks();
+ // now we have the dimensions per block
+
+ unsigned long long int ldim =
+ varRagged->blockinfo[rank].m_Dimensions[1];
+ RaggedArray.resize(ldim);
+
+ std::unique_ptr<adios::Selection> wbsel =
+ adios.SelectionWriteblock(rank);
+ varRagged->SetSelection(wbsel);
+ bpReader->Read<float>(varRagged, RaggedArray.data());
+
+ // We can use bounding box selection as well
+ std::unique_ptr<adios::Selection> rbbsel =
+ adios.SelectionBoundingBox({1, ldim}, {rank, 0});
+ varRagged->SetSelection(rbbsel);
+ bpReader->Read<float>(varRagged, RaggedArray.data());
+ }
+
+ /* Extra help to process Ragged */
+ int maxRaggedDim =
+ varRagged->GetMaxGlobalDimensions(1); // contains the largest
+ std::vector<int> raggedDims = varRagged->GetVaryingGlobalDimensions(
+ 1); // contains all individual sizes in that dimension
+
+ // Close file/stream
+ bpReader->Close();
}
-
- /* Extra help to process Ragged */
- int maxRaggedDim =
- varRagged->GetMaxGlobalDimensions(1); // contains the largest
- std::vector<int> raggedDims = varRagged->GetVaryingGlobalDimensions(
- 1); // contains all individual sizes in that dimension
-
- // Close file/stream
- bpReader->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
+ catch (std::invalid_argument &e)
{
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
+ catch (std::ios_base::failure &e)
{
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
+ catch (std::exception &e)
{
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- MPI_Finalize();
+ MPI_Finalize();
- return 0;
+ return 0;
}
diff --git a/examples/groupless/compound/writer.cpp b/examples/groupless/compound/writer.cpp
index a235ebb4205ec148af8653717fc2407d26c8790c..f8c105e2f0508cccdf3d5322342afe0dc50c4286 100644
--- a/examples/groupless/compound/writer.cpp
+++ b/examples/groupless/compound/writer.cpp
@@ -21,146 +21,159 @@ typedef enum { VARYING_DIMENSION = -1, LOCAL_VALUE = 0, GLOBAL_VALUE = 1 };
int main(int argc, char *argv[])
{
- int rank, nproc;
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- MPI_Comm_size(MPI_COMM_WORLD, &nproc);
- const bool adiosDebug = true;
-
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
-
- // Application variable
- const unsigned int Nx = 10;
- // GSE === user-defined structure
- typedef struct s1_t
- {
- int a;
- float b;
- double c;
- };
- const int Nparts = rand() % 6 + 5; // random size per process, 5..10 each
-
- std::vector<s1_t> NiceArray(Nx);
- for (int i = 0; i < Nx; i++)
- {
- NiceArray.push_back(ss1_t());
- NiceArray[i].a = rank * Nx + (double)i;
- NiceArray[i].b = 100.0 * rank * Nx + 100.0 * (double)i;
- NiceArray[i].c = 10000.0 * rank * Nx + 10000.0 * (double)i;
- }
-
- try
- {
- /* GSE === compound type declaration borrowed heavily from HDF5 style */
- adios::CompType mtype(sizeof(s1_t));
- mtype.insertMember("a_name", OFFSET(s1_t, a), PredType::NATIVE_INT);
- mtype.insertMember("c_name", OFFSET(s1_t, c), PredType::NATIVE_DOUBLE);
- mtype.insertMember("b_name", OFFSET(s1_t, b), PredType::NATIVE_FLOAT);
-
- // Define group and variables with transforms, variables don't have
- // functions, only group can access variables
- adios::Variable<unsigned int> &varNX = adios.DefineVariable<unsigned int>(
- "NX"); // global single-value across processes
- adios::Variable<int> &varNproc = adios.DefineVariable<int>(
- "nproc", adios::GLOBAL_VALUE); // same def for global value
- adios::Variable<int> &varNparts = adios.DefineVariable<int>(
- "Nparts",
- adios::LOCAL_VALUE); // a single-value different on every process
-
- // GSE === template necessary or useful here? Extra argument for
- // previously-built compound type information */
- adios::Variable<s1_t> &varNice = adios.DefineVariable<s1_t>(
- "Nice", {nproc * Nx}, mtype); // 1D global array
-
- // add transform to variable in group...not executed (just testing API)
- adios::Transform bzip2 = adios::transform::BZIP2();
- varNice->AddTransform(bzip2, 1);
-
- // Define method for engine creation
- // 1. Get method def from config file or define new one
- adios::Method &bpWriterSettings = adios.GetMethod("output");
- if (bpWriterSettings.undeclared())
+ int rank, nproc;
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &nproc);
+ const bool adiosDebug = true;
+
+ adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
+
+ // Application variable
+ const unsigned int Nx = 10;
+ // GSE === user-defined structure
+ typedef struct s1_t
{
- // if not defined by user, we can change the default settings
- bpWriterSettings.SetEngine("BP"); // BP is the default engine
- bpWriterSettings.AddTransport(
- "File", "lucky=yes"); // ISO-POSIX file is the default transport
- // Passing parameters to the transport
- bpWriterSettings.SetParameters("have_metadata_file",
- "yes"); // Passing parameters to the engine
- bpWriterSettings.SetParameters("Aggregation",
- (nproc + 1) / 2); // number of aggregators
+ int a;
+ float b;
+ double c;
+ };
+ const int Nparts = rand() % 6 + 5; // random size per process, 5..10 each
+
+ std::vector<s1_t> NiceArray(Nx);
+ for (int i = 0; i < Nx; i++)
+ {
+ NiceArray.push_back(ss1_t());
+ NiceArray[i].a = rank * Nx + (double)i;
+ NiceArray[i].b = 100.0 * rank * Nx + 100.0 * (double)i;
+ NiceArray[i].c = 10000.0 * rank * Nx + 10000.0 * (double)i;
}
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- // "w" means we overwrite any existing file on disk, but AdvanceStep will
- // append steps later.
- auto bpWriter = adios.Open("myNumbers.bp", "w", bpWriterSettings);
-
- if (bpWriter == nullptr)
- throw std::ios_base::failure("ERROR: failed to open ADIOS bpWriter\n");
-
- if (rank == 0)
+ try
{
- // Writing a global scalar from only one process
- bpWriter->Write<unsigned int>(varNX, Nx);
+ /* GSE === compound type declaration borrowed heavily from HDF5 style */
+ adios::CompType mtype(sizeof(s1_t));
+ mtype.insertMember("a_name", OFFSET(s1_t, a), PredType::NATIVE_INT);
+ mtype.insertMember("c_name", OFFSET(s1_t, c), PredType::NATIVE_DOUBLE);
+ mtype.insertMember("b_name", OFFSET(s1_t, b), PredType::NATIVE_FLOAT);
+
+ // Define group and variables with transforms, variables don't have
+ // functions, only group can access variables
+ adios::Variable<unsigned int> &varNX =
+ adios.DefineVariable<unsigned int>(
+ "NX"); // global single-value across processes
+ adios::Variable<int> &varNproc = adios.DefineVariable<int>(
+ "nproc", adios::GLOBAL_VALUE); // same def for global value
+ adios::Variable<int> &varNparts =
+ adios.DefineVariable<int>("Nparts",
+ adios::LOCAL_VALUE); // a single-value
+ // different on
+ // every process
+
+ // GSE === template necessary or useful here? Extra argument for
+ // previously-built compound type information */
+ adios::Variable<s1_t> &varNice = adios.DefineVariable<s1_t>(
+ "Nice", {nproc * Nx}, mtype); // 1D global array
+
+ // add transform to variable in group...not executed (just testing API)
+ adios::Transform bzip2 = adios::transform::BZIP2();
+ varNice->AddTransform(bzip2, 1);
+
+ // Define method for engine creation
+ // 1. Get method def from config file or define new one
+ adios::Method &bpWriterSettings = adios.GetMethod("output");
+ if (bpWriterSettings.undeclared())
+ {
+ // if not defined by user, we can change the default settings
+ bpWriterSettings.SetEngine("BP"); // BP is the default engine
+ bpWriterSettings.AddTransport(
+ "File",
+ "lucky=yes"); // ISO-POSIX file is the default transport
+ // Passing parameters to the transport
+ bpWriterSettings.SetParameters(
+ "have_metadata_file",
+ "yes"); // Passing parameters to the engine
+ bpWriterSettings.SetParameters("Aggregation",
+ (nproc + 1) /
+ 2); // number of aggregators
+ }
+
+ // Open returns a smart pointer to Engine containing the Derived class
+ // Writer
+ // "w" means we overwrite any existing file on disk, but AdvanceStep
+ // will
+ // append steps later.
+ auto bpWriter = adios.Open("myNumbers.bp", "w", bpWriterSettings);
+
+ if (bpWriter == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: failed to open ADIOS bpWriter\n");
+
+ if (rank == 0)
+ {
+ // Writing a global scalar from only one process
+ bpWriter->Write<unsigned int>(varNX, Nx);
+ }
+ // Writing a local scalar on every process. Will be shown at reading as
+ // a 1D
+ // array
+ bpWriter->Write<int>(varNparts, Nparts);
+
+ // Writing a global scalar on every process is useless. Information will
+ // be
+ // thrown away
+ // and only rank 0's data will be in the output
+ bpWriter->Write<int>(varNproc, nproc);
+
+ // Make a 1D selection to describe the local dimensions of the variable
+ // we
+ // write and
+ // its offsets in the global spaces
+ adios::Selection &sel = adios.SelectionBoundingBox(
+ {Nx}, {rank * Nx}); // local dims and offsets; both as list
+ varNice.SetSelection(sel);
+
+ // GSE === Template useful or necessary here? We have to treat this as
+ // a
+ // void* inside ADIOS...
+ bpWriter->Write<sl_t>(varNice, NiceArray.data());
+
+ // Indicate we are done for this step
+ // N-to-M Aggregation, disk I/O will be performed during this call,
+ // unless
+ // time aggregation postpones all of that to some later step
+ bpWriter->Advance();
+ bpWriter->AdvanceAsync(callback_func_to_notify_me);
+
+ // Called once: indicate that we are done with this output for the run
+ bpWriter->Close();
}
- // Writing a local scalar on every process. Will be shown at reading as a 1D
- // array
- bpWriter->Write<int>(varNparts, Nparts);
-
- // Writing a global scalar on every process is useless. Information will be
- // thrown away
- // and only rank 0's data will be in the output
- bpWriter->Write<int>(varNproc, nproc);
-
- // Make a 1D selection to describe the local dimensions of the variable we
- // write and
- // its offsets in the global spaces
- adios::Selection &sel = adios.SelectionBoundingBox(
- {Nx}, {rank * Nx}); // local dims and offsets; both as list
- varNice.SetSelection(sel);
-
- // GSE === Template useful or necessary here? We have to treat this as a
- // void* inside ADIOS...
- bpWriter->Write<sl_t>(varNice, NiceArray.data());
-
- // Indicate we are done for this step
- // N-to-M Aggregation, disk I/O will be performed during this call, unless
- // time aggregation postpones all of that to some later step
- bpWriter->Advance();
- bpWriter->AdvanceAsync(callback_func_to_notify_me);
-
- // Called once: indicate that we are done with this output for the run
- bpWriter->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
+ catch (std::invalid_argument &e)
{
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
+ catch (std::ios_base::failure &e)
{
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
+ catch (std::exception &e)
{
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- MPI_Finalize();
+ MPI_Finalize();
- return 0;
+ return 0;
}
diff --git a/examples/groupless/multistep/reader_allsteps.cpp b/examples/groupless/multistep/reader_allsteps.cpp
index d71703dda7276d3dfc3c8bd19e495fbcb20ce011..1b28a82c72d71e1438c077f6b00ae88aa837a1f6 100644
--- a/examples/groupless/multistep/reader_allsteps.cpp
+++ b/examples/groupless/multistep/reader_allsteps.cpp
@@ -16,189 +16,201 @@
int main(int argc, char *argv[])
{
- int rank, nproc;
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- MPI_Comm_size(MPI_COMM_WORLD, &nproc);
- const bool adiosDebug = true;
-
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
-
- // Application variable
- std::vector<double> NiceArray;
- std::vector<float> RaggedArray;
-
- int Nparts;
- int Nwriters;
- int Nsteps;
-
- try
- {
- // Define method for engine creation
- // 1. Get method def from config file or define new one
- adios::Method &bpReaderSettings = adios.GetMethod("input");
- if (bpReaderSettings.undeclared())
- {
- // if not defined by user, we can change the default settings
- bpReaderSettings.SetEngine("BP"); // BP is the default engine
- // By default we see all steps available in a file, so the next line is
- // not needed
- bpReaderSettings.SetParameters("Stepping", false);
- }
+ int rank, nproc;
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &nproc);
+ const bool adiosDebug = true;
- // Create engine smart pointer due to polymorphism,
- // Default behavior
- // auto bpReader = adios.Open( "myNumbers.bp", "r" );
- // this would just open with a default transport, which is "BP"
- auto bpReader = adios.Open("myNumbers.bp", "r", bpReaderSettings);
-
- // All the above is same as default use:
- // auto bpReader = adios.Open( "myNumbers.bp", "r");
-
- if (bpReader == nullptr)
- throw std::ios_base::failure("ERROR: failed to open ADIOS bpReader\n");
-
- /* Note: there is no global number of steps. Each variable has its own
- * number of steps */
-
- /* NX */
- /* There is a single value for each step. We can read all into a 1D array
- * with a step selection.
- * We can also just conveniently get the first with a simple read statement.
- * Steps are not automatically presented as an array dimension and read does
- * not read it as array.
- */
- unsigned int Nx;
- bpReader->Read<unsigned int>(
- "NX", &Nx); // read a Global scalar which has a single value in a step
-
- std::shared_ptr<adios::Variable<void>> varNx =
- bpReader.InquiryVariable("Nx");
- std::vector<int> Nxs(varNx->nsteps()); // number of steps available
- // make a StepSelection to select multiple steps. Args: From, #of
- // consecutive steps
- std::unique_ptr<adios::StepSelection> stepsNx =
- adios.StepSelection(0, varNx->nsteps());
- // ? How do we make a selection for an arbitrary list of steps ?
- varNX.SetStepSelection(stepsNx);
- bpReader->Read<unsigned int>(varNx, Nxs.data());
-
- auto itmax = std::max_element(std::begin(Nxs), std::end(Nxs));
- auto itmin = std::min_element(std::begin(Nxs), std::end(Nxs));
- if (*itmin != *itmax)
- {
- throw std::ios_base::failure("ERROR: NX is not the same at all steps!\n");
- }
+ adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
- /* nproc */
- bpReader->Read<int>("nproc", &Nwriters); // also a global scalar
-
- /* Nparts */
- // Nparts local scalar is presented as a 1D array of Nwriters elements.
- // We can read all steps into a 2D array of nproc * Nwriters
- std::shared_ptr<adios::Variable<void>> varNparts =
- bpReader.InquiryVariable("Nparts");
- std::vector<int> partsV(Nproc * Nwriters);
- varNparts->SetStepSelection(adios.StepSelection(0, varNparts->nsteps()));
- bpReader->Read<int>(
- varNparts,
- partsV.data()); // missing spatial selection = whole array at each step
-
- /* Nice */
- // inquiry about a variable, whose name we know
- std::shared_ptr<adios::Variable<void>> varNice =
- bpReader.InquiryVariable("Nice");
-
- if (varNice == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to find variable 'myDoubles' in input file\n");
-
- // ? how do we know about the type? std::string varNice->m_Type
- unsigned long long int gdim =
- varMyDoubles->m_GlobalDimensions[0]; // ?member var or member func?
- unsigned long long int ldim = gdim / nproc;
- unsigned long long int offs = rank * ldim;
- if (rank == nproc - 1)
- {
- ldim = gdim - (ldim * gdim);
- }
+ // Application variable
+ std::vector<double> NiceArray;
+ std::vector<float> RaggedArray;
- NiceArray.reserve(ldim);
-
- // Make a 1D selection to describe the local dimensions of the variable we
- // READ and
- // its offsets in the global spaces
- std::unique_ptr<adios::Selection> bbsel = adios.SelectionBoundingBox(
- {ldim}, {offs}); // local dims and offsets; both as list
- bpReader->Read<double>("Nice", bbsel,
- NiceArray.data()); // Base class Engine own the
- // Read<T> that will call
- // overloaded Read from Derived
-
- /* Ragged */
- // inquiry about a variable, whose name we know
- std::shared_ptr<adios::Variable<void>> varRagged =
- bpReader.InquiryVariable("Ragged");
- if (varRagged->m_GlobalDimensions[1] != adios::VARYING_DIMENSION)
- {
- throw std::ios_base::failure(
- "Unexpected condition: Ragged array's fast dimension "
- "is supposed to be VARYING_DIMENSION\n");
- }
- // We have here varRagged->sum_nblocks, nsteps, nblocks[], global
- if (rank < varRagged->nblocks[0]) // same as rank < Nwriters in this example
- {
- // get per-writer size information
- varRagged->InquiryBlocks();
- // now we have the dimensions per block
-
- unsigned long long int ldim = varRagged->blockinfo[rank].m_Dimensions[0];
- RaggedArray.resize(ldim);
+ int Nparts;
+ int Nwriters;
+ int Nsteps;
- std::unique_ptr<adios::Selection> wbsel = adios.SelectionWriteblock(rank);
- bpReader->Read<float>("Ragged", wbsel, RaggedArray.data());
-
- // We can use bounding box selection as well
- std::unique_ptr<adios::Selection> rbbsel =
- adios.SelectionBoundingBox({1, ldim}, {rank, 0});
- bpReader->Read<float>("Ragged", rbbsel, RaggedArray.data());
+ try
+ {
+ // Define method for engine creation
+ // 1. Get method def from config file or define new one
+ adios::Method &bpReaderSettings = adios.GetMethod("input");
+ if (bpReaderSettings.undeclared())
+ {
+ // if not defined by user, we can change the default settings
+ bpReaderSettings.SetEngine("BP"); // BP is the default engine
+ // By default we see all steps available in a file, so the next line
+ // is
+ // not needed
+ bpReaderSettings.SetParameters("Stepping", false);
+ }
+
+ // Create engine smart pointer due to polymorphism,
+ // Default behavior
+ // auto bpReader = adios.Open( "myNumbers.bp", "r" );
+ // this would just open with a default transport, which is "BP"
+ auto bpReader = adios.Open("myNumbers.bp", "r", bpReaderSettings);
+
+ // All the above is same as default use:
+ // auto bpReader = adios.Open( "myNumbers.bp", "r");
+
+ if (bpReader == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: failed to open ADIOS bpReader\n");
+
+ /* Note: there is no global number of steps. Each variable has its own
+ * number of steps */
+
+ /* NX */
+ /* There is a single value for each step. We can read all into a 1D
+ * array
+ * with a step selection.
+ * We can also just conveniently get the first with a simple read
+ * statement.
+ * Steps are not automatically presented as an array dimension and read
+ * does
+ * not read it as array.
+ */
+ unsigned int Nx;
+ bpReader->Read<unsigned int>(
+ "NX",
+ &Nx); // read a Global scalar which has a single value in a step
+
+ std::shared_ptr<adios::Variable<void>> varNx =
+ bpReader.InquiryVariable("Nx");
+ std::vector<int> Nxs(varNx->nsteps()); // number of steps available
+ // make a StepSelection to select multiple steps. Args: From, #of
+ // consecutive steps
+ std::unique_ptr<adios::StepSelection> stepsNx =
+ adios.StepSelection(0, varNx->nsteps());
+ // ? How do we make a selection for an arbitrary list of steps ?
+ varNX.SetStepSelection(stepsNx);
+ bpReader->Read<unsigned int>(varNx, Nxs.data());
+
+ auto itmax = std::max_element(std::begin(Nxs), std::end(Nxs));
+ auto itmin = std::min_element(std::begin(Nxs), std::end(Nxs));
+ if (*itmin != *itmax)
+ {
+ throw std::ios_base::failure(
+ "ERROR: NX is not the same at all steps!\n");
+ }
+
+ /* nproc */
+ bpReader->Read<int>("nproc", &Nwriters); // also a global scalar
+
+ /* Nparts */
+ // Nparts local scalar is presented as a 1D array of Nwriters elements.
+ // We can read all steps into a 2D array of nproc * Nwriters
+ std::shared_ptr<adios::Variable<void>> varNparts =
+ bpReader.InquiryVariable("Nparts");
+ std::vector<int> partsV(Nproc * Nwriters);
+ varNparts->SetStepSelection(
+ adios.StepSelection(0, varNparts->nsteps()));
+ bpReader->Read<int>(varNparts,
+ partsV.data()); // missing spatial selection = whole
+ // array at each step
+
+ /* Nice */
+ // inquiry about a variable, whose name we know
+ std::shared_ptr<adios::Variable<void>> varNice =
+ bpReader.InquiryVariable("Nice");
+
+ if (varNice == nullptr)
+ throw std::ios_base::failure("ERROR: failed to find variable "
+ "'myDoubles' in input file\n");
+
+ // ? how do we know about the type? std::string varNice->m_Type
+ unsigned long long int gdim =
+ varMyDoubles->m_GlobalDimensions[0]; // ?member var or member func?
+ unsigned long long int ldim = gdim / nproc;
+ unsigned long long int offs = rank * ldim;
+ if (rank == nproc - 1)
+ {
+ ldim = gdim - (ldim * gdim);
+ }
+
+ NiceArray.reserve(ldim);
+
+ // Make a 1D selection to describe the local dimensions of the variable
+ // we
+ // READ and
+ // its offsets in the global spaces
+ std::unique_ptr<adios::Selection> bbsel = adios.SelectionBoundingBox(
+ {ldim}, {offs}); // local dims and offsets; both as list
+ bpReader->Read<double>("Nice", bbsel,
+ NiceArray.data()); // Base class Engine own the
+ // Read<T> that will call
+ // overloaded Read from Derived
+
+ /* Ragged */
+ // inquiry about a variable, whose name we know
+ std::shared_ptr<adios::Variable<void>> varRagged =
+ bpReader.InquiryVariable("Ragged");
+ if (varRagged->m_GlobalDimensions[1] != adios::VARYING_DIMENSION)
+ {
+ throw std::ios_base::failure(
+ "Unexpected condition: Ragged array's fast dimension "
+ "is supposed to be VARYING_DIMENSION\n");
+ }
+ // We have here varRagged->sum_nblocks, nsteps, nblocks[], global
+ if (rank <
+ varRagged->nblocks[0]) // same as rank < Nwriters in this example
+ {
+ // get per-writer size information
+ varRagged->InquiryBlocks();
+ // now we have the dimensions per block
+
+ unsigned long long int ldim =
+ varRagged->blockinfo[rank].m_Dimensions[0];
+ RaggedArray.resize(ldim);
+
+ std::unique_ptr<adios::Selection> wbsel =
+ adios.SelectionWriteblock(rank);
+ bpReader->Read<float>("Ragged", wbsel, RaggedArray.data());
+
+ // We can use bounding box selection as well
+ std::unique_ptr<adios::Selection> rbbsel =
+ adios.SelectionBoundingBox({1, ldim}, {rank, 0});
+ bpReader->Read<float>("Ragged", rbbsel, RaggedArray.data());
+ }
+
+ /* Extra help to process Ragged */
+ int maxRaggedDim =
+ varRagged->GetMaxGlobalDimensions(1); // contains the largest
+ std::vector<int> raggedDims = varRagged->GetVaryingGlobalDimensions(
+ 1); // contains all individual sizes in that dimension
+
+ // Close file/stream
+ bpReader->Close();
}
-
- /* Extra help to process Ragged */
- int maxRaggedDim =
- varRagged->GetMaxGlobalDimensions(1); // contains the largest
- std::vector<int> raggedDims = varRagged->GetVaryingGlobalDimensions(
- 1); // contains all individual sizes in that dimension
-
- // Close file/stream
- bpReader->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
+ catch (std::invalid_argument &e)
{
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
+ catch (std::ios_base::failure &e)
{
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
+ catch (std::exception &e)
{
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- MPI_Finalize();
+ MPI_Finalize();
- return 0;
+ return 0;
}
diff --git a/examples/groupless/multistep/reader_stepping.cpp b/examples/groupless/multistep/reader_stepping.cpp
index df5adb7d542b9c031c6312bd6db4613b0c40467c..5328408da4249e62be66d2157a3cdb43a57ae703 100644
--- a/examples/groupless/multistep/reader_stepping.cpp
+++ b/examples/groupless/multistep/reader_stepping.cpp
@@ -16,185 +16,196 @@
int main(int argc, char *argv[])
{
- int rank, nproc;
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- MPI_Comm_size(MPI_COMM_WORLD, &nproc);
- const bool adiosDebug = true;
-
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
-
- // Application variable
- std::vector<double> NiceArray;
- std::vector<float> RaggedArray;
- unsigned int Nx;
- int Nparts;
- int Nwriters;
- int Nsteps;
-
- try
- {
- // Define method for engine creation
- // 1. Get method def from config file or define new one
- adios::Method &bpReaderSettings = adios.GetMethod("input");
- if (bpReaderSettings.undeclared())
- {
- // if not defined by user, we can change the default settings
- bpReaderSettings.SetEngine("BP"); // BP is the default engine
- bpReaderSettings.SetParameters("Stepping",
- true); // see only one step at a time
- }
+ int rank, nproc;
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &nproc);
+ const bool adiosDebug = true;
+
+ adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
+
+ // Application variable
+ std::vector<double> NiceArray;
+ std::vector<float> RaggedArray;
+ unsigned int Nx;
+ int Nparts;
+ int Nwriters;
+ int Nsteps;
- // Create engine smart pointer due to polymorphism,
- // Default behavior
- // auto bpReader = adios.Open( "myNumbers.bp", "r" );
- // this would just open with a default transport, which is "BP"
try
{
- auto bpReader = adios.Open("myNumbers.bp", "r", bpReaderSettings);
-
- while (true)
- {
- /* NX */
- bpReader->Read<unsigned int>(
- "NX",
- &Nx); // read a Global scalar which has a single value in a step
-
- /* nproc */
- bpReader->Read<int>("nproc", &Nwriters); // also a global scalar
-
- /* Nparts */
- // Nparts local scalar is presented as a 1D array of Nwriters elements.
- // We can read all as a 1D array
- std::vector<int> partsV(Nwriters);
- bpReader->Read<int>(
- "Nparts",
- &partsV); // read with string name, no selection => read whole array
-
- /* Nice */
- // inquiry about a variable, whose name we know
- std::shared_ptr<adios::Variable<void>> varNice =
- bpReader.InquiryVariable("Nice");
-
- if (varNice == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to find variable 'myDoubles' in input file\n");
-
- // ? how do we know about the type? std::string varNice->m_Type
- unsigned long long int gdim =
- varMyDoubles->m_GlobalDimensions[0]; // ?member var or member func?
- unsigned long long int ldim = gdim / nproc;
- unsigned long long int offs = rank * ldim;
- if (rank == nproc - 1)
+ // Define method for engine creation
+ // 1. Get method def from config file or define new one
+ adios::Method &bpReaderSettings = adios.GetMethod("input");
+ if (bpReaderSettings.undeclared())
{
- ldim = gdim - (ldim * gdim);
+ // if not defined by user, we can change the default settings
+ bpReaderSettings.SetEngine("BP"); // BP is the default engine
+ bpReaderSettings.SetParameters("Stepping",
+ true); // see only one step at a time
}
- NiceArray.reserve(ldim);
-
- // Make a 1D selection to describe the local dimensions of the variable
- // we READ and
- // its offsets in the global spaces
- std::unique_ptr<adios::Selection> bbsel = adios.SelectionBoundingBox(
- {ldim}, {offs}); // local dims and offsets; both as list
- varNice->SetSelection(bbsel);
- bpReader->Read<double>(varNice, NiceArray.data());
-
- /* Ragged */
- // inquiry about a variable, whose name we know
- std::shared_ptr<adios::Variable<void>> varRagged =
- bpReader.InquiryVariable("Ragged");
- if (varRagged->m_GlobalDimensions[1] != adios::VARYING_DIMENSION)
+ // Create engine smart pointer due to polymorphism,
+ // Default behavior
+ // auto bpReader = adios.Open( "myNumbers.bp", "r" );
+ // this would just open with a default transport, which is "BP"
+ try
{
- throw std::ios_base::failure(
- "Unexpected condition: Ragged array's fast dimension "
- "is supposed to be VARYING_DIMENSION\n");
+ auto bpReader = adios.Open("myNumbers.bp", "r", bpReaderSettings);
+
+ while (true)
+ {
+ /* NX */
+ bpReader->Read<unsigned int>("NX",
+ &Nx); // read a Global scalar which
+ // has a single value in a
+ // step
+
+ /* nproc */
+ bpReader->Read<int>("nproc", &Nwriters); // also a global scalar
+
+ /* Nparts */
+ // Nparts local scalar is presented as a 1D array of Nwriters
+ // elements.
+ // We can read all as a 1D array
+ std::vector<int> partsV(Nwriters);
+ bpReader->Read<int>("Nparts",
+ &partsV); // read with string name, no
+ // selection => read whole array
+
+ /* Nice */
+ // inquiry about a variable, whose name we know
+ std::shared_ptr<adios::Variable<void>> varNice =
+ bpReader.InquiryVariable("Nice");
+
+ if (varNice == nullptr)
+ throw std::ios_base::failure("ERROR: failed to find "
+ "variable 'myDoubles' in "
+ "input file\n");
+
+ // ? how do we know about the type? std::string varNice->m_Type
+ unsigned long long int gdim =
+ varMyDoubles->m_GlobalDimensions[0]; // ?member var or
+ // member func?
+ unsigned long long int ldim = gdim / nproc;
+ unsigned long long int offs = rank * ldim;
+ if (rank == nproc - 1)
+ {
+ ldim = gdim - (ldim * gdim);
+ }
+
+ NiceArray.reserve(ldim);
+
+ // Make a 1D selection to describe the local dimensions of the
+ // variable
+ // we READ and
+ // its offsets in the global spaces
+ std::unique_ptr<adios::Selection> bbsel =
+ adios.SelectionBoundingBox(
+ {ldim}, {offs}); // local dims and offsets; both as list
+ varNice->SetSelection(bbsel);
+ bpReader->Read<double>(varNice, NiceArray.data());
+
+ /* Ragged */
+ // inquiry about a variable, whose name we know
+ std::shared_ptr<adios::Variable<void>> varRagged =
+ bpReader.InquiryVariable("Ragged");
+ if (varRagged->m_GlobalDimensions[1] !=
+ adios::VARYING_DIMENSION)
+ {
+ throw std::ios_base::failure(
+ "Unexpected condition: Ragged array's fast "
+ "dimension "
+ "is supposed to be VARYING_DIMENSION\n");
+ }
+ // We have here varRagged->sum_nblocks, nsteps, nblocks[],
+ // global
+ if (rank < varRagged->nblocks[0]) // same as rank < Nwriters in
+ // this example
+ {
+ // get per-writer size information
+ varRagged->InquiryBlocks();
+ // now we have the dimensions per block
+
+ unsigned long long int ldim =
+ varRagged->blockinfo[rank].m_Dimensions[0];
+ RaggedArray.resize(ldim);
+
+ std::unique_ptr<adios::Selection> wbsel =
+ adios.SelectionWriteblock(rank);
+ varRagged->SetSelection(wbsel);
+ bpReader->Read<float>(varRagged, RaggedArray.data());
+
+ // We can use bounding box selection as well
+ std::unique_ptr<adios::Selection> rbbsel =
+ adios.SelectionBoundingBox({1, ldim}, {rank, 0});
+ varRagged->SetSelection(rbbsel);
+ bpReader->Read<float>(varRagged, RaggedArray.data());
+ }
+
+ /* Extra help to process Ragged */
+ int maxRaggedDim = varRagged->GetMaxGlobalDimensions(
+ 1); // contains the largest
+ std::vector<int> raggedDims =
+ varRagged->GetVaryingGlobalDimensions(
+ 1); // contains all individual sizes in that
+ // dimension
+
+ // promise to not read more from this step
+ bpReader->Release();
+
+ // want to move on to the next available step
+ // bpReader->Advance(adios::NextStep);
+ // bpReader->Advance(adios::LatestStep);
+ bpReader->Advance(); // default is adios::NextStep
+ }
+
+ // Close file/stream
+ bpReader->Close();
}
- // We have here varRagged->sum_nblocks, nsteps, nblocks[], global
- if (rank <
- varRagged->nblocks[0]) // same as rank < Nwriters in this example
+ catch (adios::end_of_stream &e)
{
- // get per-writer size information
- varRagged->InquiryBlocks();
- // now we have the dimensions per block
-
- unsigned long long int ldim =
- varRagged->blockinfo[rank].m_Dimensions[0];
- RaggedArray.resize(ldim);
-
- std::unique_ptr<adios::Selection> wbsel =
- adios.SelectionWriteblock(rank);
- varRagged->SetSelection(wbsel);
- bpReader->Read<float>(varRagged, RaggedArray.data());
-
- // We can use bounding box selection as well
- std::unique_ptr<adios::Selection> rbbsel =
- adios.SelectionBoundingBox({1, ldim}, {rank, 0});
- varRagged->SetSelection(rbbsel);
- bpReader->Read<float>(varRagged, RaggedArray.data());
+ if (rank == 0)
+ {
+ std::cout << "Reached end of stream, end processing loop.\n";
+ }
+ // Close file/stream
+ bpReader->Close();
+ }
+ catch (adios::file_not_found &e)
+ {
+ if (rank == 0)
+ {
+ std::cout << "File/stream does not exist, quit.\n";
+ }
}
-
- /* Extra help to process Ragged */
- int maxRaggedDim =
- varRagged->GetMaxGlobalDimensions(1); // contains the largest
- std::vector<int> raggedDims = varRagged->GetVaryingGlobalDimensions(
- 1); // contains all individual sizes in that dimension
-
- // promise to not read more from this step
- bpReader->Release();
-
- // want to move on to the next available step
- // bpReader->Advance(adios::NextStep);
- // bpReader->Advance(adios::LatestStep);
- bpReader->Advance(); // default is adios::NextStep
- }
-
- // Close file/stream
- bpReader->Close();
- }
- catch (adios::end_of_stream &e)
- {
- if (rank == 0)
- {
- std::cout << "Reached end of stream, end processing loop.\n";
- }
- // Close file/stream
- bpReader->Close();
- }
- catch (adios::file_not_found &e)
- {
- if (rank == 0)
- {
- std::cout << "File/stream does not exist, quit.\n";
- }
}
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
+ catch (std::invalid_argument &e)
{
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
+ catch (std::ios_base::failure &e)
{
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
+ catch (std::exception &e)
{
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- MPI_Finalize();
+ MPI_Finalize();
- return 0;
+ return 0;
}
diff --git a/examples/groupless/multistep/writer_multistep.cpp b/examples/groupless/multistep/writer_multistep.cpp
index 946d20f951356e8121dceef8a27f31b38f5b2d29..696d4bdb636ed422d4872ae043505551a84e05a9 100644
--- a/examples/groupless/multistep/writer_multistep.cpp
+++ b/examples/groupless/multistep/writer_multistep.cpp
@@ -21,152 +21,165 @@ typedef enum { VARYING_DIMENSION = -1, LOCAL_VALUE = 0, GLOBAL_VALUE = 1 };
int main(int argc, char *argv[])
{
- int rank, nproc;
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- MPI_Comm_size(MPI_COMM_WORLD, &nproc);
- const bool adiosDebug = true;
- const int NSTEPS = 5;
-
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
-
- // Application variable
- const unsigned int Nx = 10;
- int Nparts; // random size per process, 5..10 each
-
- std::vector<double> NiceArray(Nx);
- for (int i = 0; i < Nx; i++)
- {
- NiceArray[i] = rank * Nx + (double)i;
- }
-
- std::vector<float> RaggedArray;
-
- try
- {
- // Define group and variables with transforms, variables don't have
- // functions, only group can access variables
- adios::Variable<unsigned int> &varNX = adios.DefineVariable<unsigned int>(
- "NX"); // global single-value across processes
- adios::Variable<int> &varNproc = adios.DefineVariable<int>(
- "nproc", adios::GLOBAL_VALUE); // same def for global value
- adios::Variable<int> &varNparts = adios.DefineVariable<int>(
- "Nparts",
- adios::LOCAL_VALUE); // a single-value different on every process
- adios::Variable<double> &varNice =
- adios.DefineVariable<double>("Nice", {nproc * Nx}); // 1D global array
- adios::Variable<float> &varRagged = adios.DefineVariable<float>(
- "Ragged", {nproc, adios::VARYING_DIMENSION}); // ragged array
-
- // add transform to variable in group...not executed (just testing API)
- adios::Transform bzip2 = adios::transform::BZIP2();
- varNice->AddTransform(bzip2, 1);
-
- // Define method for engine creation
- // 1. Get method def from config file or define new one
- adios::Method &bpWriterSettings = adios.GetMethod("output");
- if (bpWriterSettings.undeclared())
- {
- // if not defined by user, we can change the default settings
- bpWriterSettings.SetEngine("BP"); // BP is the default engine
- bpWriterSettings.AddTransport(
- "File", "lucky=yes"); // ISO-POSIX file is the default transport
- // Passing parameters to the transport
- bpWriterSettings.SetParameters("have_metadata_file",
- "yes"); // Passing parameters to the engine
- bpWriterSettings.SetParameters("Aggregation",
- (nproc + 1) / 2); // number of aggregators
- }
+ int rank, nproc;
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &nproc);
+ const bool adiosDebug = true;
+ const int NSTEPS = 5;
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- // "w" means we overwrite any existing file on disk, but AdvanceStep will
- // append steps later.
- auto bpWriter = adios.Open("myNumbers.bp", "w", bpWriterSettings);
+ adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
- if (bpWriter == nullptr)
- throw std::ios_base::failure("ERROR: failed to open ADIOS bpWriter\n");
+ // Application variable
+ const unsigned int Nx = 10;
+ int Nparts; // random size per process, 5..10 each
- for (int step; step < NSTEPS; step++)
+ std::vector<double> NiceArray(Nx);
+ for (int i = 0; i < Nx; i++)
{
- int Nparts = rand() % 6 + 5; // random size per process, 5..10 each
- RaggedArray.reserve(Nparts);
- for (int i = 0; i < Nparts; i++)
- {
- RaggedArray[i] = rank * Nx + (float)i;
- }
-
- if (rank == 0)
- {
- // Writing a global scalar from only one process
- bpWriter->Write<unsigned int>(varNX, &Nx);
- }
- // Writing a local scalar on every process. Will be shown at reading as a
- // 1D array
- bpWriter->Write<int>(varNparts, &Nparts);
-
- // Writing a global scalar on every process is useless. Information will
- // be thrown away
- // and only rank 0's data will be in the output
- bpWriter->Write<int>(varNproc, &nproc);
-
- // Make a 1D selection to describe the local dimensions of the variable we
- // write and
- // its offsets in the global spaces
- adios::Selection &sel = adios.SelectionBoundingBox(
- {Nx}, {rank * Nx}); // local dims and offsets; both as list
- NiceArray.SetSelection(sel);
- bpWriter->Write<double>(varNice, NiceArray.data()); // Base class Engine
- // own the Write<T>
- // that will call
- // overloaded Write
- // from Derived
-
- adios::Selection &lsel =
- adios.SelectionBoundingBox({1, Nparts}, {rank, 0});
- RaggedArray.SetSelection(sel);
- bpWriter->Write<float>(varRagged, RaggedArray.data()); // Base class
- // Engine own the
- // Write<T> that
- // will call
- // overloaded Write
- // from Derived
-
- // Indicate we are done for this step
- // N-to-M Aggregation, disk I/O will be performed during this call, unless
- // time aggregation postpones all of that to some later step
- bpWriter->Advance();
+ NiceArray[i] = rank * Nx + (double)i;
}
- // Called once: indicate that we are done with this output for the run
- bpWriter->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
+ std::vector<float> RaggedArray;
+
+ try
+ {
+ // Define group and variables with transforms, variables don't have
+ // functions, only group can access variables
+ adios::Variable<unsigned int> &varNX =
+ adios.DefineVariable<unsigned int>(
+ "NX"); // global single-value across processes
+ adios::Variable<int> &varNproc = adios.DefineVariable<int>(
+ "nproc", adios::GLOBAL_VALUE); // same def for global value
+ adios::Variable<int> &varNparts =
+ adios.DefineVariable<int>("Nparts",
+ adios::LOCAL_VALUE); // a single-value
+ // different on
+ // every process
+ adios::Variable<double> &varNice = adios.DefineVariable<double>(
+ "Nice", {nproc * Nx}); // 1D global array
+ adios::Variable<float> &varRagged = adios.DefineVariable<float>(
+ "Ragged", {nproc, adios::VARYING_DIMENSION}); // ragged array
+
+ // add transform to variable in group...not executed (just testing API)
+ adios::Transform bzip2 = adios::transform::BZIP2();
+ varNice->AddTransform(bzip2, 1);
+
+ // Define method for engine creation
+ // 1. Get method def from config file or define new one
+ adios::Method &bpWriterSettings = adios.GetMethod("output");
+ if (bpWriterSettings.undeclared())
+ {
+ // if not defined by user, we can change the default settings
+ bpWriterSettings.SetEngine("BP"); // BP is the default engine
+ bpWriterSettings.AddTransport(
+ "File",
+ "lucky=yes"); // ISO-POSIX file is the default transport
+ // Passing parameters to the transport
+ bpWriterSettings.SetParameters(
+ "have_metadata_file",
+ "yes"); // Passing parameters to the engine
+ bpWriterSettings.SetParameters("Aggregation",
+ (nproc + 1) /
+ 2); // number of aggregators
+ }
+
+ // Open returns a smart pointer to Engine containing the Derived class
+ // Writer
+ // "w" means we overwrite any existing file on disk, but AdvanceStep
+ // will
+ // append steps later.
+ auto bpWriter = adios.Open("myNumbers.bp", "w", bpWriterSettings);
+
+ if (bpWriter == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: failed to open ADIOS bpWriter\n");
+
+ for (int step; step < NSTEPS; step++)
+ {
+ int Nparts = rand() % 6 + 5; // random size per process, 5..10 each
+ RaggedArray.reserve(Nparts);
+ for (int i = 0; i < Nparts; i++)
+ {
+ RaggedArray[i] = rank * Nx + (float)i;
+ }
+
+ if (rank == 0)
+ {
+ // Writing a global scalar from only one process
+ bpWriter->Write<unsigned int>(varNX, &Nx);
+ }
+ // Writing a local scalar on every process. Will be shown at reading
+ // as a
+ // 1D array
+ bpWriter->Write<int>(varNparts, &Nparts);
+
+ // Writing a global scalar on every process is useless. Information
+ // will
+ // be thrown away
+ // and only rank 0's data will be in the output
+ bpWriter->Write<int>(varNproc, &nproc);
+
+ // Make a 1D selection to describe the local dimensions of the
+ // variable we
+ // write and
+ // its offsets in the global spaces
+ adios::Selection &sel = adios.SelectionBoundingBox(
+ {Nx}, {rank * Nx}); // local dims and offsets; both as list
+ NiceArray.SetSelection(sel);
+ bpWriter->Write<double>(varNice,
+ NiceArray.data()); // Base class Engine
+ // own the Write<T>
+ // that will call
+ // overloaded Write
+ // from Derived
+
+ adios::Selection &lsel =
+ adios.SelectionBoundingBox({1, Nparts}, {rank, 0});
+ RaggedArray.SetSelection(sel);
+ bpWriter->Write<float>(varRagged, RaggedArray.data()); // Base class
+ // Engine own the
+ // Write<T> that
+ // will call
+ // overloaded Write
+ // from Derived
+
+ // Indicate we are done for this step
+ // N-to-M Aggregation, disk I/O will be performed during this call,
+ // unless
+ // time aggregation postpones all of that to some later step
+ bpWriter->Advance();
+ }
+
+ // Called once: indicate that we are done with this output for the run
+ bpWriter->Close();
+ }
+ catch (std::invalid_argument &e)
{
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
+ catch (std::ios_base::failure &e)
{
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
+ catch (std::exception &e)
{
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- MPI_Finalize();
+ MPI_Finalize();
- return 0;
+ return 0;
}
diff --git a/examples/heatTransfer/HeatTransfer.cpp b/examples/heatTransfer/HeatTransfer.cpp
index 5cac74fc91b389d6a6167b95e9fc8a58a0737dd7..ac706e4c66d75c5e342faa915ae2edb8aa4519e2 100644
--- a/examples/heatTransfer/HeatTransfer.cpp
+++ b/examples/heatTransfer/HeatTransfer.cpp
@@ -23,212 +23,213 @@
HeatTransfer::HeatTransfer(const Settings &settings) : m_s{settings}
{
- m_T1 = new double *[m_s.ndx + 2];
- m_T1[0] = new double[(m_s.ndx + 2) * (m_s.ndy + 2)];
- m_T2 = new double *[m_s.ndx + 2];
- m_T2[0] = new double[(m_s.ndx + 2) * (m_s.ndy + 2)];
- for (unsigned int i = 1; i < m_s.ndx + 2; i++)
- {
- m_T1[i] = m_T1[i - 1] + m_s.ndy + 2;
- m_T2[i] = m_T2[i - 1] + m_s.ndy + 2;
- }
- m_TCurrent = m_T1;
- m_TNext = m_T2;
+ m_T1 = new double *[m_s.ndx + 2];
+ m_T1[0] = new double[(m_s.ndx + 2) * (m_s.ndy + 2)];
+ m_T2 = new double *[m_s.ndx + 2];
+ m_T2[0] = new double[(m_s.ndx + 2) * (m_s.ndy + 2)];
+ for (unsigned int i = 1; i < m_s.ndx + 2; i++)
+ {
+ m_T1[i] = m_T1[i - 1] + m_s.ndy + 2;
+ m_T2[i] = m_T2[i - 1] + m_s.ndy + 2;
+ }
+ m_TCurrent = m_T1;
+ m_TNext = m_T2;
}
HeatTransfer::~HeatTransfer()
{
- delete[] m_T1[0];
- delete[] m_T1;
- delete[] m_T2[0];
- delete[] m_T2;
+ delete[] m_T1[0];
+ delete[] m_T1;
+ delete[] m_T2[0];
+ delete[] m_T2;
}
void HeatTransfer::init(bool init_with_rank)
{
- if (init_with_rank)
- {
- for (unsigned int i = 0; i < m_s.ndx + 2; i++)
- for (unsigned int j = 0; j < m_s.ndy + 2; j++)
- m_T1[i][j] = m_s.rank;
- }
- else
- {
- const double hx = 2.0 * 4.0 * atan(1.0) / m_s.ndx;
- const double hy = 2.0 * 4.0 * atan(1.0) / m_s.ndy;
-
- double x, y;
- for (unsigned int i = 0; i < m_s.ndx + 2; i++)
+ if (init_with_rank)
+ {
+ for (unsigned int i = 0; i < m_s.ndx + 2; i++)
+ for (unsigned int j = 0; j < m_s.ndy + 2; j++)
+ m_T1[i][j] = m_s.rank;
+ }
+ else
{
- x = 0.0 + hx * (i - 1);
- for (unsigned int j = 0; j < m_s.ndy + 2; j++)
- {
- y = 0.0 + hy * (j - 1);
- m_T1[i][j] = cos(8 * x) + cos(6 * x) - cos(4 * x) + cos(2 * x) -
- cos(x) + sin(8 * y) - sin(6 * y) + sin(4 * y) -
- sin(2 * y) + sin(y);
- }
- }
- }
- m_TCurrent = m_T1;
- m_TNext = m_T2;
+ const double hx = 2.0 * 4.0 * atan(1.0) / m_s.ndx;
+ const double hy = 2.0 * 4.0 * atan(1.0) / m_s.ndy;
+
+ double x, y;
+ for (unsigned int i = 0; i < m_s.ndx + 2; i++)
+ {
+ x = 0.0 + hx * (i - 1);
+ for (unsigned int j = 0; j < m_s.ndy + 2; j++)
+ {
+ y = 0.0 + hy * (j - 1);
+ m_T1[i][j] = cos(8 * x) + cos(6 * x) - cos(4 * x) + cos(2 * x) -
+ cos(x) + sin(8 * y) - sin(6 * y) + sin(4 * y) -
+ sin(2 * y) + sin(y);
+ }
+ }
+ }
+ m_TCurrent = m_T1;
+ m_TNext = m_T2;
}
void HeatTransfer::printT(std::string message, MPI_Comm comm) const
{
- int rank, size;
- int tag = 1;
- int token;
- MPI_Status status;
- MPI_Comm_rank(comm, &rank);
- MPI_Comm_size(comm, &size);
- if (rank > 0)
- {
- MPI_Recv(&token, 1, MPI_INT, rank - 1, tag, comm, &status);
- }
-
- std::cout << "Rank " << rank << " " << message << std::endl;
- for (unsigned int i = 0; i < m_s.ndx + 2; i++)
- {
- std::cout << " T[" << i << "][] = ";
- for (unsigned int j = 0; j < m_s.ndy + 2; j++)
- {
- std::cout << std::setw(6) << m_TCurrent[i][j];
- }
- std::cout << std::endl;
- }
- std::cout << std::flush << std::endl;
-
- if (rank < size - 1)
- {
- MPI_Send(&token, 1, MPI_INT, rank + 1, tag, comm);
- }
+ int rank, size;
+ int tag = 1;
+ int token;
+ MPI_Status status;
+ MPI_Comm_rank(comm, &rank);
+ MPI_Comm_size(comm, &size);
+ if (rank > 0)
+ {
+ MPI_Recv(&token, 1, MPI_INT, rank - 1, tag, comm, &status);
+ }
+
+ std::cout << "Rank " << rank << " " << message << std::endl;
+ for (unsigned int i = 0; i < m_s.ndx + 2; i++)
+ {
+ std::cout << " T[" << i << "][] = ";
+ for (unsigned int j = 0; j < m_s.ndy + 2; j++)
+ {
+ std::cout << std::setw(6) << m_TCurrent[i][j];
+ }
+ std::cout << std::endl;
+ }
+ std::cout << std::flush << std::endl;
+
+ if (rank < size - 1)
+ {
+ MPI_Send(&token, 1, MPI_INT, rank + 1, tag, comm);
+ }
}
void HeatTransfer::switchCurrentNext()
{
- double **tmp = m_TCurrent;
- m_TCurrent = m_TNext;
- m_TNext = tmp;
+ double **tmp = m_TCurrent;
+ m_TCurrent = m_TNext;
+ m_TNext = tmp;
}
void HeatTransfer::iterate()
{
- for (unsigned int i = 1; i <= m_s.ndx; ++i)
- {
- for (unsigned int j = 1; j <= m_s.ndy; ++j)
+ for (unsigned int i = 1; i <= m_s.ndx; ++i)
{
- m_TNext[i][j] =
- omega / 4 * (m_TCurrent[i - 1][j] + m_TCurrent[i + 1][j] +
- m_TCurrent[i][j - 1] + m_TCurrent[i][j + 1]) +
- (1.0 - omega) * m_TCurrent[i][j];
+ for (unsigned int j = 1; j <= m_s.ndy; ++j)
+ {
+ m_TNext[i][j] =
+ omega / 4 * (m_TCurrent[i - 1][j] + m_TCurrent[i + 1][j] +
+ m_TCurrent[i][j - 1] + m_TCurrent[i][j + 1]) +
+ (1.0 - omega) * m_TCurrent[i][j];
+ }
}
- }
- switchCurrentNext();
+ switchCurrentNext();
}
void HeatTransfer::heatEdges()
{
- // Heat the whole global edges
- if (m_s.posx == 0)
- for (unsigned int j = 0; j < m_s.ndy + 2; ++j)
- m_TCurrent[0][j] = edgetemp;
-
- if (m_s.posx == m_s.npx - 1)
- for (unsigned int j = 0; j < m_s.ndy + 2; ++j)
- m_TCurrent[m_s.ndx + 1][j] = edgetemp;
-
- if (m_s.posy == 0)
- for (unsigned int i = 0; i < m_s.ndx + 2; ++i)
- m_TCurrent[i][0] = edgetemp;
-
- if (m_s.posy == m_s.npy - 1)
- for (unsigned int i = 0; i < m_s.ndx + 2; ++i)
- m_TCurrent[i][m_s.ndy + 1] = edgetemp;
+ // Heat the whole global edges
+ if (m_s.posx == 0)
+ for (unsigned int j = 0; j < m_s.ndy + 2; ++j)
+ m_TCurrent[0][j] = edgetemp;
+
+ if (m_s.posx == m_s.npx - 1)
+ for (unsigned int j = 0; j < m_s.ndy + 2; ++j)
+ m_TCurrent[m_s.ndx + 1][j] = edgetemp;
+
+ if (m_s.posy == 0)
+ for (unsigned int i = 0; i < m_s.ndx + 2; ++i)
+ m_TCurrent[i][0] = edgetemp;
+
+ if (m_s.posy == m_s.npy - 1)
+ for (unsigned int i = 0; i < m_s.ndx + 2; ++i)
+ m_TCurrent[i][m_s.ndy + 1] = edgetemp;
}
void HeatTransfer::exchange(MPI_Comm comm)
{
- // Exchange ghost cells, in the order left-right-up-down
-
- double *send_x = new double[m_s.ndx + 2];
- double *recv_x = new double[m_s.ndx + 2];
-
- // send to left + receive from right
- int tag = 1;
- MPI_Status status;
- if (m_s.rank_left >= 0)
- {
- std::cout << "Rank " << m_s.rank << " send left to rank " << m_s.rank_left
- << std::endl;
- for (unsigned int i = 0; i < m_s.ndx + 2; ++i)
- send_x[i] = m_TCurrent[i][1];
- MPI_Send(send_x, m_s.ndx + 2, MPI_REAL8, m_s.rank_left, tag, comm);
- }
- if (m_s.rank_right >= 0)
- {
- std::cout << "Rank " << m_s.rank << " receive from right from rank "
- << m_s.rank_right << std::endl;
- MPI_Recv(recv_x, m_s.ndx + 2, MPI_REAL8, m_s.rank_right, tag, comm,
- &status);
- for (unsigned int i = 0; i < m_s.ndx + 2; ++i)
- m_TCurrent[i][m_s.ndy + 1] = recv_x[i];
- }
-
- // send to right + receive from left
- tag = 2;
- if (m_s.rank_right >= 0)
- {
- std::cout << "Rank " << m_s.rank << " send right to rank " << m_s.rank_right
- << std::endl;
- for (unsigned int i = 0; i < m_s.ndx + 2; ++i)
- send_x[i] = m_TCurrent[i][m_s.ndy];
- MPI_Send(send_x, m_s.ndx + 2, MPI_REAL8, m_s.rank_right, tag, comm);
- }
- if (m_s.rank_left >= 0)
- {
- std::cout << "Rank " << m_s.rank << " receive from left from rank "
- << m_s.rank_left << std::endl;
- MPI_Recv(recv_x, m_s.ndx + 2, MPI_REAL8, m_s.rank_left, tag, comm, &status);
- for (unsigned int i = 0; i < m_s.ndx + 2; ++i)
- m_TCurrent[i][0] = recv_x[i];
- }
-
- // send down + receive from above
- tag = 3;
- if (m_s.rank_down >= 0)
- {
- std::cout << "Rank " << m_s.rank << " send down to rank " << m_s.rank_down
- << std::endl;
- MPI_Send(m_TCurrent[m_s.ndx], m_s.ndy + 2, MPI_REAL8, m_s.rank_down, tag,
- comm);
- }
- if (m_s.rank_up >= 0)
- {
- std::cout << "Rank " << m_s.rank << " receive from above from rank "
- << m_s.rank_up << std::endl;
- MPI_Recv(m_TCurrent[0], m_s.ndy + 2, MPI_REAL8, m_s.rank_up, tag, comm,
- &status);
- }
-
- // send up + receive from below
- tag = 4;
- if (m_s.rank_up >= 0)
- {
- std::cout << "Rank " << m_s.rank << " send up to rank " << m_s.rank_up
- << std::endl;
- MPI_Send(m_TCurrent[1], m_s.ndy + 2, MPI_REAL8, m_s.rank_up, tag, comm);
- }
- if (m_s.rank_down >= 0)
- {
- std::cout << "Rank " << m_s.rank << " receive from below from rank "
- << m_s.rank_down << std::endl;
- MPI_Recv(m_TCurrent[m_s.ndx + 1], m_s.ndy + 2, MPI_REAL8, m_s.rank_down,
- tag, comm, &status);
- }
-
- delete[] send_x;
- delete[] recv_x;
+ // Exchange ghost cells, in the order left-right-up-down
+
+ double *send_x = new double[m_s.ndx + 2];
+ double *recv_x = new double[m_s.ndx + 2];
+
+ // send to left + receive from right
+ int tag = 1;
+ MPI_Status status;
+ if (m_s.rank_left >= 0)
+ {
+ std::cout << "Rank " << m_s.rank << " send left to rank "
+ << m_s.rank_left << std::endl;
+ for (unsigned int i = 0; i < m_s.ndx + 2; ++i)
+ send_x[i] = m_TCurrent[i][1];
+ MPI_Send(send_x, m_s.ndx + 2, MPI_REAL8, m_s.rank_left, tag, comm);
+ }
+ if (m_s.rank_right >= 0)
+ {
+ std::cout << "Rank " << m_s.rank << " receive from right from rank "
+ << m_s.rank_right << std::endl;
+ MPI_Recv(recv_x, m_s.ndx + 2, MPI_REAL8, m_s.rank_right, tag, comm,
+ &status);
+ for (unsigned int i = 0; i < m_s.ndx + 2; ++i)
+ m_TCurrent[i][m_s.ndy + 1] = recv_x[i];
+ }
+
+ // send to right + receive from left
+ tag = 2;
+ if (m_s.rank_right >= 0)
+ {
+ std::cout << "Rank " << m_s.rank << " send right to rank "
+ << m_s.rank_right << std::endl;
+ for (unsigned int i = 0; i < m_s.ndx + 2; ++i)
+ send_x[i] = m_TCurrent[i][m_s.ndy];
+ MPI_Send(send_x, m_s.ndx + 2, MPI_REAL8, m_s.rank_right, tag, comm);
+ }
+ if (m_s.rank_left >= 0)
+ {
+ std::cout << "Rank " << m_s.rank << " receive from left from rank "
+ << m_s.rank_left << std::endl;
+ MPI_Recv(recv_x, m_s.ndx + 2, MPI_REAL8, m_s.rank_left, tag, comm,
+ &status);
+ for (unsigned int i = 0; i < m_s.ndx + 2; ++i)
+ m_TCurrent[i][0] = recv_x[i];
+ }
+
+ // send down + receive from above
+ tag = 3;
+ if (m_s.rank_down >= 0)
+ {
+ std::cout << "Rank " << m_s.rank << " send down to rank "
+ << m_s.rank_down << std::endl;
+ MPI_Send(m_TCurrent[m_s.ndx], m_s.ndy + 2, MPI_REAL8, m_s.rank_down,
+ tag, comm);
+ }
+ if (m_s.rank_up >= 0)
+ {
+ std::cout << "Rank " << m_s.rank << " receive from above from rank "
+ << m_s.rank_up << std::endl;
+ MPI_Recv(m_TCurrent[0], m_s.ndy + 2, MPI_REAL8, m_s.rank_up, tag, comm,
+ &status);
+ }
+
+ // send up + receive from below
+ tag = 4;
+ if (m_s.rank_up >= 0)
+ {
+ std::cout << "Rank " << m_s.rank << " send up to rank " << m_s.rank_up
+ << std::endl;
+ MPI_Send(m_TCurrent[1], m_s.ndy + 2, MPI_REAL8, m_s.rank_up, tag, comm);
+ }
+ if (m_s.rank_down >= 0)
+ {
+ std::cout << "Rank " << m_s.rank << " receive from below from rank "
+ << m_s.rank_down << std::endl;
+ MPI_Recv(m_TCurrent[m_s.ndx + 1], m_s.ndy + 2, MPI_REAL8, m_s.rank_down,
+ tag, comm, &status);
+ }
+
+ delete[] send_x;
+ delete[] recv_x;
}
#include <cstring>
@@ -238,11 +239,11 @@ void HeatTransfer::exchange(MPI_Comm comm)
*/
std::vector<double> HeatTransfer::data_noghost() const
{
- std::vector<double> d(m_s.ndx * m_s.ndy);
- for (unsigned int i = 1; i <= m_s.ndx; ++i)
- {
- std::memcpy(&d[(i - 1) * m_s.ndy], m_TCurrent[i] + 1,
- m_s.ndy * sizeof(double));
- }
- return d;
+ std::vector<double> d(m_s.ndx * m_s.ndy);
+ for (unsigned int i = 1; i <= m_s.ndx; ++i)
+ {
+ std::memcpy(&d[(i - 1) * m_s.ndy], m_TCurrent[i] + 1,
+ m_s.ndy * sizeof(double));
+ }
+ return d;
}
diff --git a/examples/heatTransfer/HeatTransfer.h b/examples/heatTransfer/HeatTransfer.h
index 12334f0664a36eaf54b86aa1b83e2d607a5cd4d8..7d48eb558d2db274218e8b0030ad53cc2aa0f7f3 100644
--- a/examples/heatTransfer/HeatTransfer.h
+++ b/examples/heatTransfer/HeatTransfer.h
@@ -19,34 +19,36 @@
class HeatTransfer
{
public:
- HeatTransfer(const Settings &settings); // Create two 2D arrays with ghost
- // cells to compute
- ~HeatTransfer();
- void init(bool init_with_rank); // set up array values with either rank or
- // real demo values
- void iterate(); // one local calculation step
- void heatEdges(); // reset the heat values at the global edge
- void exchange(MPI_Comm comm); // send updates to neighbors
-
- // return a single value at index i,j. 0 <= i <= ndx+2, 0 <= j <= ndy+2
- double T(int i, int j) const { return m_TCurrent[i][j]; };
- // return (1D) pointer to current T data, ndx+2 * ndy+2 elements
- double *data() const { return m_TCurrent[0]; };
- // return (1D) pointer to current T data without ghost cells, ndx*ndy elements
- std::vector<double> data_noghost() const;
-
- void printT(std::string message,
- MPI_Comm comm) const; // debug: print local TCurrent on stdout
+ HeatTransfer(const Settings &settings); // Create two 2D arrays with ghost
+ // cells to compute
+ ~HeatTransfer();
+ void init(bool init_with_rank); // set up array values with either rank or
+ // real demo values
+ void iterate(); // one local calculation step
+ void heatEdges(); // reset the heat values at the global edge
+ void exchange(MPI_Comm comm); // send updates to neighbors
+
+ // return a single value at index i,j. 0 <= i <= ndx+2, 0 <= j <= ndy+2
+ double T(int i, int j) const { return m_TCurrent[i][j]; };
+ // return (1D) pointer to current T data, ndx+2 * ndy+2 elements
+ double *data() const { return m_TCurrent[0]; };
+ // return (1D) pointer to current T data without ghost cells, ndx*ndy
+ // elements
+ std::vector<double> data_noghost() const;
+
+ void printT(std::string message,
+ MPI_Comm comm) const; // debug: print local TCurrent on stdout
private:
- const double edgetemp = 3.0; // temperature at the edges of the global plate
- const double omega = 0.8; // weight for current temp is (1-omega) in iteration
- double **m_T1; // 2D array (ndx+2) * (ndy+2) size, including ghost cells
- double **m_T2; // another 2D array
- double **m_TCurrent; // pointer to T1 or T2
- double **m_TNext; // pointer to T2 or T1
- const Settings &m_s;
- void switchCurrentNext(); // switch the current array with the next array
+ const double edgetemp = 3.0; // temperature at the edges of the global plate
+ const double omega =
+ 0.8; // weight for current temp is (1-omega) in iteration
+ double **m_T1; // 2D array (ndx+2) * (ndy+2) size, including ghost cells
+ double **m_T2; // another 2D array
+ double **m_TCurrent; // pointer to T1 or T2
+ double **m_TNext; // pointer to T2 or T1
+ const Settings &m_s;
+ void switchCurrentNext(); // switch the current array with the next array
};
#endif /* HEATTRANSFER_H_ */
diff --git a/examples/heatTransfer/IO.h b/examples/heatTransfer/IO.h
index e9c7c6195b24fab12590f009f9c0b024d7009b59..999866112e471e46f2136f804ed2ee5226bb0a0a 100644
--- a/examples/heatTransfer/IO.h
+++ b/examples/heatTransfer/IO.h
@@ -19,13 +19,13 @@ class IO
{
public:
- IO(const Settings &s, MPI_Comm comm);
- ~IO();
- void write(int step, const HeatTransfer &ht, const Settings &s,
- MPI_Comm comm);
+ IO(const Settings &s, MPI_Comm comm);
+ ~IO();
+ void write(int step, const HeatTransfer &ht, const Settings &s,
+ MPI_Comm comm);
private:
- std::string m_outputfilename;
+ std::string m_outputfilename;
};
#endif /* IO_H_ */
diff --git a/examples/heatTransfer/IO_adios1.cpp b/examples/heatTransfer/IO_adios1.cpp
index 806c654d09ed8e73b6ef0d656953b4fcc5fc48fa..8bc8753c264d3562eb792e7ba39184ed349e957b 100644
--- a/examples/heatTransfer/IO_adios1.cpp
+++ b/examples/heatTransfer/IO_adios1.cpp
@@ -20,24 +20,24 @@ static int rank_saved;
IO::IO(const Settings &s, MPI_Comm comm)
{
- rank_saved = s.rank;
- m_outputfilename = s.outputfile + ".bp";
- adios_init_noxml(comm);
- adios_declare_group(&group, "heat", "", adios_stat_default);
- adios_select_method(group, "MPI", "", "");
+ rank_saved = s.rank;
+ m_outputfilename = s.outputfile + ".bp";
+ adios_init_noxml(comm);
+ adios_declare_group(&group, "heat", "", adios_stat_default);
+ adios_select_method(group, "MPI", "", "");
- adios_define_var(group, "gndx", "", adios_integer, "", "", "");
- adios_define_var(group, "gndy", "", adios_integer, "", "", "");
+ adios_define_var(group, "gndx", "", adios_integer, "", "", "");
+ adios_define_var(group, "gndy", "", adios_integer, "", "", "");
- std::string ldims(std::to_string(s.ndx) + "," + std::to_string(s.ndy));
- std::string gdims(std::to_string(s.gndx) + "," + std::to_string(s.gndy));
- std::string offs(std::to_string(s.offsx) + "," + std::to_string(s.offsy));
- uint64_t T_id;
- T_id = adios_define_var(group, "T", "", adios_double, ldims.c_str(),
- gdims.c_str(), offs.c_str());
+ std::string ldims(std::to_string(s.ndx) + "," + std::to_string(s.ndy));
+ std::string gdims(std::to_string(s.gndx) + "," + std::to_string(s.gndy));
+ std::string offs(std::to_string(s.offsx) + "," + std::to_string(s.offsy));
+ uint64_t T_id;
+ T_id = adios_define_var(group, "T", "", adios_double, ldims.c_str(),
+ gdims.c_str(), offs.c_str());
- adios_set_transform(T_id, "none");
- // adios_set_transform( T_id, "zfp:accuracy=0.001");
+ adios_set_transform(T_id, "none");
+ // adios_set_transform( T_id, "zfp:accuracy=0.001");
}
IO::~IO() { adios_finalize(rank_saved); }
@@ -45,31 +45,31 @@ IO::~IO() { adios_finalize(rank_saved); }
void IO::write(int step, const HeatTransfer &ht, const Settings &s,
MPI_Comm comm)
{
- char mode[2] = "w";
- if (step > 0)
- {
- mode[0] = 'a';
- }
+ char mode[2] = "w";
+ if (step > 0)
+ {
+ mode[0] = 'a';
+ }
- // for time measurements, let's synchronize the processes
- MPI_Barrier(comm);
- double time_start = MPI_Wtime();
+ // for time measurements, let's synchronize the processes
+ MPI_Barrier(comm);
+ double time_start = MPI_Wtime();
- int64_t f;
- adios_open(&f, "heat", m_outputfilename.c_str(), mode, comm);
- adios_write(f, "gndx", &s.gndx);
- adios_write(f, "gndy", &s.gndy);
- adios_write(f, "T", ht.data_noghost().data());
- adios_close(f);
+ int64_t f;
+ adios_open(&f, "heat", m_outputfilename.c_str(), mode, comm);
+ adios_write(f, "gndx", &s.gndx);
+ adios_write(f, "gndy", &s.gndy);
+ adios_write(f, "T", ht.data_noghost().data());
+ adios_close(f);
- MPI_Barrier(comm);
- double total_time = MPI_Wtime() - time_start;
- uint64_t adios_totalsize =
- 2 * sizeof(int) + 2 * s.ndx * s.ndy * sizeof(double);
- uint64_t sizeMB =
- adios_totalsize * s.nproc / 1024 / 1024 / 1024; // size in MB
- uint64_t mbs = sizeMB / total_time;
- if (s.rank == 0)
- std::cout << "Step " << step << ": " << m_outputfilename << " " << sizeMB
- << " " << total_time << "" << mbs << std::endl;
+ MPI_Barrier(comm);
+ double total_time = MPI_Wtime() - time_start;
+ uint64_t adios_totalsize =
+ 2 * sizeof(int) + 2 * s.ndx * s.ndy * sizeof(double);
+ uint64_t sizeMB =
+ adios_totalsize * s.nproc / 1024 / 1024 / 1024; // size in MB
+ uint64_t mbs = sizeMB / total_time;
+ if (s.rank == 0)
+ std::cout << "Step " << step << ": " << m_outputfilename << " "
+ << sizeMB << " " << total_time << "" << mbs << std::endl;
}
diff --git a/examples/heatTransfer/IO_adios2.cpp b/examples/heatTransfer/IO_adios2.cpp
index 49e9c58602b8dd5bcf05d4c2502746af42b14e54..ac0567820549d3300ca410c9686fe8552fb9578f 100644
--- a/examples/heatTransfer/IO_adios2.cpp
+++ b/examples/heatTransfer/IO_adios2.cpp
@@ -20,90 +20,95 @@ adios::Variable<double> *varT = nullptr;
IO::IO(const Settings &s, MPI_Comm comm)
{
- rank_saved = s.rank;
- m_outputfilename = s.outputfile + ".bp";
- ad = new adios::ADIOS("adios2.xml", comm, adios::Verbose::INFO);
+ rank_saved = s.rank;
+ m_outputfilename = s.outputfile + ".bp";
+ ad = new adios::ADIOS("adios2.xml", comm, adios::Verbose::INFO);
- // Define method for engine creation
- // 1. Get method def from config file or define new one
+ // Define method for engine creation
+ // 1. Get method def from config file or define new one
- adios::Method &bpWriterSettings = ad->DeclareMethod("output");
- if (!bpWriterSettings.isUserDefined())
- {
- // if not defined by user, we can change the default settings
- bpWriterSettings.SetEngine("BP"); // BP is the default engine
- bpWriterSettings.AllowThreads(
- 1); // allow 1 extra thread for data processing
- bpWriterSettings.AddTransport(
- "File", "lucky=yes"); // ISO-POSIX file is the default transport
- // Passing parameters to the transport
- bpWriterSettings.SetParameters("have_metadata_file",
- "yes"); // Passing parameters to the engine
- bpWriterSettings.SetParameters(
- "Aggregation",
- std::to_string((s.nproc + 1) / 2)); // number of aggregators
- }
+ adios::Method &bpWriterSettings = ad->DeclareMethod("output");
+ if (!bpWriterSettings.isUserDefined())
+ {
+ // if not defined by user, we can change the default settings
+ bpWriterSettings.SetEngine("BP"); // BP is the default engine
+ bpWriterSettings.AllowThreads(
+ 1); // allow 1 extra thread for data processing
+ bpWriterSettings.AddTransport(
+ "File", "lucky=yes"); // ISO-POSIX file is the default transport
+ // Passing parameters to the transport
+ bpWriterSettings.SetParameters(
+ "have_metadata_file",
+ "yes"); // Passing parameters to the engine
+ bpWriterSettings.SetParameters(
+ "Aggregation",
+ std::to_string((s.nproc + 1) / 2)); // number of aggregators
+ }
- // define T as 2D global array
- varT = &ad->DefineVariable<double>(
- "T", {s.gndx, s.gndy}, // Global dimensions
- {s.ndx, s.ndy}, // local size, could be defined later using SetSelection()
- {s.offsx, s.offsy} // offset of the local array in the global space
- );
+ // define T as 2D global array
+ varT = &ad->DefineVariable<double>(
+ "T", {s.gndx, s.gndy}, // Global dimensions
+ {s.ndx,
+ s.ndy}, // local size, could be defined later using SetSelection()
+ {s.offsx, s.offsy} // offset of the local array in the global space
+ );
- // add transform to variable
- // adios::Transform tr = adios::transform::BZIP2( );
- // varT.AddTransform( tr, "" );
- // varT.AddTransform( tr,"accuracy=0.001" ); // for ZFP
+ // add transform to variable
+ // adios::Transform tr = adios::transform::BZIP2( );
+ // varT.AddTransform( tr, "" );
+ // varT.AddTransform( tr,"accuracy=0.001" ); // for ZFP
- bpWriter = ad->Open(m_outputfilename, "w", comm, bpWriterSettings,
- adios::IOMode::COLLECTIVE);
+ bpWriter = ad->Open(m_outputfilename, "w", comm, bpWriterSettings,
+ adios::IOMode::COLLECTIVE);
- if (bpWriter == nullptr)
- throw std::ios_base::failure("ERROR: failed to open ADIOS bpWriter\n");
+ if (bpWriter == nullptr)
+ throw std::ios_base::failure("ERROR: failed to open ADIOS bpWriter\n");
}
IO::~IO()
{
- bpWriter->Close();
- delete ad;
+ bpWriter->Close();
+ delete ad;
}
void /*IO::*/ old_style_write(int step, const HeatTransfer &ht,
const Settings &s, MPI_Comm comm)
{
- bpWriter->Write<double>(*varT, ht.data_noghost().data());
- bpWriter->Advance();
+ bpWriter->Write<double>(*varT, ht.data_noghost().data());
+ bpWriter->Advance();
}
void IO::write(int step, const HeatTransfer &ht, const Settings &s,
MPI_Comm comm)
{
- /* This selection is redundant and not required, since we defined
- * the selection already in DefineVariable(). It is here just as an example.
- */
- // Make a selection to describe the local dimensions of the variable we write
- // and
- // its offsets in the global spaces. This could have been done in
- // adios.DefineVariable()
- adios::Selection sel = adios.SelectionBoundingBox(
- {s.ndx, s.ndy},
- {s.offsx, s.offsy}); // local dims and offsets; both as list
- var2D.SetSelection(sel);
+ /* This selection is redundant and not required, since we defined
+ * the selection already in DefineVariable(). It is here just as an example.
+ */
+ // Make a selection to describe the local dimensions of the variable we
+ // write
+ // and
+ // its offsets in the global spaces. This could have been done in
+ // adios.DefineVariable()
+ adios::Selection sel = adios.SelectionBoundingBox(
+ {s.ndx, s.ndy},
+ {s.offsx, s.offsy}); // local dims and offsets; both as list
+ var2D.SetSelection(sel);
- /* Select the area that we want to write from the data pointer we pass to the
- writer.
- Think HDF5 memspace, just not hyperslabs, only a bounding box selection.
- Engine will copy this bounding box from the data pointer into the output
- buffer.
- Size of the bounding box should match the "space" selection which was given
- above.
- Default memspace is always the full selection.
- */
- adios::Selection memspace =
- adios.SelectionBoundingBox({s.ndx, s.ndy}, {1, 1});
- var2D.SetMemorySelection(memspace);
+ /* Select the area that we want to write from the data pointer we pass to
+ the
+ writer.
+ Think HDF5 memspace, just not hyperslabs, only a bounding box selection.
+ Engine will copy this bounding box from the data pointer into the output
+ buffer.
+ Size of the bounding box should match the "space" selection which was
+ given
+ above.
+ Default memspace is always the full selection.
+ */
+ adios::Selection memspace =
+ adios.SelectionBoundingBox({s.ndx, s.ndy}, {1, 1});
+ var2D.SetMemorySelection(memspace);
- bpWriter->Write<double>(*varT, ht.data());
- bpWriter->Advance();
+ bpWriter->Write<double>(*varT, ht.data());
+ bpWriter->Advance();
}
diff --git a/examples/heatTransfer/IO_ascii.cpp b/examples/heatTransfer/IO_ascii.cpp
index ccf158dabdf8b373fb47290165556f6bb40e8254..5f16aa05f9ed1ac75892d903ec7af0fe794e64db 100644
--- a/examples/heatTransfer/IO_ascii.cpp
+++ b/examples/heatTransfer/IO_ascii.cpp
@@ -19,60 +19,61 @@ static std::streambuf *buf;
IO::IO(const Settings &s, MPI_Comm comm)
{
- m_outputfilename = s.outputfile;
+ m_outputfilename = s.outputfile;
- if (m_outputfilename == "cout")
- {
- buf = std::cout.rdbuf();
- }
- else
- {
- int rank;
- MPI_Comm_rank(comm, &rank);
- std::string rs = std::to_string(rank);
- of.open(m_outputfilename + rs + ".txt");
- buf = of.rdbuf();
- }
+ if (m_outputfilename == "cout")
+ {
+ buf = std::cout.rdbuf();
+ }
+ else
+ {
+ int rank;
+ MPI_Comm_rank(comm, &rank);
+ std::string rs = std::to_string(rank);
+ of.open(m_outputfilename + rs + ".txt");
+ buf = of.rdbuf();
+ }
}
IO::~IO()
{
- if (m_outputfilename != "cout")
- {
- of.close();
- }
+ if (m_outputfilename != "cout")
+ {
+ of.close();
+ }
}
void IO::write(int step, const HeatTransfer &ht, const Settings &s,
MPI_Comm comm)
{
- std::ostream out(buf);
- if (step == 0)
- {
- out << "rank=" << s.rank << " size=" << s.ndx << "x" << s.ndy
- << " offsets=" << s.offsx << ":" << s.offsy << " step=" << step
- << std::endl;
- out << " time row columns " << s.offsy << "..." << s.offsy + s.ndy - 1
- << std::endl;
- out << " ";
- for (int j = 1; j <= s.ndy; ++j)
+ std::ostream out(buf);
+ if (step == 0)
+ {
+ out << "rank=" << s.rank << " size=" << s.ndx << "x" << s.ndy
+ << " offsets=" << s.offsx << ":" << s.offsy << " step=" << step
+ << std::endl;
+ out << " time row columns " << s.offsy << "..."
+ << s.offsy + s.ndy - 1 << std::endl;
+ out << " ";
+ for (int j = 1; j <= s.ndy; ++j)
+ {
+ out << std::setw(9) << s.offsy + j - 1;
+ }
+ out << "\n-------------------------------------------------------------"
+ "-\n";
+ }
+ else
{
- out << std::setw(9) << s.offsy + j - 1;
+ out << std::endl;
}
- out << "\n--------------------------------------------------------------\n";
- }
- else
- {
- out << std::endl;
- }
- for (int i = 1; i <= s.ndx; ++i)
- {
- out << std::setw(5) << step << std::setw(5) << s.offsx + i - 1;
- for (int j = 1; j <= s.ndy; ++j)
+ for (int i = 1; i <= s.ndx; ++i)
{
- out << std::setw(9) << ht.T(i, j);
+ out << std::setw(5) << step << std::setw(5) << s.offsx + i - 1;
+ for (int j = 1; j <= s.ndy; ++j)
+ {
+ out << std::setw(9) << ht.T(i, j);
+ }
+ out << std::endl;
}
- out << std::endl;
- }
}
diff --git a/examples/heatTransfer/IO_hdf5_a.cpp b/examples/heatTransfer/IO_hdf5_a.cpp
index 881085f0c59a28aa4a8547fb3a67853d99c35f9a..c0514b803dff617f24d732f8dbcae60a50f6dd7c 100644
--- a/examples/heatTransfer/IO_hdf5_a.cpp
+++ b/examples/heatTransfer/IO_hdf5_a.cpp
@@ -26,37 +26,38 @@ IO::~IO() {}
void IO::write(int step, const HeatTransfer &ht, const Settings &s,
MPI_Comm comm)
{
- std::string rs = std::to_string(s.rank);
- std::string ts = std::to_string(step);
- std::string fname = s.outputfile + "." + rs + "." + ts + ".h5";
-
- // for time measurements, let's synchronize the processes
- MPI_Barrier(comm);
- double time_start = MPI_Wtime();
-
- hsize_t dims[2] = {static_cast<hsize_t>(s.ndx), static_cast<hsize_t>(s.ndy)};
-
- hid_t space = H5Screate_simple(2, dims, NULL);
- hid_t file =
- H5Fcreate(fname.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
- hid_t dset = H5Dcreate(file, "T", H5T_NATIVE_DOUBLE, space, H5P_DEFAULT,
- H5P_DEFAULT, H5P_DEFAULT);
-
- H5Dwrite(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT,
- ht.data_noghost().data());
-
- H5Dclose(dset);
- H5Sclose(space);
- H5Fclose(file);
-
- MPI_Barrier(comm);
- double total_time = MPI_Wtime() - time_start;
- uint64_t adios_totalsize =
- 2 * sizeof(int) + 2 * s.ndx * s.ndy * sizeof(double);
- uint64_t sizeMB =
- adios_totalsize * s.nproc / 1024 / 1024 / 1024; // size in MB
- uint64_t mbs = sizeMB / total_time;
- if (s.rank == 0)
- std::cout << "Step " << step << ": " << m_outputfilename << " " << sizeMB
- << " " << total_time << "" << mbs << std::endl;
+ std::string rs = std::to_string(s.rank);
+ std::string ts = std::to_string(step);
+ std::string fname = s.outputfile + "." + rs + "." + ts + ".h5";
+
+ // for time measurements, let's synchronize the processes
+ MPI_Barrier(comm);
+ double time_start = MPI_Wtime();
+
+ hsize_t dims[2] = {static_cast<hsize_t>(s.ndx),
+ static_cast<hsize_t>(s.ndy)};
+
+ hid_t space = H5Screate_simple(2, dims, NULL);
+ hid_t file =
+ H5Fcreate(fname.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+ hid_t dset = H5Dcreate(file, "T", H5T_NATIVE_DOUBLE, space, H5P_DEFAULT,
+ H5P_DEFAULT, H5P_DEFAULT);
+
+ H5Dwrite(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+ ht.data_noghost().data());
+
+ H5Dclose(dset);
+ H5Sclose(space);
+ H5Fclose(file);
+
+ MPI_Barrier(comm);
+ double total_time = MPI_Wtime() - time_start;
+ uint64_t adios_totalsize =
+ 2 * sizeof(int) + 2 * s.ndx * s.ndy * sizeof(double);
+ uint64_t sizeMB =
+ adios_totalsize * s.nproc / 1024 / 1024 / 1024; // size in MB
+ uint64_t mbs = sizeMB / total_time;
+ if (s.rank == 0)
+ std::cout << "Step " << step << ": " << m_outputfilename << " "
+ << sizeMB << " " << total_time << "" << mbs << std::endl;
}
diff --git a/examples/heatTransfer/Settings.cpp b/examples/heatTransfer/Settings.cpp
index f5e0459ed2f989dcc08cb3a0c466e476369af247..4337a00a33f7b3865bceb1feeb569537f1e6271c 100644
--- a/examples/heatTransfer/Settings.cpp
+++ b/examples/heatTransfer/Settings.cpp
@@ -15,70 +15,70 @@
static unsigned int convertToUint(std::string varName, char *arg)
{
- char *end;
- int retval = std::strtoll(arg, &end, 10);
- if (end[0] || errno == ERANGE)
- {
- throw std::invalid_argument("Invalid value given for " + varName + ": " +
- std::string(arg));
- }
- if (retval < 0)
- {
- throw std::invalid_argument("Negative value given for " + varName + ": " +
- std::string(arg));
- }
- return (unsigned int)retval;
+ char *end;
+ int retval = std::strtoll(arg, &end, 10);
+ if (end[0] || errno == ERANGE)
+ {
+ throw std::invalid_argument("Invalid value given for " + varName +
+ ": " + std::string(arg));
+ }
+ if (retval < 0)
+ {
+ throw std::invalid_argument("Negative value given for " + varName +
+ ": " + std::string(arg));
+ }
+ return (unsigned int)retval;
}
Settings::Settings(int argc, char *argv[], int rank, int nproc) : rank{rank}
{
- if (argc < 8)
- {
- throw std::invalid_argument("Not enough arguments");
- }
- this->nproc = (unsigned int)nproc;
+ if (argc < 8)
+ {
+ throw std::invalid_argument("Not enough arguments");
+ }
+ this->nproc = (unsigned int)nproc;
- outputfile = argv[1];
- npx = convertToUint("N", argv[2]);
- npy = convertToUint("M", argv[3]);
- ndx = convertToUint("nx", argv[4]);
- ndy = convertToUint("ny", argv[5]);
- steps = convertToUint("steps", argv[6]);
- iterations = convertToUint("iterations", argv[7]);
+ outputfile = argv[1];
+ npx = convertToUint("N", argv[2]);
+ npy = convertToUint("M", argv[3]);
+ ndx = convertToUint("nx", argv[4]);
+ ndy = convertToUint("ny", argv[5]);
+ steps = convertToUint("steps", argv[6]);
+ iterations = convertToUint("iterations", argv[7]);
- if (npx * npy != this->nproc)
- {
- throw std::invalid_argument("N*M must equal the number of processes");
- }
+ if (npx * npy != this->nproc)
+ {
+ throw std::invalid_argument("N*M must equal the number of processes");
+ }
- // calculate global array size and the local offsets in that global space
- gndx = npx * ndx;
- gndy = npy * ndy;
- posx = rank % npx;
- posy = rank / npx;
- offsx = posx * ndx;
- offsy = posy * ndy;
+ // calculate global array size and the local offsets in that global space
+ gndx = npx * ndx;
+ gndy = npy * ndy;
+ posx = rank % npx;
+ posy = rank / npx;
+ offsx = posx * ndx;
+ offsy = posy * ndy;
- // determine neighbors
- if (posx == 0)
- rank_left = -1;
- else
- rank_left = rank - 1;
+ // determine neighbors
+ if (posx == 0)
+ rank_left = -1;
+ else
+ rank_left = rank - 1;
- if (posx == npx - 1)
- rank_right = -1;
- else
- rank_right = rank + 1;
+ if (posx == npx - 1)
+ rank_right = -1;
+ else
+ rank_right = rank + 1;
- if (posy == 0)
- rank_up = -1;
- else
- rank_up = rank - npx;
+ if (posy == 0)
+ rank_up = -1;
+ else
+ rank_up = rank - npx;
- if (posy == npy - 1)
- rank_down = -1;
- else
- rank_down = rank + npx;
+ if (posy == npy - 1)
+ rank_down = -1;
+ else
+ rank_down = rank + npx;
}
Settings::~Settings() {}
diff --git a/examples/heatTransfer/Settings.h b/examples/heatTransfer/Settings.h
index 85382656abff49205a77422ec5b880588ff74af6..97e85ea310adcd55a2ccc10ca8333346461b3949 100644
--- a/examples/heatTransfer/Settings.h
+++ b/examples/heatTransfer/Settings.h
@@ -17,37 +17,38 @@ class Settings
{
public:
- // user arguments
- std::string outputfile;
- unsigned int npx; // Number of processes in X (slow) dimension
- unsigned int npy; // Number of processes in Y (fast) dimension
- unsigned int ndx; // Local array size in X dimension per process
- unsigned int ndy; // Local array size in y dimension per process
- unsigned int steps; // Number of output steps
- unsigned int iterations; // Number of computing iterations between steps
-
- // calculated values from those arguments and number of processes
- unsigned int gndx; // Global array size in slow dimension
- unsigned int gndy; // Global array size in fast dimension
- // X dim positions: rank 0, npx, 2npx... are in the same X position
- // Y dim positions: npx number of consecutive processes belong to one row (npx
- // columns)
- unsigned int posx; // Position of this process in X dimension
- unsigned int posy; // Position of this process in Y dimension
- unsigned int offsx; // Offset of local array in X dimension on this process
- unsigned int offsy; // Offset of local array in Y dimension on this process
-
- int rank; // MPI rank
- unsigned int nproc; // number of processors
-
- // neighbors by their MPI ranks, -1 if there is no such neighbor
- int rank_left;
- int rank_right;
- int rank_up;
- int rank_down;
-
- Settings(int argc, char *argv[], int rank, int nproc);
- ~Settings();
+ // user arguments
+ std::string outputfile;
+ unsigned int npx; // Number of processes in X (slow) dimension
+ unsigned int npy; // Number of processes in Y (fast) dimension
+ unsigned int ndx; // Local array size in X dimension per process
+ unsigned int ndy; // Local array size in y dimension per process
+ unsigned int steps; // Number of output steps
+ unsigned int iterations; // Number of computing iterations between steps
+
+ // calculated values from those arguments and number of processes
+ unsigned int gndx; // Global array size in slow dimension
+ unsigned int gndy; // Global array size in fast dimension
+ // X dim positions: rank 0, npx, 2npx... are in the same X position
+ // Y dim positions: npx number of consecutive processes belong to one row
+ // (npx
+ // columns)
+ unsigned int posx; // Position of this process in X dimension
+ unsigned int posy; // Position of this process in Y dimension
+ unsigned int offsx; // Offset of local array in X dimension on this process
+ unsigned int offsy; // Offset of local array in Y dimension on this process
+
+ int rank; // MPI rank
+ unsigned int nproc; // number of processors
+
+ // neighbors by their MPI ranks, -1 if there is no such neighbor
+ int rank_left;
+ int rank_right;
+ int rank_up;
+ int rank_down;
+
+ Settings(int argc, char *argv[], int rank, int nproc);
+ ~Settings();
};
#endif /* SETTINGS_H_ */
diff --git a/examples/heatTransfer/main.cpp b/examples/heatTransfer/main.cpp
index d15216eb8f775819f037eba802772949dd369bbb..1d1372f401ff641f3dc0da71a1b175b9b5c5b1fb 100644
--- a/examples/heatTransfer/main.cpp
+++ b/examples/heatTransfer/main.cpp
@@ -23,86 +23,87 @@
void printUsage()
{
- std::cout << "Usage: heatTransfer output N M nx ny steps iterations\n"
- << " output: name of output file\n"
- << " N: number of processes in X dimension\n"
- << " M: number of processes in Y dimension\n"
- << " nx: local array size in X dimension per processor\n"
- << " ny: local array size in Y dimension per processor\n"
- << " steps: the total number of steps to output\n"
- << " iterations: one step consist of this many iterations\n\n";
+ std::cout
+ << "Usage: heatTransfer output N M nx ny steps iterations\n"
+ << " output: name of output file\n"
+ << " N: number of processes in X dimension\n"
+ << " M: number of processes in Y dimension\n"
+ << " nx: local array size in X dimension per processor\n"
+ << " ny: local array size in Y dimension per processor\n"
+ << " steps: the total number of steps to output\n"
+ << " iterations: one step consist of this many iterations\n\n";
}
int main(int argc, char *argv[])
{
- MPI_Init(&argc, &argv);
- /* World comm spans all applications started with the same aprun command
- on a Cray XK6. So we have to split and create the local
- 'world' communicator for heat_transfer only.
- In normal start-up, the communicator will just equal the MPI_COMM_WORLD.
- */
+ MPI_Init(&argc, &argv);
+ /* World comm spans all applications started with the same aprun command
+ on a Cray XK6. So we have to split and create the local
+ 'world' communicator for heat_transfer only.
+ In normal start-up, the communicator will just equal the MPI_COMM_WORLD.
+ */
- int wrank, wnproc;
- MPI_Comm_rank(MPI_COMM_WORLD, &wrank);
- MPI_Comm_size(MPI_COMM_WORLD, &wnproc);
- MPI_Barrier(MPI_COMM_WORLD);
+ int wrank, wnproc;
+ MPI_Comm_rank(MPI_COMM_WORLD, &wrank);
+ MPI_Comm_size(MPI_COMM_WORLD, &wnproc);
+ MPI_Barrier(MPI_COMM_WORLD);
- const unsigned int color = 1;
- MPI_Comm mpiHeatTransferComm;
- MPI_Comm_split(MPI_COMM_WORLD, color, wrank, &mpiHeatTransferComm);
+ const unsigned int color = 1;
+ MPI_Comm mpiHeatTransferComm;
+ MPI_Comm_split(MPI_COMM_WORLD, color, wrank, &mpiHeatTransferComm);
- int rank, nproc;
- MPI_Comm_rank(mpiHeatTransferComm, &rank);
- MPI_Comm_size(mpiHeatTransferComm, &nproc);
+ int rank, nproc;
+ MPI_Comm_rank(mpiHeatTransferComm, &rank);
+ MPI_Comm_size(mpiHeatTransferComm, &nproc);
- try
- {
- double timeStart = MPI_Wtime();
- Settings settings(argc, argv, rank, nproc);
- HeatTransfer ht(settings);
- IO io(settings, mpiHeatTransferComm);
+ try
+ {
+ double timeStart = MPI_Wtime();
+ Settings settings(argc, argv, rank, nproc);
+ HeatTransfer ht(settings);
+ IO io(settings, mpiHeatTransferComm);
+
+ ht.init(true);
+ ht.printT("Initialized T:", mpiHeatTransferComm);
+ ht.heatEdges();
+ // ht.exchange( mpiHeatTransferComm );
+ ht.printT("Heated T:", mpiHeatTransferComm);
+ io.write(0, ht, settings, mpiHeatTransferComm);
- ht.init(true);
- ht.printT("Initialized T:", mpiHeatTransferComm);
- ht.heatEdges();
- // ht.exchange( mpiHeatTransferComm );
- ht.printT("Heated T:", mpiHeatTransferComm);
- io.write(0, ht, settings, mpiHeatTransferComm);
+ for (unsigned int t = 1; t <= settings.steps; ++t)
+ {
+ if (rank == 0)
+ std::cout << "Step " << t << ":\n";
+ for (unsigned int iter = 1; iter <= settings.iterations; ++iter)
+ {
+ ht.iterate();
+ ht.exchange(mpiHeatTransferComm);
+ ht.heatEdges();
+ }
+ io.write(t, ht, settings, mpiHeatTransferComm);
+ }
+ MPI_Barrier(mpiHeatTransferComm);
- for (unsigned int t = 1; t <= settings.steps; ++t)
+ double timeEnd = MPI_Wtime();
+ if (rank == 0)
+ std::cout << "Total runtime = " << timeEnd - timeStart << "s\n";
+ }
+ catch (std::invalid_argument &e) // command-line argument errors
{
- if (rank == 0)
- std::cout << "Step " << t << ":\n";
- for (unsigned int iter = 1; iter <= settings.iterations; ++iter)
- {
- ht.iterate();
- ht.exchange(mpiHeatTransferComm);
- ht.heatEdges();
- }
- io.write(t, ht, settings, mpiHeatTransferComm);
+ std::cout << e.what() << std::endl;
+ printUsage();
+ }
+ catch (std::ios_base::failure &e) // I/O failure (e.g. file not found)
+ {
+ std::cout << "I/O base exception caught\n";
+ std::cout << e.what() << std::endl;
+ }
+ catch (std::exception &e) // All other exceptions
+ {
+ std::cout << "Exception caught\n";
+ std::cout << e.what() << std::endl;
}
- MPI_Barrier(mpiHeatTransferComm);
-
- double timeEnd = MPI_Wtime();
- if (rank == 0)
- std::cout << "Total runtime = " << timeEnd - timeStart << "s\n";
- }
- catch (std::invalid_argument &e) // command-line argument errors
- {
- std::cout << e.what() << std::endl;
- printUsage();
- }
- catch (std::ios_base::failure &e) // I/O failure (e.g. file not found)
- {
- std::cout << "I/O base exception caught\n";
- std::cout << e.what() << std::endl;
- }
- catch (std::exception &e) // All other exceptions
- {
- std::cout << "Exception caught\n";
- std::cout << e.what() << std::endl;
- }
- MPI_Finalize();
- return 0;
+ MPI_Finalize();
+ return 0;
}
diff --git a/examples/hello/adios1Writer/helloADIOS1Writer.cpp b/examples/hello/adios1Writer/helloADIOS1Writer.cpp
index 9543ec43b2530c7f64d1435092dee25e8b6719e0..2a7803ab6edac9adc2618699fb3be45c3960b6c7 100644
--- a/examples/hello/adios1Writer/helloADIOS1Writer.cpp
+++ b/examples/hello/adios1Writer/helloADIOS1Writer.cpp
@@ -17,104 +17,107 @@
int main(int argc, char *argv[])
{
- MPI_Init(&argc, &argv);
- int rank, nproc;
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- MPI_Comm_size(MPI_COMM_WORLD, &nproc);
- const bool adiosDebug = true;
- adios::ADIOS adios(MPI_COMM_WORLD, adios::Verbose::INFO, adiosDebug);
-
- // Application variable
- float frank = (float)rank;
- std::vector<double> myDoubles = {
- frank, frank + 0.1f, frank + 0.2f, frank + 0.3f, frank + 0.4f,
- frank + 0.5f, frank + 0.6f, frank + 0.7f, frank + 0.8f, frank + 0.9f};
- const std::size_t Nx = myDoubles.size();
-
- const std::size_t rows = 3;
- const std::size_t columns = 3;
-
- std::vector<float> myMatrix;
- myMatrix.reserve(rows * columns);
- myMatrix.push_back(frank + 0.0);
- myMatrix.push_back(frank + 0.1), myMatrix.push_back(frank + 0.2);
- myMatrix.push_back(frank + 0.3);
- myMatrix.push_back(frank + 0.4), myMatrix.push_back(frank + 0.5);
- myMatrix.push_back(frank + 0.6);
- myMatrix.push_back(frank + 0.7), myMatrix.push_back(frank + 0.8);
-
- frank = -(float)rank;
- std::vector<float> myMatrix2 = {frank - 0.1f, frank - 0.2f, frank - 0.3f,
- frank - 0.4f, frank - 0.5f, frank - 0.6f,
- frank - 0.7f, frank - 0.8f, frank - 0.9f};
-
- try
- {
- // Define variable and local size
- adios::Variable<double> &ioMyDoubles = adios.DefineVariable<double>(
- "myDoubles", {1, Nx}, {nproc, Nx}, {rank, 0});
- adios::Variable<float> &ioMyMatrix = adios.DefineVariable<float>(
- "myMatrix", {rows, columns}, {nproc * rows, columns}, {rank * rows, 0});
- adios::Variable<float> &ioMyMatrix2 = adios.DefineVariable<float>(
- "myMatrix2", {rows, columns}, {rows, nproc * columns},
- {0, rank * columns});
-
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &bpWriterSettings =
- adios.DeclareMethod("SingleFile"); // default method type is BPWriter
- bpWriterSettings.SetEngine("ADIOS1Writer");
- bpWriterSettings.SetParameters("profile_units=mus");
- bpWriterSettings.AddTransport(
- "File", "profile_units=mus",
- "have_metadata_file=no"); // uses default POSIX library
-
- // Create engine smart pointer due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- auto bpWriter = adios.Open("myDoubles.bp", "w", bpWriterSettings,
- adios::IOMode::COLLECTIVE);
-
- if (bpWriter == nullptr)
- throw std::ios_base::failure("ERROR: couldn't create bpWriter at Open\n");
-
- bpWriter->Write<double>(ioMyDoubles, myDoubles.data()); // Base class Engine
- // own the Write<T>
- // that will call
- // overloaded Write
- // from Derived
-
- bpWriter->Write<float>(ioMyMatrix, myMatrix.data());
- bpWriter->Write<float>(ioMyMatrix2, myMatrix2.data());
-
- bpWriter->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
+ MPI_Init(&argc, &argv);
+ int rank, nproc;
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ MPI_Comm_size(MPI_COMM_WORLD, &nproc);
+ const bool adiosDebug = true;
+ adios::ADIOS adios(MPI_COMM_WORLD, adios::Verbose::INFO, adiosDebug);
+
+ // Application variable
+ float frank = (float)rank;
+ std::vector<double> myDoubles = {
+ frank, frank + 0.1f, frank + 0.2f, frank + 0.3f, frank + 0.4f,
+ frank + 0.5f, frank + 0.6f, frank + 0.7f, frank + 0.8f, frank + 0.9f};
+ const std::size_t Nx = myDoubles.size();
+
+ const std::size_t rows = 3;
+ const std::size_t columns = 3;
+
+ std::vector<float> myMatrix;
+ myMatrix.reserve(rows * columns);
+ myMatrix.push_back(frank + 0.0);
+ myMatrix.push_back(frank + 0.1), myMatrix.push_back(frank + 0.2);
+ myMatrix.push_back(frank + 0.3);
+ myMatrix.push_back(frank + 0.4), myMatrix.push_back(frank + 0.5);
+ myMatrix.push_back(frank + 0.6);
+ myMatrix.push_back(frank + 0.7), myMatrix.push_back(frank + 0.8);
+
+ frank = -(float)rank;
+ std::vector<float> myMatrix2 = {frank - 0.1f, frank - 0.2f, frank - 0.3f,
+ frank - 0.4f, frank - 0.5f, frank - 0.6f,
+ frank - 0.7f, frank - 0.8f, frank - 0.9f};
+
+ try
{
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ // Define variable and local size
+ adios::Variable<double> &ioMyDoubles = adios.DefineVariable<double>(
+ "myDoubles", {1, Nx}, {nproc, Nx}, {rank, 0});
+ adios::Variable<float> &ioMyMatrix = adios.DefineVariable<float>(
+ "myMatrix", {rows, columns}, {nproc * rows, columns},
+ {rank * rows, 0});
+ adios::Variable<float> &ioMyMatrix2 = adios.DefineVariable<float>(
+ "myMatrix2", {rows, columns}, {rows, nproc * columns},
+ {0, rank * columns});
+
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &bpWriterSettings = adios.DeclareMethod(
+ "SingleFile"); // default method type is BPWriter
+ bpWriterSettings.SetEngine("ADIOS1Writer");
+ bpWriterSettings.SetParameters("profile_units=mus");
+ bpWriterSettings.AddTransport(
+ "File", "profile_units=mus",
+ "have_metadata_file=no"); // uses default POSIX library
+
+ // Create engine smart pointer due to polymorphism,
+ // Open returns a smart pointer to Engine containing the Derived class
+ // Writer
+ auto bpWriter = adios.Open("myDoubles.bp", "w", bpWriterSettings,
+ adios::IOMode::COLLECTIVE);
+
+ if (bpWriter == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: couldn't create bpWriter at Open\n");
+
+ bpWriter->Write<double>(ioMyDoubles,
+ myDoubles.data()); // Base class Engine
+ // own the Write<T>
+ // that will call
+ // overloaded Write
+ // from Derived
+
+ bpWriter->Write<float>(ioMyMatrix, myMatrix.data());
+ bpWriter->Write<float>(ioMyMatrix2, myMatrix2.data());
+
+ bpWriter->Close();
}
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
+ catch (std::invalid_argument &e)
{
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
+ catch (std::ios_base::failure &e)
{
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+ catch (std::exception &e)
+ {
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- MPI_Finalize();
+ MPI_Finalize();
- return 0;
+ return 0;
}
diff --git a/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp b/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp
index eb282251d2de28fbf726628c99dddfcc6bc62eb2..44d4d5547050e79ef4a3cb3b0222b4d21433438f 100644
--- a/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp
+++ b/examples/hello/adios1Writer/helloADIOS1Writer_nompi.cpp
@@ -15,73 +15,76 @@
int main(int argc, char *argv[])
{
- const bool adiosDebug = true;
- adios::ADIOS adios(adiosDebug);
+ const bool adiosDebug = true;
+ adios::ADIOS adios(adiosDebug);
- // Application variable
- std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
- const std::size_t Nx = myDoubles.size();
+ // Application variable
+ std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+ const std::size_t Nx = myDoubles.size();
- const std::size_t rows = 3;
- const std::size_t columns = 3;
- std::vector<float> myMatrix = {1, 2, 3, 4, 5, 6, 7, 8, 9};
+ const std::size_t rows = 3;
+ const std::size_t columns = 3;
+ std::vector<float> myMatrix = {1, 2, 3, 4, 5, 6, 7, 8, 9};
- std::vector<float> myMatrix2 = {-1, -2, -3, -4, -5, -6, -7, -8, -9};
+ std::vector<float> myMatrix2 = {-1, -2, -3, -4, -5, -6, -7, -8, -9};
- try
- {
- // Define variable and local size
- adios::Variable<double> &ioMyDoubles =
- adios.DefineVariable<double>("myDoubles", adios::Dims{Nx});
- adios::Variable<float> &ioMyMatrix =
- adios.DefineVariable<float>("myMatrix", adios::Dims{rows, columns});
- adios::Variable<float> &ioMyMatrix2 =
- adios.DefineVariable<float>("myMatrix2", adios::Dims{rows, columns});
- adios::Variable<float> &ioMyMatrix3 =
- adios.DefineVariable<float>("myMatrix3", adios::Dims{rows, columns});
+ try
+ {
+ // Define variable and local size
+ adios::Variable<double> &ioMyDoubles =
+ adios.DefineVariable<double>("myDoubles", adios::Dims{Nx});
+ adios::Variable<float> &ioMyMatrix =
+ adios.DefineVariable<float>("myMatrix", adios::Dims{rows, columns});
+ adios::Variable<float> &ioMyMatrix2 = adios.DefineVariable<float>(
+ "myMatrix2", adios::Dims{rows, columns});
+ adios::Variable<float> &ioMyMatrix3 = adios.DefineVariable<float>(
+ "myMatrix3", adios::Dims{rows, columns});
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &bpWriterSettings =
- adios.DeclareMethod("SinglePOSIXFile"); // default method type is Writer
- bpWriterSettings.SetParameters("profile_units=mus");
- bpWriterSettings.AddTransport("File", "have_metadata_file=yes",
- "profile_units=mus");
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &bpWriterSettings = adios.DeclareMethod(
+ "SinglePOSIXFile"); // default method type is Writer
+ bpWriterSettings.SetParameters("profile_units=mus");
+ bpWriterSettings.AddTransport("File", "have_metadata_file=yes",
+ "profile_units=mus");
- // Create engine smart pointer due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- auto bpFileWriter = adios.Open("myDoubles_nompi.bp", "w", bpWriterSettings,
- adios::IOMode::COLLECTIVE);
+ // Create engine smart pointer due to polymorphism,
+ // Open returns a smart pointer to Engine containing the Derived class
+ // Writer
+ auto bpFileWriter =
+ adios.Open("myDoubles_nompi.bp", "w", bpWriterSettings,
+ adios::IOMode::COLLECTIVE);
- if (bpFileWriter == nullptr)
- throw std::ios_base::failure("ERROR: couldn't create bpWriter at Open\n");
+ if (bpFileWriter == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: couldn't create bpWriter at Open\n");
- bpFileWriter->Write<double>(
- ioMyDoubles, myDoubles.data()); // Base class Engine own the Write<T>
- // that will call overloaded Write from
- // Derived
- bpFileWriter->Write<float>(ioMyMatrix, myMatrix.data()); // 2d Example
- bpFileWriter->Write<float>(ioMyMatrix2, myMatrix2.data()); // 2d Example
- bpFileWriter->Write<float>(ioMyMatrix3, myMatrix2.data()); // 2d Example
- bpFileWriter->Close();
- //
- }
- catch (std::invalid_argument &e)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::ios_base::failure &e)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
+ bpFileWriter->Write<double>(
+ ioMyDoubles,
+ myDoubles.data()); // Base class Engine own the Write<T>
+ // that will call overloaded Write from
+ // Derived
+ bpFileWriter->Write<float>(ioMyMatrix, myMatrix.data()); // 2d Example
+ bpFileWriter->Write<float>(ioMyMatrix2, myMatrix2.data()); // 2d Example
+ bpFileWriter->Write<float>(ioMyMatrix3, myMatrix2.data()); // 2d Example
+ bpFileWriter->Close();
+ //
+ }
+ catch (std::invalid_argument &e)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::ios_base::failure &e)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
- return 0;
+ return 0;
}
diff --git a/examples/hello/bpReader/helloBPReader.cpp b/examples/hello/bpReader/helloBPReader.cpp
index 5558ee04a5ff9e00ccc772986689c0a348a3d295..934439584aad6c69509e2191e4a5d1ee3e38e0d0 100644
--- a/examples/hello/bpReader/helloBPReader.cpp
+++ b/examples/hello/bpReader/helloBPReader.cpp
@@ -17,54 +17,55 @@
int main(int argc, char *argv[])
{
- MPI_Init(&argc, &argv);
- int rank;
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- const bool adiosDebug = true;
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
+ MPI_Init(&argc, &argv);
+ int rank;
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ const bool adiosDebug = true;
+ adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
- try
- {
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &bpReaderSettings =
- adios.DeclareMethod("SingleFile"); // default method type is BPWriter
- bpReaderSettings.AddTransport("File"); // uses default POSIX library
+ try
+ {
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &bpReaderSettings = adios.DeclareMethod(
+ "SingleFile"); // default method type is BPWriter
+ bpReaderSettings.AddTransport("File"); // uses default POSIX library
- // Create engine smart pointer due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- auto bpReader = adios.Open("myDoubles_nompi.bp", "r", bpReaderSettings);
+ // Create engine smart pointer due to polymorphism,
+ // Open returns a smart pointer to Engine containing the Derived class
+ // Writer
+ auto bpReader = adios.Open("myDoubles_nompi.bp", "r", bpReaderSettings);
- if (bpReader == nullptr)
- throw std::ios_base::failure("ERROR: couldn't create bpReader at Open\n");
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
+ if (bpReader == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: couldn't create bpReader at Open\n");
+ }
+ catch (std::invalid_argument &e)
{
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
+ catch (std::ios_base::failure &e)
{
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
+ catch (std::exception &e)
{
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- MPI_Finalize();
+ MPI_Finalize();
- return 0;
+ return 0;
}
diff --git a/examples/hello/bpReader/helloBPReader_nompi.cpp b/examples/hello/bpReader/helloBPReader_nompi.cpp
index d5a604fbddb59f33f8f8a38ad09a825ec940d737..79de6af15eb5b0c6892d57a8a2c4b5a92d6f7009 100644
--- a/examples/hello/bpReader/helloBPReader_nompi.cpp
+++ b/examples/hello/bpReader/helloBPReader_nompi.cpp
@@ -15,40 +15,41 @@
int main(int argc, char *argv[])
{
- const bool adiosDebug = true;
- adios::ADIOS adios(adiosDebug);
+ const bool adiosDebug = true;
+ adios::ADIOS adios(adiosDebug);
- try
- {
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &bpReaderSettings = adios.DeclareMethod(
- "SingleFile"); // default method type is BPWriter/BPReader
- bpReaderSettings.AddTransport("File"); // uses default POSIX library
+ try
+ {
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &bpReaderSettings = adios.DeclareMethod(
+ "SingleFile"); // default method type is BPWriter/BPReader
+ bpReaderSettings.AddTransport("File"); // uses default POSIX library
- // Create engine smart pointer due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- auto bpReader = adios.Open("myDoubles.bp", "r", bpReaderSettings);
+ // Create engine smart pointer due to polymorphism,
+ // Open returns a smart pointer to Engine containing the Derived class
+ // Writer
+ auto bpReader = adios.Open("myDoubles.bp", "r", bpReaderSettings);
- if (bpReader == nullptr)
- throw std::ios_base::failure("ERROR: couldn't create bpReader at Open\n");
- }
- catch (std::invalid_argument &e)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::ios_base::failure &e)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
+ if (bpReader == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: couldn't create bpReader at Open\n");
+ }
+ catch (std::invalid_argument &e)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::ios_base::failure &e)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
- return 0;
+ return 0;
}
diff --git a/examples/hello/bpWriter/helloBPWriter.cpp b/examples/hello/bpWriter/helloBPWriter.cpp
index abc680ffdcfb93be169f51dc41570122713c2458..29d46647d65a0673ff523d234a56a415df115aaf 100644
--- a/examples/hello/bpWriter/helloBPWriter.cpp
+++ b/examples/hello/bpWriter/helloBPWriter.cpp
@@ -17,101 +17,103 @@
int main(int argc, char *argv[])
{
- MPI_Init(&argc, &argv);
- int rank;
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- const bool adiosDebug = true;
- adios::ADIOS adios(MPI_COMM_WORLD, adios::Verbose::INFO, adiosDebug);
-
- // Application variable
- std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
- const std::size_t Nx = myDoubles.size();
-
- const std::size_t rows = 3;
- const std::size_t columns = 3;
-
- std::vector<float> myMatrix;
- if (rank % 2 == 0) // even rank
- {
- myMatrix.reserve(rows * columns);
- myMatrix.push_back(1);
- myMatrix.push_back(2), myMatrix.push_back(3);
- myMatrix.push_back(4);
- myMatrix.push_back(5), myMatrix.push_back(6);
- myMatrix.push_back(7);
- myMatrix.push_back(8), myMatrix.push_back(8);
- }
-
- std::vector<float> myMatrix2 = {-1, -2, -3, -4, -5, -6, -7, -8, -9};
-
- try
- {
- // Define variable and local size
- adios::Variable<double> &ioMyDoubles =
- adios.DefineVariable<double>("myDoubles", {Nx});
- adios::Variable<float> &ioMyMatrix =
- adios.DefineVariable<float>("myMatrix", {rows, columns});
- adios::Variable<float> &ioMyMatrix2 =
- adios.DefineVariable<float>("myMatrix2", {rows, columns});
-
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &bpWriterSettings =
- adios.DeclareMethod("SingleFile"); // default method type is BPWriter
- bpWriterSettings.SetParameters("profile_units=mus");
- bpWriterSettings.AddTransport(
- "File", "profile_units=mus",
- "have_metadata_file=no"); // uses default POSIX library
-
- // Create engine smart pointer due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- auto bpWriter = adios.Open("myDoubles.bp", "w", bpWriterSettings,
- adios::IOMode::COLLECTIVE);
-
- if (bpWriter == nullptr)
- throw std::ios_base::failure("ERROR: couldn't create bpWriter at Open\n");
-
- bpWriter->Write<double>(ioMyDoubles, myDoubles.data()); // Base class Engine
- // own the Write<T>
- // that will call
- // overloaded Write
- // from Derived
+ MPI_Init(&argc, &argv);
+ int rank;
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ const bool adiosDebug = true;
+ adios::ADIOS adios(MPI_COMM_WORLD, adios::Verbose::INFO, adiosDebug);
+ // Application variable
+ std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+ const std::size_t Nx = myDoubles.size();
+
+ const std::size_t rows = 3;
+ const std::size_t columns = 3;
+
+ std::vector<float> myMatrix;
if (rank % 2 == 0) // even rank
{
- bpWriter->Write<float>(ioMyMatrix, myMatrix.data());
- bpWriter->Write<float>(ioMyMatrix2, myMatrix2.data());
+ myMatrix.reserve(rows * columns);
+ myMatrix.push_back(1);
+ myMatrix.push_back(2), myMatrix.push_back(3);
+ myMatrix.push_back(4);
+ myMatrix.push_back(5), myMatrix.push_back(6);
+ myMatrix.push_back(7);
+ myMatrix.push_back(8), myMatrix.push_back(8);
}
- bpWriter->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
+ std::vector<float> myMatrix2 = {-1, -2, -3, -4, -5, -6, -7, -8, -9};
+
+ try
+ {
+ // Define variable and local size
+ adios::Variable<double> &ioMyDoubles =
+ adios.DefineVariable<double>("myDoubles", {Nx});
+ adios::Variable<float> &ioMyMatrix =
+ adios.DefineVariable<float>("myMatrix", {rows, columns});
+ adios::Variable<float> &ioMyMatrix2 =
+ adios.DefineVariable<float>("myMatrix2", {rows, columns});
+
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &bpWriterSettings = adios.DeclareMethod(
+ "SingleFile"); // default method type is BPWriter
+ bpWriterSettings.SetParameters("profile_units=mus");
+ bpWriterSettings.AddTransport(
+ "File", "profile_units=mus",
+ "have_metadata_file=no"); // uses default POSIX library
+
+ // Create engine smart pointer due to polymorphism,
+ // Open returns a smart pointer to Engine containing the Derived class
+ // Writer
+ auto bpWriter = adios.Open("myDoubles.bp", "w", bpWriterSettings,
+ adios::IOMode::COLLECTIVE);
+
+ if (bpWriter == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: couldn't create bpWriter at Open\n");
+
+ bpWriter->Write<double>(ioMyDoubles,
+ myDoubles.data()); // Base class Engine
+ // own the Write<T>
+ // that will call
+ // overloaded Write
+ // from Derived
+
+ if (rank % 2 == 0) // even rank
+ {
+ bpWriter->Write<float>(ioMyMatrix, myMatrix.data());
+ bpWriter->Write<float>(ioMyMatrix2, myMatrix2.data());
+ }
+
+ bpWriter->Close();
+ }
+ catch (std::invalid_argument &e)
{
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
+ catch (std::ios_base::failure &e)
{
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
+ catch (std::exception &e)
{
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- MPI_Finalize();
+ MPI_Finalize();
- return 0;
+ return 0;
}
diff --git a/examples/hello/bpWriter/helloBPWriter_nompi.cpp b/examples/hello/bpWriter/helloBPWriter_nompi.cpp
index 3936d3eab4aa6f06db4188809cc7a32e0a6d6263..7c8b7ee24119d01ea4cc32ce4b72af09b789603b 100644
--- a/examples/hello/bpWriter/helloBPWriter_nompi.cpp
+++ b/examples/hello/bpWriter/helloBPWriter_nompi.cpp
@@ -17,75 +17,78 @@
int main(int /*argc*/, char ** /*argv*/)
{
- const bool adiosDebug = true;
- adios::ADIOS adios(adios::Verbose::WARN, adiosDebug);
+ const bool adiosDebug = true;
+ adios::ADIOS adios(adios::Verbose::WARN, adiosDebug);
- // Application variable
- std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
- const std::size_t Nx = myDoubles.size();
+ // Application variable
+ std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+ const std::size_t Nx = myDoubles.size();
- const std::size_t rows = 3;
- const std::size_t columns = 3;
- std::vector<float> myMatrix = {1, 2, 3, 4, 5, 6, 7, 8, 9};
+ const std::size_t rows = 3;
+ const std::size_t columns = 3;
+ std::vector<float> myMatrix = {1, 2, 3, 4, 5, 6, 7, 8, 9};
- std::vector<float> myMatrix2 = {-1, -2, -3, -4, -5, -6, -7, -8, -9};
+ std::vector<float> myMatrix2 = {-1, -2, -3, -4, -5, -6, -7, -8, -9};
- try
- {
- // Define variable and local size
- adios::Variable<double> &ioMyDoubles =
- adios.DefineVariable<double>("myDoubles", adios::Dims{Nx});
- adios::Variable<float> &ioMyMatrix =
- adios.DefineVariable<float>("myMatrix", adios::Dims{rows, columns});
- adios::Variable<float> &ioMyMatrix2 =
- adios.DefineVariable<float>("myMatrix2", adios::Dims{rows, columns});
- adios::Variable<float> &ioMyMatrix3 =
- adios.DefineVariable<float>("myMatrix3", adios::Dims{rows, columns});
+ try
+ {
+ // Define variable and local size
+ adios::Variable<double> &ioMyDoubles =
+ adios.DefineVariable<double>("myDoubles", adios::Dims{Nx});
+ adios::Variable<float> &ioMyMatrix =
+ adios.DefineVariable<float>("myMatrix", adios::Dims{rows, columns});
+ adios::Variable<float> &ioMyMatrix2 = adios.DefineVariable<float>(
+ "myMatrix2", adios::Dims{rows, columns});
+ adios::Variable<float> &ioMyMatrix3 = adios.DefineVariable<float>(
+ "myMatrix3", adios::Dims{rows, columns});
+
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &bpWriterSettings = adios.DeclareMethod(
+ "SinglePOSIXFile"); // default method type is Writer
+ bpWriterSettings.SetParameters("profile_units=mus");
+ bpWriterSettings.AddTransport("File", "have_metadata_file=yes",
+ "profile_units=mus");
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &bpWriterSettings =
- adios.DeclareMethod("SinglePOSIXFile"); // default method type is Writer
- bpWriterSettings.SetParameters("profile_units=mus");
- bpWriterSettings.AddTransport("File", "have_metadata_file=yes",
- "profile_units=mus");
+ // Create engine smart pointer due to polymorphism,
+ // Open returns a smart pointer to Engine containing the Derived class
+ // Writer
+ auto bpFileWriter =
+ adios.Open("myDoubles_nompi.bp", "w", bpWriterSettings,
+ adios::IOMode::COLLECTIVE);
- // Create engine smart pointer due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- auto bpFileWriter = adios.Open("myDoubles_nompi.bp", "w", bpWriterSettings,
- adios::IOMode::COLLECTIVE);
+ if (bpFileWriter == nullptr)
+ {
+ throw std::ios_base::failure(
+ "ERROR: couldn't create bpWriter at Open\n");
+ }
- if (bpFileWriter == nullptr)
+ bpFileWriter->Write<double>(
+ ioMyDoubles,
+ myDoubles.data()); // Base class Engine own the Write<T>
+ // that will call overloaded Write from
+ // Derived
+ bpFileWriter->Write<float>(ioMyMatrix, myMatrix.data()); // 2d Example
+ bpFileWriter->Write<float>(ioMyMatrix2, myMatrix2.data()); // 2d Example
+ bpFileWriter->Write<float>(ioMyMatrix3, myMatrix2.data()); // 2d Example
+ bpFileWriter->Close();
+ //
+ }
+ catch (std::invalid_argument &e)
{
- throw std::ios_base::failure("ERROR: couldn't create bpWriter at Open\n");
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::ios_base::failure &e)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
}
- bpFileWriter->Write<double>(
- ioMyDoubles, myDoubles.data()); // Base class Engine own the Write<T>
- // that will call overloaded Write from
- // Derived
- bpFileWriter->Write<float>(ioMyMatrix, myMatrix.data()); // 2d Example
- bpFileWriter->Write<float>(ioMyMatrix2, myMatrix2.data()); // 2d Example
- bpFileWriter->Write<float>(ioMyMatrix3, myMatrix2.data()); // 2d Example
- bpFileWriter->Close();
- //
- }
- catch (std::invalid_argument &e)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::ios_base::failure &e)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
-
- return 0;
+ return 0;
}
diff --git a/examples/hello/compound/helloCompound.cpp b/examples/hello/compound/helloCompound.cpp
index fac04ed5936bf0d7fe4c7865435df32f2a84c96f..32ccddd7f70ffd8f0b992f36dda2839118d07c55 100644
--- a/examples/hello/compound/helloCompound.cpp
+++ b/examples/hello/compound/helloCompound.cpp
@@ -18,94 +18,98 @@
struct Particle
{
- char Type[10]; ///< alpha, beta, gamma, etc.
- double Position[3]; ///< x, y, z
- double Velocity[3]; ///< Vx, Vy, Vz
+ char Type[10]; ///< alpha, beta, gamma, etc.
+ double Position[3]; ///< x, y, z
+ double Velocity[3]; ///< Vx, Vy, Vz
};
int main(int argc, char *argv[])
{
- MPI_Init(&argc, &argv);
- int rank;
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- const bool adiosDebug = true;
- adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
-
- // Application variable
- std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
- const std::size_t Nx = myDoubles.size();
-
- Particle myParticle;
- sprintf(myParticle.Type, "%s", "photon");
- myParticle.Position[0] = 0;
- myParticle.Position[1] = 1;
- myParticle.Position[2] = 2;
-
- myParticle.Velocity[0] = 10;
- myParticle.Velocity[1] = 11;
- myParticle.Velocity[2] = 12;
-
- try
- {
- // Define variable and local size
- adios::Variable<double> &ioMyDoubles =
- adios.DefineVariable<double>("myDoubles", adios::Dims{Nx});
-
- adios::VariableCompound &ioMyParticle =
- adios.DefineVariableCompound<Particle>("myParticle", adios::Dims{1});
- ioMyParticle.InsertMember<std::string>("Type", offsetof(Particle, Type));
- ioMyParticle.InsertMember<std::vector<double>>(
- "Position", offsetof(Particle, Position));
- ioMyParticle.InsertMember<std::vector<double>>(
- "Velocity", offsetof(Particle, Velocity));
-
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &bpWriterSettings =
- adios.DeclareMethod("SingleFile"); // default method type is BPWriter
- bpWriterSettings.AddTransport(
- "File", "have_metadata_file=yes"); // uses default POSIX library
-
- // Create engine smart pointer due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- auto bpWriter = adios.Open("myDoubles.bp", "w", bpWriterSettings);
-
- if (bpWriter == nullptr)
- throw std::ios_base::failure("ERROR: couldn't create bpWriter at Open\n");
-
- bpWriter->Write(ioMyDoubles, myDoubles.data()); // Base class Engine own the
- // Write<T> that will call
- // overloaded Write from
- // Derived
- bpWriter->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
+ MPI_Init(&argc, &argv);
+ int rank;
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ const bool adiosDebug = true;
+ adios::ADIOS adios(MPI_COMM_WORLD, adiosDebug);
+
+ // Application variable
+ std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+ const std::size_t Nx = myDoubles.size();
+
+ Particle myParticle;
+ sprintf(myParticle.Type, "%s", "photon");
+ myParticle.Position[0] = 0;
+ myParticle.Position[1] = 1;
+ myParticle.Position[2] = 2;
+
+ myParticle.Velocity[0] = 10;
+ myParticle.Velocity[1] = 11;
+ myParticle.Velocity[2] = 12;
+
+ try
{
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ // Define variable and local size
+ adios::Variable<double> &ioMyDoubles =
+ adios.DefineVariable<double>("myDoubles", adios::Dims{Nx});
+
+ adios::VariableCompound &ioMyParticle =
+ adios.DefineVariableCompound<Particle>("myParticle",
+ adios::Dims{1});
+ ioMyParticle.InsertMember<std::string>("Type",
+ offsetof(Particle, Type));
+ ioMyParticle.InsertMember<std::vector<double>>(
+ "Position", offsetof(Particle, Position));
+ ioMyParticle.InsertMember<std::vector<double>>(
+ "Velocity", offsetof(Particle, Velocity));
+
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &bpWriterSettings = adios.DeclareMethod(
+ "SingleFile"); // default method type is BPWriter
+ bpWriterSettings.AddTransport(
+ "File", "have_metadata_file=yes"); // uses default POSIX library
+
+ // Create engine smart pointer due to polymorphism,
+ // Open returns a smart pointer to Engine containing the Derived class
+ // Writer
+ auto bpWriter = adios.Open("myDoubles.bp", "w", bpWriterSettings);
+
+ if (bpWriter == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: couldn't create bpWriter at Open\n");
+
+ bpWriter->Write(ioMyDoubles,
+ myDoubles.data()); // Base class Engine own the
+ // Write<T> that will call
+ // overloaded Write from
+ // Derived
+ bpWriter->Close();
}
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
+ catch (std::invalid_argument &e)
{
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
+ catch (std::ios_base::failure &e)
{
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+ catch (std::exception &e)
+ {
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- MPI_Finalize();
+ MPI_Finalize();
- return 0;
+ return 0;
}
diff --git a/examples/hello/compound/helloCompound_nompi.cpp b/examples/hello/compound/helloCompound_nompi.cpp
index 08b7debffa9c5f46ed2d2e129bde24f0b8e75778..52d4075ccde051180437ba06a1f7b66b9121c293 100644
--- a/examples/hello/compound/helloCompound_nompi.cpp
+++ b/examples/hello/compound/helloCompound_nompi.cpp
@@ -17,78 +17,82 @@
struct Particle
{
- char Type[10]; ///< alpha, beta, gamma, etc.
- double Position[3]; ///< x, y, z
- double Velocity[3]; ///< Vx, Vy, Vz
+ char Type[10]; ///< alpha, beta, gamma, etc.
+ double Position[3]; ///< x, y, z
+ double Velocity[3]; ///< Vx, Vy, Vz
};
int main(int argc, char *argv[])
{
- const bool adiosDebug = true;
- adios::ADIOS adios(adiosDebug);
+ const bool adiosDebug = true;
+ adios::ADIOS adios(adiosDebug);
- // Application variable
- std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
- const std::size_t Nx = myDoubles.size();
+ // Application variable
+ std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+ const std::size_t Nx = myDoubles.size();
- Particle myParticle;
- sprintf(myParticle.Type, "%s", "photon");
- myParticle.Position[0] = 0;
- myParticle.Position[1] = 1;
- myParticle.Position[2] = 2;
+ Particle myParticle;
+ sprintf(myParticle.Type, "%s", "photon");
+ myParticle.Position[0] = 0;
+ myParticle.Position[1] = 1;
+ myParticle.Position[2] = 2;
- myParticle.Velocity[0] = 10;
- myParticle.Velocity[1] = 11;
- myParticle.Velocity[2] = 12;
+ myParticle.Velocity[0] = 10;
+ myParticle.Velocity[1] = 11;
+ myParticle.Velocity[2] = 12;
- try
- {
- // Define variable and local size
- adios::Variable<double> &ioMyDoubles =
- adios.DefineVariable<double>("myDoubles", adios::Dims{Nx});
+ try
+ {
+ // Define variable and local size
+ adios::Variable<double> &ioMyDoubles =
+ adios.DefineVariable<double>("myDoubles", adios::Dims{Nx});
- adios::VariableCompound &ioMyParticle =
- adios.DefineVariableCompound<Particle>("myParticle");
- ioMyParticle.InsertMember<char>("Type", offsetof(Particle, Type));
- ioMyParticle.InsertMember<double>("Position", offsetof(Particle, Position));
- ioMyParticle.InsertMember<double>("Velocity", offsetof(Particle, Velocity));
+ adios::VariableCompound &ioMyParticle =
+ adios.DefineVariableCompound<Particle>("myParticle");
+ ioMyParticle.InsertMember<char>("Type", offsetof(Particle, Type));
+ ioMyParticle.InsertMember<double>("Position",
+ offsetof(Particle, Position));
+ ioMyParticle.InsertMember<double>("Velocity",
+ offsetof(Particle, Velocity));
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &bpWriterSettings =
- adios.DeclareMethod("SingleFile"); // default method type is BPWriter
- bpWriterSettings.AddTransport(
- "File", "have_metadata_file=yes"); // uses default POSIX library
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &bpWriterSettings = adios.DeclareMethod(
+ "SingleFile"); // default method type is BPWriter
+ bpWriterSettings.AddTransport(
+ "File", "have_metadata_file=yes"); // uses default POSIX library
- // Create engine smart pointer due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- auto bpWriter = adios.Open("myDoubles.bp", "w", bpWriterSettings);
+ // Create engine smart pointer due to polymorphism,
+ // Open returns a smart pointer to Engine containing the Derived class
+ // Writer
+ auto bpWriter = adios.Open("myDoubles.bp", "w", bpWriterSettings);
- if (bpWriter == nullptr)
- throw std::ios_base::failure("ERROR: couldn't create bpWriter at Open\n");
+ if (bpWriter == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: couldn't create bpWriter at Open\n");
- bpWriter->Write(ioMyDoubles, myDoubles.data()); // Base class Engine own the
- // Write<T> that will call
- // overloaded Write from
- // Derived
- bpWriter->Close();
- }
- catch (std::invalid_argument &e)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::ios_base::failure &e)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
+ bpWriter->Write(ioMyDoubles,
+ myDoubles.data()); // Base class Engine own the
+ // Write<T> that will call
+ // overloaded Write from
+ // Derived
+ bpWriter->Close();
+ }
+ catch (std::invalid_argument &e)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::ios_base::failure &e)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
- return 0;
+ return 0;
}
diff --git a/examples/hello/datamanReader/helloDataManReader.cpp b/examples/hello/datamanReader/helloDataManReader.cpp
index ec1713e73fa3368f0048caeba5abdb59b0efb37d..6c1c87897cd7f8bfef280a045586d5c94131d195 100644
--- a/examples/hello/datamanReader/helloDataManReader.cpp
+++ b/examples/hello/datamanReader/helloDataManReader.cpp
@@ -21,88 +21,91 @@
void getcb(const void *data, std::string doid, std::string var,
std::string dtype, std::vector<std::size_t> varshape)
{
- std::cout << "data object ID = " << doid << "\n"; // do you need to flush?
- std::cout << "variable name = " << var << "\n";
- std::cout << "data type = " << dtype << "\n";
+ std::cout << "data object ID = " << doid << "\n"; // do you need to flush?
+ std::cout << "variable name = " << var << "\n";
+ std::cout << "data type = " << dtype << "\n";
- std::size_t varsize = std::accumulate(varshape.begin(), varshape.end(), 1,
- std::multiplies<std::size_t>());
+ std::size_t varsize = std::accumulate(varshape.begin(), varshape.end(), 1,
+ std::multiplies<std::size_t>());
- for (unsigned int i = 0; i < varsize; ++i)
- std::cout << ((float *)data)[i] << " ";
- std::cout << std::endl;
+ for (unsigned int i = 0; i < varsize; ++i)
+ std::cout << ((float *)data)[i] << " ";
+ std::cout << std::endl;
}
int main(int argc, char *argv[])
{
- MPI_Init(&argc, &argv);
- int rank;
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- const bool adiosDebug = true;
- adios::ADIOS adios(MPI_COMM_WORLD, adios::Verbose::WARN, adiosDebug);
+ MPI_Init(&argc, &argv);
+ int rank;
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ const bool adiosDebug = true;
+ adios::ADIOS adios(MPI_COMM_WORLD, adios::Verbose::WARN, adiosDebug);
- try
- {
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &datamanSettings = adios.DeclareMethod("WAN");
- if (!datamanSettings.isUserDefined())
+ try
{
- // if not defined by user, we can change the default settings
- datamanSettings.SetEngine("DataManReader");
- datamanSettings.SetParameters("peer-to-peer=yes");
- datamanSettings.AddTransport("Mdtm", "localIP=128.0.0.0.1",
- "remoteIP=128.0.0.0.2", "tolerances=1,2,3");
- // datamanSettings.AddTransport( "ZeroMQ", "localIP=128.0.0.0.1.1",
- // "remoteIP=128.0.0.0.2.1", "tolerances=1,2,3" ); not yet supported ,
- // will throw an exception
- }
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &datamanSettings = adios.DeclareMethod("WAN");
+ if (!datamanSettings.isUserDefined())
+ {
+ // if not defined by user, we can change the default settings
+ datamanSettings.SetEngine("DataManReader");
+ datamanSettings.SetParameters("peer-to-peer=yes");
+ datamanSettings.AddTransport("Mdtm", "localIP=128.0.0.0.1",
+ "remoteIP=128.0.0.0.2",
+ "tolerances=1,2,3");
+ // datamanSettings.AddTransport( "ZeroMQ", "localIP=128.0.0.0.1.1",
+ // "remoteIP=128.0.0.0.2.1", "tolerances=1,2,3" ); not yet supported
+ // ,
+ // will throw an exception
+ }
- // Create engine smart pointer to DataManReader Engine due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // DataManReader
- auto datamanReader = adios.Open("myDoubles.bp", "r", datamanSettings,
- adios::IOMode::INDEPENDENT);
+ // Create engine smart pointer to DataManReader Engine due to
+ // polymorphism,
+ // Open returns a smart pointer to Engine containing the Derived class
+ // DataManReader
+ auto datamanReader = adios.Open("myDoubles.bp", "r", datamanSettings,
+ adios::IOMode::INDEPENDENT);
- if (datamanReader == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to create DataMan I/O engine at Open\n");
+ if (datamanReader == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: failed to create DataMan I/O engine at Open\n");
- datamanReader->SetCallBack(getcb);
+ datamanReader->SetCallBack(getcb);
- adios::Variable<double> *ioMyDoubles =
- datamanReader->InquireVariableDouble("ioMyDoubles");
- if (ioMyDoubles == nullptr)
- std::cout << "Variable ioMyDoubles not read...yet\n";
+ adios::Variable<double> *ioMyDoubles =
+ datamanReader->InquireVariableDouble("ioMyDoubles");
+ if (ioMyDoubles == nullptr)
+ std::cout << "Variable ioMyDoubles not read...yet\n";
- datamanReader->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
+ datamanReader->Close();
+ }
+ catch (std::invalid_argument &e)
{
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
+ catch (std::ios_base::failure &e)
{
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
+ catch (std::exception &e)
{
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- MPI_Finalize();
+ MPI_Finalize();
- return 0;
+ return 0;
}
diff --git a/examples/hello/datamanReader/helloDataManReader_nompi.cpp b/examples/hello/datamanReader/helloDataManReader_nompi.cpp
index 28973cbc19a94c8dc6b5b9cd111b85a19c0b30fa..db7a717be43dbfe7809d1dbcc21f3645c03eda5d 100644
--- a/examples/hello/datamanReader/helloDataManReader_nompi.cpp
+++ b/examples/hello/datamanReader/helloDataManReader_nompi.cpp
@@ -17,81 +17,83 @@
void getcb(const void *data, std::string doid, std::string var,
std::string dtype, std::vector<std::size_t> varshape)
{
- std::cout << "data object ID = " << doid << "\n"; // do you need to flush?
- std::cout << "variable name = " << var << "\n";
- std::cout << "data type = " << dtype << "\n";
+ std::cout << "data object ID = " << doid << "\n"; // do you need to flush?
+ std::cout << "variable name = " << var << "\n";
+ std::cout << "data type = " << dtype << "\n";
- std::size_t varsize = std::accumulate(varshape.begin(), varshape.end(), 1,
- std::multiplies<std::size_t>());
+ std::size_t varsize = std::accumulate(varshape.begin(), varshape.end(), 1,
+ std::multiplies<std::size_t>());
- for (unsigned int i = 0; i < varsize; ++i)
- std::cout << ((float *)data)[i] << " ";
- std::cout << std::endl;
+ for (unsigned int i = 0; i < varsize; ++i)
+ std::cout << ((float *)data)[i] << " ";
+ std::cout << std::endl;
}
int main(int argc, char *argv[])
{
- const bool adiosDebug = true;
- adios::ADIOS adios(adios::Verbose::WARN, adiosDebug);
+ const bool adiosDebug = true;
+ adios::ADIOS adios(adios::Verbose::WARN, adiosDebug);
- try
- {
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &datamanSettings = adios.DeclareMethod("WAN");
- if (!datamanSettings.isUserDefined())
+ try
{
- // if not defined by user, we can change the default settings
- datamanSettings.SetEngine("DataManReader");
- datamanSettings.SetParameters("real_time=yes", "method_type=stream",
- "method=zmq", "local_ip=127.0.0.1",
- "remote_ip=127.0.0.1", "local_port=12307",
- "remote_port=12306");
- // datamanSettings.AddTransport( "Mdtm", "localIP=128.0.0.0.1",
- // "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
- // datamanSettings.AddTransport( "ZeroMQ", "localIP=128.0.0.0.1.1",
- // "remoteIP=128.0.0.0.2.1", "tolerances=1,2,3" ); not yet supported ,
- // will throw an exception
- }
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &datamanSettings = adios.DeclareMethod("WAN");
+ if (!datamanSettings.isUserDefined())
+ {
+ // if not defined by user, we can change the default settings
+ datamanSettings.SetEngine("DataManReader");
+ datamanSettings.SetParameters(
+ "real_time=yes", "method_type=stream", "method=zmq",
+ "local_ip=127.0.0.1", "remote_ip=127.0.0.1", "local_port=12307",
+ "remote_port=12306");
+ // datamanSettings.AddTransport( "Mdtm", "localIP=128.0.0.0.1",
+ // "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
+ // datamanSettings.AddTransport( "ZeroMQ", "localIP=128.0.0.0.1.1",
+ // "remoteIP=128.0.0.0.2.1", "tolerances=1,2,3" ); not yet supported
+ // ,
+ // will throw an exception
+ }
- // Create engine smart pointer to DataManReader Engine due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // DataManReader
- auto datamanReader = adios.Open("myDoubles.bp", "r", datamanSettings,
- adios::IOMode::INDEPENDENT);
+ // Create engine smart pointer to DataManReader Engine due to
+ // polymorphism,
+ // Open returns a smart pointer to Engine containing the Derived class
+ // DataManReader
+ auto datamanReader = adios.Open("myDoubles.bp", "r", datamanSettings,
+ adios::IOMode::INDEPENDENT);
- if (datamanReader == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to create DataMan I/O engine at Open\n");
+ if (datamanReader == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: failed to create DataMan I/O engine at Open\n");
- datamanReader->SetCallBack(getcb);
+ datamanReader->SetCallBack(getcb);
- while (1)
- {
- }
+ while (1)
+ {
+ }
- adios::Variable<double> *ioMyDoubles =
- datamanReader->InquireVariableDouble("ioMyDoubles");
- if (ioMyDoubles == nullptr)
- std::cout << "Variable ioMyDoubles not read...yet\n";
+ adios::Variable<double> *ioMyDoubles =
+ datamanReader->InquireVariableDouble("ioMyDoubles");
+ if (ioMyDoubles == nullptr)
+ std::cout << "Variable ioMyDoubles not read...yet\n";
- datamanReader->Close();
- }
- catch (std::invalid_argument &e)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::ios_base::failure &e)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
+ datamanReader->Close();
+ }
+ catch (std::invalid_argument &e)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::ios_base::failure &e)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
- return 0;
+ return 0;
}
diff --git a/examples/hello/datamanWriter/helloDataManWriter.cpp b/examples/hello/datamanWriter/helloDataManWriter.cpp
index 138abbcec405bed0ac6847667438387bf22b1ca1..b2276254e98cb3075c77518a786b9f05b1840129 100644
--- a/examples/hello/datamanWriter/helloDataManWriter.cpp
+++ b/examples/hello/datamanWriter/helloDataManWriter.cpp
@@ -17,99 +17,103 @@
int main(int argc, char *argv[])
{
- MPI_Init(&argc, &argv);
- int rank;
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- const bool adiosDebug = true;
- adios::ADIOS adios(MPI_COMM_WORLD, adios::Verbose::WARN, adiosDebug);
+ MPI_Init(&argc, &argv);
+ int rank;
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ const bool adiosDebug = true;
+ adios::ADIOS adios(MPI_COMM_WORLD, adios::Verbose::WARN, adiosDebug);
- // Application variable
- std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
- const std::size_t Nx = myDoubles.size();
+ // Application variable
+ std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+ const std::size_t Nx = myDoubles.size();
- std::vector<std::complex<float>> myCFloats;
- myCFloats.reserve(3);
- myCFloats.emplace_back(1, 3);
- myCFloats.emplace_back(2, 2);
- myCFloats.emplace_back(3, 1);
+ std::vector<std::complex<float>> myCFloats;
+ myCFloats.reserve(3);
+ myCFloats.emplace_back(1, 3);
+ myCFloats.emplace_back(2, 2);
+ myCFloats.emplace_back(3, 1);
- try
- {
- // Define variable and local size
- auto ioMyDoubles = adios.DefineVariable<double>("myDoubles", {Nx});
- auto ioMyCFloats =
- adios.DefineVariable<std::complex<float>>("myCFloats", {3});
-
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &datamanSettings = adios.DeclareMethod("WAN");
- if (!datamanSettings.isUserDefined())
+ try
{
- // if not defined by user, we can change the default settings
- datamanSettings.SetEngine("DatamanWriter");
- datamanSettings.SetParameters("peer-to-peer=yes", "real_time=yes",
- "compress=no");
- datamanSettings.AddTransport("Mdtm", "localIP=128.0.0.0.1",
- "remoteIP=128.0.0.0.2", "tolerances=1,2,3");
- // datamanSettings.AddTransport( "file", "name=myfile.bp",
- // "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
- // datamanSettings.AddTransport( "file", "name=myfile.bp",
- // "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
- // datamanSettings.AddTransport( "Mdtm", "localIP=128.0.0.0.1",
- // "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
- // datamanSettings.AddTransport( "ZeroMQ", "localIP=128.0.0.0.1",
- // "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
- // datamanSettings.AddTransport( "ZeroMQ", "localIP=128.0.0.0.1.1",
- // "remoteIP=128.0.0.0.2.1", "tolerances=1,2,3" ); not yet supported, will
- // throw an exception
- }
+ // Define variable and local size
+ auto ioMyDoubles = adios.DefineVariable<double>("myDoubles", {Nx});
+ auto ioMyCFloats =
+ adios.DefineVariable<std::complex<float>>("myCFloats", {3});
- // Create engine smart pointer to DataMan Engine due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // DataMan
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &datamanSettings = adios.DeclareMethod("WAN");
+ if (!datamanSettings.isUserDefined())
+ {
+ // if not defined by user, we can change the default settings
+ datamanSettings.SetEngine("DatamanWriter");
+ datamanSettings.SetParameters("peer-to-peer=yes", "real_time=yes",
+ "compress=no");
+ datamanSettings.AddTransport("Mdtm", "localIP=128.0.0.0.1",
+ "remoteIP=128.0.0.0.2",
+ "tolerances=1,2,3");
+ // datamanSettings.AddTransport( "file", "name=myfile.bp",
+ // "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
+ // datamanSettings.AddTransport( "file", "name=myfile.bp",
+ // "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
+ // datamanSettings.AddTransport( "Mdtm", "localIP=128.0.0.0.1",
+ // "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
+ // datamanSettings.AddTransport( "ZeroMQ", "localIP=128.0.0.0.1",
+ // "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
+ // datamanSettings.AddTransport( "ZeroMQ", "localIP=128.0.0.0.1.1",
+ // "remoteIP=128.0.0.0.2.1", "tolerances=1,2,3" ); not yet
+ // supported, will
+ // throw an exception
+ }
- // adios::DataManWriter datamanWriter;
+ // Create engine smart pointer to DataMan Engine due to polymorphism,
+ // Open returns a smart pointer to Engine containing the Derived class
+ // DataMan
- auto datamanWriter = adios.Open("myDoubles.bp", "w", datamanSettings,
- adios::IOMode::INDEPENDENT);
+ // adios::DataManWriter datamanWriter;
- if (datamanWriter == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to create DataMan I/O engine at Open\n");
+ auto datamanWriter = adios.Open("myDoubles.bp", "w", datamanSettings,
+ adios::IOMode::INDEPENDENT);
- datamanWriter->Write<double>(
- ioMyDoubles, myDoubles.data()); // Base class Engine own the Write<T>
- // that will call overloaded Write from
- // Derived
- datamanWriter->Write<std::complex<float>>(ioMyCFloats, myCFloats.data());
- datamanWriter->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
+ if (datamanWriter == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: failed to create DataMan I/O engine at Open\n");
+
+ datamanWriter->Write<double>(
+ ioMyDoubles,
+ myDoubles.data()); // Base class Engine own the Write<T>
+ // that will call overloaded Write from
+ // Derived
+ datamanWriter->Write<std::complex<float>>(ioMyCFloats,
+ myCFloats.data());
+ datamanWriter->Close();
+ }
+ catch (std::invalid_argument &e)
{
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
+ catch (std::ios_base::failure &e)
{
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
+ catch (std::exception &e)
{
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- MPI_Finalize();
+ MPI_Finalize();
- return 0;
+ return 0;
}
diff --git a/examples/hello/datamanWriter/helloDataManWriter_nompi.cpp b/examples/hello/datamanWriter/helloDataManWriter_nompi.cpp
index 75114e8721323d17809359be69bbd2bfa32e4e03..d6b1e3068f6447cd2985fb16b5983227972230cf 100644
--- a/examples/hello/datamanWriter/helloDataManWriter_nompi.cpp
+++ b/examples/hello/datamanWriter/helloDataManWriter_nompi.cpp
@@ -15,85 +15,89 @@
int main(int argc, char *argv[])
{
- const bool adiosDebug = true;
- adios::ADIOS adios(adios::Verbose::WARN, adiosDebug);
+ const bool adiosDebug = true;
+ adios::ADIOS adios(adios::Verbose::WARN, adiosDebug);
- // Application variable
- std::vector<float> myFloats = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
- std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
- const std::size_t Nx = myDoubles.size();
+ // Application variable
+ std::vector<float> myFloats = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+ std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+ const std::size_t Nx = myDoubles.size();
- std::vector<std::complex<float>> myCFloats;
- myCFloats.reserve(3);
- myCFloats.emplace_back(1, 3);
- myCFloats.emplace_back(2, 2);
- myCFloats.emplace_back(3, 1);
+ std::vector<std::complex<float>> myCFloats;
+ myCFloats.reserve(3);
+ myCFloats.emplace_back(1, 3);
+ myCFloats.emplace_back(2, 2);
+ myCFloats.emplace_back(3, 1);
- try
- {
- // Define variable and local size
- // Define variable and local size
- auto ioMyFloats = adios.DefineVariable<float>("myfloats", adios::Dims{Nx});
- auto ioMyFloat = adios.DefineVariable<float>("myfloat", adios::Dims{1});
- // auto& ioMyDoubles = adios.DefineVariable<double>( "myDoubles",
- // adios::Dims{Nx} );
- // auto& ioMyCFloats = adios.DefineVariable<std::complex<float>>(
- // "myCFloats", {3} );
-
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &datamanSettings = adios.DeclareMethod("WAN");
- if (!datamanSettings.isUserDefined())
+ try
{
- // if not defined by user, we can change the default settings
- datamanSettings.SetEngine("DataManWriter");
- datamanSettings.SetParameters("real_time=yes", "method_type=stream",
- "method=dump", "monitoring=yes",
- "local_ip=127.0.0.1", "remote_ip=127.0.0.1",
- "local_port=12306", "remote_port=12307");
- // datamanSettings.AddTransport( "Mdtm", "localIP=128.0.0.0.1",
- // "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
- // datamanSettings.AddTransport( "ZeroMQ", "localIP=128.0.0.0.1.1",
- // "remoteIP=128.0.0.0.2.1", "tolerances=1,2,3" ); not yet supported ,
- // will throw an exception
- }
+ // Define variable and local size
+ // Define variable and local size
+ auto ioMyFloats =
+ adios.DefineVariable<float>("myfloats", adios::Dims{Nx});
+ auto ioMyFloat = adios.DefineVariable<float>("myfloat", adios::Dims{1});
+ // auto& ioMyDoubles = adios.DefineVariable<double>( "myDoubles",
+ // adios::Dims{Nx} );
+ // auto& ioMyCFloats = adios.DefineVariable<std::complex<float>>(
+ // "myCFloats", {3} );
+
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &datamanSettings = adios.DeclareMethod("WAN");
+ if (!datamanSettings.isUserDefined())
+ {
+ // if not defined by user, we can change the default settings
+ datamanSettings.SetEngine("DataManWriter");
+ datamanSettings.SetParameters(
+ "real_time=yes", "method_type=stream", "method=dump",
+ "monitoring=yes", "local_ip=127.0.0.1", "remote_ip=127.0.0.1",
+ "local_port=12306", "remote_port=12307");
+ // datamanSettings.AddTransport( "Mdtm", "localIP=128.0.0.0.1",
+ // "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
+ // datamanSettings.AddTransport( "ZeroMQ", "localIP=128.0.0.0.1.1",
+ // "remoteIP=128.0.0.0.2.1", "tolerances=1,2,3" ); not yet supported
+ // ,
+ // will throw an exception
+ }
- // Create engine smart pointer to DataMan Engine due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // DataMan
- auto datamanWriter = adios.Open("myDoubles.bp", "w", datamanSettings,
- adios::IOMode::INDEPENDENT);
+ // Create engine smart pointer to DataMan Engine due to polymorphism,
+ // Open returns a smart pointer to Engine containing the Derived class
+ // DataMan
+ auto datamanWriter = adios.Open("myDoubles.bp", "w", datamanSettings,
+ adios::IOMode::INDEPENDENT);
- if (datamanWriter == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to create DataMan I/O engine at Open\n");
+ if (datamanWriter == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: failed to create DataMan I/O engine at Open\n");
- datamanWriter->Write<float>(
- ioMyFloats, myFloats.data()); // Base class Engine own the Write<T> that
- // will call overloaded Write from Derived
- const float num = 1.12;
- datamanWriter->Write<float>(ioMyFloat, &num); // Base class Engine own the
- // Write<T> that will call
- // overloaded Write from
- // Derived
- // datamanWriter->Write( ioMyCFloats, myCFloats.data() );
- datamanWriter->Close();
- }
- catch (std::invalid_argument &e)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::ios_base::failure &e)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
+ datamanWriter->Write<float>(
+ ioMyFloats,
+ myFloats.data()); // Base class Engine own the Write<T> that
+ // will call overloaded Write from Derived
+ const float num = 1.12;
+ datamanWriter->Write<float>(ioMyFloat,
+ &num); // Base class Engine own the
+ // Write<T> that will call
+ // overloaded Write from
+ // Derived
+ // datamanWriter->Write( ioMyCFloats, myCFloats.data() );
+ datamanWriter->Close();
+ }
+ catch (std::invalid_argument &e)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::ios_base::failure &e)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
- return 0;
+ return 0;
}
diff --git a/examples/hello/timeBP/timeBPWriter.cpp b/examples/hello/timeBP/timeBPWriter.cpp
index 280e97e1e7eb08761a1b7ce5f0eba11bb4ed66e6..b9ae445debe12905c0614549778632eb32758a6b 100644
--- a/examples/hello/timeBP/timeBPWriter.cpp
+++ b/examples/hello/timeBP/timeBPWriter.cpp
@@ -17,107 +17,109 @@
int main(int argc, char *argv[])
{
- MPI_Init(&argc, &argv);
- int rank;
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- const bool adiosDebug = true;
- adios::ADIOS adios(MPI_COMM_WORLD, adios::Verbose::ERROR, adiosDebug);
-
- // Application variable
- std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
- const std::size_t Nx = myDoubles.size();
-
- const std::size_t rows = 3;
- const std::size_t columns = 3;
-
- std::vector<float> myMatrix;
- if (rank % 2 == 0) // even rank
- {
- myMatrix.reserve(rows * columns);
- myMatrix.push_back(1);
- myMatrix.push_back(2), myMatrix.push_back(3);
- myMatrix.push_back(4);
- myMatrix.push_back(5), myMatrix.push_back(6);
- myMatrix.push_back(7);
- myMatrix.push_back(8), myMatrix.push_back(8);
- }
-
- std::vector<float> myMatrix2 = {-1, -2, -3, -4, -5, -6, -7, -8, -9};
-
- try
- {
- // Define variable and local size
- adios::Variable<double> &ioMyDoubles =
- adios.DefineVariable<double>("myDoubles", {Nx});
- adios::Variable<float> &ioMyMatrix =
- adios.DefineVariable<float>("myMatrix", {rows, columns});
- adios::Variable<float> &ioMyMatrix2 =
- adios.DefineVariable<float>("myMatrix2", {rows, columns});
-
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &bpWriterSettings =
- adios.DeclareMethod("MyMethod"); // default method type is BPWriter
- bpWriterSettings.SetParameters("profile_units=mus");
- bpWriterSettings.AddTransport(
- "File", "profile_units=mus",
- "have_metadata_file=no"); // uses default POSIX library
-
- // Create engine smart pointer due to polymorphism,
- // Open returns a smart pointer to Engine containing the Derived class
- // Writer
- auto bpWriter = adios.Open("time.bp", "w", bpWriterSettings);
-
- if (bpWriter == nullptr)
- throw std::ios_base::failure("ERROR: couldn't create bpWriter at Open\n");
-
- for (unsigned int t = 0; t < 10; ++t)
+ MPI_Init(&argc, &argv);
+ int rank;
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ const bool adiosDebug = true;
+ adios::ADIOS adios(MPI_COMM_WORLD, adios::Verbose::ERROR, adiosDebug);
+
+ // Application variable
+ std::vector<double> myDoubles = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+ const std::size_t Nx = myDoubles.size();
+
+ const std::size_t rows = 3;
+ const std::size_t columns = 3;
+
+ std::vector<float> myMatrix;
+ if (rank % 2 == 0) // even rank
{
- myDoubles[0] = t;
- bpWriter->Write<double>(
- ioMyDoubles, myDoubles.data()); // Base class Engine own the Write<T>
- // that will call overloaded Write
- // from Derived
-
- if (rank % 2 == 0) // even rank
- {
- myMatrix[0] = t;
- myMatrix2[0] = t;
-
- bpWriter->Write<float>(ioMyMatrix, myMatrix.data());
- bpWriter->Write<float>(ioMyMatrix2, myMatrix2.data());
- }
- bpWriter->Advance();
+ myMatrix.reserve(rows * columns);
+ myMatrix.push_back(1);
+ myMatrix.push_back(2), myMatrix.push_back(3);
+ myMatrix.push_back(4);
+ myMatrix.push_back(5), myMatrix.push_back(6);
+ myMatrix.push_back(7);
+ myMatrix.push_back(8), myMatrix.push_back(8);
}
- bpWriter->Close();
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
+ std::vector<float> myMatrix2 = {-1, -2, -3, -4, -5, -6, -7, -8, -9};
+
+ try
+ {
+ // Define variable and local size
+ adios::Variable<double> &ioMyDoubles =
+ adios.DefineVariable<double>("myDoubles", {Nx});
+ adios::Variable<float> &ioMyMatrix =
+ adios.DefineVariable<float>("myMatrix", {rows, columns});
+ adios::Variable<float> &ioMyMatrix2 =
+ adios.DefineVariable<float>("myMatrix2", {rows, columns});
+
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &bpWriterSettings =
+ adios.DeclareMethod("MyMethod"); // default method type is BPWriter
+ bpWriterSettings.SetParameters("profile_units=mus");
+ bpWriterSettings.AddTransport(
+ "File", "profile_units=mus",
+ "have_metadata_file=no"); // uses default POSIX library
+
+ // Create engine smart pointer due to polymorphism,
+ // Open returns a smart pointer to Engine containing the Derived class
+ // Writer
+ auto bpWriter = adios.Open("time.bp", "w", bpWriterSettings);
+
+ if (bpWriter == nullptr)
+ throw std::ios_base::failure(
+ "ERROR: couldn't create bpWriter at Open\n");
+
+ for (unsigned int t = 0; t < 10; ++t)
+ {
+ myDoubles[0] = t;
+ bpWriter->Write<double>(
+ ioMyDoubles,
+ myDoubles.data()); // Base class Engine own the Write<T>
+ // that will call overloaded Write
+ // from Derived
+
+ if (rank % 2 == 0) // even rank
+ {
+ myMatrix[0] = t;
+ myMatrix2[0] = t;
+
+ bpWriter->Write<float>(ioMyMatrix, myMatrix.data());
+ bpWriter->Write<float>(ioMyMatrix2, myMatrix2.data());
+ }
+ bpWriter->Advance();
+ }
+
+ bpWriter->Close();
+ }
+ catch (std::invalid_argument &e)
{
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::ios_base::failure &e)
- {
- if (rank == 0)
+ catch (std::ios_base::failure &e)
{
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
+ catch (std::exception &e)
{
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- MPI_Finalize();
+ MPI_Finalize();
- return 0;
+ return 0;
}
diff --git a/examples/hello/timeBP/timeBPWriter_nompi.cpp b/examples/hello/timeBP/timeBPWriter_nompi.cpp
index 48fdd2bbf3111f3c36b550c927d03b475893bf4e..42af66f238ff9e7dad277d0d7c89e4dee30de5d0 100644
--- a/examples/hello/timeBP/timeBPWriter_nompi.cpp
+++ b/examples/hello/timeBP/timeBPWriter_nompi.cpp
@@ -15,82 +15,83 @@
int main(int /*argc*/, char ** /*argv*/)
{
- const bool adiosDebug = true;
- adios::ADIOS adios(adios::Verbose::ERROR, adiosDebug);
+ const bool adiosDebug = true;
+ adios::ADIOS adios(adios::Verbose::ERROR, adiosDebug);
- // Application variable
- std::vector<double> myDoubles = {10, 1, 2, 3, 4, 5, 6, 7, 8, 9};
- const std::size_t Nx = myDoubles.size();
+ // Application variable
+ std::vector<double> myDoubles = {10, 1, 2, 3, 4, 5, 6, 7, 8, 9};
+ const std::size_t Nx = myDoubles.size();
- const std::size_t rows = 3;
- const std::size_t columns = 3;
+ const std::size_t rows = 3;
+ const std::size_t columns = 3;
- std::vector<float> myMatrix;
- myMatrix.reserve(rows * columns);
- myMatrix.push_back(1);
- myMatrix.push_back(2), myMatrix.push_back(3);
- myMatrix.push_back(4);
- myMatrix.push_back(5), myMatrix.push_back(6);
- myMatrix.push_back(7);
- myMatrix.push_back(8), myMatrix.push_back(8);
+ std::vector<float> myMatrix;
+ myMatrix.reserve(rows * columns);
+ myMatrix.push_back(1);
+ myMatrix.push_back(2), myMatrix.push_back(3);
+ myMatrix.push_back(4);
+ myMatrix.push_back(5), myMatrix.push_back(6);
+ myMatrix.push_back(7);
+ myMatrix.push_back(8), myMatrix.push_back(8);
- std::vector<float> myMatrix2 = {-1, -2, -3, -4, -5, -6, -7, -8, -9};
+ std::vector<float> myMatrix2 = {-1, -2, -3, -4, -5, -6, -7, -8, -9};
- try
- {
- // Define variable and local size
- adios::Variable<double> &ioMyDoubles =
- adios.DefineVariable<double>("myDoubles", {Nx});
- adios::Variable<float> &ioMyMatrix =
- adios.DefineVariable<float>("myMatrix", {rows, columns});
- adios::Variable<float> &ioMyMatrix2 =
- adios.DefineVariable<float>("myMatrix2", {rows, columns});
+ try
+ {
+ // Define variable and local size
+ adios::Variable<double> &ioMyDoubles =
+ adios.DefineVariable<double>("myDoubles", {Nx});
+ adios::Variable<float> &ioMyMatrix =
+ adios.DefineVariable<float>("myMatrix", {rows, columns});
+ adios::Variable<float> &ioMyMatrix2 =
+ adios.DefineVariable<float>("myMatrix2", {rows, columns});
- // Define method for engine creation, it is basically straight-forward
- // parameters
- adios::Method &bpWriterSettings =
- adios.DeclareMethod("SingleFile"); // default method type is BPWriter
- bpWriterSettings.SetParameters("profile_units=mus");
- bpWriterSettings.AddTransport(
- "File", "profile_units=mus",
- "have_metadata_file=no"); // uses default POSIX library
+ // Define method for engine creation, it is basically straight-forward
+ // parameters
+ adios::Method &bpWriterSettings = adios.DeclareMethod(
+ "SingleFile"); // default method type is BPWriter
+ bpWriterSettings.SetParameters("profile_units=mus");
+ bpWriterSettings.AddTransport(
+ "File", "profile_units=mus",
+ "have_metadata_file=no"); // uses default POSIX library
- // Create object directly rather than using polymorphism with ADIOS.Open
- adios::BPFileWriter bpWriter(adios, "time_nompi.bp", "w", adios.m_MPIComm,
- bpWriterSettings);
+ // Create object directly rather than using polymorphism with ADIOS.Open
+ adios::BPFileWriter bpWriter(adios, "time_nompi.bp", "w",
+ adios.m_MPIComm, bpWriterSettings);
- for (unsigned int t = 0; t < 3; ++t)
- {
- myDoubles[0] = t; // t * -1;
- myMatrix[0] = t;
- myMatrix2[0] = t;
+ for (unsigned int t = 0; t < 3; ++t)
+ {
+ myDoubles[0] = t; // t * -1;
+ myMatrix[0] = t;
+ myMatrix2[0] = t;
- bpWriter.Write(ioMyDoubles, myDoubles.data()); // Base class Engine own
- // the Write<T> that will
- // call overloaded Write
- // from Derived
- bpWriter.Write(ioMyMatrix, myMatrix.data());
- bpWriter.Write(ioMyMatrix2, myMatrix2.data());
- bpWriter.Advance();
- }
+ bpWriter.Write(ioMyDoubles,
+ myDoubles.data()); // Base class Engine own
+ // the Write<T> that will
+ // call overloaded Write
+ // from Derived
+ bpWriter.Write(ioMyMatrix, myMatrix.data());
+ bpWriter.Write(ioMyMatrix2, myMatrix2.data());
+ bpWriter.Advance();
+ }
- bpWriter.Close();
- }
- catch (std::invalid_argument &e)
- {
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::ios_base::failure &e)
- {
- std::cout << "System exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- std::cout << "Exception, STOPPING PROGRAM\n";
- std::cout << e.what() << "\n";
- }
+ bpWriter.Close();
+ }
+ catch (std::invalid_argument &e)
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::ios_base::failure &e)
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
- return 0;
+ return 0;
}
diff --git a/examples/solidfluid/solidfluid_read.cpp b/examples/solidfluid/solidfluid_read.cpp
index 97f7f950563cf91b85747b32b3ba02f69b6ef6a4..028590601b9cdefaae4eeb6ebd37206726d70357 100644
--- a/examples/solidfluid/solidfluid_read.cpp
+++ b/examples/solidfluid/solidfluid_read.cpp
@@ -19,9 +19,9 @@
struct MYDATA
{
- int NX;
- double *t;
- std::vector<double> p;
+ int NX;
+ double *t;
+ std::vector<double> p;
};
const int N = 10;
@@ -31,276 +31,284 @@ int rank, size;
void read_ckpt(adios::ADIOS adios, struct MYDATA &solid, struct MYDATA &fluid)
{
- try
- {
- // Open an input which was written with an expected Method
- // The write transport is associated with the group in the XML
- // ADIOS pairs that with the corresponding read transport
- // "r" is required to indicate we are reading
- auto ckptfile = adios.Open("checkpoint.bp", "r", comm, "checkpoint");
- // We can also manually set the read transport
- // auto ckptfile = adios.Open("checkpoint.bp", adios::READ_METHOD_BP, "r",
- // comm);
-
- // Note: we only see a single step in the input but the checkpoint has
- // only one step anyway. This makes this code simple
-
- // simple immediate read of a scalar
- ckptfile->ReadScalar("solid/NX", &solid.NX);
- // solid.NX is filled at this point
-
- // scheduled version of read of another scalar
- // //ckptfile->ScheduleRead ("fluid/NX", &fluid.NX);
- // //ckptfile->Read(); // perform reading now
- ckptfile->Read("fluid/NX", &fluid.NX);
- // fluid.NX is filled at this point
-
- solid.t = new double(solid.NX);
- solid.p = std::vector<double>(solid.NX);
-
- fluid.t = new double(fluid.NX);
- fluid.p = std::vector<double>(fluid.NX);
-
- adios::ADIOS_SELECTION_WRITEBLOCK sel(rank);
- adios.Read(ckptfile, sel, "solid/temperature", solid.t);
- adios.Read(ckptfile, sel, "solid/pressure", solid.p);
- adios.Read(ckptfile, sel, "fluid/temperature", fluid.t);
- // force checking if the allocated space equals to the size of the
- // selection:
- adios.Read(ckptfile, sel, "fluid/pressure", fluid.p,
- fluid.NX * sizeof(double));
- adios.Read(ckptfile, true); // true: blocking read, which is also default
- adios.Close(ckptfile); // Should this do Read() if user misses or should we
- // complain?
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
+ try
+ {
+ // Open an input which was written with an expected Method
+ // The write transport is associated with the group in the XML
+ // ADIOS pairs that with the corresponding read transport
+ // "r" is required to indicate we are reading
+ auto ckptfile = adios.Open("checkpoint.bp", "r", comm, "checkpoint");
+ // We can also manually set the read transport
+ // auto ckptfile = adios.Open("checkpoint.bp", adios::READ_METHOD_BP,
+ // "r",
+ // comm);
+
+ // Note: we only see a single step in the input but the checkpoint has
+ // only one step anyway. This makes this code simple
+
+ // simple immediate read of a scalar
+ ckptfile->ReadScalar("solid/NX", &solid.NX);
+ // solid.NX is filled at this point
+
+ // scheduled version of read of another scalar
+ // //ckptfile->ScheduleRead ("fluid/NX", &fluid.NX);
+ // //ckptfile->Read(); // perform reading now
+ ckptfile->Read("fluid/NX", &fluid.NX);
+ // fluid.NX is filled at this point
+
+ solid.t = new double(solid.NX);
+ solid.p = std::vector<double>(solid.NX);
+
+ fluid.t = new double(fluid.NX);
+ fluid.p = std::vector<double>(fluid.NX);
+
+ adios::ADIOS_SELECTION_WRITEBLOCK sel(rank);
+ adios.Read(ckptfile, sel, "solid/temperature", solid.t);
+ adios.Read(ckptfile, sel, "solid/pressure", solid.p);
+ adios.Read(ckptfile, sel, "fluid/temperature", fluid.t);
+ // force checking if the allocated space equals to the size of the
+ // selection:
+ adios.Read(ckptfile, sel, "fluid/pressure", fluid.p,
+ fluid.NX * sizeof(double));
+ adios.Read(ckptfile,
+ true); // true: blocking read, which is also default
+ adios.Close(
+ ckptfile); // Should this do Read() if user misses or should we
+ // complain?
+ }
+ catch (std::exception &e) // need to think carefully how to handle C++
+ // exceptions with MPI to avoid deadlocking
{
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << e.what() << "\n";
+ }
}
- }
}
void read_solid(adios::ADIOS adios, struct MYDATA &solid)
{
- float timeout_sec = 1.0;
- int retval = 0;
-
- try
- {
- // Open a file for input, no group defined
- // A reading transport should be defined if not file based
- // "r" is required to indicate we are reading
- int solidfile = adios.Open("solid.bp", "r",
- comm); //, ADIOS_LOCKMODE_NONE, timeout_sec);
- // int solidfile = adios.Open("solid.bp", adios::READ_METHOD_BP, "r", comm);
- /* process file here... */
- const adios::ADIOS_VARINFO &v = adios.InqVar(solidfile, "temperature");
- v.GetBlockInfo();
-
- printf("ndim = %d\n", v.ndim);
- // printf ("nsteps = %d\n", v.nsteps);
- printf("dims[%" PRIu64 "][%" PRIu64 "]\n", v.dims[0], v.dims[1]);
-
- uint64_t slice_size = v.dims[0] / size;
+ float timeout_sec = 1.0;
+ int retval = 0;
- if (rank == size - 1)
- slice_size = slice_size + v.dims[0] % size;
+ try
+ {
+ // Open a file for input, no group defined
+ // A reading transport should be defined if not file based
+ // "r" is required to indicate we are reading
+ int solidfile = adios.Open("solid.bp", "r",
+ comm); //, ADIOS_LOCKMODE_NONE, timeout_sec);
+ // int solidfile = adios.Open("solid.bp", adios::READ_METHOD_BP, "r",
+ // comm);
+ /* process file here... */
+ const adios::ADIOS_VARINFO &v = adios.InqVar(solidfile, "temperature");
+ v.GetBlockInfo();
- start[0] = rank * slice_size;
- count[0] = slice_size;
- start[1] = 0;
- count[1] = v.dims[1];
+ printf("ndim = %d\n", v.ndim);
+ // printf ("nsteps = %d\n", v.nsteps);
+ printf("dims[%" PRIu64 "][%" PRIu64 "]\n", v.dims[0], v.dims[1]);
- auto data = std::make_unique<double[]>(slice_size * v.dims[1] * 8);
+ uint64_t slice_size = v.dims[0] / size;
- adios::ADIOS_SELECTION_BOUNDINGBOX sel(v.ndim, start, count);
+ if (rank == size - 1)
+ slice_size = slice_size + v.dims[0] % size;
- /* Processing loop over the steps (we are already in the first one) */
- while (adios_errno != err_end_of_stream)
- {
- steps++; // steps start counting from 1
+ start[0] = rank * slice_size;
+ count[0] = slice_size;
+ start[1] = 0;
+ count[1] = v.dims[1];
- solidfile.ScheduleRead(sel, "temperature", solid.t);
- solidfile.Read(true);
+ auto data = std::make_unique<double[]>(slice_size * v.dims[1] * 8);
- if (rank == 0)
- printf("--------- Step: %d --------------------------------\n",
- solidfile.getCurrentStep());
+ adios::ADIOS_SELECTION_BOUNDINGBOX sel(v.ndim, start, count);
- printf("rank=%d: [0:%" PRIu64 ",0:%" PRIu64 "] = [", rank, v.dims[0],
- v.dims[1]);
- for (i = 0; i < slice_size; i++)
- {
- printf(" [");
- for (j = 0; j < v.dims[1]; j++)
+ /* Processing loop over the steps (we are already in the first one) */
+ while (adios_errno != err_end_of_stream)
{
- printf("%g ", *((double *)data + i * v.dims[1] + j));
+ steps++; // steps start counting from 1
+
+ solidfile.ScheduleRead(sel, "temperature", solid.t);
+ solidfile.Read(true);
+
+ if (rank == 0)
+ printf("--------- Step: %d --------------------------------\n",
+ solidfile.getCurrentStep());
+
+ printf("rank=%d: [0:%" PRIu64 ",0:%" PRIu64 "] = [", rank,
+ v.dims[0], v.dims[1]);
+ for (i = 0; i < slice_size; i++)
+ {
+ printf(" [");
+ for (j = 0; j < v.dims[1]; j++)
+ {
+ printf("%g ", *((double *)data + i * v.dims[1] + j));
+ }
+ printf("]");
+ }
+ printf(" ]\n\n");
+
+ // advance to 1) next available step with 2) blocking wait
+ solidfile.AdvanceStep(false, timeout_sec);
+ if (adios_errno == err_step_notready)
+ {
+ printf("rank %d: No new step arrived within the timeout. Quit. "
+ "%s\n",
+ rank, adios_errmsg());
+ break; // quit while loop
+ }
}
- printf("]");
- }
- printf(" ]\n\n");
-
- // advance to 1) next available step with 2) blocking wait
- solidfile.AdvanceStep(false, timeout_sec);
- if (adios_errno == err_step_notready)
- {
- printf("rank %d: No new step arrived within the timeout. Quit. %s\n",
- rank, adios_errmsg());
- break; // quit while loop
- }
- }
- solidfile.Close();
- }
- catch (std::exception &e)
- {
- if (adios_errno == err_file_not_found)
- {
- printf("rank %d: Stream not found after waiting %f seconds: %s\n", rank,
- timeout_sec, adios_errmsg());
- retval = adios_errno;
- }
- else if (adios_errno == err_end_of_stream)
- {
- printf("rank %d: Stream terminated before open. %s\n", rank,
- adios_errmsg());
- retval = adios_errno;
+ solidfile.Close();
}
- else if (f == NULL)
+ catch (std::exception &e)
{
- printf("rank %d: Error at opening stream: %s\n", rank, adios_errmsg());
- retval = adios_errno;
+ if (adios_errno == err_file_not_found)
+ {
+ printf("rank %d: Stream not found after waiting %f seconds: %s\n",
+ rank, timeout_sec, adios_errmsg());
+ retval = adios_errno;
+ }
+ else if (adios_errno == err_end_of_stream)
+ {
+ printf("rank %d: Stream terminated before open. %s\n", rank,
+ adios_errmsg());
+ retval = adios_errno;
+ }
+ else if (f == NULL)
+ {
+ printf("rank %d: Error at opening stream: %s\n", rank,
+ adios_errmsg());
+ retval = adios_errno;
+ }
}
- }
}
void read_fluid(adios::ADIOS adios, struct MYDATA &fluid)
{
- float timeout_sec = 1.0;
- int retval = 0;
+ float timeout_sec = 1.0;
+ int retval = 0;
- // Open a file for input, no group defined
- // A reading transport should be defined if not file based
- // "r" is required to indicate we are reading
- adios::ADIOS_INPUT fluidfile(comm, "r");
-
- try
- {
- fluidfile.Open("fluid.bp"); //, ADIOS_LOCKMODE_NONE, timeout_sec);
-
- /* process file here... */
- const adios::ADIOS_VARINFO &v = fluidfile.InqVar("temperature");
- v.GetBlockInfo();
-
- printf("ndim = %d\n", v.ndim);
- // printf ("nsteps = %d\n", v.nsteps);
- printf("dims[%" PRIu64 "][%" PRIu64 "]\n", v.dims[0], v.dims[1]);
+ // Open a file for input, no group defined
+ // A reading transport should be defined if not file based
+ // "r" is required to indicate we are reading
+ adios::ADIOS_INPUT fluidfile(comm, "r");
- uint64_t slice_size = v.dims[0] / size;
+ try
+ {
+ fluidfile.Open("fluid.bp"); //, ADIOS_LOCKMODE_NONE, timeout_sec);
- if (rank == size - 1)
- slice_size = slice_size + v.dims[0] % size;
+ /* process file here... */
+ const adios::ADIOS_VARINFO &v = fluidfile.InqVar("temperature");
+ v.GetBlockInfo();
- start[0] = rank * slice_size;
- count[0] = slice_size;
- start[1] = 0;
- count[1] = v.dims[1];
+ printf("ndim = %d\n", v.ndim);
+ // printf ("nsteps = %d\n", v.nsteps);
+ printf("dims[%" PRIu64 "][%" PRIu64 "]\n", v.dims[0], v.dims[1]);
- data = malloc(slice_size * v.dims[1] * 8);
+ uint64_t slice_size = v.dims[0] / size;
- adios::ADIOS_SELECTION_BOUNDINGBOX sel(v.ndim, start, count);
+ if (rank == size - 1)
+ slice_size = slice_size + v.dims[0] % size;
- /* Processing loop over the steps (we are already in the first one) */
- while (adios_errno != err_end_of_stream)
- {
- steps++; // steps start counting from 1
+ start[0] = rank * slice_size;
+ count[0] = slice_size;
+ start[1] = 0;
+ count[1] = v.dims[1];
- fluidfile.ScheduleRead(sel, "temperature", fluid.t);
- fluidfile.Read(true);
+ data = malloc(slice_size * v.dims[1] * 8);
- if (rank == 0)
- printf("--------- Step: %d --------------------------------\n",
- fluidfile.getCurrentStep());
+ adios::ADIOS_SELECTION_BOUNDINGBOX sel(v.ndim, start, count);
- printf("rank=%d: [0:%" PRIu64 ",0:%" PRIu64 "] = [", rank, v.dims[0],
- v.dims[1]);
- for (i = 0; i < slice_size; i++)
- {
- printf(" [");
- for (j = 0; j < v.dims[1]; j++)
+ /* Processing loop over the steps (we are already in the first one) */
+ while (adios_errno != err_end_of_stream)
{
- printf("%g ", *((double *)data + i * v.dims[1] + j));
+ steps++; // steps start counting from 1
+
+ fluidfile.ScheduleRead(sel, "temperature", fluid.t);
+ fluidfile.Read(true);
+
+ if (rank == 0)
+ printf("--------- Step: %d --------------------------------\n",
+ fluidfile.getCurrentStep());
+
+ printf("rank=%d: [0:%" PRIu64 ",0:%" PRIu64 "] = [", rank,
+ v.dims[0], v.dims[1]);
+ for (i = 0; i < slice_size; i++)
+ {
+ printf(" [");
+ for (j = 0; j < v.dims[1]; j++)
+ {
+ printf("%g ", *((double *)data + i * v.dims[1] + j));
+ }
+ printf("]");
+ }
+ printf(" ]\n\n");
+
+ // advance to 1) next available step with 2) blocking wait
+ fluidfile.AdvanceStep(false, timeout_sec);
+ if (adios_errno == err_step_notready)
+ {
+ printf("rank %d: No new step arrived within the timeout. Quit. "
+ "%s\n",
+ rank, adios_errmsg());
+ break; // quit while loop
+ }
}
- printf("]");
- }
- printf(" ]\n\n");
-
- // advance to 1) next available step with 2) blocking wait
- fluidfile.AdvanceStep(false, timeout_sec);
- if (adios_errno == err_step_notready)
- {
- printf("rank %d: No new step arrived within the timeout. Quit. %s\n",
- rank, adios_errmsg());
- break; // quit while loop
- }
- }
- fluidfile.Close();
- }
- catch (std::exception &e)
- {
- if (adios_errno == err_file_not_found)
- {
- printf("rank %d: Stream not found after waiting %f seconds: %s\n", rank,
- timeout_sec, adios_errmsg());
- retval = adios_errno;
- }
- else if (adios_errno == err_end_of_stream)
- {
- printf("rank %d: Stream terminated before open. %s\n", rank,
- adios_errmsg());
- retval = adios_errno;
+ fluidfile.Close();
}
- else if (f == NULL)
+ catch (std::exception &e)
{
- printf("rank %d: Error at opening stream: %s\n", rank, adios_errmsg());
- retval = adios_errno;
+ if (adios_errno == err_file_not_found)
+ {
+ printf("rank %d: Stream not found after waiting %f seconds: %s\n",
+ rank, timeout_sec, adios_errmsg());
+ retval = adios_errno;
+ }
+ else if (adios_errno == err_end_of_stream)
+ {
+ printf("rank %d: Stream terminated before open. %s\n", rank,
+ adios_errmsg());
+ retval = adios_errno;
+ }
+ else if (f == NULL)
+ {
+ printf("rank %d: Error at opening stream: %s\n", rank,
+ adios_errmsg());
+ retval = adios_errno;
+ }
}
- }
}
int main(int argc, char **argv)
{
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(comm, &rank);
- MPI_Comm_size(comm, &size);
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(comm, &rank);
+ MPI_Comm_size(comm, &size);
- try
- {
- // ADIOS manager object creation. MPI must be initialized
- adios::ADIOS adios("globalArrayXML.xml", comm, true);
+ try
+ {
+ // ADIOS manager object creation. MPI must be initialized
+ adios::ADIOS adios("globalArrayXML.xml", comm, true);
- read_ckpt(adios, solid, fluid);
+ read_ckpt(adios, solid, fluid);
- read_solid(adios, solid);
+ read_solid(adios, solid);
- read_fluid(adios, fluid);
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
+ read_fluid(adios, fluid);
+ }
+ catch (std::exception &e) // need to think carefully how to handle C++
+ // exceptions with MPI to avoid deadlocking
{
- std::cout << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << e.what() << "\n";
+ }
}
- }
- if (rank == 0)
- printf("We have processed %d steps\n", steps);
+ if (rank == 0)
+ printf("We have processed %d steps\n", steps);
- free(data);
- MPI_Finalize();
+ free(data);
+ MPI_Finalize();
- return retval;
+ return retval;
}
diff --git a/examples/solidfluid/solidfluid_write.cpp b/examples/solidfluid/solidfluid_write.cpp
index fd17df803d8c77336a471649e31c7543e1bec75f..68992800e2c9496ad51caa01b2e3e3a30e4eb66d 100644
--- a/examples/solidfluid/solidfluid_write.cpp
+++ b/examples/solidfluid/solidfluid_write.cpp
@@ -20,9 +20,9 @@ using adiosFile = std::shared_ptr<adios::Engine>;
struct MYDATA
{
- int NX;
- double *t;
- std::vector<double> p;
+ int NX;
+ double *t;
+ std::vector<double> p;
};
const int N = 10;
@@ -32,206 +32,218 @@ int rank, size;
void write_data(adiosFile writer, struct MYDATA &data)
{
- writer->Write("NX", &data.NX);
- writer->Write("rank", &rank);
- writer->Write("size", &size);
- writer->Write("temperature", data.t);
- writer->Write("pressure", data.p.data());
- // writer->Flush(); AdvanceStep()???
+ writer->Write("NX", &data.NX);
+ writer->Write("rank", &rank);
+ writer->Write("size", &size);
+ writer->Write("temperature", data.t);
+ writer->Write("pressure", data.p.data());
+ // writer->Flush(); AdvanceStep()???
}
void write_checkpoint(adiosFile ckptfile, const struct MYDATA &solid,
const struct MYDATA &fluid)
{
- try
- {
- ckptfile->Write("solid/NX", &solid.NX);
- ckptfile->Write("solid/rank", &rank);
- ckptfile->Write("solid/size", &size);
- ckptfile->Write("solid/temperature", solid.t);
- ckptfile->Write("solid/pressure", &solid.p[0]);
-
- ckptfile->Write("fluid/NX", &fluid.NX);
- ckptfile->Write("fluid/rank", &rank);
- ckptfile->Write("fluid/size", &size);
- ckptfile->Write("fluid/temperature", fluid.t);
- ckptfile->Write("fluid/pressure", fluid.p.data());
- // ckptfile->AdvanceStep(); ??
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
+ try
{
- std::cout << "ERROR: caught an exception from write_checkpoint\n";
- std::cout << e.what() << "\n";
+ ckptfile->Write("solid/NX", &solid.NX);
+ ckptfile->Write("solid/rank", &rank);
+ ckptfile->Write("solid/size", &size);
+ ckptfile->Write("solid/temperature", solid.t);
+ ckptfile->Write("solid/pressure", &solid.p[0]);
+
+ ckptfile->Write("fluid/NX", &fluid.NX);
+ ckptfile->Write("fluid/rank", &rank);
+ ckptfile->Write("fluid/size", &size);
+ ckptfile->Write("fluid/temperature", fluid.t);
+ ckptfile->Write("fluid/pressure", fluid.p.data());
+ // ckptfile->AdvanceStep(); ??
+ }
+ catch (std::exception &e) // need to think carefully how to handle C++
+ // exceptions with MPI to avoid deadlocking
+ {
+ if (rank == 0)
+ {
+ std::cout << "ERROR: caught an exception from write_checkpoint\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
}
void write_viz(std::shared_ptr<adios::Engine> vizstream, struct MYDATA &solid,
struct MYDATA &fluid)
{
- // This stream is not associated with a group, so we must say for each write
- // which group to use
- // The output variable is re-defined inside as <groupname>/<varname>, unless
- // given as third string argument
- // An array variable's dimension definitions are also re-defined with
- // dimensions <groupname>/<dimensionvar>
+ // This stream is not associated with a group, so we must say for each write
+ // which group to use
+ // The output variable is re-defined inside as <groupname>/<varname>, unless
+ // given as third string argument
+ // An array variable's dimension definitions are also re-defined with
+ // dimensions <groupname>/<dimensionvar>
- // vizstream->Write ("solid", "NX", &solid.NX);
- // vizstream->Write ("solid", "rank", &rank);
- // vizstream->Write ("solid", "size", &size);
+ // vizstream->Write ("solid", "NX", &solid.NX);
+ // vizstream->Write ("solid", "rank", &rank);
+ // vizstream->Write ("solid", "size", &size);
- // write solid group's temperature simply as temperature, risking overloading
- // the 'temperature' variable when
- // reading from a file
+ // write solid group's temperature simply as temperature, risking
+ // overloading
+ // the 'temperature' variable when
+ // reading from a file
- // vizstream->Write ("solid", "temperature", "my/tempvarinfile", solid.t);
+ // vizstream->Write ("solid", "temperature", "my/tempvarinfile", solid.t);
- // vizstream->Write ("fluid", "NX", &fluid.NX);
- // vizstream->Write ("fluid", "rank", &rank);
- // vizstream->Write ("fluid", "size", &size);
+ // vizstream->Write ("fluid", "NX", &fluid.NX);
+ // vizstream->Write ("fluid", "rank", &rank);
+ // vizstream->Write ("fluid", "size", &size);
- // vizstream->Write ("fluid", "temperature", "temperature", fluid.t);
+ // vizstream->Write ("fluid", "temperature", "temperature", fluid.t);
- // vizstream->Flush(); // flushes all data to disk; required operation
- // vizstream.AdvanceStep();
+ // vizstream->Flush(); // flushes all data to disk; required operation
+ // vizstream.AdvanceStep();
}
void compute(int it, struct MYDATA &solid, struct MYDATA &fluid)
{
- for (int i = 0; i < solid.NX; i++)
- {
- solid.t[i] = it * 100.0 + rank * solid.NX + i;
- solid.p[i] = it * 1000.0 + rank * solid.NX + i;
- }
- for (int i = 0; i < fluid.NX; i++)
- {
- fluid.t[i] = it * 200.0 + rank * fluid.NX + i;
- fluid.p[i] = it * 2000.0 + rank * fluid.NX + i;
- }
+ for (int i = 0; i < solid.NX; i++)
+ {
+ solid.t[i] = it * 100.0 + rank * solid.NX + i;
+ solid.p[i] = it * 1000.0 + rank * solid.NX + i;
+ }
+ for (int i = 0; i < fluid.NX; i++)
+ {
+ fluid.t[i] = it * 200.0 + rank * fluid.NX + i;
+ fluid.p[i] = it * 2000.0 + rank * fluid.NX + i;
+ }
}
int main(int argc, char *argv[])
{
- MPI_Init(&argc, &argv);
- MPI_Comm_rank(comm, &rank);
- MPI_Comm_size(comm, &size);
-
- solid.NX = N;
- solid.t = new double[N];
- solid.p = std::vector<double>(N);
-
- fluid.NX = N;
- fluid.t = new double[N];
- fluid.p = std::vector<double>(N);
-
- try
- {
- // ADIOS manager object creation. MPI must be initialized
- adios::ADIOS adios(comm, true);
-
- adios::Method &fileSettings =
- adios.DeclareMethod("Reusable"); // default engine is BP writer
- fileSettings.AddTransport("POSIX", "have_metadata_file=no");
-
- // Open a file with a Method which has selected a group and a transport in
- // the XML.
- // "a" will append to an already existing file, "w" would create a new file
- // Multiple writes to the same file work as append in this application run
- // FIXME: how do we support Update to same step?
-
- auto solidfile = adios.Open("solid.bp", "w", comm, fileSettings);
-
- // "solid" is a method but incidentally also a group
- // Constructor only creates an object and what is needed there but does not
- // open a stream/file
- // It can be used to initialize a staging connection if not declared before
- // FIXME: which argument can be post-poned into Open() instead of
- // constructor?
- // solidfile.Open("solid.bp");
-
- // Open a file with a Method that has selected a group and an engine in the
- // XML
- // The transport method(s) are (must be) associated with the engines
- // "a" will append to an already existing file, "w" would create a new file
- // Multiple writes to the same file work as append in this application run
- // FIXME: how do we support Update to same step?
- auto fluidfile = adios.Open("fluid.bp", "w", comm, fileSettings);
-
- auto checkpointFile = adios.Open("checkpoint.bp", "w", comm, fileSettings);
-
- // int ckptfile = adios.Open("checkpoint.bp", "checkpoint", "w", comm);
- // we do not open this here, but every time when needed in a function
-
- // Another output not associated with a single group, so that we can mix
- // variables to it
- // adios:handle vizstream = adios.Open( "stream.bp", comm, "w", "STAGING",
- // "options to staging method");
- auto vizstream = adios.Open("stream.bp", "w", comm, fileSettings);
-
- // This creates an empty group inside, and we can write all kinds of
- // variables to it
-
- // Get Monitor info
- std::ofstream logStream("info_" + std::to_string(rank) + ".log");
- adios.MonitorVariables(logStream);
-
- int checkPointSteps = 10;
-
- for (int it = 1; it <= 100; it++)
- {
- compute(it, solid, fluid);
+ MPI_Init(&argc, &argv);
+ MPI_Comm_rank(comm, &rank);
+ MPI_Comm_size(comm, &size);
- write_data(solidfile, solid);
- write_data(fluidfile, fluid);
+ solid.NX = N;
+ solid.t = new double[N];
+ solid.p = std::vector<double>(N);
- if (it % checkPointSteps == 0)
- {
- write_checkpoint(checkpointFile, solid, fluid);
+ fluid.NX = N;
+ fluid.t = new double[N];
+ fluid.p = std::vector<double>(N);
- MPI_Barrier(comm);
- if (rank == 0)
+ try
+ {
+ // ADIOS manager object creation. MPI must be initialized
+ adios::ADIOS adios(comm, true);
+
+ adios::Method &fileSettings =
+ adios.DeclareMethod("Reusable"); // default engine is BP writer
+ fileSettings.AddTransport("POSIX", "have_metadata_file=no");
+
+ // Open a file with a Method which has selected a group and a transport
+ // in
+ // the XML.
+ // "a" will append to an already existing file, "w" would create a new
+ // file
+ // Multiple writes to the same file work as append in this application
+ // run
+ // FIXME: how do we support Update to same step?
+
+ auto solidfile = adios.Open("solid.bp", "w", comm, fileSettings);
+
+ // "solid" is a method but incidentally also a group
+ // Constructor only creates an object and what is needed there but does
+ // not
+ // open a stream/file
+ // It can be used to initialize a staging connection if not declared
+ // before
+ // FIXME: which argument can be post-poned into Open() instead of
+ // constructor?
+ // solidfile.Open("solid.bp");
+
+ // Open a file with a Method that has selected a group and an engine in
+ // the
+ // XML
+ // The transport method(s) are (must be) associated with the engines
+ // "a" will append to an already existing file, "w" would create a new
+ // file
+ // Multiple writes to the same file work as append in this application
+ // run
+ // FIXME: how do we support Update to same step?
+ auto fluidfile = adios.Open("fluid.bp", "w", comm, fileSettings);
+
+ auto checkpointFile =
+ adios.Open("checkpoint.bp", "w", comm, fileSettings);
+
+ // int ckptfile = adios.Open("checkpoint.bp", "checkpoint", "w", comm);
+ // we do not open this here, but every time when needed in a function
+
+ // Another output not associated with a single group, so that we can mix
+ // variables to it
+ // adios:handle vizstream = adios.Open( "stream.bp", comm, "w",
+ // "STAGING",
+ // "options to staging method");
+ auto vizstream = adios.Open("stream.bp", "w", comm, fileSettings);
+
+ // This creates an empty group inside, and we can write all kinds of
+ // variables to it
+
+ // Get Monitor info
+ std::ofstream logStream("info_" + std::to_string(rank) + ".log");
+ adios.MonitorVariables(logStream);
+
+ int checkPointSteps = 10;
+
+ for (int it = 1; it <= 100; it++)
{
- std::cout << "New checkpoint step, current = " << checkPointSteps
- << "\n";
- std::cin >> checkPointSteps;
- MPI_Bcast(&checkPointSteps, 1, MPI_INT, 0, comm);
+ compute(it, solid, fluid);
+
+ write_data(solidfile, solid);
+ write_data(fluidfile, fluid);
+
+ if (it % checkPointSteps == 0)
+ {
+ write_checkpoint(checkpointFile, solid, fluid);
+
+ MPI_Barrier(comm);
+ if (rank == 0)
+ {
+ std::cout
+ << "New checkpoint step, current = " << checkPointSteps
+ << "\n";
+ std::cin >> checkPointSteps;
+ MPI_Bcast(&checkPointSteps, 1, MPI_INT, 0, comm);
+ }
+ MPI_Barrier(comm);
+ }
+
+ write_viz(vizstream, solid, fluid);
+
+ MPI_Barrier(comm);
+ if (rank == 0)
+ printf("Timestep %d written\n", it);
}
- MPI_Barrier(comm);
- }
- write_viz(vizstream, solid, fluid);
+ solidfile->Close();
+ fluidfile->Close();
+ vizstream->Close();
- MPI_Barrier(comm);
- if (rank == 0)
- printf("Timestep %d written\n", it);
+ // need barrier before we destroy the ADIOS object here automatically
+ MPI_Barrier(comm);
+ if (rank == 0)
+ printf("Finalize adios\n");
}
-
- solidfile->Close();
- fluidfile->Close();
- vizstream->Close();
-
- // need barrier before we destroy the ADIOS object here automatically
- MPI_Barrier(comm);
- if (rank == 0)
- printf("Finalize adios\n");
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
+ catch (std::exception &e) // need to think carefully how to handle C++
+ // exceptions with MPI to avoid deadlocking
{
- std::cout << "ERROR: " << e.what() << "\n";
+ if (rank == 0)
+ {
+ std::cout << "ERROR: " << e.what() << "\n";
+ }
}
- }
- delete[] solid.t;
- delete[] fluid.t;
+ delete[] solid.t;
+ delete[] fluid.t;
- if (rank == 0)
- printf("Finalize MPI\n");
- MPI_Finalize();
- return 0;
+ if (rank == 0)
+ printf("Finalize MPI\n");
+ MPI_Finalize();
+ return 0;
}
diff --git a/examples/solidfluid/solidfluid_write_nompi.cpp b/examples/solidfluid/solidfluid_write_nompi.cpp
index c5342e9a755746b62dbad7c9118e68f4154247c5..37e641fdfcc455f318cbccfabfdf6f459ef362d7 100644
--- a/examples/solidfluid/solidfluid_write_nompi.cpp
+++ b/examples/solidfluid/solidfluid_write_nompi.cpp
@@ -20,9 +20,9 @@ using adiosFile = std::shared_ptr<adios::Engine>;
struct MYDATA
{
- int NX;
- double *t;
- std::vector<double> p;
+ int NX;
+ double *t;
+ std::vector<double> p;
};
const int N = 10;
@@ -31,200 +31,212 @@ int rank = 0, size = 1;
void set_io_variables(adios::ADIOS &adios, const std::string process)
{
- adios.DefineVariable<int>(process + "/NX");
- adios.DefineVariable<int>(process + "/rank");
- adios.DefineVariable<int>(process + "/size");
- adios.DefineVariable<double>(process + "/temperature", adios::Dims{N});
- adios.DefineVariable<double>(process + "/pressure", adios::Dims{N});
+ adios.DefineVariable<int>(process + "/NX");
+ adios.DefineVariable<int>(process + "/rank");
+ adios.DefineVariable<int>(process + "/size");
+ adios.DefineVariable<double>(process + "/temperature", adios::Dims{N});
+ adios.DefineVariable<double>(process + "/pressure", adios::Dims{N});
}
void write_data(adiosFile writer, const std::string process,
struct MYDATA &data)
{
- writer->Write(process + "/NX", &data.NX);
- writer->Write(process + "/rank", &rank);
- writer->Write(process + "/size", &size);
- writer->Write(process + "/temperature", data.t);
- writer->Write(process + "/pressure", data.p.data());
- // writer->Flush(); AdvanceStep()???
+ writer->Write(process + "/NX", &data.NX);
+ writer->Write(process + "/rank", &rank);
+ writer->Write(process + "/size", &size);
+ writer->Write(process + "/temperature", data.t);
+ writer->Write(process + "/pressure", data.p.data());
+ // writer->Flush(); AdvanceStep()???
}
void write_checkpoint(adiosFile ckptfile, const struct MYDATA &solid,
const struct MYDATA &fluid)
{
- try
- {
- ckptfile->Write("solid/NX", &solid.NX);
- ckptfile->Write("solid/rank", &rank);
- ckptfile->Write("solid/size", &size);
- ckptfile->Write("solid/temperature", solid.t);
- ckptfile->Write("solid/pressure", &solid.p[0]);
-
- ckptfile->Write("fluid/NX", &fluid.NX);
- ckptfile->Write("fluid/rank", &rank);
- ckptfile->Write("fluid/size", &size);
- ckptfile->Write("fluid/temperature", fluid.t);
- ckptfile->Write("fluid/pressure", fluid.p.data());
- // ckptfile->AdvanceStep(); ??
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- if (rank == 0)
+ try
{
- std::cout << "ERROR: caught an exception from write_checkpoint\n";
- std::cout << e.what() << "\n";
+ ckptfile->Write("solid/NX", &solid.NX);
+ ckptfile->Write("solid/rank", &rank);
+ ckptfile->Write("solid/size", &size);
+ ckptfile->Write("solid/temperature", solid.t);
+ ckptfile->Write("solid/pressure", &solid.p[0]);
+
+ ckptfile->Write("fluid/NX", &fluid.NX);
+ ckptfile->Write("fluid/rank", &rank);
+ ckptfile->Write("fluid/size", &size);
+ ckptfile->Write("fluid/temperature", fluid.t);
+ ckptfile->Write("fluid/pressure", fluid.p.data());
+ // ckptfile->AdvanceStep(); ??
+ }
+ catch (std::exception &e) // need to think carefully how to handle C++
+ // exceptions with MPI to avoid deadlocking
+ {
+ if (rank == 0)
+ {
+ std::cout << "ERROR: caught an exception from write_checkpoint\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
}
void write_viz(adiosFile vizstream, struct MYDATA &solid, struct MYDATA &fluid)
{
- // This stream is not associated with a group, so we must say for each write
- // which group to use
- // The output variable is re-defined inside as <groupname>/<varname>, unless
- // given as third string argument
- // An array variable's dimension definitions are also re-defined with
- // dimensions <groupname>/<dimensionvar>
+ // This stream is not associated with a group, so we must say for each write
+ // which group to use
+ // The output variable is re-defined inside as <groupname>/<varname>, unless
+ // given as third string argument
+ // An array variable's dimension definitions are also re-defined with
+ // dimensions <groupname>/<dimensionvar>
- // vizstream->Write ("solid", "NX", &solid.NX);
- // vizstream->Write ("solid", "rank", &rank);
- // vizstream->Write ("solid", "size", &size);
+ // vizstream->Write ("solid", "NX", &solid.NX);
+ // vizstream->Write ("solid", "rank", &rank);
+ // vizstream->Write ("solid", "size", &size);
- // write solid group's temperature simply as temperature, risking overloading
- // the 'temperature' variable when
- // reading from a file
+ // write solid group's temperature simply as temperature, risking
+ // overloading
+ // the 'temperature' variable when
+ // reading from a file
- // vizstream->Write ("solid", "temperature", "my/tempvarinfile", solid.t);
+ // vizstream->Write ("solid", "temperature", "my/tempvarinfile", solid.t);
- // vizstream->Write ("fluid", "NX", &fluid.NX);
- // vizstream->Write ("fluid", "rank", &rank);
- // vizstream->Write ("fluid", "size", &size);
+ // vizstream->Write ("fluid", "NX", &fluid.NX);
+ // vizstream->Write ("fluid", "rank", &rank);
+ // vizstream->Write ("fluid", "size", &size);
- // vizstream->Write ("fluid", "temperature", "temperature", fluid.t);
+ // vizstream->Write ("fluid", "temperature", "temperature", fluid.t);
- // vizstream->Flush(); // flushes all data to disk; required operation
- // vizstream.AdvanceStep();
+ // vizstream->Flush(); // flushes all data to disk; required operation
+ // vizstream.AdvanceStep();
}
void compute(int it, struct MYDATA &solid, struct MYDATA &fluid)
{
- for (int i = 0; i < solid.NX; i++)
- {
- solid.t[i] = it * 100.0 + rank * solid.NX + i;
- solid.p[i] = it * 1000.0 + rank * solid.NX + i;
- }
- for (int i = 0; i < fluid.NX; i++)
- {
- fluid.t[i] = it * 200.0 + rank * fluid.NX + i;
- fluid.p[i] = it * 2000.0 + rank * fluid.NX + i;
- }
+ for (int i = 0; i < solid.NX; i++)
+ {
+ solid.t[i] = it * 100.0 + rank * solid.NX + i;
+ solid.p[i] = it * 1000.0 + rank * solid.NX + i;
+ }
+ for (int i = 0; i < fluid.NX; i++)
+ {
+ fluid.t[i] = it * 200.0 + rank * fluid.NX + i;
+ fluid.p[i] = it * 2000.0 + rank * fluid.NX + i;
+ }
}
int main(int argc, char *argv[])
{
- solid.NX = N;
- solid.t = new double[N];
- solid.p = std::vector<double>(N);
-
- fluid.NX = N;
- fluid.t = new double[N];
- fluid.p = std::vector<double>(N);
-
- try
- {
- // ADIOS manager object creation. MPI must be initialized
- adios::ADIOS adios(true);
- set_io_variables(adios, "solid");
- set_io_variables(adios, "fluid");
-
- adios::Method &fileSettings =
- adios.DeclareMethod("Reusable"); // default engine is BP writer
- fileSettings.AddTransport("POSIX", "have_metadata_file=no");
-
- // Open a file with a Method which has selected a group and a transport in
- // the XML.
- // "a" will append to an already existing file, "w" would create a new file
- // Multiple writes to the same file work as append in this application run
- // FIXME: how do we support Update to same step?
-
- auto solidfile = adios.Open("solid.bp", "w", fileSettings);
-
- // "solid" is a method but incidentally also a group
- // Constructor only creates an object and what is needed there but does not
- // open a stream/file
- // It can be used to initialize a staging connection if not declared before
- // FIXME: which argument can be post-poned into Open() instead of
- // constructor?
- // solidfile.Open("solid.bp");
-
- // Open a file with a Method that has selected a group and an engine in the
- // XML
- // The transport method(s) are (must be) associated with the engines
- // "a" will append to an already existing file, "w" would create a new file
- // Multiple writes to the same file work as append in this application run
- // FIXME: how do we support Update to same step?
- auto fluidfile = adios.Open("fluid.bp", "w", fileSettings);
-
- auto checkpointFile = adios.Open("checkpoint.bp", "w", fileSettings);
-
- // int ckptfile = adios.Open("checkpoint.bp", "checkpoint", "w", comm);
- // we do not open this here, but every time when needed in a function
-
- // Another output not associated with a single group, so that we can mix
- // variables to it
- // adios:handle vizstream = adios.Open( "stream.bp", comm, "w", "STAGING",
- // "options to staging method");
- auto vizstream = adios.Open("stream.bp", "w", fileSettings);
-
- // This creates an empty group inside, and we can write all kinds of
- // variables to it
-
- // Get Monitor info
- std::ofstream logStream("info_nompi.log");
- adios.MonitorVariables(logStream);
-
- int checkPointSteps = 10;
-
- for (int it = 1; it <= 100; it++)
+ solid.NX = N;
+ solid.t = new double[N];
+ solid.p = std::vector<double>(N);
+
+ fluid.NX = N;
+ fluid.t = new double[N];
+ fluid.p = std::vector<double>(N);
+
+ try
{
- compute(it, solid, fluid);
+ // ADIOS manager object creation. MPI must be initialized
+ adios::ADIOS adios(true);
+ set_io_variables(adios, "solid");
+ set_io_variables(adios, "fluid");
+
+ adios::Method &fileSettings =
+ adios.DeclareMethod("Reusable"); // default engine is BP writer
+ fileSettings.AddTransport("POSIX", "have_metadata_file=no");
+
+ // Open a file with a Method which has selected a group and a transport
+ // in
+ // the XML.
+ // "a" will append to an already existing file, "w" would create a new
+ // file
+ // Multiple writes to the same file work as append in this application
+ // run
+ // FIXME: how do we support Update to same step?
+
+ auto solidfile = adios.Open("solid.bp", "w", fileSettings);
+
+ // "solid" is a method but incidentally also a group
+ // Constructor only creates an object and what is needed there but does
+ // not
+ // open a stream/file
+ // It can be used to initialize a staging connection if not declared
+ // before
+ // FIXME: which argument can be post-poned into Open() instead of
+ // constructor?
+ // solidfile.Open("solid.bp");
+
+ // Open a file with a Method that has selected a group and an engine in
+ // the
+ // XML
+ // The transport method(s) are (must be) associated with the engines
+ // "a" will append to an already existing file, "w" would create a new
+ // file
+ // Multiple writes to the same file work as append in this application
+ // run
+ // FIXME: how do we support Update to same step?
+ auto fluidfile = adios.Open("fluid.bp", "w", fileSettings);
+
+ auto checkpointFile = adios.Open("checkpoint.bp", "w", fileSettings);
+
+ // int ckptfile = adios.Open("checkpoint.bp", "checkpoint", "w", comm);
+ // we do not open this here, but every time when needed in a function
+
+ // Another output not associated with a single group, so that we can mix
+ // variables to it
+ // adios:handle vizstream = adios.Open( "stream.bp", comm, "w",
+ // "STAGING",
+ // "options to staging method");
+ auto vizstream = adios.Open("stream.bp", "w", fileSettings);
+
+ // This creates an empty group inside, and we can write all kinds of
+ // variables to it
+
+ // Get Monitor info
+ std::ofstream logStream("info_nompi.log");
+ adios.MonitorVariables(logStream);
+
+ int checkPointSteps = 10;
+
+ for (int it = 1; it <= 100; it++)
+ {
+ compute(it, solid, fluid);
- write_data(solidfile, "solid", solid);
- write_data(fluidfile, "fluid", fluid);
+ write_data(solidfile, "solid", solid);
+ write_data(fluidfile, "fluid", fluid);
- if (it % checkPointSteps == 0)
- {
- write_checkpoint(checkpointFile, solid, fluid);
+ if (it % checkPointSteps == 0)
+ {
+ write_checkpoint(checkpointFile, solid, fluid);
- {
- std::cout << "New checkpoint step, current = " << checkPointSteps
- << "\n";
- std::cin >> checkPointSteps;
- }
- }
+ {
+ std::cout
+ << "New checkpoint step, current = " << checkPointSteps
+ << "\n";
+ std::cin >> checkPointSteps;
+ }
+ }
- write_viz(vizstream, solid, fluid);
+ write_viz(vizstream, solid, fluid);
- std::cout << "Timestep " << it << " written\n";
- }
+ std::cout << "Timestep " << it << " written\n";
+ }
- solidfile->Close();
- fluidfile->Close();
- vizstream->Close();
- checkpointFile->Close();
+ solidfile->Close();
+ fluidfile->Close();
+ vizstream->Close();
+ checkpointFile->Close();
- // need barrier before we destroy the ADIOS object here automatically ...no!
- std::cout << "Finalize adios\n";
- }
- catch (std::exception &e) // need to think carefully how to handle C++
- // exceptions with MPI to avoid deadlocking
- {
- std::cout << e.what() << "\n";
- }
+ // need barrier before we destroy the ADIOS object here automatically
+ // ...no!
+ std::cout << "Finalize adios\n";
+ }
+ catch (std::exception &e) // need to think carefully how to handle C++
+ // exceptions with MPI to avoid deadlocking
+ {
+ std::cout << e.what() << "\n";
+ }
- delete[] solid.t;
- delete[] fluid.t;
+ delete[] solid.t;
+ delete[] fluid.t;
- return 0;
+ return 0;
}
diff --git a/examples/xmlParser/xmlParser.cpp b/examples/xmlParser/xmlParser.cpp
index 358f4467888e4b44e34f3b8290dd1c5fed9f0e4e..98624de22bb771c31a2b9a5de2b9a62fb17ace88 100644
--- a/examples/xmlParser/xmlParser.cpp
+++ b/examples/xmlParser/xmlParser.cpp
@@ -25,40 +25,40 @@ static void Usage();
int main(int argc, char *argv[])
{
- MPI_Init(&argc, &argv);
- int rank;
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+ MPI_Init(&argc, &argv);
+ int rank;
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
- try
- {
- if (argc != 2)
+ try
{
- Usage();
+ if (argc != 2)
+ {
+ Usage();
+ }
+ else
+ {
+ const std::string xmlConfigFile(argv[1]);
+ adios::ADIOS adios(xmlConfigFile, MPI_COMM_WORLD, true);
+ adios.MonitorGroups(std::cout);
+ }
}
- else
+ catch (std::exception &e)
{
- const std::string xmlConfigFile(argv[1]);
- adios::ADIOS adios(xmlConfigFile, MPI_COMM_WORLD, true);
- adios.MonitorGroups(std::cout);
+ if (rank == 0)
+ {
+ std::cout << "ERROR: exception caught\n";
+ std::cout << e.what() << "\n";
+ }
}
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- {
- std::cout << "ERROR: exception caught\n";
- std::cout << e.what() << "\n";
- }
- }
- MPI_Finalize();
- return 0;
+ MPI_Finalize();
+ return 0;
}
static void Usage()
{
- std::cout << "Program to test XML Config file parsing\n";
- std::cout << "Usage: \n";
- std::cout << "\t MPI version: ./xmlParser_mpi xmlConfigFile\n";
- std::cout << "\t Non-MPI version: ./xmlParser_nompi xmlConfigFile\n";
+ std::cout << "Program to test XML Config file parsing\n";
+ std::cout << "Usage: \n";
+ std::cout << "\t MPI version: ./xmlParser_mpi xmlConfigFile\n";
+ std::cout << "\t Non-MPI version: ./xmlParser_nompi xmlConfigFile\n";
}
diff --git a/include/ADIOS.h b/include/ADIOS.h
index 85bd4825950c9fceb4865a906c5bdd4cea3d48a5..be624488c96a3fb1c8baf00abf41dcbd2d0eecef 100644
--- a/include/ADIOS.h
+++ b/include/ADIOS.h
@@ -42,320 +42,333 @@ class Engine;
class ADIOS
{
public:
- MPI_Comm m_MPIComm = MPI_COMM_SELF; ///< only used as reference to MPI
- /// communicator passed from parallel
- /// constructor, MPI_Comm is a pointer
- /// itself. Public as called from C
-
- int m_RankMPI = 0; ///< current MPI rank process
- int m_SizeMPI = 1; ///< current MPI processes size
-
- std::string m_HostLanguage = "C++";
-
- /**
- * @brief ADIOS empty constructor. Used for non XML config file API calls.
- */
- ADIOS(const Verbose verbose = Verbose::WARN, const bool debugMode = false);
-
- /**
- * @brief Serial constructor for config file, only allowed and compiled in
- * libadios_nompi.a
- * @param config XML config file
- * @param debugMode true: on throws exceptions and do additional checks,
- * false: off (faster, but unsafe)
- */
- ADIOS(std::string config, const Verbose verbose = Verbose::WARN,
- const bool debugMode = false);
-
- /**
- * @brief Parallel constructor for XML config file and MPI
- * @param config XML config file
- * @param mpiComm MPI communicator ...const to be discussed
- * @param debugMode true: on, false: off (faster, but unsafe)
- */
-
- ADIOS(std::string config, MPI_Comm mpiComm,
- const Verbose verbose = Verbose::WARN, const bool debugMode = false);
-
- /**
- * @brief Parallel MPI communicator without XML config file
- * @param mpiComm MPI communicator passed to m_MPIComm*
- * @param debugMode true: on, false: off (faster)
- */
- ADIOS(MPI_Comm mpiComm, const Verbose verbose = Verbose::WARN,
- const bool debugMode = false);
-
- ~ADIOS() = default;
-
- void InitMPI(); ///< sets rank and size in m_rank and m_Size, respectively.
-
- /**
- * Look for template specialization
- * @param name
- * @param dimensions
- * @param globalDimensions
- * @param globalOffsets
- * @return
- */
- template <class T>
- inline Variable<T> &DefineVariable(const std::string &name,
- const Dims dimensions = Dims{1},
- const Dims globalDimensions = Dims(),
- const Dims globalOffsets = Dims())
- {
- throw std::invalid_argument("ERROR: type not supported for variable " +
- name + " in call to DefineVariable\n");
- }
-
- template <class T> inline Variable<T> &GetVariable(const std::string &name)
- {
- throw std::invalid_argument("ERROR: type not supported for variable " +
- name + " in call to GetVariable\n");
- }
-
- template <class T>
- VariableCompound &DefineVariableCompound(const std::string &name,
- const Dims dimensions = Dims{1},
- const Dims globalDimensions = Dims(),
- const Dims globalOffsets = Dims())
- {
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_Compound.size();
- m_Compound.emplace(size, VariableCompound(name, sizeof(T), dimensions,
- globalDimensions, globalOffsets,
- m_DebugMode));
- m_Variables.emplace(name, std::make_pair(GetType<T>(), size));
- return m_Compound.at(size);
- }
-
- VariableCompound &GetVariableCompound(const std::string &name);
-
- /**
- * Declares a new method. If the method is defined in the user config file,
- * it will be already created during processing the config file,
- * the method is set up with the user settings and this function just returns
- * that method.
- * Otherwise it will create and return a new Method with default settings.
- * Use method.isUserDefined() to distinguish between the two cases.
- * @param methodName must be unique
- */
- Method &DeclareMethod(const std::string &methodName);
-
- /**
- * @brief Open to Write, Read. Creates a new engine from previously defined
- * method
- * @param streamName unique stream or file name
- * @param accessMode "w" or "write", "r" or "read", "a" or "append", "u" or
- * "update"
- * @param mpiComm option to modify communicator from ADIOS class constructor
- * @param method looks for corresponding Method object in ADIOS to initialize
- * the engine
- * @param iomode Independent or collective open/advance by writers/readers?
- * Write() operations are always independent.
- * @param timeout_sec Wait some time before reporting on missing stream (i.e.
- * wait for it for a while)
- * @return Derived class of base Engine depending on Method parameters,
- * shared_ptr for potential flexibility
- */
- std::shared_ptr<Engine> Open(const std::string &streamName,
- const std::string &accessMode, MPI_Comm mpiComm,
- const Method &method,
- const IOMode iomode = IOMode::INDEPENDENT,
- const float timeout_sec = 0.0);
-
- /**
- * @brief Open to Write, Read. Creates a new engine from previously defined
- * method.
- * Reuses MPI communicator from ADIOS constructor.
- * @param streamName unique stream or file name
- * @param accessMode "w" or "write", "r" or "read", "a" or "append", "u" or
- * "update"
- * @param method contains engine parameters
- * @param iomode Independent or collective open/advance by writers/readers?
- * Write() operations are always independent.
- * @param timeout_sec Wait some time before reporting on missing stream (i.e.
- * wait for it for a while)
- * @return Derived class of base Engine depending on Method parameters,
- * shared_ptr for potential flexibility
- */
- std::shared_ptr<Engine> Open(const std::string &streamName,
- const std::string &accessMode,
- const Method &method,
- const IOMode iomode = IOMode::INDEPENDENT,
- const float timeout_sec = 0.0);
-
- /**
- * Version required by the XML config file implementation, searches method
- * inside ADIOS through a unique name
- * @param streamName unique stream or file name
- * @param accessMode "w" or "write", "r" or "read", "a" or "append"
- * @param mpiComm mpi Communicator
- * @param methodName used to search method object inside ADIOS object
- * @param iomode Independent or collective open/advance by writers/readers?
- * Write() operations are always independent.
- * @param timeout_sec Wait some time before reporting on missing stream (i.e.
- * wait for it for a while)
- * @return Derived class of base Engine depending on Method parameters,
- * shared_ptr for potential flexibility
- */
- std::shared_ptr<Engine> Open(const std::string &streamName,
- const std::string &accessMode, MPI_Comm mpiComm,
- const std::string &methodName,
- const IOMode iomode = IOMode::INDEPENDENT,
- const float timeout_sec = 0.0);
-
- /**
- * Version required by the XML config file implementation, searches method
- * inside ADIOS through a unique name.
- * Reuses ADIOS MPI Communicator from constructor.
- * @param streamName unique stream or file name
- * @param accessMode "w" or "write", "r" or "read", "a" or "append"
- * @param methodName used to search method object inside ADIOS object
- * @param iomode Independent or collective open/advance by writers/readers?
- * Write() operations are always independent.
- * @param timeout_sec Wait some time before reporting on missing stream (i.e.
- * wait for it for a while)
- * @return Derived class of base Engine depending on Method parameters,
- * shared_ptr for potential flexibility
- */
- std::shared_ptr<Engine> Open(const std::string &streamName,
- const std::string &accessMode,
- const std::string &methodName,
- const IOMode iomode = IOMode::INDEPENDENT,
- const float timeout_sec = 0.0);
-
- /**
- * @brief Open to Read all steps from a file. No streaming, advancing is
- * possible here. All steps in the file
- * are immediately available for reading. Creates a new engine from previously
- * defined method.
- * @param fileName file name
- * @param mpiComm option to modify communicator from ADIOS class constructor
- * @param method looks for corresponding Method object in ADIOS to initialize
- * the engine
- * @param iomode Independent or collective open/advance by writers/readers?
- * Write() operations are always independent.
- * @return Derived class of base Engine depending on Method parameters,
- * shared_ptr for potential flexibility
- */
- std::shared_ptr<Engine>
- OpenFileReader(const std::string &fileName, MPI_Comm mpiComm,
- const Method &method,
- const IOMode iomode = IOMode::INDEPENDENT);
-
- /**
- * @brief Open to Read all steps from a file. No streaming, advancing is
- * possible here. All steps in the file
- * are immediately available for reading. Creates a new engine from previously
- * defined method.
- * Version required by the XML config file implementation, searches method
- * inside ADIOS through a unique name.
- * @param fileName file name
- * @param mpiComm option to modify communicator from ADIOS class constructor
- * @param methodName used to search method object inside ADIOS object
- * @param iomode Independent or collective open/advance by writers/readers?
- * Write() operations are always independent.
- * @return Derived class of base Engine depending on Method parameters,
- * shared_ptr for potential flexibility
- */
- std::shared_ptr<Engine>
- OpenFileReader(const std::string &fileName, MPI_Comm mpiComm,
- const std::string &methodName,
- const IOMode iomode = IOMode::INDEPENDENT);
-
- /**
- * @brief Dumps groups information to a file stream or standard output.
- * Note that either the user closes this fileStream or it's closed at the end.
- * @param logStream either std::cout standard output, or a std::ofstream file
- */
- void MonitorVariables(std::ostream &logStream);
+ MPI_Comm m_MPIComm = MPI_COMM_SELF; ///< only used as reference to MPI
+ /// communicator passed from parallel
+ /// constructor, MPI_Comm is a pointer
+ /// itself. Public as called from C
+
+ int m_RankMPI = 0; ///< current MPI rank process
+ int m_SizeMPI = 1; ///< current MPI processes size
+
+ std::string m_HostLanguage = "C++";
+
+ /**
+ * @brief ADIOS empty constructor. Used for non XML config file API calls.
+ */
+ ADIOS(const Verbose verbose = Verbose::WARN, const bool debugMode = false);
+
+ /**
+ * @brief Serial constructor for config file, only allowed and compiled in
+ * libadios_nompi.a
+ * @param config XML config file
+ * @param debugMode true: on throws exceptions and do additional checks,
+ * false: off (faster, but unsafe)
+ */
+ ADIOS(std::string config, const Verbose verbose = Verbose::WARN,
+ const bool debugMode = false);
+
+ /**
+ * @brief Parallel constructor for XML config file and MPI
+ * @param config XML config file
+ * @param mpiComm MPI communicator ...const to be discussed
+ * @param debugMode true: on, false: off (faster, but unsafe)
+ */
+
+ ADIOS(std::string config, MPI_Comm mpiComm,
+ const Verbose verbose = Verbose::WARN, const bool debugMode = false);
+
+ /**
+ * @brief Parallel MPI communicator without XML config file
+ * @param mpiComm MPI communicator passed to m_MPIComm*
+ * @param debugMode true: on, false: off (faster)
+ */
+ ADIOS(MPI_Comm mpiComm, const Verbose verbose = Verbose::WARN,
+ const bool debugMode = false);
+
+ ~ADIOS() = default;
+
+ void InitMPI(); ///< sets rank and size in m_rank and m_Size, respectively.
+
+ /**
+ * Look for template specialization
+ * @param name
+ * @param dimensions
+ * @param globalDimensions
+ * @param globalOffsets
+ * @return
+ */
+ template <class T>
+ inline Variable<T> &DefineVariable(const std::string &name,
+ const Dims dimensions = Dims{1},
+ const Dims globalDimensions = Dims(),
+ const Dims globalOffsets = Dims())
+ {
+ throw std::invalid_argument("ERROR: type not supported for variable " +
+ name + " in call to DefineVariable\n");
+ }
+
+ template <class T> inline Variable<T> &GetVariable(const std::string &name)
+ {
+ throw std::invalid_argument("ERROR: type not supported for variable " +
+ name + " in call to GetVariable\n");
+ }
+
+ template <class T>
+ VariableCompound &DefineVariableCompound(
+ const std::string &name, const Dims dimensions = Dims{1},
+ const Dims globalDimensions = Dims(), const Dims globalOffsets = Dims())
+ {
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_Compound.size();
+ m_Compound.emplace(size, VariableCompound(name, sizeof(T), dimensions,
+ globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name, std::make_pair(GetType<T>(), size));
+ return m_Compound.at(size);
+ }
+
+ VariableCompound &GetVariableCompound(const std::string &name);
+
+ /**
+ * Declares a new method. If the method is defined in the user config file,
+ * it will be already created during processing the config file,
+ * the method is set up with the user settings and this function just
+ * returns
+ * that method.
+ * Otherwise it will create and return a new Method with default settings.
+ * Use method.isUserDefined() to distinguish between the two cases.
+ * @param methodName must be unique
+ */
+ Method &DeclareMethod(const std::string &methodName);
+
+ /**
+ * @brief Open to Write, Read. Creates a new engine from previously defined
+ * method
+ * @param streamName unique stream or file name
+ * @param accessMode "w" or "write", "r" or "read", "a" or "append", "u" or
+ * "update"
+ * @param mpiComm option to modify communicator from ADIOS class constructor
+ * @param method looks for corresponding Method object in ADIOS to
+ * initialize
+ * the engine
+ * @param iomode Independent or collective open/advance by writers/readers?
+ * Write() operations are always independent.
+ * @param timeout_sec Wait some time before reporting on missing stream
+ * (i.e.
+ * wait for it for a while)
+ * @return Derived class of base Engine depending on Method parameters,
+ * shared_ptr for potential flexibility
+ */
+ std::shared_ptr<Engine> Open(const std::string &streamName,
+ const std::string &accessMode,
+ MPI_Comm mpiComm, const Method &method,
+ const IOMode iomode = IOMode::INDEPENDENT,
+ const float timeout_sec = 0.0);
+
+ /**
+ * @brief Open to Write, Read. Creates a new engine from previously defined
+ * method.
+ * Reuses MPI communicator from ADIOS constructor.
+ * @param streamName unique stream or file name
+ * @param accessMode "w" or "write", "r" or "read", "a" or "append", "u" or
+ * "update"
+ * @param method contains engine parameters
+ * @param iomode Independent or collective open/advance by writers/readers?
+ * Write() operations are always independent.
+ * @param timeout_sec Wait some time before reporting on missing stream
+ * (i.e.
+ * wait for it for a while)
+ * @return Derived class of base Engine depending on Method parameters,
+ * shared_ptr for potential flexibility
+ */
+ std::shared_ptr<Engine> Open(const std::string &streamName,
+ const std::string &accessMode,
+ const Method &method,
+ const IOMode iomode = IOMode::INDEPENDENT,
+ const float timeout_sec = 0.0);
+
+ /**
+ * Version required by the XML config file implementation, searches method
+ * inside ADIOS through a unique name
+ * @param streamName unique stream or file name
+ * @param accessMode "w" or "write", "r" or "read", "a" or "append"
+ * @param mpiComm mpi Communicator
+ * @param methodName used to search method object inside ADIOS object
+ * @param iomode Independent or collective open/advance by writers/readers?
+ * Write() operations are always independent.
+ * @param timeout_sec Wait some time before reporting on missing stream
+ * (i.e.
+ * wait for it for a while)
+ * @return Derived class of base Engine depending on Method parameters,
+ * shared_ptr for potential flexibility
+ */
+ std::shared_ptr<Engine> Open(const std::string &streamName,
+ const std::string &accessMode,
+ MPI_Comm mpiComm,
+ const std::string &methodName,
+ const IOMode iomode = IOMode::INDEPENDENT,
+ const float timeout_sec = 0.0);
+
+ /**
+ * Version required by the XML config file implementation, searches method
+ * inside ADIOS through a unique name.
+ * Reuses ADIOS MPI Communicator from constructor.
+ * @param streamName unique stream or file name
+ * @param accessMode "w" or "write", "r" or "read", "a" or "append"
+ * @param methodName used to search method object inside ADIOS object
+ * @param iomode Independent or collective open/advance by writers/readers?
+ * Write() operations are always independent.
+ * @param timeout_sec Wait some time before reporting on missing stream
+ * (i.e.
+ * wait for it for a while)
+ * @return Derived class of base Engine depending on Method parameters,
+ * shared_ptr for potential flexibility
+ */
+ std::shared_ptr<Engine> Open(const std::string &streamName,
+ const std::string &accessMode,
+ const std::string &methodName,
+ const IOMode iomode = IOMode::INDEPENDENT,
+ const float timeout_sec = 0.0);
+
+ /**
+ * @brief Open to Read all steps from a file. No streaming, advancing is
+ * possible here. All steps in the file
+ * are immediately available for reading. Creates a new engine from
+ * previously
+ * defined method.
+ * @param fileName file name
+ * @param mpiComm option to modify communicator from ADIOS class constructor
+ * @param method looks for corresponding Method object in ADIOS to
+ * initialize
+ * the engine
+ * @param iomode Independent or collective open/advance by writers/readers?
+ * Write() operations are always independent.
+ * @return Derived class of base Engine depending on Method parameters,
+ * shared_ptr for potential flexibility
+ */
+ std::shared_ptr<Engine>
+ OpenFileReader(const std::string &fileName, MPI_Comm mpiComm,
+ const Method &method,
+ const IOMode iomode = IOMode::INDEPENDENT);
+
+ /**
+ * @brief Open to Read all steps from a file. No streaming, advancing is
+ * possible here. All steps in the file
+ * are immediately available for reading. Creates a new engine from
+ * previously
+ * defined method.
+ * Version required by the XML config file implementation, searches method
+ * inside ADIOS through a unique name.
+ * @param fileName file name
+ * @param mpiComm option to modify communicator from ADIOS class constructor
+ * @param methodName used to search method object inside ADIOS object
+ * @param iomode Independent or collective open/advance by writers/readers?
+ * Write() operations are always independent.
+ * @return Derived class of base Engine depending on Method parameters,
+ * shared_ptr for potential flexibility
+ */
+ std::shared_ptr<Engine>
+ OpenFileReader(const std::string &fileName, MPI_Comm mpiComm,
+ const std::string &methodName,
+ const IOMode iomode = IOMode::INDEPENDENT);
+
+ /**
+ * @brief Dumps groups information to a file stream or standard output.
+ * Note that either the user closes this fileStream or it's closed at the
+ * end.
+ * @param logStream either std::cout standard output, or a std::ofstream
+ * file
+ */
+ void MonitorVariables(std::ostream &logStream);
protected: // no const to allow default empty and copy constructors
- std::map<unsigned int, Variable<char>> m_Char;
- std::map<unsigned int, Variable<unsigned char>> m_UChar;
- std::map<unsigned int, Variable<short>> m_Short;
- std::map<unsigned int, Variable<unsigned short>> m_UShort;
- std::map<unsigned int, Variable<int>> m_Int;
- std::map<unsigned int, Variable<unsigned int>> m_UInt;
- std::map<unsigned int, Variable<long int>> m_LInt;
- std::map<unsigned int, Variable<unsigned long int>> m_ULInt;
- std::map<unsigned int, Variable<long long int>> m_LLInt;
- std::map<unsigned int, Variable<unsigned long long int>> m_ULLInt;
- std::map<unsigned int, Variable<float>> m_Float;
- std::map<unsigned int, Variable<double>> m_Double;
- std::map<unsigned int, Variable<long double>> m_LDouble;
- std::map<unsigned int, Variable<std::complex<float>>> m_CFloat;
- std::map<unsigned int, Variable<std::complex<double>>> m_CDouble;
- std::map<unsigned int, Variable<std::complex<long double>>> m_CLDouble;
- std::map<unsigned int, VariableCompound> m_Compound;
-
- std::string m_ConfigFile; ///< XML File to be read containing configuration
- /// information
- bool m_DebugMode = false; ///< if true will do more checks, exceptions,
- /// warnings, expect slower code
-
- // Variables
- std::map<std::string, std::pair<std::string, unsigned int>>
- m_Variables; ///< Makes variable name unique, key: variable name, value:
- /// pair.first = type, pair.second = index in corresponding
- /// vector of Variable
-
- std::vector<std::shared_ptr<Transform>>
- m_Transforms; ///< transforms associated with ADIOS run
-
- /**
- * @brief List of Methods (engine metadata) defined from either ADIOS XML
- * configuration file or the DeclareMethod function.
- * <pre>
- * Key: std::string unique method name
- * Value: Method class
- * </pre>
- */
- std::map<std::string, Method> m_Methods;
- std::set<std::string>
- m_EngineNames; ///< set used to check Engine name uniqueness in debug mode
-
- /**
- * @brief Checks for group existence in m_Groups, if failed throws
- * std::invalid_argument exception
- * @param itGroup m_Groups iterator, usually from find function
- * @param groupName unique name, passed for thrown exception only
- * @param hint adds information to thrown exception
- */
- void CheckVariableInput(const std::string &name,
- const Dims &dimensions) const;
-
- /**
- * Checks for variable name, if not found throws an invalid exception
- * @param itVariable iterator pointing to the variable name in m_Variables
- * @param name variable name
- * @param hint message to be thrown for debugging purporses
- */
- void CheckVariableName(
- std::map<std::string,
- std::pair<std::string, unsigned int>>::const_iterator itVariable,
- const std::string &name, const std::string &hint) const;
-
- /**
- * @brief Checks for method existence in m_Methods, if failed throws
- * std::invalid_argument exception
- * @param itMethod m_Methods iterator, usually from find function
- * @param methodName unique name, passed for thrown exception only
- * @param hint adds information to thrown exception
- */
- void CheckMethod(std::map<std::string, Method>::const_iterator itMethod,
- const std::string &methodName,
- const std::string &hint) const;
-
- template <class T> unsigned int GetVariableIndex(const std::string &name)
- {
- auto itVariable = m_Variables.find(name);
- CheckVariableName(
- itVariable, name,
- "in call to GetVariable<" + GetType<T>() +
- ">, or call to GetVariableCompound if <T> = <compound>\n");
- return itVariable->second.second;
- }
+ std::map<unsigned int, Variable<char>> m_Char;
+ std::map<unsigned int, Variable<unsigned char>> m_UChar;
+ std::map<unsigned int, Variable<short>> m_Short;
+ std::map<unsigned int, Variable<unsigned short>> m_UShort;
+ std::map<unsigned int, Variable<int>> m_Int;
+ std::map<unsigned int, Variable<unsigned int>> m_UInt;
+ std::map<unsigned int, Variable<long int>> m_LInt;
+ std::map<unsigned int, Variable<unsigned long int>> m_ULInt;
+ std::map<unsigned int, Variable<long long int>> m_LLInt;
+ std::map<unsigned int, Variable<unsigned long long int>> m_ULLInt;
+ std::map<unsigned int, Variable<float>> m_Float;
+ std::map<unsigned int, Variable<double>> m_Double;
+ std::map<unsigned int, Variable<long double>> m_LDouble;
+ std::map<unsigned int, Variable<std::complex<float>>> m_CFloat;
+ std::map<unsigned int, Variable<std::complex<double>>> m_CDouble;
+ std::map<unsigned int, Variable<std::complex<long double>>> m_CLDouble;
+ std::map<unsigned int, VariableCompound> m_Compound;
+
+ std::string m_ConfigFile; ///< XML File to be read containing configuration
+ /// information
+ bool m_DebugMode = false; ///< if true will do more checks, exceptions,
+ /// warnings, expect slower code
+
+ // Variables
+ std::map<std::string, std::pair<std::string, unsigned int>>
+ m_Variables; ///< Makes variable name unique, key: variable name,
+ /// value:
+ /// pair.first = type, pair.second = index in corresponding
+ /// vector of Variable
+
+ std::vector<std::shared_ptr<Transform>>
+ m_Transforms; ///< transforms associated with ADIOS run
+
+ /**
+ * @brief List of Methods (engine metadata) defined from either ADIOS XML
+ * configuration file or the DeclareMethod function.
+ * <pre>
+ * Key: std::string unique method name
+ * Value: Method class
+ * </pre>
+ */
+ std::map<std::string, Method> m_Methods;
+ std::set<std::string> m_EngineNames; ///< set used to check Engine name
+ /// uniqueness in debug mode
+
+ /**
+ * @brief Checks for group existence in m_Groups, if failed throws
+ * std::invalid_argument exception
+ * @param itGroup m_Groups iterator, usually from find function
+ * @param groupName unique name, passed for thrown exception only
+ * @param hint adds information to thrown exception
+ */
+ void CheckVariableInput(const std::string &name,
+ const Dims &dimensions) const;
+
+ /**
+ * Checks for variable name, if not found throws an invalid exception
+ * @param itVariable iterator pointing to the variable name in m_Variables
+ * @param name variable name
+ * @param hint message to be thrown for debugging purporses
+ */
+ void CheckVariableName(
+ std::map<std::string,
+ std::pair<std::string, unsigned int>>::const_iterator
+ itVariable,
+ const std::string &name, const std::string &hint) const;
+
+ /**
+ * @brief Checks for method existence in m_Methods, if failed throws
+ * std::invalid_argument exception
+ * @param itMethod m_Methods iterator, usually from find function
+ * @param methodName unique name, passed for thrown exception only
+ * @param hint adds information to thrown exception
+ */
+ void CheckMethod(std::map<std::string, Method>::const_iterator itMethod,
+ const std::string &methodName,
+ const std::string &hint) const;
+
+ template <class T> unsigned int GetVariableIndex(const std::string &name)
+ {
+ auto itVariable = m_Variables.find(name);
+ CheckVariableName(itVariable, name,
+ "in call to GetVariable<" + GetType<T>() +
+ ">, or call to GetVariableCompound if <T> = "
+ "<compound>\n");
+ return itVariable->second.second;
+ }
};
// template specializations of DefineVariable:
@@ -364,12 +377,12 @@ inline Variable<char> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_Char.size();
- m_Char.emplace(size, Variable<char>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name, std::make_pair(GetType<char>(), size));
- return m_Char.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_Char.size();
+ m_Char.emplace(size, Variable<char>(name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name, std::make_pair(GetType<char>(), size));
+ return m_Char.at(size);
}
template <>
@@ -377,13 +390,13 @@ inline Variable<unsigned char> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_UChar.size();
- m_UChar.emplace(size,
- Variable<unsigned char>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name, std::make_pair(GetType<unsigned char>(), size));
- return m_UChar.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_UChar.size();
+ m_UChar.emplace(size,
+ Variable<unsigned char>(name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name, std::make_pair(GetType<unsigned char>(), size));
+ return m_UChar.at(size);
}
template <>
@@ -391,12 +404,12 @@ inline Variable<short> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_Short.size();
- m_Short.emplace(size, Variable<short>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name, std::make_pair(GetType<unsigned char>(), size));
- return m_Short.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_Short.size();
+ m_Short.emplace(size, Variable<short>(name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name, std::make_pair(GetType<unsigned char>(), size));
+ return m_Short.at(size);
}
template <>
@@ -404,13 +417,13 @@ inline Variable<unsigned short> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_UShort.size();
- m_UShort.emplace(size,
- Variable<unsigned short>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name, std::make_pair(GetType<unsigned short>(), size));
- return m_UShort.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_UShort.size();
+ m_UShort.emplace(
+ size, Variable<unsigned short>(name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name, std::make_pair(GetType<unsigned short>(), size));
+ return m_UShort.at(size);
}
template <>
@@ -418,12 +431,12 @@ inline Variable<int> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_Int.size();
- m_Int.emplace(size, Variable<int>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name, std::make_pair(GetType<int>(), size));
- return m_Int.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_Int.size();
+ m_Int.emplace(size, Variable<int>(name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name, std::make_pair(GetType<int>(), size));
+ return m_Int.at(size);
}
template <>
@@ -431,13 +444,13 @@ inline Variable<unsigned int> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_UInt.size();
- m_UInt.emplace(size,
- Variable<unsigned int>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name, std::make_pair(GetType<unsigned int>(), size));
- return m_UInt.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_UInt.size();
+ m_UInt.emplace(size,
+ Variable<unsigned int>(name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name, std::make_pair(GetType<unsigned int>(), size));
+ return m_UInt.at(size);
}
template <>
@@ -445,12 +458,12 @@ inline Variable<long int> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_LInt.size();
- m_LInt.emplace(size, Variable<long int>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name, std::make_pair(GetType<long int>(), size));
- return m_LInt.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_LInt.size();
+ m_LInt.emplace(size, Variable<long int>(name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name, std::make_pair(GetType<long int>(), size));
+ return m_LInt.at(size);
}
template <>
@@ -458,13 +471,14 @@ inline Variable<unsigned long int> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_LInt.size();
- m_ULInt.emplace(
- size, Variable<unsigned long int>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name, std::make_pair(GetType<unsigned long int>(), size));
- return m_ULInt.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_LInt.size();
+ m_ULInt.emplace(
+ size, Variable<unsigned long int>(name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name,
+ std::make_pair(GetType<unsigned long int>(), size));
+ return m_ULInt.at(size);
}
template <>
@@ -472,13 +486,13 @@ inline Variable<long long int> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_LLInt.size();
- m_LLInt.emplace(size,
- Variable<long long int>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name, std::make_pair(GetType<long long int>(), size));
- return m_LLInt.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_LLInt.size();
+ m_LLInt.emplace(size,
+ Variable<long long int>(name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name, std::make_pair(GetType<long long int>(), size));
+ return m_LLInt.at(size);
}
template <>
@@ -486,14 +500,14 @@ inline Variable<unsigned long long int> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_ULLInt.size();
- m_ULLInt.emplace(
- size, Variable<unsigned long long int>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name,
- std::make_pair(GetType<unsigned long long int>(), size));
- return m_ULLInt.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_ULLInt.size();
+ m_ULLInt.emplace(size, Variable<unsigned long long int>(
+ name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(
+ name, std::make_pair(GetType<unsigned long long int>(), size));
+ return m_ULLInt.at(size);
}
template <>
@@ -501,12 +515,12 @@ inline Variable<float> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_Float.size();
- m_Float.emplace(size, Variable<float>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name, std::make_pair(GetType<float>(), size));
- return m_Float.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_Float.size();
+ m_Float.emplace(size, Variable<float>(name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name, std::make_pair(GetType<float>(), size));
+ return m_Float.at(size);
}
template <>
@@ -514,12 +528,12 @@ inline Variable<double> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_Double.size();
- m_Double.emplace(size, Variable<double>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name, std::make_pair(GetType<double>(), size));
- return m_Double.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_Double.size();
+ m_Double.emplace(size, Variable<double>(name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name, std::make_pair(GetType<double>(), size));
+ return m_Double.at(size);
}
template <>
@@ -527,13 +541,13 @@ inline Variable<long double> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_LDouble.size();
- m_LDouble.emplace(size,
- Variable<long double>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name, std::make_pair(GetType<long double>(), size));
- return m_LDouble.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_LDouble.size();
+ m_LDouble.emplace(size,
+ Variable<long double>(name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name, std::make_pair(GetType<long double>(), size));
+ return m_LDouble.at(size);
}
template <>
@@ -541,14 +555,14 @@ inline Variable<std::complex<float>> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_CFloat.size();
- m_CFloat.emplace(
- size, Variable<std::complex<float>>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name,
- std::make_pair(GetType<std::complex<float>>(), size));
- return m_CFloat.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_CFloat.size();
+ m_CFloat.emplace(
+ size, Variable<std::complex<float>>(name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name,
+ std::make_pair(GetType<std::complex<float>>(), size));
+ return m_CFloat.at(size);
}
template <>
@@ -556,14 +570,14 @@ inline Variable<std::complex<double>> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_CDouble.size();
- m_CDouble.emplace(
- size, Variable<std::complex<double>>(name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(name,
- std::make_pair(GetType<std::complex<double>>(), size));
- return m_CDouble.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_CDouble.size();
+ m_CDouble.emplace(
+ size, Variable<std::complex<double>>(name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(name,
+ std::make_pair(GetType<std::complex<double>>(), size));
+ return m_CDouble.at(size);
}
template <>
@@ -571,110 +585,110 @@ inline Variable<std::complex<long double>> &
ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
- CheckVariableInput(name, dimensions);
- const unsigned int size = m_CLDouble.size();
- m_CLDouble.emplace(size, Variable<std::complex<long double>>(
- name, dimensions, globalDimensions,
- globalOffsets, m_DebugMode));
- m_Variables.emplace(
- name, std::make_pair(GetType<std::complex<long double>>(), size));
- return m_CLDouble.at(size);
+ CheckVariableInput(name, dimensions);
+ const unsigned int size = m_CLDouble.size();
+ m_CLDouble.emplace(size, Variable<std::complex<long double>>(
+ name, dimensions, globalDimensions,
+ globalOffsets, m_DebugMode));
+ m_Variables.emplace(
+ name, std::make_pair(GetType<std::complex<long double>>(), size));
+ return m_CLDouble.at(size);
}
// Get template specialization
template <> inline Variable<char> &ADIOS::GetVariable(const std::string &name)
{
- return m_Char.at(GetVariableIndex<char>(name));
+ return m_Char.at(GetVariableIndex<char>(name));
}
template <>
inline Variable<unsigned char> &ADIOS::GetVariable(const std::string &name)
{
- return m_UChar.at(GetVariableIndex<unsigned char>(name));
+ return m_UChar.at(GetVariableIndex<unsigned char>(name));
}
template <> inline Variable<short> &ADIOS::GetVariable(const std::string &name)
{
- return m_Short.at(GetVariableIndex<short>(name));
+ return m_Short.at(GetVariableIndex<short>(name));
}
template <>
inline Variable<unsigned short> &ADIOS::GetVariable(const std::string &name)
{
- return m_UShort.at(GetVariableIndex<unsigned short>(name));
+ return m_UShort.at(GetVariableIndex<unsigned short>(name));
}
template <> inline Variable<int> &ADIOS::GetVariable(const std::string &name)
{
- return m_Int.at(GetVariableIndex<int>(name));
+ return m_Int.at(GetVariableIndex<int>(name));
}
template <>
inline Variable<unsigned int> &ADIOS::GetVariable(const std::string &name)
{
- return m_UInt.at(GetVariableIndex<unsigned int>(name));
+ return m_UInt.at(GetVariableIndex<unsigned int>(name));
}
template <>
inline Variable<long int> &ADIOS::GetVariable(const std::string &name)
{
- return m_LInt.at(GetVariableIndex<unsigned int>(name));
+ return m_LInt.at(GetVariableIndex<unsigned int>(name));
}
template <>
inline Variable<unsigned long int> &ADIOS::GetVariable(const std::string &name)
{
- return m_ULInt.at(GetVariableIndex<unsigned long int>(name));
+ return m_ULInt.at(GetVariableIndex<unsigned long int>(name));
}
template <>
inline Variable<long long int> &ADIOS::GetVariable(const std::string &name)
{
- return m_LLInt.at(GetVariableIndex<long long int>(name));
+ return m_LLInt.at(GetVariableIndex<long long int>(name));
}
template <>
inline Variable<unsigned long long int> &
ADIOS::GetVariable(const std::string &name)
{
- return m_ULLInt.at(GetVariableIndex<unsigned long long int>(name));
+ return m_ULLInt.at(GetVariableIndex<unsigned long long int>(name));
}
template <> inline Variable<float> &ADIOS::GetVariable(const std::string &name)
{
- return m_Float.at(GetVariableIndex<float>(name));
+ return m_Float.at(GetVariableIndex<float>(name));
}
template <> inline Variable<double> &ADIOS::GetVariable(const std::string &name)
{
- return m_Double.at(GetVariableIndex<double>(name));
+ return m_Double.at(GetVariableIndex<double>(name));
}
template <>
inline Variable<long double> &ADIOS::GetVariable(const std::string &name)
{
- return m_LDouble.at(GetVariableIndex<long double>(name));
+ return m_LDouble.at(GetVariableIndex<long double>(name));
}
template <>
inline Variable<std::complex<float>> &
ADIOS::GetVariable(const std::string &name)
{
- return m_CFloat.at(GetVariableIndex<std::complex<float>>(name));
+ return m_CFloat.at(GetVariableIndex<std::complex<float>>(name));
}
template <>
inline Variable<std::complex<double>> &
ADIOS::GetVariable(const std::string &name)
{
- return m_CDouble.at(GetVariableIndex<std::complex<double>>(name));
+ return m_CDouble.at(GetVariableIndex<std::complex<double>>(name));
}
template <>
inline Variable<std::complex<long double>> &
ADIOS::GetVariable(const std::string &name)
{
- return m_CLDouble.at(GetVariableIndex<std::complex<long double>>(name));
+ return m_CLDouble.at(GetVariableIndex<std::complex<long double>>(name));
}
} // end namespace
diff --git a/include/ADIOSTypes.h b/include/ADIOSTypes.h
index 3949bbc36f98f935a5069b38ea95c567a99d00f5..a3e286d943cff87ecacae3dea7cfb58c636be47f 100644
--- a/include/ADIOSTypes.h
+++ b/include/ADIOSTypes.h
@@ -18,23 +18,23 @@ namespace adios
*/
enum
{
- VARYING_DIMENSION = -1, //!< VARYING_DIMENSION
- LOCAL_VALUE = 0, //!< LOCAL_VALUE
- GLOBAL_VALUE = 1 //!< GLOBAL_VALUE
+ VARYING_DIMENSION = -1, //!< VARYING_DIMENSION
+ LOCAL_VALUE = 0, //!< LOCAL_VALUE
+ GLOBAL_VALUE = 1 //!< GLOBAL_VALUE
};
enum class Verbose
{
- ERROR = 0,
- WARN = 1,
- INFO = 2,
- DEBUG = 3
+ ERROR = 0,
+ WARN = 1,
+ INFO = 2,
+ DEBUG = 3
};
enum class IOMode
{
- INDEPENDENT = 0,
- COLLECTIVE = 1
+ INDEPENDENT = 0,
+ COLLECTIVE = 1
};
} // end namespace
diff --git a/include/capsule/heap/STLVector.h b/include/capsule/heap/STLVector.h
index b548a64d640a3072d55b9d923174df62fc845eb7..35adb47188b1739a3c0fc114b16a009bbb67f65b 100644
--- a/include/capsule/heap/STLVector.h
+++ b/include/capsule/heap/STLVector.h
@@ -29,29 +29,30 @@ class STLVector : public Capsule
{
public:
- std::vector<char> m_Data; ///< data buffer allocated using the STL in heap
- /// memory, default size = 16 Mb
- std::vector<char> m_Metadata; ///< metadata buffer allocated using the STL in
- /// heap memory, default size = 100 Kb
-
- /**
- * Unique constructor
- * @param accessMode read, write or append
- * @param rankMPI MPI rank
- * @param debugMode true: extra checks, slower
- */
- STLVector(std::string accessMode, int rankMPI, bool debugMode = false);
-
- ~STLVector() = default;
-
- char *GetData();
- char *GetMetadata();
-
- std::size_t GetDataSize() const;
- std::size_t GetMetadataSize() const;
-
- void ResizeData(const std::size_t size);
- void ResizeMetadata(const std::size_t size);
+ std::vector<char> m_Data; ///< data buffer allocated using the STL in heap
+ /// memory, default size = 16 Mb
+ std::vector<char>
+ m_Metadata; ///< metadata buffer allocated using the STL in
+ /// heap memory, default size = 100 Kb
+
+ /**
+ * Unique constructor
+ * @param accessMode read, write or append
+ * @param rankMPI MPI rank
+ * @param debugMode true: extra checks, slower
+ */
+ STLVector(std::string accessMode, int rankMPI, bool debugMode = false);
+
+ ~STLVector() = default;
+
+ char *GetData();
+ char *GetMetadata();
+
+ std::size_t GetDataSize() const;
+ std::size_t GetMetadataSize() const;
+
+ void ResizeData(const std::size_t size);
+ void ResizeMetadata(const std::size_t size);
};
} // end namespace capsule
diff --git a/include/capsule/shmem/ShmSystemV.h b/include/capsule/shmem/ShmSystemV.h
index 4c7c5cab4ed15eb9420f0274e6a46daa4f452a2d..2e3a14c5b804736b5c2f8d4d5890bc49efde2eba 100644
--- a/include/capsule/shmem/ShmSystemV.h
+++ b/include/capsule/shmem/ShmSystemV.h
@@ -18,42 +18,44 @@ class ShmSystemV : public Capsule
{
public:
- /**
- * Create a Capsule in shared memory using System V shm API
- * @param accessMode
- * @param pathName used to create the key as a unique identifier
- * @param dataSize size of allocated memory segment for data
- * @param metadataSize size of allocated memory segment for metadata
- * @param debugMode true: extra checks, slower
- */
- ShmSystemV(std::string accessMode, int rankMPI, const std::string &pathName,
- size_t dataSize, size_t metadataSize, bool debugMode = false);
+ /**
+ * Create a Capsule in shared memory using System V shm API
+ * @param accessMode
+ * @param pathName used to create the key as a unique identifier
+ * @param dataSize size of allocated memory segment for data
+ * @param metadataSize size of allocated memory segment for metadata
+ * @param debugMode true: extra checks, slower
+ */
+ ShmSystemV(std::string accessMode, int rankMPI, const std::string &pathName,
+ size_t dataSize, size_t metadataSize, bool debugMode = false);
- ~ShmSystemV() = default;
+ ~ShmSystemV() = default;
- char *GetData(); ///< return the pointer to the raw data buffer
- char *GetMetadata(); ///< return the pointer to the raw metadata buffer
+ char *GetData(); ///< return the pointer to the raw data buffer
+ char *GetMetadata(); ///< return the pointer to the raw metadata buffer
- size_t GetDataSize() const; ///< get current data buffer size
- size_t GetMetadataSize() const; ///< get current metadata buffer size
+ size_t GetDataSize() const; ///< get current data buffer size
+ size_t GetMetadataSize() const; ///< get current metadata buffer size
private:
- char *m_Data =
- nullptr; ///< reference to a shared memory data buffer created with shmget
- const size_t m_DataSize; ///< size of the allocated shared memory segment
- key_t m_DataKey; ///< key associated with the data buffer, created with ftok
- int m_DataShmID; ///< data shared memory buffer id
-
- char *m_Metadata = nullptr; ///< reference to a shared memory metadata buffer
- /// created with shmget
- const size_t m_MetadataSize; ///< size of the allocated shared memory segment
- key_t m_MetadataKey; ///< key associated with the metadata buffer, created
- /// with ftok
- int m_MetadataShmID; ///< metadata shared memory buffer id
-
- void CheckShm() const; ///< checks if all shared memory allocations are
- /// correct, throws std::bad_alloc, called from
- /// constructor if debug mode is true
+ char *m_Data = nullptr; ///< reference to a shared memory data buffer
+ /// created with shmget
+ const size_t m_DataSize; ///< size of the allocated shared memory segment
+ key_t m_DataKey; ///< key associated with the data buffer, created with ftok
+ int m_DataShmID; ///< data shared memory buffer id
+
+ char *m_Metadata =
+ nullptr; ///< reference to a shared memory metadata buffer
+ /// created with shmget
+ const size_t
+ m_MetadataSize; ///< size of the allocated shared memory segment
+ key_t m_MetadataKey; ///< key associated with the metadata buffer, created
+ /// with ftok
+ int m_MetadataShmID; ///< metadata shared memory buffer id
+
+ void CheckShm() const; ///< checks if all shared memory allocations are
+ /// correct, throws std::bad_alloc, called from
+ /// constructor if debug mode is true
};
} // end namespace adios
diff --git a/include/core/Attribute.h b/include/core/Attribute.h
index dae2644b77d155d16c52c64aff5cf90f6c301f7f..d1384d228ff5019a9ad6fcadf7ee76ff736e3595 100644
--- a/include/core/Attribute.h
+++ b/include/core/Attribute.h
@@ -23,8 +23,8 @@ namespace adios
*/
struct Attribute
{
- const char TypeID; ///< '0': string, '1': numeric
- const std::string Value; ///< information about the attribute
+ const char TypeID; ///< '0': string, '1': numeric
+ const std::string Value; ///< information about the attribute
};
} // end namespace
diff --git a/include/core/Capsule.h b/include/core/Capsule.h
index 815c8542363f614be1c61e4023b7a9d8ffa779af..8993025f50dd2cc513ba6b868b42cde3ec06f490 100644
--- a/include/core/Capsule.h
+++ b/include/core/Capsule.h
@@ -27,42 +27,42 @@ class Capsule
{
public:
- const std::string m_Type; ///< buffer type
- const std::string m_AccessMode; ///< 'w': write, 'r': read, 'a': append
+ const std::string m_Type; ///< buffer type
+ const std::string m_AccessMode; ///< 'w': write, 'r': read, 'a': append
- size_t m_DataPosition = 0; ///< position in current data buffer (not
- /// included data flushed to transports)
- size_t m_DataAbsolutePosition =
- 0; ///< includes the data flushed to transports
+ size_t m_DataPosition = 0; ///< position in current data buffer (not
+ /// included data flushed to transports)
+ size_t m_DataAbsolutePosition =
+ 0; ///< includes the data flushed to transports
- size_t m_MetadataPosition = 0; ///< position in metadata buffer
+ size_t m_MetadataPosition = 0; ///< position in metadata buffer
- /**
- * Base class constructor providing type from derived class and accessMode
- * @param type derived class type
- * @param accessMode 'w':write, 'r':read, 'a':append
- * @param rankMPI current MPI rank
- * @param debugMode
- */
- Capsule(std::string type, std::string accessMode, int rankMPI,
- bool debugMode);
+ /**
+ * Base class constructor providing type from derived class and accessMode
+ * @param type derived class type
+ * @param accessMode 'w':write, 'r':read, 'a':append
+ * @param rankMPI current MPI rank
+ * @param debugMode
+ */
+ Capsule(std::string type, std::string accessMode, int rankMPI,
+ bool debugMode);
- virtual ~Capsule() = default;
+ virtual ~Capsule() = default;
- virtual char *GetData() = 0; ///< return the pointer to the raw data buffer
- virtual char *
- GetMetadata() = 0; ///< return the pointer to the raw metadata buffer
+ virtual char *GetData() = 0; ///< return the pointer to the raw data buffer
+ virtual char *
+ GetMetadata() = 0; ///< return the pointer to the raw metadata buffer
- virtual size_t GetDataSize() const = 0; ///< get current data buffer size
- virtual size_t
- GetMetadataSize() const = 0; ///< get current metadata buffer size
+ virtual size_t GetDataSize() const = 0; ///< get current data buffer size
+ virtual size_t
+ GetMetadataSize() const = 0; ///< get current metadata buffer size
- virtual void ResizeData(size_t size); ///< resize data buffer
- virtual void ResizeMetadata(size_t size); ///< resize metadata buffer
+ virtual void ResizeData(size_t size); ///< resize data buffer
+ virtual void ResizeMetadata(size_t size); ///< resize metadata buffer
protected:
- const int m_RankMPI = 0; ///< current MPI rank
- const bool m_DebugMode = false; ///< true: extra checks
+ const int m_RankMPI = 0; ///< current MPI rank
+ const bool m_DebugMode = false; ///< true: extra checks
};
} // end namespace
diff --git a/include/core/Engine.h b/include/core/Engine.h
index d536873c72dd08bbcd7e9307713159a73f956d4d..a206682e8f4961af7d4cc663e4efd1f2782bf23e 100644
--- a/include/core/Engine.h
+++ b/include/core/Engine.h
@@ -38,10 +38,10 @@ namespace adios
typedef enum { NONBLOCKINGREAD = 0, BLOCKINGREAD = 1 } PerformReadMode;
typedef enum {
- APPEND = 0,
- UPDATE = 1, // writer advance modes
- NEXT_AVAILABLE = 2,
- LATEST_AVAILABLE = 3, // reader advance modes
+ APPEND = 0,
+ UPDATE = 1, // writer advance modes
+ NEXT_AVAILABLE = 2,
+ LATEST_AVAILABLE = 3, // reader advance modes
} AdvanceMode;
/**
@@ -52,450 +52,465 @@ class Engine
{
public:
- MPI_Comm m_MPIComm = MPI_COMM_SELF;
-
- const std::string m_EngineType; ///< from derived class
- const std::string m_Name; ///< name used for this engine
- const std::string
- m_AccessMode; ///< accessMode for buffers used by this engine
- const Method &m_Method; ///< associated method containing engine metadata
-
- int m_RankMPI = 0; ///< current MPI rank process
- int m_SizeMPI = 1; ///< current MPI processes size
-
- const std::string m_HostLanguage = "C++"; ///< default host language
-
- /**
- * Unique constructor
- * @param adios
- * @param engineType
- * @param name
- * @param accessMode
- * @param mpiComm
- * @param method
- * @param debugMode
- * @param nthreads
- * @param endMessage
- */
- Engine(ADIOS &adios, std::string engineType, std::string name,
- std::string accessMode, MPI_Comm mpiComm, const Method &method,
- bool debugMode, unsigned int nthreads, std::string endMessage);
-
- virtual ~Engine() = default;
-
- /** @brief Let ADIOS allocate memory for a variable, which can be used by the
- * user.
- *
- * To decrease the cost of copying memory, a user may let ADIOS allocate the
- * memory for a user-variable,
- * according to the definition of an ADIOS-variable. The memory will be part
- * of the ADIOS buffer used
- * by the engine and it lives until the engine (file, stream) is closed.
- * A variable that has been allocated this way (cannot have its local
- * dimensions changed, and AdvanceAsync() should be
- * used instead of Advance() and the user-variable must not be modified by the
- * application until the notification arrives.
- * This is required so that any reader can access the written data before the
- * application overwrites it.
- * @param var Variable with defined local dimensions and offsets in global
- * space
- * @param fillValue Fill the allocated array with this value
- * @return A constant pointer to the non-constant allocated array. User should
- * not deallocate this pointer.
- */
- template <class T>
- inline T *const AllocateVariable(Variable<T> &var, T fillValue = 0)
- {
- throw std::invalid_argument("ERROR: type not supported for variable " +
- var->name + " in call to GetVariable\n");
- }
-
- /**
- * Needed for DataMan Engine
- * @param callback function passed from the user
- */
- virtual void SetCallBack(std::function<void(const void *, std::string,
- std::string, std::string, Dims)>
- callback);
-
- /**
- * Write function that adds static checking on the variable to be passed by
- * values
- * It then calls its corresponding derived class virtual function
- * This version uses m_Group to look for the variableName.
- * @param variable name of variable to the written
- * @param values pointer passed from the application
- */
- template <class T> void Write(Variable<T> &variable, const T *values)
- {
- Write(variable, values);
- }
-
- /**
- * String version
- * @param variableName
- * @param values
- */
- template <class T>
- void Write(const std::string &variableName, const T *values)
- {
- Write(variableName, values);
- }
-
- /**
- * Single value version
- * @param variable
- * @param values
- */
- template <class T> void Write(Variable<T> &variable, const T values)
- {
- const T val = values;
- Write(variable, &val);
- }
-
- /**
- * Single value version using string as variable handlers, allows rvalues to
- * be passed
- * @param variableName
- * @param values
- */
- template <class T> void Write(const std::string &variableName, const T values)
- {
- const T val = values;
- Write(variableName, &val);
- }
-
- virtual void Write(Variable<char> &variable, const char *values);
- virtual void Write(Variable<unsigned char> &variable,
- const unsigned char *values);
- virtual void Write(Variable<short> &variable, const short *values);
- virtual void Write(Variable<unsigned short> &variable,
- const unsigned short *values);
- virtual void Write(Variable<int> &variable, const int *values);
- virtual void Write(Variable<unsigned int> &variable,
- const unsigned int *values);
- virtual void Write(Variable<long int> &variable, const long int *values);
- virtual void Write(Variable<unsigned long int> &variable,
- const unsigned long int *values);
- virtual void Write(Variable<long long int> &variable,
- const long long int *values);
- virtual void Write(Variable<unsigned long long int> &variable,
- const unsigned long long int *values);
- virtual void Write(Variable<float> &variable, const float *values);
- virtual void Write(Variable<double> &variable, const double *values);
- virtual void Write(Variable<long double> &variable,
- const long double *values);
- virtual void Write(Variable<std::complex<float>> &variable,
- const std::complex<float> *values);
- virtual void Write(Variable<std::complex<double>> &variable,
- const std::complex<double> *values);
- virtual void Write(Variable<std::complex<long double>> &variable,
- const std::complex<long double> *values);
- virtual void Write(VariableCompound &variable, const void *values);
-
- /**
- * @brief Write functions can be overridden by derived classes. Base class
- * behavior is to:
- * 1) Write to Variable values (m_Values) using the pointer to default group
- * *m_Group set with SetDefaultGroup function
- * 2) Transform the data
- * 3) Write to all capsules -> data and metadata
- * @param variableName
- * @param values coming from user app
- */
- virtual void Write(const std::string &variableName, const char *values);
- virtual void Write(const std::string &variableName,
- const unsigned char *values);
- virtual void Write(const std::string &variableName, const short *values);
- virtual void Write(const std::string &variableName,
- const unsigned short *values);
- virtual void Write(const std::string &variableName, const int *values);
- virtual void Write(const std::string &variableName,
- const unsigned int *values);
- virtual void Write(const std::string &variableName, const long int *values);
- virtual void Write(const std::string &variableName,
- const unsigned long int *values);
- virtual void Write(const std::string &variableName,
- const long long int *values);
- virtual void Write(const std::string &variableName,
- const unsigned long long int *values);
- virtual void Write(const std::string &variableName, const float *values);
- virtual void Write(const std::string &variableName, const double *values);
- virtual void Write(const std::string &variableName,
- const long double *values);
- virtual void Write(const std::string &variableName,
- const std::complex<float> *values);
- virtual void Write(const std::string &variableName,
- const std::complex<double> *values);
- virtual void Write(const std::string &variableName,
- const std::complex<long double> *values);
- virtual void Write(const std::string &variableName, const void *values);
-
- /**
- * Read function that adds static checking on the variable to be passed by
- * values
- * It then calls its corresponding derived class virtual function
- * This version uses m_Group to look for the variableName.
- * @param variable name of variable to the written
- * @param values pointer passed from the application, nullptr not allowed,
- * must use Read(variable) instead intentionally
- */
- template <class T> void Read(Variable<T> &variable, const T *values)
- {
- Read(variable, values);
- }
-
- /**
- * String version
- * @param variableName
- * @param values
- */
- template <class T> void Read(const std::string variableName, const T *values)
- {
- Read(variableName, values);
- }
-
- /**
- * Single value version
- * @param variable
- * @param values
- */
- template <class T> void Read(Variable<T> &variable, const T &values)
- {
- Read(variable, &values);
- }
-
- /**
- * Single value version using string as variable handlers
- * @param variableName
- * @param values
- */
- template <class T> void Read(const std::string variableName, const T &values)
- {
- Read(variableName, &values);
- }
-
- /**
- * Unallocated version, ADIOS will allocate space for incoming data
- * @param variable
- */
- template <class T> void Read(Variable<T> &variable)
- {
- Read(variable, nullptr);
- }
-
- /**
- * Unallocated version, ADIOS will allocate space for incoming data
- * @param variableName
- */
- template <class T> void Read(const std::string variableName)
- {
- Read(variableName, nullptr);
- }
-
- virtual void Read(Variable<double> &variable, const double *values);
-
- /**
- * Read function that adds static checking on the variable to be passed by
- * values
- * It then calls its corresponding derived class virtual function
- * This version uses m_Group to look for the variableName.
- * @param variable name of variable to the written
- * @param values pointer passed from the application
- */
- template <class T> void ScheduleRead(Variable<T> &variable, const T *values)
- {
- ScheduleRead(variable, values);
- }
-
- /**
- * String version
- * @param variableName
- * @param values
- */
- template <class T>
- void ScheduleRead(const std::string variableName, const T *values)
- {
- ScheduleRead(variableName, values);
- }
-
- /**
- * Single value version
- * @param variable
- * @param values
- */
- template <class T> void ScheduleRead(Variable<T> &variable, const T &values)
- {
- ScheduleRead(variable, &values);
- }
-
- /**
- * Single value version using string as variable handlers
- * @param variableName
- * @param values
- */
- template <class T>
- void ScheduleRead(const std::string variableName, const T &values)
- {
- ScheduleRead(variableName, &values);
- }
-
- /**
- * Unallocated version, ADIOS will allocate space for incoming data
- * @param variableName
- */
- void ScheduleRead(const std::string variableName)
- {
- ScheduleRead(variableName, nullptr);
- }
-
- /**
- * Unallocated unspecified version, ADIOS will receive any variable and will
- * allocate space for incoming data
- */
- void ScheduleRead() { ScheduleRead(nullptr, nullptr); }
-
- virtual void ScheduleRead(Variable<double> &variable, const double *values);
-
- /**
- * Perform all scheduled reads, either blocking until all reads completed, or
- * return immediately.
- * @param mode Blocking or non-blocking modes
- */
- void PerformReads(PerformReadMode mode);
-
- /**
- * Reader application indicates that no more data will be read from the
- * current stream before advancing.
- * This is necessary to allow writers to advance as soon as possible.
- */
- virtual void Release();
-
- /**
- * Indicates that a new step is going to be written as new variables come in.
- */
- virtual void Advance(float timeout_sec = 0.0);
-
- /**
- * Indicates that a new step is going to be written as new variables come in.
- * @param mode Advance mode, there are different options for writers and
- * readers
- */
- virtual void Advance(AdvanceMode mode, float timeout_sec = 0.0);
-
- /** @brief Advance asynchronously and get a callback when readers release
- * access to the buffered step.
- *
- * User variables that were allocated through AllocateVariable()
- * must not be modified until advance is completed.
- * @param mode Advance mode, there are different options for writers and
- * readers
- * @param callback Will be called when advance is completed.
- */
- virtual void
- AdvanceAsync(AdvanceMode mode,
- std::function<void(std::shared_ptr<adios::Engine>)> callback);
-
- // Read API
- /**
- * Inquires and (optionally) allocates and copies the contents of a variable
- * If success: it returns a pointer to the internal stored variable object in
- * ADIOS class.
- * If failure: it returns nullptr
- * @param name variable name to look for
- * @param readIn if true: reads the full variable and payload, allocating
- * values in memory, if false: internal payload is nullptr
- * @return success: it returns a pointer to the internal stored variable
- * object in ADIOS class, failure: nullptr
- */
- virtual Variable<void> *InquireVariable(const std::string name,
- const bool readIn = true);
- virtual Variable<char> *InquireVariableChar(const std::string name,
- const bool readIn = true);
- virtual Variable<unsigned char> *
- InquireVariableUChar(const std::string name, const bool readIn = true);
- virtual Variable<short> *InquireVariableShort(const std::string name,
- const bool readIn = true);
- virtual Variable<unsigned short> *
- InquireVariableUShort(const std::string name, const bool readIn = true);
- virtual Variable<int> *InquireVariableInt(const std::string name,
+ MPI_Comm m_MPIComm = MPI_COMM_SELF;
+
+ const std::string m_EngineType; ///< from derived class
+ const std::string m_Name; ///< name used for this engine
+ const std::string
+ m_AccessMode; ///< accessMode for buffers used by this engine
+ const Method &m_Method; ///< associated method containing engine metadata
+
+ int m_RankMPI = 0; ///< current MPI rank process
+ int m_SizeMPI = 1; ///< current MPI processes size
+
+ const std::string m_HostLanguage = "C++"; ///< default host language
+
+ /**
+ * Unique constructor
+ * @param adios
+ * @param engineType
+ * @param name
+ * @param accessMode
+ * @param mpiComm
+ * @param method
+ * @param debugMode
+ * @param nthreads
+ * @param endMessage
+ */
+ Engine(ADIOS &adios, std::string engineType, std::string name,
+ std::string accessMode, MPI_Comm mpiComm, const Method &method,
+ bool debugMode, unsigned int nthreads, std::string endMessage);
+
+ virtual ~Engine() = default;
+
+ /** @brief Let ADIOS allocate memory for a variable, which can be used by
+ * the
+ * user.
+ *
+ * To decrease the cost of copying memory, a user may let ADIOS allocate the
+ * memory for a user-variable,
+ * according to the definition of an ADIOS-variable. The memory will be part
+ * of the ADIOS buffer used
+ * by the engine and it lives until the engine (file, stream) is closed.
+ * A variable that has been allocated this way (cannot have its local
+ * dimensions changed, and AdvanceAsync() should be
+ * used instead of Advance() and the user-variable must not be modified by
+ * the
+ * application until the notification arrives.
+ * This is required so that any reader can access the written data before
+ * the
+ * application overwrites it.
+ * @param var Variable with defined local dimensions and offsets in global
+ * space
+ * @param fillValue Fill the allocated array with this value
+ * @return A constant pointer to the non-constant allocated array. User
+ * should
+ * not deallocate this pointer.
+ */
+ template <class T>
+ inline T *const AllocateVariable(Variable<T> &var, T fillValue = 0)
+ {
+ throw std::invalid_argument("ERROR: type not supported for variable " +
+ var->name + " in call to GetVariable\n");
+ }
+
+ /**
+ * Needed for DataMan Engine
+ * @param callback function passed from the user
+ */
+ virtual void SetCallBack(std::function<void(const void *, std::string,
+ std::string, std::string, Dims)>
+ callback);
+
+ /**
+ * Write function that adds static checking on the variable to be passed by
+ * values
+ * It then calls its corresponding derived class virtual function
+ * This version uses m_Group to look for the variableName.
+ * @param variable name of variable to the written
+ * @param values pointer passed from the application
+ */
+ template <class T> void Write(Variable<T> &variable, const T *values)
+ {
+ Write(variable, values);
+ }
+
+ /**
+ * String version
+ * @param variableName
+ * @param values
+ */
+ template <class T>
+ void Write(const std::string &variableName, const T *values)
+ {
+ Write(variableName, values);
+ }
+
+ /**
+ * Single value version
+ * @param variable
+ * @param values
+ */
+ template <class T> void Write(Variable<T> &variable, const T values)
+ {
+ const T val = values;
+ Write(variable, &val);
+ }
+
+ /**
+ * Single value version using string as variable handlers, allows rvalues to
+ * be passed
+ * @param variableName
+ * @param values
+ */
+ template <class T>
+ void Write(const std::string &variableName, const T values)
+ {
+ const T val = values;
+ Write(variableName, &val);
+ }
+
+ virtual void Write(Variable<char> &variable, const char *values);
+ virtual void Write(Variable<unsigned char> &variable,
+ const unsigned char *values);
+ virtual void Write(Variable<short> &variable, const short *values);
+ virtual void Write(Variable<unsigned short> &variable,
+ const unsigned short *values);
+ virtual void Write(Variable<int> &variable, const int *values);
+ virtual void Write(Variable<unsigned int> &variable,
+ const unsigned int *values);
+ virtual void Write(Variable<long int> &variable, const long int *values);
+ virtual void Write(Variable<unsigned long int> &variable,
+ const unsigned long int *values);
+ virtual void Write(Variable<long long int> &variable,
+ const long long int *values);
+ virtual void Write(Variable<unsigned long long int> &variable,
+ const unsigned long long int *values);
+ virtual void Write(Variable<float> &variable, const float *values);
+ virtual void Write(Variable<double> &variable, const double *values);
+ virtual void Write(Variable<long double> &variable,
+ const long double *values);
+ virtual void Write(Variable<std::complex<float>> &variable,
+ const std::complex<float> *values);
+ virtual void Write(Variable<std::complex<double>> &variable,
+ const std::complex<double> *values);
+ virtual void Write(Variable<std::complex<long double>> &variable,
+ const std::complex<long double> *values);
+ virtual void Write(VariableCompound &variable, const void *values);
+
+ /**
+ * @brief Write functions can be overridden by derived classes. Base class
+ * behavior is to:
+ * 1) Write to Variable values (m_Values) using the pointer to default group
+ * *m_Group set with SetDefaultGroup function
+ * 2) Transform the data
+ * 3) Write to all capsules -> data and metadata
+ * @param variableName
+ * @param values coming from user app
+ */
+ virtual void Write(const std::string &variableName, const char *values);
+ virtual void Write(const std::string &variableName,
+ const unsigned char *values);
+ virtual void Write(const std::string &variableName, const short *values);
+ virtual void Write(const std::string &variableName,
+ const unsigned short *values);
+ virtual void Write(const std::string &variableName, const int *values);
+ virtual void Write(const std::string &variableName,
+ const unsigned int *values);
+ virtual void Write(const std::string &variableName, const long int *values);
+ virtual void Write(const std::string &variableName,
+ const unsigned long int *values);
+ virtual void Write(const std::string &variableName,
+ const long long int *values);
+ virtual void Write(const std::string &variableName,
+ const unsigned long long int *values);
+ virtual void Write(const std::string &variableName, const float *values);
+ virtual void Write(const std::string &variableName, const double *values);
+ virtual void Write(const std::string &variableName,
+ const long double *values);
+ virtual void Write(const std::string &variableName,
+ const std::complex<float> *values);
+ virtual void Write(const std::string &variableName,
+ const std::complex<double> *values);
+ virtual void Write(const std::string &variableName,
+ const std::complex<long double> *values);
+ virtual void Write(const std::string &variableName, const void *values);
+
+ /**
+ * Read function that adds static checking on the variable to be passed by
+ * values
+ * It then calls its corresponding derived class virtual function
+ * This version uses m_Group to look for the variableName.
+ * @param variable name of variable to the written
+ * @param values pointer passed from the application, nullptr not allowed,
+ * must use Read(variable) instead intentionally
+ */
+ template <class T> void Read(Variable<T> &variable, const T *values)
+ {
+ Read(variable, values);
+ }
+
+ /**
+ * String version
+ * @param variableName
+ * @param values
+ */
+ template <class T>
+ void Read(const std::string variableName, const T *values)
+ {
+ Read(variableName, values);
+ }
+
+ /**
+ * Single value version
+ * @param variable
+ * @param values
+ */
+ template <class T> void Read(Variable<T> &variable, const T &values)
+ {
+ Read(variable, &values);
+ }
+
+ /**
+ * Single value version using string as variable handlers
+ * @param variableName
+ * @param values
+ */
+ template <class T>
+ void Read(const std::string variableName, const T &values)
+ {
+ Read(variableName, &values);
+ }
+
+ /**
+ * Unallocated version, ADIOS will allocate space for incoming data
+ * @param variable
+ */
+ template <class T> void Read(Variable<T> &variable)
+ {
+ Read(variable, nullptr);
+ }
+
+ /**
+ * Unallocated version, ADIOS will allocate space for incoming data
+ * @param variableName
+ */
+ template <class T> void Read(const std::string variableName)
+ {
+ Read(variableName, nullptr);
+ }
+
+ virtual void Read(Variable<double> &variable, const double *values);
+
+ /**
+ * Read function that adds static checking on the variable to be passed by
+ * values
+ * It then calls its corresponding derived class virtual function
+ * This version uses m_Group to look for the variableName.
+ * @param variable name of variable to the written
+ * @param values pointer passed from the application
+ */
+ template <class T> void ScheduleRead(Variable<T> &variable, const T *values)
+ {
+ ScheduleRead(variable, values);
+ }
+
+ /**
+ * String version
+ * @param variableName
+ * @param values
+ */
+ template <class T>
+ void ScheduleRead(const std::string variableName, const T *values)
+ {
+ ScheduleRead(variableName, values);
+ }
+
+ /**
+ * Single value version
+ * @param variable
+ * @param values
+ */
+ template <class T> void ScheduleRead(Variable<T> &variable, const T &values)
+ {
+ ScheduleRead(variable, &values);
+ }
+
+ /**
+ * Single value version using string as variable handlers
+ * @param variableName
+ * @param values
+ */
+ template <class T>
+ void ScheduleRead(const std::string variableName, const T &values)
+ {
+ ScheduleRead(variableName, &values);
+ }
+
+ /**
+ * Unallocated version, ADIOS will allocate space for incoming data
+ * @param variableName
+ */
+ void ScheduleRead(const std::string variableName)
+ {
+ ScheduleRead(variableName, nullptr);
+ }
+
+ /**
+ * Unallocated unspecified version, ADIOS will receive any variable and will
+ * allocate space for incoming data
+ */
+ void ScheduleRead() { ScheduleRead(nullptr, nullptr); }
+
+ virtual void ScheduleRead(Variable<double> &variable, const double *values);
+
+ /**
+ * Perform all scheduled reads, either blocking until all reads completed,
+ * or
+ * return immediately.
+ * @param mode Blocking or non-blocking modes
+ */
+ void PerformReads(PerformReadMode mode);
+
+ /**
+ * Reader application indicates that no more data will be read from the
+ * current stream before advancing.
+ * This is necessary to allow writers to advance as soon as possible.
+ */
+ virtual void Release();
+
+ /**
+ * Indicates that a new step is going to be written as new variables come
+ * in.
+ */
+ virtual void Advance(float timeout_sec = 0.0);
+
+ /**
+ * Indicates that a new step is going to be written as new variables come
+ * in.
+ * @param mode Advance mode, there are different options for writers and
+ * readers
+ */
+ virtual void Advance(AdvanceMode mode, float timeout_sec = 0.0);
+
+ /** @brief Advance asynchronously and get a callback when readers release
+ * access to the buffered step.
+ *
+ * User variables that were allocated through AllocateVariable()
+ * must not be modified until advance is completed.
+ * @param mode Advance mode, there are different options for writers and
+ * readers
+ * @param callback Will be called when advance is completed.
+ */
+ virtual void
+ AdvanceAsync(AdvanceMode mode,
+ std::function<void(std::shared_ptr<adios::Engine>)> callback);
+
+ // Read API
+ /**
+ * Inquires and (optionally) allocates and copies the contents of a variable
+ * If success: it returns a pointer to the internal stored variable object
+ * in
+ * ADIOS class.
+ * If failure: it returns nullptr
+ * @param name variable name to look for
+ * @param readIn if true: reads the full variable and payload, allocating
+ * values in memory, if false: internal payload is nullptr
+ * @return success: it returns a pointer to the internal stored variable
+ * object in ADIOS class, failure: nullptr
+ */
+ virtual Variable<void> *InquireVariable(const std::string name,
const bool readIn = true);
- virtual Variable<unsigned int> *InquireVariableUInt(const std::string name,
- const bool readIn = true);
- virtual Variable<long int> *InquireVariableLInt(const std::string name,
- const bool readIn = true);
- virtual Variable<unsigned long int> *
- InquireVariableULInt(const std::string name, const bool readIn = true);
- virtual Variable<long long int> *
- InquireVariableLLInt(const std::string name, const bool readIn = true);
- virtual Variable<unsigned long long int> *
- InquireVariableULLInt(const std::string name, const bool readIn = true);
- virtual Variable<float> *InquireVariableFloat(const std::string name,
+ virtual Variable<char> *InquireVariableChar(const std::string name,
const bool readIn = true);
- virtual Variable<double> *InquireVariableDouble(const std::string name,
+ virtual Variable<unsigned char> *
+ InquireVariableUChar(const std::string name, const bool readIn = true);
+ virtual Variable<short> *InquireVariableShort(const std::string name,
const bool readIn = true);
- virtual Variable<long double> *
- InquireVariableLDouble(const std::string name, const bool readIn = true);
- virtual Variable<std::complex<float>> *
- InquireVariableCFloat(const std::string name, const bool readIn = true);
- virtual Variable<std::complex<double>> *
- InquireVariableCDouble(const std::string name, const bool readIn = true);
- virtual Variable<std::complex<long double>> *
- InquireVariableCLDouble(const std::string name, const bool readIn = true);
- virtual VariableCompound *InquireVariableCompound(const std::string name,
+ virtual Variable<unsigned short> *
+ InquireVariableUShort(const std::string name, const bool readIn = true);
+ virtual Variable<int> *InquireVariableInt(const std::string name,
+ const bool readIn = true);
+ virtual Variable<unsigned int> *
+ InquireVariableUInt(const std::string name, const bool readIn = true);
+ virtual Variable<long int> *InquireVariableLInt(const std::string name,
+ const bool readIn = true);
+ virtual Variable<unsigned long int> *
+ InquireVariableULInt(const std::string name, const bool readIn = true);
+ virtual Variable<long long int> *
+ InquireVariableLLInt(const std::string name, const bool readIn = true);
+ virtual Variable<unsigned long long int> *
+ InquireVariableULLInt(const std::string name, const bool readIn = true);
+ virtual Variable<float> *InquireVariableFloat(const std::string name,
+ const bool readIn = true);
+ virtual Variable<double> *InquireVariableDouble(const std::string name,
const bool readIn = true);
+ virtual Variable<long double> *
+ InquireVariableLDouble(const std::string name, const bool readIn = true);
+ virtual Variable<std::complex<float>> *
+ InquireVariableCFloat(const std::string name, const bool readIn = true);
+ virtual Variable<std::complex<double>> *
+ InquireVariableCDouble(const std::string name, const bool readIn = true);
+ virtual Variable<std::complex<long double>> *
+ InquireVariableCLDouble(const std::string name, const bool readIn = true);
+ virtual VariableCompound *InquireVariableCompound(const std::string name,
+ const bool readIn = true);
- /** Return the names of all variables present in a stream/file opened for
- * reading
- *
- * @return a vector of strings
- */
- std::vector<std::string> VariableNames();
+ /** Return the names of all variables present in a stream/file opened for
+ * reading
+ *
+ * @return a vector of strings
+ */
+ std::vector<std::string> VariableNames();
- virtual void
- Close(const int transportIndex =
- -1) = 0; ///< Closes a particular transport, or all if -1
+ virtual void
+ Close(const int transportIndex =
+ -1) = 0; ///< Closes a particular transport, or all if -1
protected:
- ADIOS
- &m_ADIOS; ///< reference to ADIOS object that creates this Engine at Open
- std::vector<std::shared_ptr<Transport>> m_Transports; ///< transports managed
- const bool m_DebugMode =
- false; ///< true: additional checks, false: by-pass checks
- unsigned int m_nThreads = 0;
- const std::string m_EndMessage; ///< added to exceptions to improve debugging
- std::set<std::string> m_WrittenVariables; ///< contains the names of the
- /// variables that are being written
-
- virtual void
- Init(); ///< Initialize m_Capsules and m_Transports, called from constructor
- virtual void InitParameters(); ///< Initialize parameters from Method, called
- /// from Initi in constructor
- virtual void InitTransports(); ///< Initialize transports from Method, called
- /// from Init in constructor
-
- /**
- * Used to verify parameters in m_Method containers
- * @param itParam iterator to a certain parameter
- * @param parameters map of parameters, from m_Method
- * @param parameterName used if exception is thrown to provide debugging
- * information
- * @param hint used if exception is thrown to provide debugging information
- */
- void CheckParameter(
- const std::map<std::string, std::string>::const_iterator itParam,
- const std::map<std::string, std::string> ¶meters,
- const std::string parameterName, const std::string hint) const;
-
- bool TransportNamesUniqueness() const; ///< checks if transport names are
- /// unique among the same types (file
- /// I/O)
-
- /**
- * Throws an exception in debug mode if transport index is out of range.
- * @param transportIndex must be in the range [ -1 , m_Transports.size()-1 ]
- */
- void CheckTransportIndex(const int transportIndex);
+ ADIOS
+ &m_ADIOS; ///< reference to ADIOS object that creates this Engine at Open
+ std::vector<std::shared_ptr<Transport>>
+ m_Transports; ///< transports managed
+ const bool m_DebugMode =
+ false; ///< true: additional checks, false: by-pass checks
+ unsigned int m_nThreads = 0;
+ const std::string
+ m_EndMessage; ///< added to exceptions to improve debugging
+ std::set<std::string> m_WrittenVariables; ///< contains the names of the
+ /// variables that are being written
+
+ virtual void
+ Init(); ///< Initialize m_Capsules and m_Transports, called from constructor
+ virtual void
+ InitParameters(); ///< Initialize parameters from Method, called
+ /// from Initi in constructor
+ virtual void
+ InitTransports(); ///< Initialize transports from Method, called
+ /// from Init in constructor
+
+ /**
+ * Used to verify parameters in m_Method containers
+ * @param itParam iterator to a certain parameter
+ * @param parameters map of parameters, from m_Method
+ * @param parameterName used if exception is thrown to provide debugging
+ * information
+ * @param hint used if exception is thrown to provide debugging information
+ */
+ void CheckParameter(
+ const std::map<std::string, std::string>::const_iterator itParam,
+ const std::map<std::string, std::string> ¶meters,
+ const std::string parameterName, const std::string hint) const;
+
+ bool TransportNamesUniqueness() const; ///< checks if transport names are
+ /// unique among the same types (file
+ /// I/O)
+
+ /**
+ * Throws an exception in debug mode if transport index is out of range.
+ * @param transportIndex must be in the range [ -1 , m_Transports.size()-1 ]
+ */
+ void CheckTransportIndex(const int transportIndex);
};
} // end namespace
diff --git a/include/core/Method.h b/include/core/Method.h
index f213022eb7ee26dab41c5ac9bad4e548dd77a4f0..0576703b6999fed3eea947642f614297c9d8771c 100644
--- a/include/core/Method.h
+++ b/include/core/Method.h
@@ -24,15 +24,15 @@ namespace adios
{
typedef enum {
- GLOBAL_READERS = 2,
- ROUNDROBIN_READERS = 3,
- FIFO_READERS = 4,
- OPEN_ALL_STEPS = 5
+ GLOBAL_READERS = 2,
+ ROUNDROBIN_READERS = 3,
+ FIFO_READERS = 4,
+ OPEN_ALL_STEPS = 5
} ReadMultiplexPattern;
typedef enum {
- NOWAITFORSTREAM = 0,
- WAITFORSTREAM = 1
+ NOWAITFORSTREAM = 0,
+ WAITFORSTREAM = 1
} StreamOpenMode; // default: wait for stream
/**
@@ -42,97 +42,99 @@ class Method
{
public:
- const std::string m_Name; ///< Method name (as defined in XML)
- const bool m_DebugMode = false; ///< true: on, throws exceptions and do
- /// additional checks, false: off, faster, but
- /// unsafe
- int m_nThreads;
- std::string m_Type; ///< Method's engine type
- std::map<std::string, std::string> m_Parameters; ///< method parameters
- std::vector<std::map<std::string, std::string>>
- m_TransportParameters; ///< each is a separate Transport containing their
- /// own parameters
-
- /**
- * Constructor
- * @param name is a label that can be used in the config file to set up the
- * method at runtime
- */
- Method(std::string name, bool debugMode = false);
-
- ~Method() = default;
-
- /** Check if the method was defined by the user in the config file.
- * @return true if the method was user-defined, false otherwise when method is
- * set with default parameters
- */
- bool isUserDefined();
-
- /**
- * Define the engine type
- * @param type must be a valid engine type
- */
- void SetEngine(const std::string type);
-
- /**
- * Set how many threads the engine can use for its operations (e.g. file io,
- * compression, staging).
- * If 1 is allowed, no extra threads will be created during the ADIOS calls
- * for asynchronous operations.
- * Note that some transports may require and use extra thread(s). See their
- * documentation for their
- * requirements. E.g. some staging transports always create an extra thread
- * for communication.
- * Set this parameter like you set it for OpenMP, i.e. count one thread for
- * the main process that calls
- * ADIOS functions.
- * @param number of threads, minimum 1 is required
- */
- void AllowThreads(const int nThreads);
-
- /**
- * Sets parameters for the method in "parameter=value" format
- * @param args list of parameters with format "parameter1=value1", ...,
- * "parameterN=valueN"
- */
- template <class... Args> void SetParameters(Args... args)
- {
- std::vector<std::string> parameters = {args...};
- m_Parameters = BuildParametersMap(parameters, m_DebugMode);
- }
-
- /**
- * Adds a transport and its parameters for the method
- * @param type must be a supported transport type under /include/transport
- * @param args list of parameters for a transport with format
- * "parameter1=value1", ..., "parameterN=valueN"
- */
- template <class... Args>
- void AddTransport(const std::string type, Args... args)
- {
- std::vector<std::string> parameters = {args...};
- AddTransportParameters(type, parameters);
- }
-
- void SetReadMultiplexPattern(
- const ReadMultiplexPattern
- pattern); // How to split stream content among readers
- void SetStreamOpenMode(const StreamOpenMode mode); // In Read mode, should
- // Open() wait for the
- // first step appear
- // (default)
-
- void SetVerbose(const Verbose verbose = Verbose::WARN)
- {
- m_Verbose = verbose;
- };
- Verbose GetVerbose() { return m_Verbose; };
+ const std::string m_Name; ///< Method name (as defined in XML)
+ const bool m_DebugMode = false; ///< true: on, throws exceptions and do
+ /// additional checks, false: off, faster, but
+ /// unsafe
+ int m_nThreads;
+ std::string m_Type; ///< Method's engine type
+ std::map<std::string, std::string> m_Parameters; ///< method parameters
+ std::vector<std::map<std::string, std::string>>
+ m_TransportParameters; ///< each is a separate Transport containing
+ /// their
+ /// own parameters
+
+ /**
+ * Constructor
+ * @param name is a label that can be used in the config file to set up the
+ * method at runtime
+ */
+ Method(std::string name, bool debugMode = false);
+
+ ~Method() = default;
+
+ /** Check if the method was defined by the user in the config file.
+ * @return true if the method was user-defined, false otherwise when method
+ * is
+ * set with default parameters
+ */
+ bool isUserDefined();
+
+ /**
+ * Define the engine type
+ * @param type must be a valid engine type
+ */
+ void SetEngine(const std::string type);
+
+ /**
+ * Set how many threads the engine can use for its operations (e.g. file io,
+ * compression, staging).
+ * If 1 is allowed, no extra threads will be created during the ADIOS calls
+ * for asynchronous operations.
+ * Note that some transports may require and use extra thread(s). See their
+ * documentation for their
+ * requirements. E.g. some staging transports always create an extra thread
+ * for communication.
+ * Set this parameter like you set it for OpenMP, i.e. count one thread for
+ * the main process that calls
+ * ADIOS functions.
+ * @param number of threads, minimum 1 is required
+ */
+ void AllowThreads(const int nThreads);
+
+ /**
+ * Sets parameters for the method in "parameter=value" format
+ * @param args list of parameters with format "parameter1=value1", ...,
+ * "parameterN=valueN"
+ */
+ template <class... Args> void SetParameters(Args... args)
+ {
+ std::vector<std::string> parameters = {args...};
+ m_Parameters = BuildParametersMap(parameters, m_DebugMode);
+ }
+
+ /**
+ * Adds a transport and its parameters for the method
+ * @param type must be a supported transport type under /include/transport
+ * @param args list of parameters for a transport with format
+ * "parameter1=value1", ..., "parameterN=valueN"
+ */
+ template <class... Args>
+ void AddTransport(const std::string type, Args... args)
+ {
+ std::vector<std::string> parameters = {args...};
+ AddTransportParameters(type, parameters);
+ }
+
+ void SetReadMultiplexPattern(
+ const ReadMultiplexPattern
+ pattern); // How to split stream content among readers
+ void SetStreamOpenMode(const StreamOpenMode mode); // In Read mode, should
+ // Open() wait for the
+ // first step appear
+ // (default)
+
+ void SetVerbose(const Verbose verbose = Verbose::WARN)
+ {
+ m_Verbose = verbose;
+ };
+ Verbose GetVerbose() { return m_Verbose; };
private:
- Verbose m_Verbose = Verbose::WARN;
+ Verbose m_Verbose = Verbose::WARN;
- void AddTransportParameters(const std::string type,
- const std::vector<std::string> ¶meters);
+ void AddTransportParameters(const std::string type,
+ const std::vector<std::string> ¶meters);
};
} // end namespace adios
diff --git a/include/core/Profiler.h b/include/core/Profiler.h
index eee51ebee869b402a6d2071a8b1a613e9367755c..7d804665bcc121ce355f200e4de0fc35460df5df 100644
--- a/include/core/Profiler.h
+++ b/include/core/Profiler.h
@@ -22,76 +22,76 @@ class Timer
{
public:
- const std::string Process;
- unsigned long long int ProcessTime = 0;
-
- Timer(const std::string process, const Support::Resolutions resolution)
- : Process{process}, Resolution{resolution}
- {
- }
-
- void SetInitialTime()
- {
- InitialTime = std::chrono::high_resolution_clock::now();
- }
-
- void SetTime()
- {
- ElapsedTime = std::chrono::high_resolution_clock::now();
- ProcessTime += GetTime();
- }
-
- long long int GetTime()
- {
- if (Resolution == Support::Resolutions::mus)
- return std::chrono::duration_cast<std::chrono::microseconds>(ElapsedTime -
- InitialTime)
- .count();
-
- else if (Resolution == Support::Resolutions::ms)
- return std::chrono::duration_cast<std::chrono::milliseconds>(ElapsedTime -
- InitialTime)
- .count();
-
- else if (Resolution == Support::Resolutions::s)
- return std::chrono::duration_cast<std::chrono::seconds>(ElapsedTime -
- InitialTime)
- .count();
-
- else if (Resolution == Support::Resolutions::m)
- return std::chrono::duration_cast<std::chrono::minutes>(ElapsedTime -
- InitialTime)
- .count();
-
- else if (Resolution == Support::Resolutions::h)
- return std::chrono::duration_cast<std::chrono::hours>(ElapsedTime -
- InitialTime)
- .count();
-
- return -1; // failure
- }
-
- std::string GetUnits() const
- {
- std::string units;
- if (Resolution == Support::Resolutions::mus)
- units = "mus";
- else if (Resolution == Support::Resolutions::ms)
- units = "ms";
- else if (Resolution == Support::Resolutions::s)
- units = "s";
- else if (Resolution == Support::Resolutions::m)
- units = "m";
- else if (Resolution == Support::Resolutions::h)
- units = "h";
- return units;
- }
+ const std::string Process;
+ unsigned long long int ProcessTime = 0;
+
+ Timer(const std::string process, const Support::Resolutions resolution)
+ : Process{process}, Resolution{resolution}
+ {
+ }
+
+ void SetInitialTime()
+ {
+ InitialTime = std::chrono::high_resolution_clock::now();
+ }
+
+ void SetTime()
+ {
+ ElapsedTime = std::chrono::high_resolution_clock::now();
+ ProcessTime += GetTime();
+ }
+
+ long long int GetTime()
+ {
+ if (Resolution == Support::Resolutions::mus)
+ return std::chrono::duration_cast<std::chrono::microseconds>(
+ ElapsedTime - InitialTime)
+ .count();
+
+ else if (Resolution == Support::Resolutions::ms)
+ return std::chrono::duration_cast<std::chrono::milliseconds>(
+ ElapsedTime - InitialTime)
+ .count();
+
+ else if (Resolution == Support::Resolutions::s)
+ return std::chrono::duration_cast<std::chrono::seconds>(
+ ElapsedTime - InitialTime)
+ .count();
+
+ else if (Resolution == Support::Resolutions::m)
+ return std::chrono::duration_cast<std::chrono::minutes>(
+ ElapsedTime - InitialTime)
+ .count();
+
+ else if (Resolution == Support::Resolutions::h)
+ return std::chrono::duration_cast<std::chrono::hours>(ElapsedTime -
+ InitialTime)
+ .count();
+
+ return -1; // failure
+ }
+
+ std::string GetUnits() const
+ {
+ std::string units;
+ if (Resolution == Support::Resolutions::mus)
+ units = "mus";
+ else if (Resolution == Support::Resolutions::ms)
+ units = "ms";
+ else if (Resolution == Support::Resolutions::s)
+ units = "s";
+ else if (Resolution == Support::Resolutions::m)
+ units = "m";
+ else if (Resolution == Support::Resolutions::h)
+ units = "h";
+ return units;
+ }
private:
- const Support::Resolutions Resolution;
- std::chrono::time_point<std::chrono::high_resolution_clock> InitialTime;
- std::chrono::time_point<std::chrono::high_resolution_clock> ElapsedTime;
- bool InitialTimeSet = false;
+ const Support::Resolutions Resolution;
+ std::chrono::time_point<std::chrono::high_resolution_clock> InitialTime;
+ std::chrono::time_point<std::chrono::high_resolution_clock> ElapsedTime;
+ bool InitialTimeSet = false;
};
/**
@@ -99,9 +99,9 @@ private:
*/
struct Profiler
{
- std::vector<Timer> m_Timers;
- std::vector<unsigned long long int> m_TotalBytes;
- bool m_IsActive = false;
+ std::vector<Timer> m_Timers;
+ std::vector<unsigned long long int> m_TotalBytes;
+ bool m_IsActive = false;
};
} // end namespace
diff --git a/include/core/Support.h b/include/core/Support.h
index bb9b451e842f07afbe38d9d3b36da864594e0c65..a36476660fb7bf34603aab6d907957ebdf606e32 100644
--- a/include/core/Support.h
+++ b/include/core/Support.h
@@ -23,32 +23,34 @@ namespace adios
struct Support
{
- static const std::string Version; ///< current ADIOS version
- static const std::set<std::string>
- HostLanguages; ///< supported languages: C, C++, Fortran, Python, Java
- static const std::set<std::string> Numbers;
- static const std::set<std::string>
- Transports; ///< supported transport methods
- static const std::set<std::string>
- Transforms; ///< supported data transform methods
- static const std::map<std::string, std::set<std::string>>
- Datatypes; ///< supported data types, key: host language, value: all
- /// supported types
- static const std::map<std::string, std::set<std::string>>
- DatatypesAliases; ///< all supported int aliases, key: C++ type (e.g.
- /// int), value: aliases to type in key (e.g. int,
- /// integer)
-
- static const std::set<std::string> FileTransports; ///< file I/O transports
-
- enum class Resolutions
- {
- mus,
- ms,
- s,
- m,
- h
- };
+ static const std::string Version; ///< current ADIOS version
+ static const std::set<std::string> HostLanguages; ///< supported languages:
+ /// C, C++, Fortran,
+ /// Python, Java
+ static const std::set<std::string> Numbers;
+ static const std::set<std::string>
+ Transports; ///< supported transport methods
+ static const std::set<std::string>
+ Transforms; ///< supported data transform methods
+ static const std::map<std::string, std::set<std::string>>
+ Datatypes; ///< supported data types, key: host language, value: all
+ /// supported types
+ static const std::map<std::string, std::set<std::string>>
+ DatatypesAliases; ///< all supported int aliases, key: C++ type
+ ///(e.g.
+ /// int), value: aliases to type in key (e.g. int,
+ /// integer)
+
+ static const std::set<std::string> FileTransports; ///< file I/O transports
+
+ enum class Resolutions
+ {
+ mus,
+ ms,
+ s,
+ m,
+ h
+ };
};
} // end namespace adios
diff --git a/include/core/Transform.h b/include/core/Transform.h
index a6a6dc75ab80f232f8f08e724837d6b83655b7e2..c133c146d7a9fc6be8fc944f38270bd66c9b393b 100644
--- a/include/core/Transform.h
+++ b/include/core/Transform.h
@@ -27,21 +27,21 @@ class Transform
{
public:
- const std::string m_Method;
+ const std::string m_Method;
- /**
- * Initialize parent method
- * @param method zlib, bzip2, szip
- */
- Transform(std::string method);
+ /**
+ * Initialize parent method
+ * @param method zlib, bzip2, szip
+ */
+ Transform(std::string method);
- virtual ~Transform() = default;
+ virtual ~Transform() = default;
- virtual void Compress(const std::vector<char> &bufferIn,
- std::vector<char> &bufferOut);
-
- virtual void Decompress(const std::vector<char> &bufferIn,
+ virtual void Compress(const std::vector<char> &bufferIn,
std::vector<char> &bufferOut);
+
+ virtual void Decompress(const std::vector<char> &bufferIn,
+ std::vector<char> &bufferOut);
};
} // end namespace adios
diff --git a/include/core/Transport.h b/include/core/Transport.h
index 0851a9b745462907db42bfd843fa224fd2471c4a..798a0db145aff5aecb9e05f0a4ab8c52149a5963 100644
--- a/include/core/Transport.h
+++ b/include/core/Transport.h
@@ -27,59 +27,62 @@ class Transport
{
public:
- const std::string m_Type; ///< transport type from derived class
- std::string m_Name; ///< from Open
- std::string m_AccessMode; ///< from Open
- bool m_IsOpen = false;
-
- MPI_Comm m_MPIComm = MPI_COMM_SELF;
-
- int m_RankMPI = 0; ///< current MPI rank process
- int m_SizeMPI = 1; ///< current MPI processes size
- Profiler m_Profiler; ///< collects information about Open and bytes Transport
-
- /**
- * Base constructor that all derived classes pass
- * @param
- * @param mpiComm passed to m_MPIComm
- * @param debugMode passed to m_DebugMode
- */
- Transport(std::string type, MPI_Comm mpiComm, bool debugMode);
-
- virtual ~Transport() = default;
-
- /**
- * Open Output file accesing a mode
- * @param name name of stream or file
- * @param accessMode r or read, w or write, a or append
- */
- virtual void Open(const std::string name, const std::string accessMode) = 0;
-
- /**
- * Set buffer and size for a particular transport
- * @param buffer raw data buffer
- * @param size raw data buffer size
- */
- virtual void SetBuffer(char *buffer, std::size_t size);
-
- /**
- * Write function for a transport
- * @param buffer pointer to buffer to be written
- * @param size size of buffer to be written
- */
- virtual void Write(const char *buffer, std::size_t size) = 0;
-
- virtual void Flush(); ///< flushes current contents to physical medium without
- /// closing the transport
-
- virtual void Close(); ///< closes current transport and flushes everything,
- /// transport becomes unreachable
-
- virtual void InitProfiler(const std::string accessMode,
- const Support::Resolutions resolution);
+ const std::string m_Type; ///< transport type from derived class
+ std::string m_Name; ///< from Open
+ std::string m_AccessMode; ///< from Open
+ bool m_IsOpen = false;
+
+ MPI_Comm m_MPIComm = MPI_COMM_SELF;
+
+ int m_RankMPI = 0; ///< current MPI rank process
+ int m_SizeMPI = 1; ///< current MPI processes size
+ Profiler
+ m_Profiler; ///< collects information about Open and bytes Transport
+
+ /**
+ * Base constructor that all derived classes pass
+ * @param
+ * @param mpiComm passed to m_MPIComm
+ * @param debugMode passed to m_DebugMode
+ */
+ Transport(std::string type, MPI_Comm mpiComm, bool debugMode);
+
+ virtual ~Transport() = default;
+
+ /**
+ * Open Output file accesing a mode
+ * @param name name of stream or file
+ * @param accessMode r or read, w or write, a or append
+ */
+ virtual void Open(const std::string name, const std::string accessMode) = 0;
+
+ /**
+ * Set buffer and size for a particular transport
+ * @param buffer raw data buffer
+ * @param size raw data buffer size
+ */
+ virtual void SetBuffer(char *buffer, std::size_t size);
+
+ /**
+ * Write function for a transport
+ * @param buffer pointer to buffer to be written
+ * @param size size of buffer to be written
+ */
+ virtual void Write(const char *buffer, std::size_t size) = 0;
+
+ virtual void
+ Flush(); ///< flushes current contents to physical medium without
+ /// closing the transport
+
+ virtual void Close(); ///< closes current transport and flushes everything,
+ /// transport becomes unreachable
+
+ virtual void InitProfiler(const std::string accessMode,
+ const Support::Resolutions resolution);
protected:
- const bool m_DebugMode = false; ///< if true: additional checks and exceptions
+ const bool m_DebugMode =
+ false; ///< if true: additional checks and exceptions
};
} // end namespace adios
diff --git a/include/core/Variable.h b/include/core/Variable.h
index 110ae7064cad92d899913204f9677e2781b9afee..93acbfc9fe94a05bef0ecc607efad4272fc50f58 100644
--- a/include/core/Variable.h
+++ b/include/core/Variable.h
@@ -26,10 +26,10 @@ namespace adios
struct TransformData
{
- Transform &Operation; ///< pointer to transform object
- std::map<std::string, std::string> Parameters; ///< transforms parameters
- std::vector<std::size_t>
- Size; ///< vector that carries the sizes after a transformation is applied
+ Transform &Operation; ///< pointer to transform object
+ std::map<std::string, std::string> Parameters; ///< transforms parameters
+ std::vector<std::size_t> Size; ///< vector that carries the sizes after a
+ /// transformation is applied
};
/**
@@ -40,77 +40,79 @@ template <class T> class Variable : public VariableBase
{
public:
- const T *m_AppValues = nullptr; ///< pointer to values passed from user in
- /// ADIOS Write, it might change in ADIOS Read
-
- std::vector<TransformData> m_Transforms; ///< associated transforms, sequence
- /// determines application order, e.g.
- /// first Transforms[0] then
- /// Transforms[1]. Pointer used as
- /// reference (no memory management).
-
- Variable<T>(const std::string name, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets,
- const bool debugMode)
- : VariableBase(name, GetType<T>(), sizeof(T), dimensions, globalDimensions,
- globalOffsets, debugMode)
- {
- if (m_Dimensions == Dims{1})
- m_IsScalar = true;
- }
-
- template <class... Args> void AddTransform(Transform &transform, Args... args)
- {
- std::vector<std::string> parameters = {args...};
- m_Transforms.emplace_back(
- transform,
- BuildParametersMap(parameters, m_DebugMode)); // need to check
- }
-
- /** Return the global dimensions of the variable
- * @return vector of std::size_t values
- */
- std::vector<std::size_t> GetGlobalDimensions();
-
- /** Return the number of steps available for the variable
- * @return Number of steps
- */
- int GetSteps();
-
- void Monitor(std::ostream &logInfo) const noexcept
- {
- logInfo << "Variable: " << m_Name << "\n";
- logInfo << "Type: " << m_Type << "\n";
- logInfo << "Size: " << TotalSize() << " elements\n";
- logInfo << "Payload: " << PayLoadSize() << " bytes\n";
-
- if (m_AppValues != nullptr)
+ const T *m_AppValues = nullptr; ///< pointer to values passed from user in
+ /// ADIOS Write, it might change in ADIOS Read
+
+ std::vector<TransformData>
+ m_Transforms; ///< associated transforms, sequence
+ /// determines application order, e.g.
+ /// first Transforms[0] then
+ /// Transforms[1]. Pointer used as
+ /// reference (no memory management).
+
+ Variable<T>(const std::string name, const Dims dimensions,
+ const Dims globalDimensions, const Dims globalOffsets,
+ const bool debugMode)
+ : VariableBase(name, GetType<T>(), sizeof(T), dimensions, globalDimensions,
+ globalOffsets, debugMode)
{
- logInfo << "Values (first 10 or max_size): \n";
- std::size_t size = TotalSize();
- if (size > 10)
- size = 10;
-
- if (m_Type.find("complex") != m_Type.npos) // it's complex
- {
- for (unsigned int i = 0; i < size; ++i)
- {
- logInfo << "( " << std::real(m_AppValues[i]) << " , "
- << std::imag(m_AppValues[i]) << " ) ";
- }
- }
- else
- {
- for (unsigned int i = 0; i < size; ++i)
+ if (m_Dimensions == Dims{1})
+ m_IsScalar = true;
+ }
+
+ template <class... Args>
+ void AddTransform(Transform &transform, Args... args)
+ {
+ std::vector<std::string> parameters = {args...};
+ m_Transforms.emplace_back(
+ transform,
+ BuildParametersMap(parameters, m_DebugMode)); // need to check
+ }
+
+ /** Return the global dimensions of the variable
+ * @return vector of std::size_t values
+ */
+ std::vector<std::size_t> GetGlobalDimensions();
+
+ /** Return the number of steps available for the variable
+ * @return Number of steps
+ */
+ int GetSteps();
+
+ void Monitor(std::ostream &logInfo) const noexcept
+ {
+ logInfo << "Variable: " << m_Name << "\n";
+ logInfo << "Type: " << m_Type << "\n";
+ logInfo << "Size: " << TotalSize() << " elements\n";
+ logInfo << "Payload: " << PayLoadSize() << " bytes\n";
+
+ if (m_AppValues != nullptr)
{
- logInfo << m_AppValues[i] << " ";
+ logInfo << "Values (first 10 or max_size): \n";
+ std::size_t size = TotalSize();
+ if (size > 10)
+ size = 10;
+
+ if (m_Type.find("complex") != m_Type.npos) // it's complex
+ {
+ for (unsigned int i = 0; i < size; ++i)
+ {
+ logInfo << "( " << std::real(m_AppValues[i]) << " , "
+ << std::imag(m_AppValues[i]) << " ) ";
+ }
+ }
+ else
+ {
+ for (unsigned int i = 0; i < size; ++i)
+ {
+ logInfo << m_AppValues[i] << " ";
+ }
+ }
+
+ logInfo << " ...";
}
- }
-
- logInfo << " ...";
+ logInfo << "\n";
}
- logInfo << "\n";
- }
};
} // end namespace
diff --git a/include/core/VariableBase.h b/include/core/VariableBase.h
index cc8c8f79a4806186e47dec2c4d5c5f691ea1039b..eea1d261c67e63b84e1db385117dfcb01781a9ce 100644
--- a/include/core/VariableBase.h
+++ b/include/core/VariableBase.h
@@ -30,71 +30,75 @@ class VariableBase
{
public:
- const std::string m_Name; ///< variable name
- const std::string m_Type; ///< variable type
- const std::size_t m_ElementSize; ///< Variable -> sizeof(T), VariableCompound
- ///-> from constructor
-
- bool m_IsScalar = false;
- const bool m_IsDimension = false;
-
- VariableBase(const std::string name, const std::string type,
- const std::size_t elementSize, const Dims dimensions,
- const Dims globalDimensions, const Dims globalOffsets,
- const bool debugMode)
- : m_Name{name}, m_Type{type}, m_ElementSize{elementSize},
- m_Dimensions{dimensions}, m_GlobalDimensions{globalDimensions},
- m_GlobalOffsets{globalOffsets}, m_DebugMode{debugMode}
- {
- }
-
- virtual ~VariableBase() {}
-
- std::size_t DimensionsSize() const noexcept { return m_Dimensions.size(); }
-
- /**
- * Returns the payload size in bytes
- * @return TotalSize * sizeof(T)
- */
- std::size_t PayLoadSize() const noexcept
- {
- return GetTotalSize(m_Dimensions) * m_ElementSize;
- }
-
- /**
- * Returns the total size
- * @return number of elements
- */
- std::size_t TotalSize() const noexcept { return GetTotalSize(m_Dimensions); }
-
- // protected: off for now
-
- Dims m_Dimensions; ///< array of local dimensions
- Dims m_GlobalDimensions; ///< array of global dimensions
- Dims m_GlobalOffsets; ///< array of global offsets
- const bool m_DebugMode = false;
-
- std::string GetDimensionAsString() { return dimsToString(m_Dimensions); }
- std::string GetGlobalDimensionAsString()
- {
- return dimsToString(m_GlobalDimensions);
- }
- std::string GetOffsetsAsString() { return dimsToString(m_GlobalOffsets); }
+ const std::string m_Name; ///< variable name
+ const std::string m_Type; ///< variable type
+ const std::size_t
+ m_ElementSize; ///< Variable -> sizeof(T), VariableCompound
+ ///-> from constructor
+
+ bool m_IsScalar = false;
+ const bool m_IsDimension = false;
+
+ VariableBase(const std::string name, const std::string type,
+ const std::size_t elementSize, const Dims dimensions,
+ const Dims globalDimensions, const Dims globalOffsets,
+ const bool debugMode)
+ : m_Name{name}, m_Type{type}, m_ElementSize{elementSize},
+ m_Dimensions{dimensions}, m_GlobalDimensions{globalDimensions},
+ m_GlobalOffsets{globalOffsets}, m_DebugMode{debugMode}
+ {
+ }
+
+ virtual ~VariableBase() {}
+
+ std::size_t DimensionsSize() const noexcept { return m_Dimensions.size(); }
+
+ /**
+ * Returns the payload size in bytes
+ * @return TotalSize * sizeof(T)
+ */
+ std::size_t PayLoadSize() const noexcept
+ {
+ return GetTotalSize(m_Dimensions) * m_ElementSize;
+ }
+
+ /**
+ * Returns the total size
+ * @return number of elements
+ */
+ std::size_t TotalSize() const noexcept
+ {
+ return GetTotalSize(m_Dimensions);
+ }
+
+ // protected: off for now
+
+ Dims m_Dimensions; ///< array of local dimensions
+ Dims m_GlobalDimensions; ///< array of global dimensions
+ Dims m_GlobalOffsets; ///< array of global offsets
+ const bool m_DebugMode = false;
+
+ std::string GetDimensionAsString() { return dimsToString(m_Dimensions); }
+ std::string GetGlobalDimensionAsString()
+ {
+ return dimsToString(m_GlobalDimensions);
+ }
+ std::string GetOffsetsAsString() { return dimsToString(m_GlobalOffsets); }
private:
- std::string dimsToString(Dims dims)
- {
- std::ostringstream oss;
- if (!dims.empty())
+ std::string dimsToString(Dims dims)
{
- // Convert all but the last element to avoid a trailing ","
- std::copy(dims.begin(), dims.end() - 1,
- std::ostream_iterator<std::size_t>(oss, ","));
- // Now add the last element with no delimiter
- oss << dims.back();
+ std::ostringstream oss;
+ if (!dims.empty())
+ {
+ // Convert all but the last element to avoid a trailing ","
+ std::copy(dims.begin(), dims.end() - 1,
+ std::ostream_iterator<std::size_t>(oss, ","));
+ // Now add the last element with no delimiter
+ oss << dims.back();
+ }
+ return oss.str();
}
- return oss.str();
- }
};
}
diff --git a/include/core/VariableCompound.h b/include/core/VariableCompound.h
index c3bacfccaae20331e45876361388eb035812cd58..322dccd4f08adc8ddc9ffd6cb18a1b2e1b159f9c 100644
--- a/include/core/VariableCompound.h
+++ b/include/core/VariableCompound.h
@@ -18,9 +18,9 @@ namespace adios
struct CompoundElement
{
- const std::string m_Name;
- const std::size_t m_Offset;
- const std::string m_Type;
+ const std::string m_Name;
+ const std::size_t m_Offset;
+ const std::string m_Type;
};
/**
@@ -31,32 +31,32 @@ class VariableCompound : public VariableBase
{
public:
- const void *m_AppValue = nullptr;
+ const void *m_AppValue = nullptr;
- VariableCompound(const std::string name, const std::size_t sizeOfStruct,
- const Dims dimensions, const Dims globalDimensions,
- const Dims globalOffsets, const bool debugMode)
- : VariableBase(name, "compound", sizeOfStruct, dimensions, globalDimensions,
- globalOffsets, debugMode)
- {
- }
+ VariableCompound(const std::string name, const std::size_t sizeOfStruct,
+ const Dims dimensions, const Dims globalDimensions,
+ const Dims globalOffsets, const bool debugMode)
+ : VariableBase(name, "compound", sizeOfStruct, dimensions, globalDimensions,
+ globalOffsets, debugMode)
+ {
+ }
- template <class U>
- void InsertMember(const std::string name, const std::size_t offset)
- {
- m_Elements.push_back(CompoundElement{name, offset, GetType<U>()});
- }
+ template <class U>
+ void InsertMember(const std::string name, const std::size_t offset)
+ {
+ m_Elements.push_back(CompoundElement{name, offset, GetType<U>()});
+ }
- void Monitor(std::ostream &logInfo) const noexcept
- {
- logInfo << "Variable Compound: " << m_Name << "\n";
- logInfo << "Type: " << m_Type << "\n";
- logInfo << "Size: " << TotalSize() << " elements\n";
- logInfo << "Payload: " << PayLoadSize() << " bytes\n";
- }
+ void Monitor(std::ostream &logInfo) const noexcept
+ {
+ logInfo << "Variable Compound: " << m_Name << "\n";
+ logInfo << "Type: " << m_Type << "\n";
+ logInfo << "Size: " << TotalSize() << " elements\n";
+ logInfo << "Payload: " << PayLoadSize() << " bytes\n";
+ }
private:
- std::vector<CompoundElement> m_Elements; ///< vector of element types
+ std::vector<CompoundElement> m_Elements; ///< vector of element types
};
} // end namespace
diff --git a/include/engine/adios1/ADIOS1Reader.h b/include/engine/adios1/ADIOS1Reader.h
index 70b89700aadabcbd4f2479d48dee4cacba480efc..22e2984765bac022d57ba63ba1b6c4b30906bd56 100644
--- a/include/engine/adios1/ADIOS1Reader.h
+++ b/include/engine/adios1/ADIOS1Reader.h
@@ -27,96 +27,100 @@ class BPFileReader : public Engine
{
public:
- /**
- * Constructor for single BP capsule engine, writes in BP format into a single
- * heap capsule
- * @param name unique name given to the engine
- * @param accessMode
- * @param mpiComm
- * @param method
- * @param debugMode
- * @param hostLanguage
- */
- BPFileReader(ADIOS &adios, const std::string name,
- const std::string accessMode, MPI_Comm mpiComm,
- const Method &method, const IOMode iomode,
- const float timeout_sec, const bool debugMode = false,
- const unsigned int nthreads = 1);
-
- ~BPFileReader();
-
- Variable<void> *InquireVariable(const std::string name,
- const bool readIn = true);
- Variable<char> *InquireVariableChar(const std::string name,
- const bool readIn = true);
- Variable<unsigned char> *InquireVariableUChar(const std::string name,
- const bool readIn = true);
- Variable<short> *InquireVariableShort(const std::string name,
+ /**
+ * Constructor for single BP capsule engine, writes in BP format into a
+ * single
+ * heap capsule
+ * @param name unique name given to the engine
+ * @param accessMode
+ * @param mpiComm
+ * @param method
+ * @param debugMode
+ * @param hostLanguage
+ */
+ BPFileReader(ADIOS &adios, const std::string name,
+ const std::string accessMode, MPI_Comm mpiComm,
+ const Method &method, const IOMode iomode,
+ const float timeout_sec, const bool debugMode = false,
+ const unsigned int nthreads = 1);
+
+ ~BPFileReader();
+
+ Variable<void> *InquireVariable(const std::string name,
+ const bool readIn = true);
+ Variable<char> *InquireVariableChar(const std::string name,
const bool readIn = true);
- Variable<unsigned short> *InquireVariableUShort(const std::string name,
+ Variable<unsigned char> *InquireVariableUChar(const std::string name,
const bool readIn = true);
- Variable<int> *InquireVariableInt(const std::string name,
- const bool readIn = true);
- Variable<unsigned int> *InquireVariableUInt(const std::string name,
- const bool readIn = true);
- Variable<long int> *InquireVariableLInt(const std::string name,
+ Variable<short> *InquireVariableShort(const std::string name,
const bool readIn = true);
- Variable<unsigned long int> *InquireVariableULInt(const std::string name,
+ Variable<unsigned short> *InquireVariableUShort(const std::string name,
const bool readIn = true);
- Variable<long long int> *InquireVariableLLInt(const std::string name,
+ Variable<int> *InquireVariableInt(const std::string name,
+ const bool readIn = true);
+ Variable<unsigned int> *InquireVariableUInt(const std::string name,
const bool readIn = true);
- Variable<unsigned long long int> *
- InquireVariableULLInt(const std::string name, const bool readIn = true);
- Variable<float> *InquireVariableFloat(const std::string name,
- const bool readIn = true);
- Variable<double> *InquireVariableDouble(const std::string name,
+ Variable<long int> *InquireVariableLInt(const std::string name,
+ const bool readIn = true);
+ Variable<unsigned long int> *InquireVariableULInt(const std::string name,
+ const bool readIn = true);
+ Variable<long long int> *InquireVariableLLInt(const std::string name,
+ const bool readIn = true);
+ Variable<unsigned long long int> *
+ InquireVariableULLInt(const std::string name, const bool readIn = true);
+ Variable<float> *InquireVariableFloat(const std::string name,
const bool readIn = true);
- Variable<long double> *InquireVariableLDouble(const std::string name,
- const bool readIn = true);
- Variable<std::complex<float>> *
- InquireVariableCFloat(const std::string name, const bool readIn = true);
- Variable<std::complex<double>> *
- InquireVariableCDouble(const std::string name, const bool readIn = true);
- Variable<std::complex<long double>> *
- InquireVariableCLDouble(const std::string name, const bool readIn = true);
-
- /**
- * Not implemented
- * @param name
- * @param readIn
- * @return
- */
- VariableCompound *InquireVariableCompound(const std::string name,
+ Variable<double> *InquireVariableDouble(const std::string name,
const bool readIn = true);
+ Variable<long double> *InquireVariableLDouble(const std::string name,
+ const bool readIn = true);
+ Variable<std::complex<float>> *
+ InquireVariableCFloat(const std::string name, const bool readIn = true);
+ Variable<std::complex<double>> *
+ InquireVariableCDouble(const std::string name, const bool readIn = true);
+ Variable<std::complex<long double>> *
+ InquireVariableCLDouble(const std::string name, const bool readIn = true);
+
+ /**
+ * Not implemented
+ * @param name
+ * @param readIn
+ * @return
+ */
+ VariableCompound *InquireVariableCompound(const std::string name,
+ const bool readIn = true);
- void Close(const int transportIndex = -1);
+ void Close(const int transportIndex = -1);
private:
- capsule::STLVector
- m_Buffer; ///< heap capsule, contains data and metadata buffers
- // format::BP1Writer m_BP1Writer; ///< format object will provide the required
- // BP functionality to be applied on m_Buffer and m_Transports
-
- void Init(); ///< calls InitCapsules and InitTransports based on Method,
- /// called from constructor
- void InitCapsules();
- void InitTransports(); ///< from Transports
-
- std::string
- GetMdtmParameter(const std::string parameter,
- const std::map<std::string, std::string> &mdtmParameters);
-
- template <class T>
- Variable<T> *InquireVariableCommon(const std::string name, const bool readIn)
- {
- std::cout << "Hello BPReaderCommon\n";
-
- // here read variable metadata (dimensions, type, etc.)...then create a
- // Variable like below:
- // Variable<T>& variable = m_ADIOS.DefineVariable<T>( m_Name + "/" + name, )
- // return &variable; //return address if success
- return nullptr; // on failure
- }
+ capsule::STLVector
+ m_Buffer; ///< heap capsule, contains data and metadata buffers
+ // format::BP1Writer m_BP1Writer; ///< format object will provide the
+ // required
+ // BP functionality to be applied on m_Buffer and m_Transports
+
+ void Init(); ///< calls InitCapsules and InitTransports based on Method,
+ /// called from constructor
+ void InitCapsules();
+ void InitTransports(); ///< from Transports
+
+ std::string
+ GetMdtmParameter(const std::string parameter,
+ const std::map<std::string, std::string> &mdtmParameters);
+
+ template <class T>
+ Variable<T> *InquireVariableCommon(const std::string name,
+ const bool readIn)
+ {
+ std::cout << "Hello BPReaderCommon\n";
+
+ // here read variable metadata (dimensions, type, etc.)...then create a
+ // Variable like below:
+ // Variable<T>& variable = m_ADIOS.DefineVariable<T>( m_Name + "/" +
+ // name, )
+ // return &variable; //return address if success
+ return nullptr; // on failure
+ }
};
} // end namespace adios
diff --git a/include/engine/adios1/ADIOS1Writer.h b/include/engine/adios1/ADIOS1Writer.h
index 054e7063a05b0f3456575c7e7fcd3bcb54a0a0a7..8f41ed432d566e370110775b13e90c051f51a531 100644
--- a/include/engine/adios1/ADIOS1Writer.h
+++ b/include/engine/adios1/ADIOS1Writer.h
@@ -27,103 +27,107 @@ class ADIOS1Writer : public Engine
{
public:
- /**
- * Constructor for Writer writes in ADIOS 1.x BP format
- * @param name unique name given to the engine
- * @param accessMode
- * @param mpiComm
- * @param method
- * @param debugMode
- */
- ADIOS1Writer(ADIOS &adios, const std::string name,
- const std::string accessMode, MPI_Comm mpiComm,
- const Method &method, const IOMode iomode,
- const float timeout_sec, const bool debugMode = false,
- const unsigned int nthreads = 1);
-
- ~ADIOS1Writer();
-
- void Write(Variable<char> &variable, const char *values);
- void Write(Variable<unsigned char> &variable, const unsigned char *values);
- void Write(Variable<short> &variable, const short *values);
- void Write(Variable<unsigned short> &variable, const unsigned short *values);
- void Write(Variable<int> &variable, const int *values);
- void Write(Variable<unsigned int> &variable, const unsigned int *values);
- void Write(Variable<long int> &variable, const long int *values);
- void Write(Variable<unsigned long int> &variable,
- const unsigned long int *values);
- void Write(Variable<long long int> &variable, const long long int *values);
- void Write(Variable<unsigned long long int> &variable,
- const unsigned long long int *values);
- void Write(Variable<float> &variable, const float *values);
- void Write(Variable<double> &variable, const double *values);
- void Write(Variable<long double> &variable, const long double *values);
- void Write(Variable<std::complex<float>> &variable,
- const std::complex<float> *values);
- void Write(Variable<std::complex<double>> &variable,
- const std::complex<double> *values);
- void Write(Variable<std::complex<long double>> &variable,
- const std::complex<long double> *values);
- void Write(VariableCompound &variable, const void *values);
-
- void Write(const std::string variableName, const char *values);
- void Write(const std::string variableName, const unsigned char *values);
- void Write(const std::string variableName, const short *values);
- void Write(const std::string variableName, const unsigned short *values);
- void Write(const std::string variableName, const int *values);
- void Write(const std::string variableName, const unsigned int *values);
- void Write(const std::string variableName, const long int *values);
- void Write(const std::string variableName, const unsigned long int *values);
- void Write(const std::string variableName, const long long int *values);
- void Write(const std::string variableName,
- const unsigned long long int *values);
- void Write(const std::string variableName, const float *values);
- void Write(const std::string variableName, const double *values);
- void Write(const std::string variableName, const long double *values);
- void Write(const std::string variableName, const std::complex<float> *values);
- void Write(const std::string variableName,
- const std::complex<double> *values);
- void Write(const std::string variableName,
- const std::complex<long double> *values);
- void Write(const std::string variableName, const void *values);
-
- void Advance();
-
- /**
- * Closes a single transport or all transports
- * @param transportIndex, if -1 (default) closes all transports, otherwise it
- * closes a transport in m_Transport[transportIndex]. In debug mode the latter
- * is bounds-checked.
- */
- void Close(const int transportIndex = -1);
+ /**
+ * Constructor for Writer writes in ADIOS 1.x BP format
+ * @param name unique name given to the engine
+ * @param accessMode
+ * @param mpiComm
+ * @param method
+ * @param debugMode
+ */
+ ADIOS1Writer(ADIOS &adios, const std::string name,
+ const std::string accessMode, MPI_Comm mpiComm,
+ const Method &method, const IOMode iomode,
+ const float timeout_sec, const bool debugMode = false,
+ const unsigned int nthreads = 1);
+
+ ~ADIOS1Writer();
+
+ void Write(Variable<char> &variable, const char *values);
+ void Write(Variable<unsigned char> &variable, const unsigned char *values);
+ void Write(Variable<short> &variable, const short *values);
+ void Write(Variable<unsigned short> &variable,
+ const unsigned short *values);
+ void Write(Variable<int> &variable, const int *values);
+ void Write(Variable<unsigned int> &variable, const unsigned int *values);
+ void Write(Variable<long int> &variable, const long int *values);
+ void Write(Variable<unsigned long int> &variable,
+ const unsigned long int *values);
+ void Write(Variable<long long int> &variable, const long long int *values);
+ void Write(Variable<unsigned long long int> &variable,
+ const unsigned long long int *values);
+ void Write(Variable<float> &variable, const float *values);
+ void Write(Variable<double> &variable, const double *values);
+ void Write(Variable<long double> &variable, const long double *values);
+ void Write(Variable<std::complex<float>> &variable,
+ const std::complex<float> *values);
+ void Write(Variable<std::complex<double>> &variable,
+ const std::complex<double> *values);
+ void Write(Variable<std::complex<long double>> &variable,
+ const std::complex<long double> *values);
+ void Write(VariableCompound &variable, const void *values);
+
+ void Write(const std::string variableName, const char *values);
+ void Write(const std::string variableName, const unsigned char *values);
+ void Write(const std::string variableName, const short *values);
+ void Write(const std::string variableName, const unsigned short *values);
+ void Write(const std::string variableName, const int *values);
+ void Write(const std::string variableName, const unsigned int *values);
+ void Write(const std::string variableName, const long int *values);
+ void Write(const std::string variableName, const unsigned long int *values);
+ void Write(const std::string variableName, const long long int *values);
+ void Write(const std::string variableName,
+ const unsigned long long int *values);
+ void Write(const std::string variableName, const float *values);
+ void Write(const std::string variableName, const double *values);
+ void Write(const std::string variableName, const long double *values);
+ void Write(const std::string variableName,
+ const std::complex<float> *values);
+ void Write(const std::string variableName,
+ const std::complex<double> *values);
+ void Write(const std::string variableName,
+ const std::complex<long double> *values);
+ void Write(const std::string variableName, const void *values);
+
+ void Advance();
+
+ /**
+ * Closes a single transport or all transports
+ * @param transportIndex, if -1 (default) closes all transports, otherwise
+ * it
+ * closes a transport in m_Transport[transportIndex]. In debug mode the
+ * latter
+ * is bounds-checked.
+ */
+ void Close(const int transportIndex = -1);
private:
- const char *m_groupname; ///< ADIOS1 group name created from the method's
- /// name. Must be a unique group name.
- const char *m_filename; ///< Save file name from constructor for Advance()
- /// when we re-open in ADIOS1
- MPI_Comm m_comm; ///< Save MPI communicator from constructor for Advance()
- /// when we re-open in ADIOS1
-
- bool m_initialized = false; ///< set to true after calling adios_init()
- int64_t m_adios_file = 0; ///< ADIOS1 file handler returned by adios_open()
- int64_t m_adios_group =
- 0; ///< ADIOS1 group pointer that holds the ADIOS1 variable definitions
- bool m_IsFileOpen = false;
-
- void Init();
- // these are unused yet, keeping here to see if we need them
- void InitParameters();
- void InitTransports();
- void InitProcessGroup();
-
- bool ReOpenAsNeeded(); // return true if file is open or reopened
- void DefineVariable(std::string name, bool isScalar,
- enum ADIOS_DATATYPES vartype, std::string ldims,
- std::string gdims, std::string offs);
- void WriteVariable(std::string name, bool isScalar,
- enum ADIOS_DATATYPES vartype, std::string ldims,
- std::string gdims, std::string offs, const void *values);
+ const char *m_groupname; ///< ADIOS1 group name created from the method's
+ /// name. Must be a unique group name.
+ const char *m_filename; ///< Save file name from constructor for Advance()
+ /// when we re-open in ADIOS1
+ MPI_Comm m_comm; ///< Save MPI communicator from constructor for Advance()
+ /// when we re-open in ADIOS1
+
+ bool m_initialized = false; ///< set to true after calling adios_init()
+ int64_t m_adios_file = 0; ///< ADIOS1 file handler returned by adios_open()
+ int64_t m_adios_group = 0; ///< ADIOS1 group pointer that holds the ADIOS1
+ /// variable definitions
+ bool m_IsFileOpen = false;
+
+ void Init();
+ // these are unused yet, keeping here to see if we need them
+ void InitParameters();
+ void InitTransports();
+ void InitProcessGroup();
+
+ bool ReOpenAsNeeded(); // return true if file is open or reopened
+ void DefineVariable(std::string name, bool isScalar,
+ enum ADIOS_DATATYPES vartype, std::string ldims,
+ std::string gdims, std::string offs);
+ void WriteVariable(std::string name, bool isScalar,
+ enum ADIOS_DATATYPES vartype, std::string ldims,
+ std::string gdims, std::string offs, const void *values);
};
} // end namespace adios
diff --git a/include/engine/bp/BPFileReader.h b/include/engine/bp/BPFileReader.h
index 4f4c451532db4769ed6f296e7b342b93cf36c857..74ef5e6a4e8ff91a78b2a08154a1b862eaf5045b 100644
--- a/include/engine/bp/BPFileReader.h
+++ b/include/engine/bp/BPFileReader.h
@@ -25,95 +25,99 @@ class BPFileReader : public Engine
{
public:
- /**
- * Constructor for single BP capsule engine, writes in BP format into a single
- * heap capsule
- * @param name unique name given to the engine
- * @param accessMode
- * @param mpiComm
- * @param method
- * @param debugMode
- * @param hostLanguage
- */
- BPFileReader(ADIOS &adios, std::string name, std::string accessMode,
- MPI_Comm mpiComm, const Method &method, IOMode iomode,
- float timeout_sec, bool debugMode = false,
- unsigned int nthreads = 1);
-
- virtual ~BPFileReader() = default;
-
- Variable<void> *InquireVariable(const std::string name,
- const bool readIn = true);
- Variable<char> *InquireVariableChar(const std::string name,
- const bool readIn = true);
- Variable<unsigned char> *InquireVariableUChar(const std::string name,
- const bool readIn = true);
- Variable<short> *InquireVariableShort(const std::string name,
+ /**
+ * Constructor for single BP capsule engine, writes in BP format into a
+ * single
+ * heap capsule
+ * @param name unique name given to the engine
+ * @param accessMode
+ * @param mpiComm
+ * @param method
+ * @param debugMode
+ * @param hostLanguage
+ */
+ BPFileReader(ADIOS &adios, std::string name, std::string accessMode,
+ MPI_Comm mpiComm, const Method &method, IOMode iomode,
+ float timeout_sec, bool debugMode = false,
+ unsigned int nthreads = 1);
+
+ virtual ~BPFileReader() = default;
+
+ Variable<void> *InquireVariable(const std::string name,
+ const bool readIn = true);
+ Variable<char> *InquireVariableChar(const std::string name,
const bool readIn = true);
- Variable<unsigned short> *InquireVariableUShort(const std::string name,
+ Variable<unsigned char> *InquireVariableUChar(const std::string name,
const bool readIn = true);
- Variable<int> *InquireVariableInt(const std::string name,
- const bool readIn = true);
- Variable<unsigned int> *InquireVariableUInt(const std::string name,
- const bool readIn = true);
- Variable<long int> *InquireVariableLInt(const std::string name,
+ Variable<short> *InquireVariableShort(const std::string name,
const bool readIn = true);
- Variable<unsigned long int> *InquireVariableULInt(const std::string name,
+ Variable<unsigned short> *InquireVariableUShort(const std::string name,
const bool readIn = true);
- Variable<long long int> *InquireVariableLLInt(const std::string name,
+ Variable<int> *InquireVariableInt(const std::string name,
+ const bool readIn = true);
+ Variable<unsigned int> *InquireVariableUInt(const std::string name,
const bool readIn = true);
- Variable<unsigned long long int> *
- InquireVariableULLInt(const std::string name, const bool readIn = true);
- Variable<float> *InquireVariableFloat(const std::string name,
- const bool readIn = true);
- Variable<double> *InquireVariableDouble(const std::string name,
+ Variable<long int> *InquireVariableLInt(const std::string name,
+ const bool readIn = true);
+ Variable<unsigned long int> *InquireVariableULInt(const std::string name,
+ const bool readIn = true);
+ Variable<long long int> *InquireVariableLLInt(const std::string name,
+ const bool readIn = true);
+ Variable<unsigned long long int> *
+ InquireVariableULLInt(const std::string name, const bool readIn = true);
+ Variable<float> *InquireVariableFloat(const std::string name,
const bool readIn = true);
- Variable<long double> *InquireVariableLDouble(const std::string name,
- const bool readIn = true);
- Variable<std::complex<float>> *
- InquireVariableCFloat(const std::string name, const bool readIn = true);
- Variable<std::complex<double>> *
- InquireVariableCDouble(const std::string name, const bool readIn = true);
- Variable<std::complex<long double>> *
- InquireVariableCLDouble(const std::string name, const bool readIn = true);
-
- /**
- * Not implemented
- * @param name
- * @param readIn
- * @return
- */
- VariableCompound *InquireVariableCompound(const std::string name,
+ Variable<double> *InquireVariableDouble(const std::string name,
const bool readIn = true);
+ Variable<long double> *InquireVariableLDouble(const std::string name,
+ const bool readIn = true);
+ Variable<std::complex<float>> *
+ InquireVariableCFloat(const std::string name, const bool readIn = true);
+ Variable<std::complex<double>> *
+ InquireVariableCDouble(const std::string name, const bool readIn = true);
+ Variable<std::complex<long double>> *
+ InquireVariableCLDouble(const std::string name, const bool readIn = true);
+
+ /**
+ * Not implemented
+ * @param name
+ * @param readIn
+ * @return
+ */
+ VariableCompound *InquireVariableCompound(const std::string name,
+ const bool readIn = true);
- void Close(const int transportIndex = -1);
+ void Close(const int transportIndex = -1);
private:
- capsule::STLVector
- m_Buffer; ///< heap capsule, contains data and metadata buffers
- // format::BP1Writer m_BP1Writer; ///< format object will provide the required
- // BP functionality to be applied on m_Buffer and m_Transports
-
- void Init(); ///< calls InitCapsules and InitTransports based on Method,
- /// called from constructor
- void InitCapsules();
- void InitTransports(); ///< from Transports
-
- std::string
- GetMdtmParameter(const std::string parameter,
- const std::map<std::string, std::string> &mdtmParameters);
-
- template <class T>
- Variable<T> *InquireVariableCommon(const std::string name, const bool readIn)
- {
- std::cout << "Hello BPReaderCommon\n";
-
- // here read variable metadata (dimensions, type, etc.)...then create a
- // Variable like below:
- // Variable<T>& variable = m_ADIOS.DefineVariable<T>( m_Name + "/" + name, )
- // return &variable; //return address if success
- return nullptr; // on failure
- }
+ capsule::STLVector
+ m_Buffer; ///< heap capsule, contains data and metadata buffers
+ // format::BP1Writer m_BP1Writer; ///< format object will provide the
+ // required
+ // BP functionality to be applied on m_Buffer and m_Transports
+
+ void Init(); ///< calls InitCapsules and InitTransports based on Method,
+ /// called from constructor
+ void InitCapsules();
+ void InitTransports(); ///< from Transports
+
+ std::string
+ GetMdtmParameter(const std::string parameter,
+ const std::map<std::string, std::string> &mdtmParameters);
+
+ template <class T>
+ Variable<T> *InquireVariableCommon(const std::string name,
+ const bool readIn)
+ {
+ std::cout << "Hello BPReaderCommon\n";
+
+ // here read variable metadata (dimensions, type, etc.)...then create a
+ // Variable like below:
+ // Variable<T>& variable = m_ADIOS.DefineVariable<T>( m_Name + "/" +
+ // name, )
+ // return &variable; //return address if success
+ return nullptr; // on failure
+ }
};
} // end namespace adios
diff --git a/include/engine/bp/BPFileWriter.h b/include/engine/bp/BPFileWriter.h
index 558eebbd9572b85a146ebd9fa2c2411a06d3901b..97db293c0defacf50cbced0b0ae84870c8e374c5 100644
--- a/include/engine/bp/BPFileWriter.h
+++ b/include/engine/bp/BPFileWriter.h
@@ -25,157 +25,165 @@ class BPFileWriter : public Engine
{
public:
- /**
- * Constructor for Writer writes in BP format into a single heap capsule,
- * manages several transports
- * @param name unique name given to the engine
- * @param accessMode
- * @param mpiComm
- * @param method
- * @param debugMode
- */
- BPFileWriter(ADIOS &adios, std::string name, const std::string &accessMode,
- MPI_Comm mpiComm, const Method &method,
- const IOMode iomode = IOMode::INDEPENDENT,
- const float timeout_sec = 0., const bool debugMode = false,
- const unsigned int nthreads = 1);
-
- ~BPFileWriter();
-
- void Write(Variable<char> &variable, const char *values);
- void Write(Variable<unsigned char> &variable, const unsigned char *values);
- void Write(Variable<short> &variable, const short *values);
- void Write(Variable<unsigned short> &variable, const unsigned short *values);
- void Write(Variable<int> &variable, const int *values);
- void Write(Variable<unsigned int> &variable, const unsigned int *values);
- void Write(Variable<long int> &variable, const long int *values);
- void Write(Variable<unsigned long int> &variable,
- const unsigned long int *values);
- void Write(Variable<long long int> &variable, const long long int *values);
- void Write(Variable<unsigned long long int> &variable,
- const unsigned long long int *values);
- void Write(Variable<float> &variable, const float *values);
- void Write(Variable<double> &variable, const double *values);
- void Write(Variable<long double> &variable, const long double *values);
- void Write(Variable<std::complex<float>> &variable,
- const std::complex<float> *values);
- void Write(Variable<std::complex<double>> &variable,
- const std::complex<double> *values);
- void Write(Variable<std::complex<long double>> &variable,
- const std::complex<long double> *values);
- void Write(VariableCompound &variable, const void *values);
-
- void Write(const std::string variableName, const char *values);
- void Write(const std::string variableName, const unsigned char *values);
- void Write(const std::string variableName, const short *values);
- void Write(const std::string variableName, const unsigned short *values);
- void Write(const std::string variableName, const int *values);
- void Write(const std::string variableName, const unsigned int *values);
- void Write(const std::string variableName, const long int *values);
- void Write(const std::string variableName, const unsigned long int *values);
- void Write(const std::string variableName, const long long int *values);
- void Write(const std::string variableName,
- const unsigned long long int *values);
- void Write(const std::string variableName, const float *values);
- void Write(const std::string variableName, const double *values);
- void Write(const std::string variableName, const long double *values);
- void Write(const std::string variableName, const std::complex<float> *values);
- void Write(const std::string variableName,
- const std::complex<double> *values);
- void Write(const std::string variableName,
- const std::complex<long double> *values);
- void Write(const std::string variableName, const void *values);
-
- void Advance(float timeout_sec = 0.0);
-
- /**
- * Closes a single transport or all transports
- * @param transportIndex, if -1 (default) closes all transports, otherwise it
- * closes a transport in m_Transport[transportIndex]. In debug mode the latter
- * is bounds-checked.
- */
- void Close(const int transportIndex = -1);
+ /**
+ * Constructor for Writer writes in BP format into a single heap capsule,
+ * manages several transports
+ * @param name unique name given to the engine
+ * @param accessMode
+ * @param mpiComm
+ * @param method
+ * @param debugMode
+ */
+ BPFileWriter(ADIOS &adios, std::string name, const std::string &accessMode,
+ MPI_Comm mpiComm, const Method &method,
+ const IOMode iomode = IOMode::INDEPENDENT,
+ const float timeout_sec = 0., const bool debugMode = false,
+ const unsigned int nthreads = 1);
+
+ ~BPFileWriter();
+
+ void Write(Variable<char> &variable, const char *values);
+ void Write(Variable<unsigned char> &variable, const unsigned char *values);
+ void Write(Variable<short> &variable, const short *values);
+ void Write(Variable<unsigned short> &variable,
+ const unsigned short *values);
+ void Write(Variable<int> &variable, const int *values);
+ void Write(Variable<unsigned int> &variable, const unsigned int *values);
+ void Write(Variable<long int> &variable, const long int *values);
+ void Write(Variable<unsigned long int> &variable,
+ const unsigned long int *values);
+ void Write(Variable<long long int> &variable, const long long int *values);
+ void Write(Variable<unsigned long long int> &variable,
+ const unsigned long long int *values);
+ void Write(Variable<float> &variable, const float *values);
+ void Write(Variable<double> &variable, const double *values);
+ void Write(Variable<long double> &variable, const long double *values);
+ void Write(Variable<std::complex<float>> &variable,
+ const std::complex<float> *values);
+ void Write(Variable<std::complex<double>> &variable,
+ const std::complex<double> *values);
+ void Write(Variable<std::complex<long double>> &variable,
+ const std::complex<long double> *values);
+ void Write(VariableCompound &variable, const void *values);
+
+ void Write(const std::string variableName, const char *values);
+ void Write(const std::string variableName, const unsigned char *values);
+ void Write(const std::string variableName, const short *values);
+ void Write(const std::string variableName, const unsigned short *values);
+ void Write(const std::string variableName, const int *values);
+ void Write(const std::string variableName, const unsigned int *values);
+ void Write(const std::string variableName, const long int *values);
+ void Write(const std::string variableName, const unsigned long int *values);
+ void Write(const std::string variableName, const long long int *values);
+ void Write(const std::string variableName,
+ const unsigned long long int *values);
+ void Write(const std::string variableName, const float *values);
+ void Write(const std::string variableName, const double *values);
+ void Write(const std::string variableName, const long double *values);
+ void Write(const std::string variableName,
+ const std::complex<float> *values);
+ void Write(const std::string variableName,
+ const std::complex<double> *values);
+ void Write(const std::string variableName,
+ const std::complex<long double> *values);
+ void Write(const std::string variableName, const void *values);
+
+ void Advance(float timeout_sec = 0.0);
+
+ /**
+ * Closes a single transport or all transports
+ * @param transportIndex, if -1 (default) closes all transports, otherwise
+ * it
+ * closes a transport in m_Transport[transportIndex]. In debug mode the
+ * latter
+ * is bounds-checked.
+ */
+ void Close(const int transportIndex = -1);
private:
- capsule::STLVector m_Buffer; ///< heap capsule using STL std::vector<char>
- format::BP1Writer m_BP1Writer; ///< format object will provide the required BP
- /// functionality to be applied on m_Buffer and
- /// m_Transports
- format::BP1MetadataSet m_MetadataSet; ///< metadata set accompanying the heap
- /// buffer data in bp format. Needed by
- /// m_BP1Writer
- format::BP1Aggregator m_BP1Aggregator;
-
- bool m_IsFirstClose = true; ///< set to false after first Close is reached so
- /// metadata doesn't have to be accommodated for a
- /// subsequent Close
- std::size_t m_MaxBufferSize; ///< maximum allowed memory to be allocated
- float m_GrowthFactor = 1.5; ///< capsule memory growth factor, new_memory =
- /// m_GrowthFactor * current_memory
-
- bool m_TransportFlush =
- false; ///< true: transport flush happened, buffer must be reset
- bool m_CloseProcessGroup = false; ///< set to true if advance is called, this
- /// prevents flattening the data and metadata
- /// in Close
-
- void Init();
- void InitParameters();
- void InitTransports();
- void InitProcessGroup();
-
- void WriteProcessGroupIndex();
-
- /**
- * Common function for primitive (including std::complex) writes
- * @param group
- * @param variableName
- * @param variable
- */
- template <class T>
- void WriteVariableCommon(Variable<T> &variable, const T *values)
- {
- if (m_MetadataSet.Log.m_IsActive == true)
- m_MetadataSet.Log.m_Timers[0].SetInitialTime();
-
- // set variable
- variable.m_AppValues = values;
- m_WrittenVariables.insert(variable.m_Name);
-
- // if first timestep Write
- if (m_MetadataSet.DataPGIsOpen == false) // create a new pg index
- WriteProcessGroupIndex();
-
- // pre-calculate new metadata and payload sizes
- // m_TransportFlush = CheckBufferAllocation(
- // m_BP1Writer.GetVariableIndexSize( variable ) +
- // variable.PayLoadSize(),
- // m_GrowthFactor,
- // m_MaxBufferSize,
- // m_Buffer.m_Data );
-
- // WRITE INDEX to data buffer and metadata structure (in memory)//
- m_BP1Writer.WriteVariableMetadata(variable, m_Buffer, m_MetadataSet);
-
- if (m_TransportFlush == true) // in batches
+ capsule::STLVector m_Buffer; ///< heap capsule using STL std::vector<char>
+ format::BP1Writer
+ m_BP1Writer; ///< format object will provide the required BP
+ /// functionality to be applied on m_Buffer and
+ /// m_Transports
+ format::BP1MetadataSet
+ m_MetadataSet; ///< metadata set accompanying the heap
+ /// buffer data in bp format. Needed by
+ /// m_BP1Writer
+ format::BP1Aggregator m_BP1Aggregator;
+
+ bool m_IsFirstClose =
+ true; ///< set to false after first Close is reached so
+ /// metadata doesn't have to be accommodated for a
+ /// subsequent Close
+ std::size_t m_MaxBufferSize; ///< maximum allowed memory to be allocated
+ float m_GrowthFactor = 1.5; ///< capsule memory growth factor, new_memory =
+ /// m_GrowthFactor * current_memory
+
+ bool m_TransportFlush =
+ false; ///< true: transport flush happened, buffer must be reset
+ bool m_CloseProcessGroup =
+ false; ///< set to true if advance is called, this
+ /// prevents flattening the data and metadata
+ /// in Close
+
+ void Init();
+ void InitParameters();
+ void InitTransports();
+ void InitProcessGroup();
+
+ void WriteProcessGroupIndex();
+
+ /**
+ * Common function for primitive (including std::complex) writes
+ * @param group
+ * @param variableName
+ * @param variable
+ */
+ template <class T>
+ void WriteVariableCommon(Variable<T> &variable, const T *values)
{
- // write pg index
-
- // flush to transports
-
- // reset relative positions to zero, update absolute position
- }
- else // Write data to buffer
- {
- m_BP1Writer.WriteVariablePayload(variable, m_Buffer, m_nThreads);
+ if (m_MetadataSet.Log.m_IsActive == true)
+ m_MetadataSet.Log.m_Timers[0].SetInitialTime();
+
+ // set variable
+ variable.m_AppValues = values;
+ m_WrittenVariables.insert(variable.m_Name);
+
+ // if first timestep Write
+ if (m_MetadataSet.DataPGIsOpen == false) // create a new pg index
+ WriteProcessGroupIndex();
+
+ // pre-calculate new metadata and payload sizes
+ // m_TransportFlush = CheckBufferAllocation(
+ // m_BP1Writer.GetVariableIndexSize( variable ) +
+ // variable.PayLoadSize(),
+ // m_GrowthFactor,
+ // m_MaxBufferSize,
+ // m_Buffer.m_Data );
+
+ // WRITE INDEX to data buffer and metadata structure (in memory)//
+ m_BP1Writer.WriteVariableMetadata(variable, m_Buffer, m_MetadataSet);
+
+ if (m_TransportFlush == true) // in batches
+ {
+ // write pg index
+
+ // flush to transports
+
+ // reset relative positions to zero, update absolute position
+ }
+ else // Write data to buffer
+ {
+ m_BP1Writer.WriteVariablePayload(variable, m_Buffer, m_nThreads);
+ }
+
+ variable.m_AppValues =
+ nullptr; // setting pointer to null as not needed after write
+
+ if (m_MetadataSet.Log.m_IsActive == true)
+ m_MetadataSet.Log.m_Timers[0].SetTime();
}
-
- variable.m_AppValues =
- nullptr; // setting pointer to null as not needed after write
-
- if (m_MetadataSet.Log.m_IsActive == true)
- m_MetadataSet.Log.m_Timers[0].SetTime();
- }
};
} // end namespace adios
diff --git a/include/engine/dataman/DataManReader.h b/include/engine/dataman/DataManReader.h
index 88ba7b65c84664dd906dca772311bd4f93e1fcbb..061d2713c2e70d828a563d96574d6ad91eb19b0d 100644
--- a/include/engine/dataman/DataManReader.h
+++ b/include/engine/dataman/DataManReader.h
@@ -28,114 +28,118 @@ class DataManReader : public Engine
{
public:
- /**
- * Constructor for dataman engine Reader for WAN communications
- * @param adios
- * @param name
- * @param accessMode
- * @param mpiComm
- * @param method
- * @param debugMode
- * @param nthreads
- */
- DataManReader(ADIOS &adios, const std::string name,
- const std::string accessMode, MPI_Comm mpiComm,
- const Method &method, const IOMode iomode,
- const float timeout_sec, const bool debugMode = false,
- const unsigned int nthreads = 1);
-
- ~DataManReader();
-
- /**
- * Set callback function from user application
- * @param callback function (get) provided by the user to be applied in
- * DataMan
- */
- void SetCallBack(std::function<void(const void *, std::string, std::string,
- std::string, Dims)>
- callback);
-
- Variable<void> *InquireVariable(const std::string name,
- const bool readIn = true);
- Variable<char> *InquireVariableChar(const std::string name,
- const bool readIn = true);
- Variable<unsigned char> *InquireVariableUChar(const std::string name,
- const bool readIn = true);
- Variable<short> *InquireVariableShort(const std::string name,
+ /**
+ * Constructor for dataman engine Reader for WAN communications
+ * @param adios
+ * @param name
+ * @param accessMode
+ * @param mpiComm
+ * @param method
+ * @param debugMode
+ * @param nthreads
+ */
+ DataManReader(ADIOS &adios, const std::string name,
+ const std::string accessMode, MPI_Comm mpiComm,
+ const Method &method, const IOMode iomode,
+ const float timeout_sec, const bool debugMode = false,
+ const unsigned int nthreads = 1);
+
+ ~DataManReader();
+
+ /**
+ * Set callback function from user application
+ * @param callback function (get) provided by the user to be applied in
+ * DataMan
+ */
+ void SetCallBack(std::function<void(const void *, std::string, std::string,
+ std::string, Dims)>
+ callback);
+
+ Variable<void> *InquireVariable(const std::string name,
+ const bool readIn = true);
+ Variable<char> *InquireVariableChar(const std::string name,
const bool readIn = true);
- Variable<unsigned short> *InquireVariableUShort(const std::string name,
+ Variable<unsigned char> *InquireVariableUChar(const std::string name,
const bool readIn = true);
- Variable<int> *InquireVariableInt(const std::string name,
- const bool readIn = true);
- Variable<unsigned int> *InquireVariableUInt(const std::string name,
- const bool readIn = true);
- Variable<long int> *InquireVariableLInt(const std::string name,
+ Variable<short> *InquireVariableShort(const std::string name,
const bool readIn = true);
- Variable<unsigned long int> *InquireVariableULInt(const std::string name,
+ Variable<unsigned short> *InquireVariableUShort(const std::string name,
const bool readIn = true);
- Variable<long long int> *InquireVariableLLInt(const std::string name,
+ Variable<int> *InquireVariableInt(const std::string name,
+ const bool readIn = true);
+ Variable<unsigned int> *InquireVariableUInt(const std::string name,
const bool readIn = true);
- Variable<unsigned long long int> *
- InquireVariableULLInt(const std::string name, const bool readIn = true);
- Variable<float> *InquireVariableFloat(const std::string name,
- const bool readIn = true);
- Variable<double> *InquireVariableDouble(const std::string name,
+ Variable<long int> *InquireVariableLInt(const std::string name,
+ const bool readIn = true);
+ Variable<unsigned long int> *InquireVariableULInt(const std::string name,
+ const bool readIn = true);
+ Variable<long long int> *InquireVariableLLInt(const std::string name,
+ const bool readIn = true);
+ Variable<unsigned long long int> *
+ InquireVariableULLInt(const std::string name, const bool readIn = true);
+ Variable<float> *InquireVariableFloat(const std::string name,
const bool readIn = true);
- Variable<long double> *InquireVariableLDouble(const std::string name,
- const bool readIn = true);
- Variable<std::complex<float>> *
- InquireVariableCFloat(const std::string name, const bool readIn = true);
- Variable<std::complex<double>> *
- InquireVariableCDouble(const std::string name, const bool readIn = true);
- Variable<std::complex<long double>> *
- InquireVariableCLDouble(const std::string name, const bool readIn = true);
-
- /**
- * Not implemented
- * @param name
- * @param readIn
- * @return
- */
- VariableCompound *InquireVariableCompound(const std::string name,
+ Variable<double> *InquireVariableDouble(const std::string name,
const bool readIn = true);
+ Variable<long double> *InquireVariableLDouble(const std::string name,
+ const bool readIn = true);
+ Variable<std::complex<float>> *
+ InquireVariableCFloat(const std::string name, const bool readIn = true);
+ Variable<std::complex<double>> *
+ InquireVariableCDouble(const std::string name, const bool readIn = true);
+ Variable<std::complex<long double>> *
+ InquireVariableCLDouble(const std::string name, const bool readIn = true);
+
+ /**
+ * Not implemented
+ * @param name
+ * @param readIn
+ * @return
+ */
+ VariableCompound *InquireVariableCompound(const std::string name,
+ const bool readIn = true);
- void Close(const int transportIndex = -1);
+ void Close(const int transportIndex = -1);
private:
- capsule::STLVector
- m_Buffer; ///< heap capsule, contains data and metadata buffers
- format::BP1Writer m_BP1Writer; ///< format object will provide the required BP
- /// functionality to be applied on m_Buffer and
- /// m_Transports
-
- bool m_DoRealTime = false;
- DataManager m_Man;
- std::function<void(const void *, std::string, std::string, std::string, Dims)>
- m_CallBack; ///< call back function
-
- void Init(); ///< calls InitCapsules and InitTransports based on Method,
- /// called from constructor
- void InitCapsules();
- void InitTransports(); ///< from Transports
-
- std::string
- GetMdtmParameter(const std::string parameter,
- const std::map<std::string, std::string> &mdtmParameters);
-
- template <class T>
- Variable<T> *InquireVariableCommon(const std::string name, const bool readIn)
- {
- std::cout << "I am hooked to the DataMan library\n";
- std::cout << "Hello DatamanReader from rank " << m_RankMPI << "\n";
- std::cout << "Trying to read variable " << name
- << " from one of the variables coming from a WAN transport\n";
-
- // here read variable metadata (dimensions, type, etc.)...then create a
- // Variable like below:
- // Variable<T>& variable = m_ADIOS.DefineVariable<T>( m_Name + "/" + name, )
- // return &variable; //return address if success
- return nullptr; // on failure
- }
+ capsule::STLVector
+ m_Buffer; ///< heap capsule, contains data and metadata buffers
+ format::BP1Writer
+ m_BP1Writer; ///< format object will provide the required BP
+ /// functionality to be applied on m_Buffer and
+ /// m_Transports
+
+ bool m_DoRealTime = false;
+ DataManager m_Man;
+ std::function<void(const void *, std::string, std::string, std::string,
+ Dims)>
+ m_CallBack; ///< call back function
+
+ void Init(); ///< calls InitCapsules and InitTransports based on Method,
+ /// called from constructor
+ void InitCapsules();
+ void InitTransports(); ///< from Transports
+
+ std::string
+ GetMdtmParameter(const std::string parameter,
+ const std::map<std::string, std::string> &mdtmParameters);
+
+ template <class T>
+ Variable<T> *InquireVariableCommon(const std::string name,
+ const bool readIn)
+ {
+ std::cout << "I am hooked to the DataMan library\n";
+ std::cout << "Hello DatamanReader from rank " << m_RankMPI << "\n";
+ std::cout << "Trying to read variable " << name
+ << " from one of the variables coming from a WAN transport\n";
+
+ // here read variable metadata (dimensions, type, etc.)...then create a
+ // Variable like below:
+ // Variable<T>& variable = m_ADIOS.DefineVariable<T>( m_Name + "/" +
+ // name, )
+ // return &variable; //return address if success
+ return nullptr; // on failure
+ }
};
} // end namespace
diff --git a/include/engine/dataman/DataManWriter.h b/include/engine/dataman/DataManWriter.h
index b60399fdcf7bc1f4e767669c862d97e74680d89c..3ca32bb3dad5f8e5b186d717c86a1609c16e0fa2 100644
--- a/include/engine/dataman/DataManWriter.h
+++ b/include/engine/dataman/DataManWriter.h
@@ -29,149 +29,155 @@ class DataManWriter : public Engine
{
public:
- /**
- * Constructor for dataman engine Writer for WAN communications
- * @param adios
- * @param name unique name given to the engine
- * @param accessMode
- * @param mpiComm
- * @param method
- * @param debugMode
- * @param nthreads
- */
- DataManWriter(ADIOS &adios, const std::string name,
- const std::string accessMode, MPI_Comm mpiComm,
- const Method &method, const IOMode iomode,
- const float timeout_sec, const bool debugMode = false,
- const unsigned int nthreads = 1);
-
- ~DataManWriter();
-
- void SetCallBack(std::function<void(const void *, std::string, std::string,
- std::string, Dims)>
- callback);
-
- void Write(Variable<char> &variable, const char *values);
- void Write(Variable<unsigned char> &variable, const unsigned char *values);
- void Write(Variable<short> &variable, const short *values);
- void Write(Variable<unsigned short> &variable, const unsigned short *values);
- void Write(Variable<int> &variable, const int *values);
- void Write(Variable<unsigned int> &variable, const unsigned int *values);
- void Write(Variable<long int> &variable, const long int *values);
- void Write(Variable<unsigned long int> &variable,
- const unsigned long int *values);
- void Write(Variable<long long int> &variable, const long long int *values);
- void Write(Variable<unsigned long long int> &variable,
- const unsigned long long int *values);
- void Write(Variable<float> &variable, const float *values);
- void Write(Variable<double> &variable, const double *values);
- void Write(Variable<long double> &variable, const long double *values);
- void Write(Variable<std::complex<float>> &variable,
- const std::complex<float> *values);
- void Write(Variable<std::complex<double>> &variable,
- const std::complex<double> *values);
- void Write(Variable<std::complex<long double>> &variable,
- const std::complex<long double> *values);
-
- void Write(const std::string variableName, const char *values);
- void Write(const std::string variableName, const unsigned char *values);
- void Write(const std::string variableName, const short *values);
- void Write(const std::string variableName, const unsigned short *values);
- void Write(const std::string variableName, const int *values);
- void Write(const std::string variableName, const unsigned int *values);
- void Write(const std::string variableName, const long int *values);
- void Write(const std::string variableName, const unsigned long int *values);
- void Write(const std::string variableName, const long long int *values);
- void Write(const std::string variableName,
- const unsigned long long int *values);
- void Write(const std::string variableName, const float *values);
- void Write(const std::string variableName, const double *values);
- void Write(const std::string variableName, const long double *values);
- void Write(const std::string variableName, const std::complex<float> *values);
- void Write(const std::string variableName,
- const std::complex<double> *values);
- void Write(const std::string variableName,
- const std::complex<long double> *values);
-
- void Close(const int transportIndex = -1);
+ /**
+ * Constructor for dataman engine Writer for WAN communications
+ * @param adios
+ * @param name unique name given to the engine
+ * @param accessMode
+ * @param mpiComm
+ * @param method
+ * @param debugMode
+ * @param nthreads
+ */
+ DataManWriter(ADIOS &adios, const std::string name,
+ const std::string accessMode, MPI_Comm mpiComm,
+ const Method &method, const IOMode iomode,
+ const float timeout_sec, const bool debugMode = false,
+ const unsigned int nthreads = 1);
+
+ ~DataManWriter();
+
+ void SetCallBack(std::function<void(const void *, std::string, std::string,
+ std::string, Dims)>
+ callback);
+
+ void Write(Variable<char> &variable, const char *values);
+ void Write(Variable<unsigned char> &variable, const unsigned char *values);
+ void Write(Variable<short> &variable, const short *values);
+ void Write(Variable<unsigned short> &variable,
+ const unsigned short *values);
+ void Write(Variable<int> &variable, const int *values);
+ void Write(Variable<unsigned int> &variable, const unsigned int *values);
+ void Write(Variable<long int> &variable, const long int *values);
+ void Write(Variable<unsigned long int> &variable,
+ const unsigned long int *values);
+ void Write(Variable<long long int> &variable, const long long int *values);
+ void Write(Variable<unsigned long long int> &variable,
+ const unsigned long long int *values);
+ void Write(Variable<float> &variable, const float *values);
+ void Write(Variable<double> &variable, const double *values);
+ void Write(Variable<long double> &variable, const long double *values);
+ void Write(Variable<std::complex<float>> &variable,
+ const std::complex<float> *values);
+ void Write(Variable<std::complex<double>> &variable,
+ const std::complex<double> *values);
+ void Write(Variable<std::complex<long double>> &variable,
+ const std::complex<long double> *values);
+
+ void Write(const std::string variableName, const char *values);
+ void Write(const std::string variableName, const unsigned char *values);
+ void Write(const std::string variableName, const short *values);
+ void Write(const std::string variableName, const unsigned short *values);
+ void Write(const std::string variableName, const int *values);
+ void Write(const std::string variableName, const unsigned int *values);
+ void Write(const std::string variableName, const long int *values);
+ void Write(const std::string variableName, const unsigned long int *values);
+ void Write(const std::string variableName, const long long int *values);
+ void Write(const std::string variableName,
+ const unsigned long long int *values);
+ void Write(const std::string variableName, const float *values);
+ void Write(const std::string variableName, const double *values);
+ void Write(const std::string variableName, const long double *values);
+ void Write(const std::string variableName,
+ const std::complex<float> *values);
+ void Write(const std::string variableName,
+ const std::complex<double> *values);
+ void Write(const std::string variableName,
+ const std::complex<long double> *values);
+
+ void Close(const int transportIndex = -1);
private:
- capsule::STLVector
- m_Buffer; ///< heap capsule, contains data and metadata buffers
- format::BP1Writer m_BP1Writer; ///< format object will provide the required BP
- /// functionality to be applied on m_Buffer and
- /// m_Transports
-
- bool m_DoRealTime = false;
- bool m_DoMonitor = false;
- DataManager m_Man;
- std::function<void(const void *, std::string, std::string, std::string, Dims)>
- m_CallBack; ///< call back function
-
- void Init(); ///< calls InitCapsules and InitTransports based on Method,
- /// called from constructor
- void InitCapsules();
- void InitTransports(); ///< from Transports
-
- /**
- * From transport Mdtm in m_Method
- * @param parameter must be an accepted parameter
- * @param mdtmParameters
- * @return value either returns user-defined from "parameter=value" or a
- * default
- */
- std::string
- GetMdtmParameter(const std::string parameter,
- const std::map<std::string, std::string> &mdtmParameters);
-
- template <class T>
- void WriteVariableCommon(Variable<T> &variable, const T *values)
- {
- // here comes your magic at Writing now variable.m_UserValues has the data
- // passed by the user
- // set variable
- variable.m_AppValues = values;
- m_WrittenVariables.insert(variable.m_Name);
-
- // This part will go away, this is just to monitor variables per rank
-
- json jmsg;
- jmsg["doid"] = m_Name;
- jmsg["var"] = variable.m_Name;
- jmsg["dtype"] = GetType<T>();
- jmsg["putshape"] = variable.m_Dimensions;
- if (variable.m_GlobalDimensions.size() == 0)
- variable.m_GlobalDimensions = variable.m_Dimensions;
- jmsg["varshape"] = variable.m_GlobalDimensions;
- if (variable.m_GlobalOffsets.size() == 0)
- variable.m_GlobalOffsets.assign(variable.m_Dimensions.size(), 0);
- jmsg["offset"] = variable.m_GlobalOffsets;
- jmsg["timestep"] = 0;
- m_Man.put(values, jmsg);
-
- if (m_DoMonitor)
+ capsule::STLVector
+ m_Buffer; ///< heap capsule, contains data and metadata buffers
+ format::BP1Writer
+ m_BP1Writer; ///< format object will provide the required BP
+ /// functionality to be applied on m_Buffer and
+ /// m_Transports
+
+ bool m_DoRealTime = false;
+ bool m_DoMonitor = false;
+ DataManager m_Man;
+ std::function<void(const void *, std::string, std::string, std::string,
+ Dims)>
+ m_CallBack; ///< call back function
+
+ void Init(); ///< calls InitCapsules and InitTransports based on Method,
+ /// called from constructor
+ void InitCapsules();
+ void InitTransports(); ///< from Transports
+
+ /**
+ * From transport Mdtm in m_Method
+ * @param parameter must be an accepted parameter
+ * @param mdtmParameters
+ * @return value either returns user-defined from "parameter=value" or a
+ * default
+ */
+ std::string
+ GetMdtmParameter(const std::string parameter,
+ const std::map<std::string, std::string> &mdtmParameters);
+
+ template <class T>
+ void WriteVariableCommon(Variable<T> &variable, const T *values)
{
- MPI_Barrier(m_MPIComm);
- std::cout << "I am hooked to the DataMan library\n";
- std::cout << "putshape " << variable.m_Dimensions.size() << endl;
- std::cout << "varshape " << variable.m_GlobalDimensions.size() << endl;
- std::cout << "offset " << variable.m_GlobalOffsets.size() << endl;
- for (int i = 0; i < m_SizeMPI; ++i)
- {
- if (i == m_RankMPI)
+ // here comes your magic at Writing now variable.m_UserValues has the
+ // data
+ // passed by the user
+ // set variable
+ variable.m_AppValues = values;
+ m_WrittenVariables.insert(variable.m_Name);
+
+ // This part will go away, this is just to monitor variables per rank
+
+ json jmsg;
+ jmsg["doid"] = m_Name;
+ jmsg["var"] = variable.m_Name;
+ jmsg["dtype"] = GetType<T>();
+ jmsg["putshape"] = variable.m_Dimensions;
+ if (variable.m_GlobalDimensions.size() == 0)
+ variable.m_GlobalDimensions = variable.m_Dimensions;
+ jmsg["varshape"] = variable.m_GlobalDimensions;
+ if (variable.m_GlobalOffsets.size() == 0)
+ variable.m_GlobalOffsets.assign(variable.m_Dimensions.size(), 0);
+ jmsg["offset"] = variable.m_GlobalOffsets;
+ jmsg["timestep"] = 0;
+ m_Man.put(values, jmsg);
+
+ if (m_DoMonitor)
{
- std::cout << "Rank: " << m_RankMPI << "\n";
- variable.Monitor(std::cout);
- std::cout << std::endl;
+ MPI_Barrier(m_MPIComm);
+ std::cout << "I am hooked to the DataMan library\n";
+ std::cout << "putshape " << variable.m_Dimensions.size() << endl;
+ std::cout << "varshape " << variable.m_GlobalDimensions.size()
+ << endl;
+ std::cout << "offset " << variable.m_GlobalOffsets.size() << endl;
+ for (int i = 0; i < m_SizeMPI; ++i)
+ {
+ if (i == m_RankMPI)
+ {
+ std::cout << "Rank: " << m_RankMPI << "\n";
+ variable.Monitor(std::cout);
+ std::cout << std::endl;
+ }
+ else
+ {
+ sleep(1);
+ }
+ }
+ MPI_Barrier(m_MPIComm);
}
- else
- {
- sleep(1);
- }
- }
- MPI_Barrier(m_MPIComm);
}
- }
};
} // end namespace adios
diff --git a/include/format/BP1.h b/include/format/BP1.h
index fd2e16a4a3bb872631d0053baea7cba40ca7c29f..518325ecdbabfa44403bb3306853a101fccdaa82 100644
--- a/include/format/BP1.h
+++ b/include/format/BP1.h
@@ -35,15 +35,15 @@ namespace format
*/
struct BP1Index
{
- std::vector<char> Buffer; ///< metadata variable index, start with 100Kb
- std::uint64_t Count =
- 0; ///< number of characteristics sets (time and spatial aggregation)
- const std::uint32_t MemberID;
-
- BP1Index(const std::uint32_t memberID) : MemberID{memberID}
- {
- Buffer.reserve(500);
- }
+ std::vector<char> Buffer; ///< metadata variable index, start with 100Kb
+ std::uint64_t Count = 0; ///< number of characteristics sets (time and
+ /// spatial aggregation)
+ const std::uint32_t MemberID;
+
+ BP1Index(const std::uint32_t memberID) : MemberID{memberID}
+ {
+ Buffer.reserve(500);
+ }
};
/**
@@ -51,36 +51,39 @@ struct BP1Index
*/
struct BP1MetadataSet
{
- std::uint32_t TimeStep; ///< current time step, updated with advance step, if
- /// append it will be updated to last, starts with one
- /// in ADIOS1
-
- BP1Index PGIndex = BP1Index(0); ///< single buffer for PGIndex
-
- // no priority for now
- std::unordered_map<std::string, BP1Index>
- VarsIndices; ///< key: variable name, value: bp metadata variable index
- std::unordered_map<std::string, BP1Index> AttributesIndices; ///< key:
- /// attribute
- /// name, value:
- /// bp metadata
- /// attribute
- /// index
-
- const unsigned int MiniFooterSize = 28; ///< from bpls reader
-
- // PG (relative) positions in Data buffer to be updated
- std::uint64_t DataPGCount = 0;
- std::size_t DataPGLengthPosition = 0; ///< current PG initial ( relative )
- /// position, needs to be updated in
- /// every advance step or init
- std::uint32_t DataPGVarsCount = 0; ///< variables in current PG
- std::size_t DataPGVarsCountPosition =
- 0; ///< current PG variable count ( relative ) position, needs to be
- /// updated in every advance step or init
- bool DataPGIsOpen = false;
-
- Profiler Log; ///< object that takes buffering profiling info
+ std::uint32_t
+ TimeStep; ///< current time step, updated with advance step, if
+ /// append it will be updated to last, starts with one
+ /// in ADIOS1
+
+ BP1Index PGIndex = BP1Index(0); ///< single buffer for PGIndex
+
+ // no priority for now
+ std::unordered_map<std::string, BP1Index> VarsIndices; ///< key: variable
+ /// name, value: bp
+ /// metadata variable
+ /// index
+ std::unordered_map<std::string, BP1Index> AttributesIndices; ///< key:
+ /// attribute
+ /// name, value:
+ /// bp metadata
+ /// attribute
+ /// index
+
+ const unsigned int MiniFooterSize = 28; ///< from bpls reader
+
+ // PG (relative) positions in Data buffer to be updated
+ std::uint64_t DataPGCount = 0;
+ std::size_t DataPGLengthPosition = 0; ///< current PG initial ( relative )
+ /// position, needs to be updated in
+ /// every advance step or init
+ std::uint32_t DataPGVarsCount = 0; ///< variables in current PG
+ std::size_t DataPGVarsCountPosition =
+ 0; ///< current PG variable count ( relative ) position, needs to be
+ /// updated in every advance step or init
+ bool DataPGIsOpen = false;
+
+ Profiler Log; ///< object that takes buffering profiling info
};
/**
@@ -90,228 +93,228 @@ class BP1
{
public:
- /**
- * Checks if input name has .bp extension and returns a .bp directory name
- * @param name input (might or not have .bp)
- * @return either name.bp (name has no .bp) or name (name has .bp extension)
- */
- std::string GetDirectoryName(const std::string name) const noexcept;
-
- /**
- * Opens rank files in the following format:
- * if transport.m_MPIComm different from MPI_Comm_SELF -->
- * name.bp.dir/name.bp.rank
- * @param name might contain .bp or not, if not .bp will be added
- * @param accessMode "write" "w", "r" "read", "append" "a"
- * @param transport file I/O transport
- */
- void OpenRankFiles(const std::string name, const std::string accessMode,
- Transport &transport) const;
+ /**
+ * Checks if input name has .bp extension and returns a .bp directory name
+ * @param name input (might or not have .bp)
+ * @return either name.bp (name has no .bp) or name (name has .bp extension)
+ */
+ std::string GetDirectoryName(const std::string name) const noexcept;
+
+ /**
+ * Opens rank files in the following format:
+ * if transport.m_MPIComm different from MPI_Comm_SELF -->
+ * name.bp.dir/name.bp.rank
+ * @param name might contain .bp or not, if not .bp will be added
+ * @param accessMode "write" "w", "r" "read", "append" "a"
+ * @param transport file I/O transport
+ */
+ void OpenRankFiles(const std::string name, const std::string accessMode,
+ Transport &transport) const;
protected:
- /**
- * method type for file I/O
- */
- enum IO_METHOD
- {
- METHOD_UNKNOWN = -2 //!< ADIOS_METHOD_UNKNOWN
- ,
- METHOD_NULL = -1 //!< ADIOS_METHOD_NULL
- ,
- METHOD_MPI = 0 //!< METHOD_MPI
- ,
- METHOD_DATATAP = 1 // OBSOLETE
- ,
- METHOD_POSIX = 2 //!< METHOD_POSIX
- ,
- METHOD_DATASPACES = 3 //!< METHOD_DATASPACES
- ,
- METHOD_VTK = 4 // non-existent
- ,
- METHOD_POSIX_ASCII = 5 // non-existent
- ,
- METHOD_MPI_CIO = 6 // OBSOLETE
- ,
- METHOD_PHDF5 = 7 //!< METHOD_PHDF5
- ,
- METHOD_PROVENANCE = 8 // OBSOLETE
- ,
- METHOD_MPI_STRIPE = 9 // OBSOLETE
- ,
- METHOD_MPI_LUSTRE = 10 //!< METHOD_MPI_LUSTRE
- ,
- METHOD_MPI_STAGGER = 11 // OBSOLETE
- ,
- METHOD_MPI_AGG = 12 // OBSOLETE
- ,
- METHOD_ADAPTIVE = 13 // OBSOLETE
- ,
- METHOD_POSIX1 = 14 // OBSOLETE
- ,
- METHOD_NC4 = 15 //!< METHOD_NC4
- ,
- METHOD_MPI_AMR = 16 //!< METHOD_MPI_AMR
- ,
- METHOD_MPI_AMR1 = 17 // OBSOLETE
- ,
- METHOD_FLEXPATH = 18 //!< METHOD_FLEXPATH
- ,
- METHOD_NSSI_STAGING = 19 //!< METHOD_NSSI_STAGING
- ,
- METHOD_NSSI_FILTER = 20 //!< METHOD_NSSI_FILTER
- ,
- METHOD_DIMES = 21 //!< METHOD_DIMES
- ,
- METHOD_VAR_MERGE = 22 //!< METHOD_VAR_MERGE
- ,
- METHOD_MPI_BGQ = 23 //!< METHOD_MPI_BGQ
- ,
- METHOD_ICEE = 24 //!< METHOD_ICEE
- ,
- METHOD_COUNT = 25 //!< METHOD_COUNT
- ,
- METHOD_FSTREAM = 26,
- METHOD_FILE = 27,
- METHOD_ZMQ = 28,
- METHOD_MDTM = 29
- };
-
- /**
- * DataTypes mapping in BP Format
- */
- enum DataTypes
- {
- type_unknown = -1, //!< type_unknown
- type_byte = 0, //!< type_byte
- type_short = 1, //!< type_short
- type_integer = 2, //!< type_integer
- type_long = 4, //!< type_long
-
- type_unsigned_byte = 50, //!< type_unsigned_byte
- type_unsigned_short = 51, //!< type_unsigned_short
- type_unsigned_integer = 52, //!< type_unsigned_integer
- type_unsigned_long = 54, //!< type_unsigned_long
-
- type_real = 5, //!< type_real or float
- type_double = 6, //!< type_double
- type_long_double = 7, //!< type_long_double
-
- type_string = 9, //!< type_string
- type_complex = 10, //!< type_complex
- type_double_complex = 11, //!< type_double_complex
- type_string_array = 12 //!< type_string_array
- };
-
- /**
- * Characteristic ID in variable metadata
- */
- enum VariableCharacteristicID
- {
- characteristic_value = 0, //!< characteristic_value
- characteristic_min = 1, //!< Used to read in older bp file format
- characteristic_max = 2, //!< Used to read in older bp file format
- characteristic_offset = 3, //!< characteristic_offset
- characteristic_dimensions = 4, //!< characteristic_dimensions
- characteristic_var_id = 5, //!< characteristic_var_id
- characteristic_payload_offset = 6, //!< characteristic_payload_offset
- characteristic_file_index = 7, //!< characteristic_file_index
- characteristic_time_index = 8, //!< characteristic_time_index
- characteristic_bitmap = 9, //!< characteristic_bitmap
- characteristic_stat = 10, //!< characteristic_stat
- characteristic_transform_type = 11 //!< characteristic_transform_type
- };
-
- /** Define statistics type for characteristic ID = 10 in bp1 format */
- enum VariableStatistics
- {
- statistic_min = 0,
- statistic_max = 1,
- statistic_cnt = 2,
- statistic_sum = 3,
- statistic_sum_square = 4,
- statistic_hist = 5,
- statistic_finite = 6
- };
-
- template <class T> struct Stats
- {
- T Min;
- T Max;
- std::uint64_t Offset;
- std::uint64_t PayloadOffset;
- std::uint32_t TimeIndex;
- std::uint32_t MemberID;
-
- // unsigned long int count;
- // long double sum;
- // long double sumSquare;
- // unsigned long int histogram
- // bool finite??
- };
-
- /**
- * Returns data type index from enum Datatypes
- * @param variable input variable
- * @return data type
- */
- template <class T> inline std::int8_t GetDataType() const noexcept
- {
- return type_unknown;
- }
-
- std::vector<std::uint8_t>
- GetMethodIDs(const std::vector<std::shared_ptr<Transport>> &transports) const
- noexcept;
+ /**
+ * method type for file I/O
+ */
+ enum IO_METHOD
+ {
+ METHOD_UNKNOWN = -2 //!< ADIOS_METHOD_UNKNOWN
+ ,
+ METHOD_NULL = -1 //!< ADIOS_METHOD_NULL
+ ,
+ METHOD_MPI = 0 //!< METHOD_MPI
+ ,
+ METHOD_DATATAP = 1 // OBSOLETE
+ ,
+ METHOD_POSIX = 2 //!< METHOD_POSIX
+ ,
+ METHOD_DATASPACES = 3 //!< METHOD_DATASPACES
+ ,
+ METHOD_VTK = 4 // non-existent
+ ,
+ METHOD_POSIX_ASCII = 5 // non-existent
+ ,
+ METHOD_MPI_CIO = 6 // OBSOLETE
+ ,
+ METHOD_PHDF5 = 7 //!< METHOD_PHDF5
+ ,
+ METHOD_PROVENANCE = 8 // OBSOLETE
+ ,
+ METHOD_MPI_STRIPE = 9 // OBSOLETE
+ ,
+ METHOD_MPI_LUSTRE = 10 //!< METHOD_MPI_LUSTRE
+ ,
+ METHOD_MPI_STAGGER = 11 // OBSOLETE
+ ,
+ METHOD_MPI_AGG = 12 // OBSOLETE
+ ,
+ METHOD_ADAPTIVE = 13 // OBSOLETE
+ ,
+ METHOD_POSIX1 = 14 // OBSOLETE
+ ,
+ METHOD_NC4 = 15 //!< METHOD_NC4
+ ,
+ METHOD_MPI_AMR = 16 //!< METHOD_MPI_AMR
+ ,
+ METHOD_MPI_AMR1 = 17 // OBSOLETE
+ ,
+ METHOD_FLEXPATH = 18 //!< METHOD_FLEXPATH
+ ,
+ METHOD_NSSI_STAGING = 19 //!< METHOD_NSSI_STAGING
+ ,
+ METHOD_NSSI_FILTER = 20 //!< METHOD_NSSI_FILTER
+ ,
+ METHOD_DIMES = 21 //!< METHOD_DIMES
+ ,
+ METHOD_VAR_MERGE = 22 //!< METHOD_VAR_MERGE
+ ,
+ METHOD_MPI_BGQ = 23 //!< METHOD_MPI_BGQ
+ ,
+ METHOD_ICEE = 24 //!< METHOD_ICEE
+ ,
+ METHOD_COUNT = 25 //!< METHOD_COUNT
+ ,
+ METHOD_FSTREAM = 26,
+ METHOD_FILE = 27,
+ METHOD_ZMQ = 28,
+ METHOD_MDTM = 29
+ };
+
+ /**
+ * DataTypes mapping in BP Format
+ */
+ enum DataTypes
+ {
+ type_unknown = -1, //!< type_unknown
+ type_byte = 0, //!< type_byte
+ type_short = 1, //!< type_short
+ type_integer = 2, //!< type_integer
+ type_long = 4, //!< type_long
+
+ type_unsigned_byte = 50, //!< type_unsigned_byte
+ type_unsigned_short = 51, //!< type_unsigned_short
+ type_unsigned_integer = 52, //!< type_unsigned_integer
+ type_unsigned_long = 54, //!< type_unsigned_long
+
+ type_real = 5, //!< type_real or float
+ type_double = 6, //!< type_double
+ type_long_double = 7, //!< type_long_double
+
+ type_string = 9, //!< type_string
+ type_complex = 10, //!< type_complex
+ type_double_complex = 11, //!< type_double_complex
+ type_string_array = 12 //!< type_string_array
+ };
+
+ /**
+ * Characteristic ID in variable metadata
+ */
+ enum VariableCharacteristicID
+ {
+ characteristic_value = 0, //!< characteristic_value
+ characteristic_min = 1, //!< Used to read in older bp file format
+ characteristic_max = 2, //!< Used to read in older bp file format
+ characteristic_offset = 3, //!< characteristic_offset
+ characteristic_dimensions = 4, //!< characteristic_dimensions
+ characteristic_var_id = 5, //!< characteristic_var_id
+ characteristic_payload_offset = 6, //!< characteristic_payload_offset
+ characteristic_file_index = 7, //!< characteristic_file_index
+ characteristic_time_index = 8, //!< characteristic_time_index
+ characteristic_bitmap = 9, //!< characteristic_bitmap
+ characteristic_stat = 10, //!< characteristic_stat
+ characteristic_transform_type = 11 //!< characteristic_transform_type
+ };
+
+ /** Define statistics type for characteristic ID = 10 in bp1 format */
+ enum VariableStatistics
+ {
+ statistic_min = 0,
+ statistic_max = 1,
+ statistic_cnt = 2,
+ statistic_sum = 3,
+ statistic_sum_square = 4,
+ statistic_hist = 5,
+ statistic_finite = 6
+ };
+
+ template <class T> struct Stats
+ {
+ T Min;
+ T Max;
+ std::uint64_t Offset;
+ std::uint64_t PayloadOffset;
+ std::uint32_t TimeIndex;
+ std::uint32_t MemberID;
+
+ // unsigned long int count;
+ // long double sum;
+ // long double sumSquare;
+ // unsigned long int histogram
+ // bool finite??
+ };
+
+ /**
+ * Returns data type index from enum Datatypes
+ * @param variable input variable
+ * @return data type
+ */
+ template <class T> inline std::int8_t GetDataType() const noexcept
+ {
+ return type_unknown;
+ }
+
+ std::vector<std::uint8_t> GetMethodIDs(
+ const std::vector<std::shared_ptr<Transport>> &transports) const
+ noexcept;
};
// Moving template BP1Writer::GetDataType template specializations outside of
// the class
template <> inline std::int8_t BP1::GetDataType<char>() const noexcept
{
- return type_byte;
+ return type_byte;
}
template <> inline std::int8_t BP1::GetDataType<short>() const noexcept
{
- return type_short;
+ return type_short;
}
template <> inline std::int8_t BP1::GetDataType<int>() const noexcept
{
- return type_integer;
+ return type_integer;
}
template <> inline std::int8_t BP1::GetDataType<long int>() const noexcept
{
- return type_long;
+ return type_long;
}
template <> inline std::int8_t BP1::GetDataType<unsigned char>() const noexcept
{
- return type_unsigned_byte;
+ return type_unsigned_byte;
}
template <> inline std::int8_t BP1::GetDataType<unsigned short>() const noexcept
{
- return type_unsigned_short;
+ return type_unsigned_short;
}
template <> inline std::int8_t BP1::GetDataType<unsigned int>() const noexcept
{
- return type_unsigned_integer;
+ return type_unsigned_integer;
}
template <>
inline std::int8_t BP1::GetDataType<unsigned long int>() const noexcept
{
- return type_unsigned_long;
+ return type_unsigned_long;
}
template <> inline std::int8_t BP1::GetDataType<float>() const noexcept
{
- return type_real;
+ return type_real;
}
template <> inline std::int8_t BP1::GetDataType<double>() const noexcept
{
- return type_double;
+ return type_double;
}
template <> inline std::int8_t BP1::GetDataType<long double>() const noexcept
{
- return type_long_double;
+ return type_long_double;
}
} // end namespace format
diff --git a/include/format/BP1Aggregator.h b/include/format/BP1Aggregator.h
index a8cf13372fd7b105b0d59967498af1589fd55c18..0522975a19d843c929deeffc3c0c9076ca23779b 100644
--- a/include/format/BP1Aggregator.h
+++ b/include/format/BP1Aggregator.h
@@ -25,28 +25,29 @@ class BP1Aggregator
{
public:
- MPI_Comm m_MPIComm = MPI_COMM_SELF; ///< MPI communicator from Engine
- int m_RankMPI = 0; ///< current MPI rank process
- int m_SizeMPI = 1; ///< current MPI processes size
-
- /**
- * Unique constructor
- * @param mpiComm coming from engine
- */
- BP1Aggregator(MPI_Comm mpiComm, const bool debugMode = false);
-
- ~BP1Aggregator();
-
- /**
- * Function that aggregates and writes (from rank = 0) profiling.log in python
- * dictionary format
- * @param rankLog contain rank profiling info to be aggregated
- */
- void WriteProfilingLog(const std::string fileName,
- const std::string &rankLog);
+ MPI_Comm m_MPIComm = MPI_COMM_SELF; ///< MPI communicator from Engine
+ int m_RankMPI = 0; ///< current MPI rank process
+ int m_SizeMPI = 1; ///< current MPI processes size
+
+ /**
+ * Unique constructor
+ * @param mpiComm coming from engine
+ */
+ BP1Aggregator(MPI_Comm mpiComm, const bool debugMode = false);
+
+ ~BP1Aggregator();
+
+ /**
+ * Function that aggregates and writes (from rank = 0) profiling.log in
+ * python
+ * dictionary format
+ * @param rankLog contain rank profiling info to be aggregated
+ */
+ void WriteProfilingLog(const std::string fileName,
+ const std::string &rankLog);
private:
- const bool m_DebugMode = false;
+ const bool m_DebugMode = false;
};
} // end namespace format
diff --git a/include/format/BP1Writer.h b/include/format/BP1Writer.h
index 1a08598a4b2a4fa55c8b2ce86301eeb20354dc38..765961978bcb4c5a15040981e342b87ac865e996 100644
--- a/include/format/BP1Writer.h
+++ b/include/format/BP1Writer.h
@@ -34,487 +34,502 @@ class BP1Writer : public BP1
{
public:
- unsigned int m_Threads =
- 1; ///< number of threads for thread operations in large array (min,max)
- unsigned int m_Verbosity =
- 0; ///< statistics verbosity, can change if redefined in Engine method.
- float m_GrowthFactor =
- 1.5; ///< memory growth factor, can change if redefined in Engine method.
- const std::uint8_t m_Version = 3; ///< BP format version
-
- /**
- * Calculates the Process Index size in bytes according to the BP format,
- * including list of method with no parameters (for now)
- * @param name
- * @param timeStepName
- * @param numberOfTransports
- * @return size of pg index
- */
- std::size_t
- GetProcessGroupIndexSize(const std::string name,
- const std::string timeStepName,
- const std::size_t numberOfTransports) const noexcept;
-
- /**
- * Writes a process group index PGIndex and list of methods (from transports),
- * done at Open or aggregation of new time step
- * Version that operates on a single heap buffer and metadataset.
- * @param isFortran
- * @param name
- * @param processID
- * @param transports
- * @param buffer
- * @param metadataSet
- */
- void WriteProcessGroupIndex(
- const bool isFortran, const std::string name,
- const std::uint32_t processID,
- const std::vector<std::shared_ptr<Transport>> &transports,
- capsule::STLVector &heap, BP1MetadataSet &metadataSet) const noexcept;
-
- /**
- * Returns the estimated variable index size
- * @param group
- * @param variableName
- * @param variable
- * @param verbosity
- * @return variable index size
- */
- template <class T>
- size_t GetVariableIndexSize(const Variable<T> &variable) const noexcept
- {
- // size_t indexSize = varEntryLength + memberID + lengthGroupName +
- // groupName + lengthVariableName + lengthOfPath + path + datatype
- size_t indexSize = 23; // without characteristics
- indexSize += variable.m_Name.size();
-
- // characteristics 3 and 4, check variable number of dimensions
- const std::size_t dimensions =
- variable.DimensionsSize(); // number of commas in CSV + 1
- indexSize += 28 * dimensions; // 28 bytes per dimension
- indexSize += 1; // id
-
- // characteristics, offset + payload offset in data
- indexSize += 2 * (1 + 8);
- // characteristic 0, if scalar add value, for now only allowing string
- if (dimensions == 1)
+ unsigned int m_Threads = 1; ///< number of threads for thread operations in
+ /// large array (min,max)
+ unsigned int m_Verbosity = 0; ///< statistics verbosity, can change if
+ /// redefined in Engine method.
+ float m_GrowthFactor = 1.5; ///< memory growth factor, can change if
+ /// redefined in Engine method.
+ const std::uint8_t m_Version = 3; ///< BP format version
+
+ /**
+ * Calculates the Process Index size in bytes according to the BP format,
+ * including list of method with no parameters (for now)
+ * @param name
+ * @param timeStepName
+ * @param numberOfTransports
+ * @return size of pg index
+ */
+ std::size_t GetProcessGroupIndexSize(
+ const std::string name, const std::string timeStepName,
+ const std::size_t numberOfTransports) const noexcept;
+
+ /**
+ * Writes a process group index PGIndex and list of methods (from
+ * transports),
+ * done at Open or aggregation of new time step
+ * Version that operates on a single heap buffer and metadataset.
+ * @param isFortran
+ * @param name
+ * @param processID
+ * @param transports
+ * @param buffer
+ * @param metadataSet
+ */
+ void WriteProcessGroupIndex(
+ const bool isFortran, const std::string name,
+ const std::uint32_t processID,
+ const std::vector<std::shared_ptr<Transport>> &transports,
+ capsule::STLVector &heap, BP1MetadataSet &metadataSet) const noexcept;
+
+ /**
+ * Returns the estimated variable index size
+ * @param group
+ * @param variableName
+ * @param variable
+ * @param verbosity
+ * @return variable index size
+ */
+ template <class T>
+ size_t GetVariableIndexSize(const Variable<T> &variable) const noexcept
{
- indexSize += sizeof(T);
- indexSize += 1; // id
- // must have an if here
- indexSize += 2 + variable.m_Name.size();
- indexSize += 1; // id
+ // size_t indexSize = varEntryLength + memberID + lengthGroupName +
+ // groupName + lengthVariableName + lengthOfPath + path + datatype
+ size_t indexSize = 23; // without characteristics
+ indexSize += variable.m_Name.size();
+
+ // characteristics 3 and 4, check variable number of dimensions
+ const std::size_t dimensions =
+ variable.DimensionsSize(); // number of commas in CSV + 1
+ indexSize += 28 * dimensions; // 28 bytes per dimension
+ indexSize += 1; // id
+
+ // characteristics, offset + payload offset in data
+ indexSize += 2 * (1 + 8);
+ // characteristic 0, if scalar add value, for now only allowing string
+ if (dimensions == 1)
+ {
+ indexSize += sizeof(T);
+ indexSize += 1; // id
+ // must have an if here
+ indexSize += 2 + variable.m_Name.size();
+ indexSize += 1; // id
+ }
+
+ // characteristic statistics
+ if (m_Verbosity == 0) // default, only min and max
+ {
+ indexSize += 2 * (sizeof(T) + 1);
+ indexSize += 1 + 1; // id
+ }
+
+ return indexSize + 12; /// extra 12 bytes in case of attributes
+ // need to add transform characteristics
}
- // characteristic statistics
- if (m_Verbosity == 0) // default, only min and max
+ /**
+ * Version for primitive types (except std::complex<T>)
+ * @param variable
+ * @param heap
+ * @param metadataSet
+ */
+ template <class T>
+ inline void WriteVariableMetadata(const Variable<T> &variable,
+ capsule::STLVector &heap,
+ BP1MetadataSet &metadataSet) const
+ noexcept
{
- indexSize += 2 * (sizeof(T) + 1);
- indexSize += 1 + 1; // id
+ Stats<T> stats = GetStats(variable);
+ WriteVariableMetadataCommon(variable, stats, heap, metadataSet);
}
- return indexSize + 12; /// extra 12 bytes in case of attributes
- // need to add transform characteristics
- }
-
- /**
- * Version for primitive types (except std::complex<T>)
- * @param variable
- * @param heap
- * @param metadataSet
- */
- template <class T>
- inline void WriteVariableMetadata(const Variable<T> &variable,
- capsule::STLVector &heap,
- BP1MetadataSet &metadataSet) const noexcept
- {
- Stats<T> stats = GetStats(variable);
- WriteVariableMetadataCommon(variable, stats, heap, metadataSet);
- }
-
- /**
- * Overloaded version for std::complex<T> variables
- * @param variable
- * @param heap
- * @param metadataSet
- */
- template <class T>
- void WriteVariableMetadata(const Variable<std::complex<T>> &variable,
- capsule::STLVector &heap,
- BP1MetadataSet &metadataSet) const noexcept
- {
- Stats<T> stats = GetStats(variable);
- WriteVariableMetadataCommon(variable, stats, heap, metadataSet);
- }
-
- /**
- * Expensive part this is only for heap buffers need to adapt to vector of
- * capsules
- * @param variable
- * @param buffer
- */
- template <class T>
- void WriteVariablePayload(const Variable<T> &variable,
- capsule::STLVector &heap,
- const unsigned int nthreads = 1) const noexcept
- {
- // EXPENSIVE part, might want to use threads if large, serial for now
- CopyToBuffer(heap.m_Data, variable.m_AppValues, variable.TotalSize());
- heap.m_DataAbsolutePosition += variable.PayLoadSize();
- }
-
- void Advance(BP1MetadataSet &metadataSet, capsule::STLVector &buffer);
-
- /**
- * Function that sets metadata (if first close) and writes to a single
- * transport
- * @param metadataSet current rank metadata set
- * @param heap contains data buffer
- * @param transport does a write after data and metadata is setup
- * @param isFirstClose true: metadata has been set and aggregated
- * @param doAggregation true: for N-to-M, false: for N-to-N
- */
- void Close(BP1MetadataSet &metadataSet, capsule::STLVector &heap,
- Transport &transport, bool &isFirstClose,
- const bool doAggregation) const noexcept;
-
- /**
- * Writes the ADIOS log information (buffering, open, write and close) for a
- * rank process
- * @param rank current rank
- * @param metadataSet contains Profile info for buffering
- * @param transports contains Profile info for transport open, writes and
- * close
- * @return string for this rank that will be aggregated into profiling.log
- */
- std::string GetRankProfilingLog(
- const int rank, const BP1MetadataSet &metadataSet,
- const std::vector<std::shared_ptr<Transport>> &transports) const noexcept;
+ /**
+ * Overloaded version for std::complex<T> variables
+ * @param variable
+ * @param heap
+ * @param metadataSet
+ */
+ template <class T>
+ void WriteVariableMetadata(const Variable<std::complex<T>> &variable,
+ capsule::STLVector &heap,
+ BP1MetadataSet &metadataSet) const noexcept
+ {
+ Stats<T> stats = GetStats(variable);
+ WriteVariableMetadataCommon(variable, stats, heap, metadataSet);
+ }
-private:
- template <class T, class U>
- void WriteVariableMetadataCommon(const Variable<T> &variable, Stats<U> &stats,
- capsule::STLVector &heap,
- BP1MetadataSet &metadataSet) const noexcept
- {
- stats.TimeIndex = metadataSet.TimeStep;
-
- // Get new Index or point to existing index
- bool isNew = true; // flag to check if variable is new
- BP1Index &varIndex =
- GetBP1Index(variable.m_Name, metadataSet.VarsIndices, isNew);
- stats.MemberID = varIndex.MemberID;
-
- // write metadata header in data and extract offsets
- stats.Offset = heap.m_DataAbsolutePosition;
- WriteVariableMetadataInData(variable, stats, heap);
- stats.PayloadOffset = heap.m_DataAbsolutePosition;
-
- // write to metadata index
- WriteVariableMetadataInIndex(variable, stats, isNew, varIndex);
-
- ++metadataSet.DataPGVarsCount;
- }
-
- template <class T, class U>
- void WriteVariableMetadataInData(const Variable<T> &variable,
- const Stats<U> &stats,
- capsule::STLVector &heap) const noexcept
- {
- auto &buffer = heap.m_Data;
-
- const std::size_t varLengthPosition =
- buffer.size(); // capture initial position for variable length
- buffer.insert(buffer.end(), 8, 0); // skip var length (8)
- CopyToBuffer(buffer, &stats.MemberID); // memberID
- WriteNameRecord(variable.m_Name, buffer); // variable name
- buffer.insert(buffer.end(), 2, 0); // skip path
- const std::uint8_t dataType = GetDataType<T>(); // dataType
- CopyToBuffer(buffer, &dataType);
- constexpr char no = 'n'; // isDimension
- CopyToBuffer(buffer, &no);
-
- // write variable dimensions
- const std::uint8_t dimensions = variable.m_Dimensions.size();
- CopyToBuffer(buffer, &dimensions); // count
- std::uint16_t dimensionsLength =
- 27 * dimensions; // 27 is from 9 bytes for each: var y/n + local, var
- // y/n + global dimension, var y/n + global offset,
- // changed for characteristic
- CopyToBuffer(buffer, &dimensionsLength); // length
- WriteDimensionsRecord(buffer, variable.m_Dimensions,
- variable.m_GlobalDimensions, variable.m_GlobalOffsets,
- 18, true);
-
- // CHARACTERISTICS
- WriteVariableCharacteristics(variable, stats, buffer, true);
-
- // Back to varLength including payload size
- const std::uint64_t varLength = buffer.size() - varLengthPosition +
- variable.PayLoadSize() -
- 8; // remove its own size
- CopyToBuffer(buffer, varLengthPosition, &varLength); // length
-
- heap.m_DataAbsolutePosition +=
- buffer.size() - varLengthPosition; // update absolute position to be
- // used as payload position
- }
-
- template <class T, class U>
- void WriteVariableMetadataInIndex(const Variable<T> &variable,
- const Stats<U> &stats, const bool isNew,
- BP1Index &index) const noexcept
- {
- auto &buffer = index.Buffer;
-
- if (isNew ==
- true) // write variable header (might be shared with attributes index)
+ /**
+ * Expensive part this is only for heap buffers need to adapt to vector of
+ * capsules
+ * @param variable
+ * @param buffer
+ */
+ template <class T>
+ void WriteVariablePayload(const Variable<T> &variable,
+ capsule::STLVector &heap,
+ const unsigned int nthreads = 1) const noexcept
{
- buffer.insert(buffer.end(), 4, 0); // skip var length (4)
- CopyToBuffer(buffer, &stats.MemberID);
- buffer.insert(buffer.end(), 2, 0); // skip group name
- WriteNameRecord(variable.m_Name, buffer);
- buffer.insert(buffer.end(), 2, 0); // skip path
-
- const std::uint8_t dataType = GetDataType<T>();
- CopyToBuffer(buffer, &dataType);
-
- // Characteristics Sets Count in Metadata
- index.Count = 1;
- CopyToBuffer(buffer, &index.Count);
+ // EXPENSIVE part, might want to use threads if large, serial for now
+ CopyToBuffer(heap.m_Data, variable.m_AppValues, variable.TotalSize());
+ heap.m_DataAbsolutePosition += variable.PayLoadSize();
}
- else // update characteristics sets count
+
+ void Advance(BP1MetadataSet &metadataSet, capsule::STLVector &buffer);
+
+ /**
+ * Function that sets metadata (if first close) and writes to a single
+ * transport
+ * @param metadataSet current rank metadata set
+ * @param heap contains data buffer
+ * @param transport does a write after data and metadata is setup
+ * @param isFirstClose true: metadata has been set and aggregated
+ * @param doAggregation true: for N-to-M, false: for N-to-N
+ */
+ void Close(BP1MetadataSet &metadataSet, capsule::STLVector &heap,
+ Transport &transport, bool &isFirstClose,
+ const bool doAggregation) const noexcept;
+
+ /**
+ * Writes the ADIOS log information (buffering, open, write and close) for a
+ * rank process
+ * @param rank current rank
+ * @param metadataSet contains Profile info for buffering
+ * @param transports contains Profile info for transport open, writes and
+ * close
+ * @return string for this rank that will be aggregated into profiling.log
+ */
+ std::string GetRankProfilingLog(
+ const int rank, const BP1MetadataSet &metadataSet,
+ const std::vector<std::shared_ptr<Transport>> &transports) const
+ noexcept;
+
+private:
+ template <class T, class U>
+ void WriteVariableMetadataCommon(const Variable<T> &variable,
+ Stats<U> &stats, capsule::STLVector &heap,
+ BP1MetadataSet &metadataSet) const noexcept
{
- const std::size_t characteristicsSetsCountPosition =
- 15 + variable.m_Name.size();
- ++index.Count;
- CopyToBuffer(buffer, characteristicsSetsCountPosition,
- &index.Count); // test
+ stats.TimeIndex = metadataSet.TimeStep;
+
+ // Get new Index or point to existing index
+ bool isNew = true; // flag to check if variable is new
+ BP1Index &varIndex =
+ GetBP1Index(variable.m_Name, metadataSet.VarsIndices, isNew);
+ stats.MemberID = varIndex.MemberID;
+
+ // write metadata header in data and extract offsets
+ stats.Offset = heap.m_DataAbsolutePosition;
+ WriteVariableMetadataInData(variable, stats, heap);
+ stats.PayloadOffset = heap.m_DataAbsolutePosition;
+
+ // write to metadata index
+ WriteVariableMetadataInIndex(variable, stats, isNew, varIndex);
+
+ ++metadataSet.DataPGVarsCount;
}
- WriteVariableCharacteristics(variable, stats, buffer);
- }
-
- template <class T, class U>
- void WriteVariableCharacteristics(const Variable<T> &variable,
- const Stats<U> &stats,
- std::vector<char> &buffer,
- const bool addLength = false) const noexcept
- {
- const std::size_t characteristicsCountPosition =
- buffer.size(); // very important to track as writer is going back to
- // this position
- buffer.insert(buffer.end(), 5,
- 0); // skip characteristics count(1) + length (4)
- std::uint8_t characteristicsCounter = 0;
-
- // DIMENSIONS
- std::uint8_t characteristicID = characteristic_dimensions;
- CopyToBuffer(buffer, &characteristicID);
- const std::uint8_t dimensions = variable.m_Dimensions.size();
-
- if (addLength == true)
+ template <class T, class U>
+ void WriteVariableMetadataInData(const Variable<T> &variable,
+ const Stats<U> &stats,
+ capsule::STLVector &heap) const noexcept
{
- const std::int16_t lengthOfDimensionsCharacteristic =
- 24 * dimensions +
- 3; // 24 = 3 local, global, global offset x 8 bytes/each
- CopyToBuffer(buffer, &lengthOfDimensionsCharacteristic);
+ auto &buffer = heap.m_Data;
+
+ const std::size_t varLengthPosition =
+ buffer.size(); // capture initial position for variable length
+ buffer.insert(buffer.end(), 8, 0); // skip var length (8)
+ CopyToBuffer(buffer, &stats.MemberID); // memberID
+ WriteNameRecord(variable.m_Name, buffer); // variable name
+ buffer.insert(buffer.end(), 2, 0); // skip path
+ const std::uint8_t dataType = GetDataType<T>(); // dataType
+ CopyToBuffer(buffer, &dataType);
+ constexpr char no = 'n'; // isDimension
+ CopyToBuffer(buffer, &no);
+
+ // write variable dimensions
+ const std::uint8_t dimensions = variable.m_Dimensions.size();
+ CopyToBuffer(buffer, &dimensions); // count
+ std::uint16_t dimensionsLength =
+ 27 *
+ dimensions; // 27 is from 9 bytes for each: var y/n + local, var
+ // y/n + global dimension, var y/n + global offset,
+ // changed for characteristic
+ CopyToBuffer(buffer, &dimensionsLength); // length
+ WriteDimensionsRecord(buffer, variable.m_Dimensions,
+ variable.m_GlobalDimensions,
+ variable.m_GlobalOffsets, 18, true);
+
+ // CHARACTERISTICS
+ WriteVariableCharacteristics(variable, stats, buffer, true);
+
+ // Back to varLength including payload size
+ const std::uint64_t varLength = buffer.size() - varLengthPosition +
+ variable.PayLoadSize() -
+ 8; // remove its own size
+ CopyToBuffer(buffer, varLengthPosition, &varLength); // length
+
+ heap.m_DataAbsolutePosition +=
+ buffer.size() - varLengthPosition; // update absolute position to be
+ // used as payload position
}
- CopyToBuffer(buffer, &dimensions); // count
- const std::uint16_t dimensionsLength = 24 * dimensions;
- CopyToBuffer(buffer, &dimensionsLength); // length
- WriteDimensionsRecord(buffer, variable.m_Dimensions,
- variable.m_GlobalDimensions, variable.m_GlobalOffsets,
- 16, addLength);
- ++characteristicsCounter;
-
- // VALUE for SCALAR or STAT min, max for ARRAY
- WriteBoundsRecord(variable.m_IsScalar, stats, buffer,
- characteristicsCounter, addLength);
- // TIME INDEX
- WriteCharacteristicRecord(characteristic_time_index, stats.TimeIndex,
- buffer, characteristicsCounter, addLength);
-
- if (addLength == false) // only in metadata offset and payload offset
+ template <class T, class U>
+ void WriteVariableMetadataInIndex(const Variable<T> &variable,
+ const Stats<U> &stats, const bool isNew,
+ BP1Index &index) const noexcept
{
- WriteCharacteristicRecord(characteristic_offset, stats.Offset, buffer,
- characteristicsCounter);
- WriteCharacteristicRecord(characteristic_payload_offset,
- stats.PayloadOffset, buffer,
- characteristicsCounter);
+ auto &buffer = index.Buffer;
+
+ if (isNew == true) // write variable header (might be shared with
+ // attributes index)
+ {
+ buffer.insert(buffer.end(), 4, 0); // skip var length (4)
+ CopyToBuffer(buffer, &stats.MemberID);
+ buffer.insert(buffer.end(), 2, 0); // skip group name
+ WriteNameRecord(variable.m_Name, buffer);
+ buffer.insert(buffer.end(), 2, 0); // skip path
+
+ const std::uint8_t dataType = GetDataType<T>();
+ CopyToBuffer(buffer, &dataType);
+
+ // Characteristics Sets Count in Metadata
+ index.Count = 1;
+ CopyToBuffer(buffer, &index.Count);
+ }
+ else // update characteristics sets count
+ {
+ const std::size_t characteristicsSetsCountPosition =
+ 15 + variable.m_Name.size();
+ ++index.Count;
+ CopyToBuffer(buffer, characteristicsSetsCountPosition,
+ &index.Count); // test
+ }
+
+ WriteVariableCharacteristics(variable, stats, buffer);
}
- // END OF CHARACTERISTICS
-
- // Back to characteristics count and length
- CopyToBuffer(buffer, characteristicsCountPosition,
- &characteristicsCounter); // count (1)
- const std::uint32_t characteristicsLength =
- buffer.size() - characteristicsCountPosition - 4 -
- 1; // remove its own length (4 bytes) + characteristic counter ( 1 byte
- // )
- CopyToBuffer(buffer, characteristicsCountPosition + 1,
- &characteristicsLength); // length
- }
-
- /**
- * Writes from &buffer[position]: [2 bytes:string.length()][string.length():
- * string.c_str()]
- * @param name
- * @param buffer
- * @param position
- */
- void WriteNameRecord(const std::string name, std::vector<char> &buffer) const
- noexcept;
-
- /**
- * Write a dimension record for a global variable used by WriteVariableCommon
- * @param buffer
- * @param position
- * @param localDimensions
- * @param globalDimensions
- * @param globalOffsets
- * @param addType true: for data buffers, false: for metadata buffer and data
- * characteristic
- */
- void WriteDimensionsRecord(std::vector<char> &buffer,
- const std::vector<std::size_t> &localDimensions,
- const std::vector<std::size_t> &globalDimensions,
- const std::vector<std::size_t> &globalOffsets,
- const unsigned int skip,
- const bool addType = false) const noexcept;
-
- /**
- * GetStats for primitive types except std::complex<T> types
- * @param variable
- * @return stats
- */
- template <class T>
- Stats<T> GetStats(const Variable<T> &variable) const noexcept
- {
- Stats<T> stats;
- const std::size_t valuesSize = variable.TotalSize();
-
- if (m_Verbosity == 0)
+
+ template <class T, class U>
+ void WriteVariableCharacteristics(const Variable<T> &variable,
+ const Stats<U> &stats,
+ std::vector<char> &buffer,
+ const bool addLength = false) const
+ noexcept
{
- if (valuesSize >= 10000000) // ten million? this needs actual results
- // //here we can make decisions for threads
- // based on valuesSize
- GetMinMax(variable.m_AppValues, valuesSize, stats.Min, stats.Max,
- m_Threads); // here we can add cores from constructor
- else
- GetMinMax(variable.m_AppValues, valuesSize, stats.Min, stats.Max);
+ const std::size_t characteristicsCountPosition =
+ buffer.size(); // very important to track as writer is going
+ // back to
+ // this position
+ buffer.insert(buffer.end(), 5,
+ 0); // skip characteristics count(1) + length (4)
+ std::uint8_t characteristicsCounter = 0;
+
+ // DIMENSIONS
+ std::uint8_t characteristicID = characteristic_dimensions;
+ CopyToBuffer(buffer, &characteristicID);
+ const std::uint8_t dimensions = variable.m_Dimensions.size();
+
+ if (addLength == true)
+ {
+ const std::int16_t lengthOfDimensionsCharacteristic =
+ 24 * dimensions +
+ 3; // 24 = 3 local, global, global offset x 8 bytes/each
+ CopyToBuffer(buffer, &lengthOfDimensionsCharacteristic);
+ }
+
+ CopyToBuffer(buffer, &dimensions); // count
+ const std::uint16_t dimensionsLength = 24 * dimensions;
+ CopyToBuffer(buffer, &dimensionsLength); // length
+ WriteDimensionsRecord(buffer, variable.m_Dimensions,
+ variable.m_GlobalDimensions,
+ variable.m_GlobalOffsets, 16, addLength);
+ ++characteristicsCounter;
+
+ // VALUE for SCALAR or STAT min, max for ARRAY
+ WriteBoundsRecord(variable.m_IsScalar, stats, buffer,
+ characteristicsCounter, addLength);
+ // TIME INDEX
+ WriteCharacteristicRecord(characteristic_time_index, stats.TimeIndex,
+ buffer, characteristicsCounter, addLength);
+
+ if (addLength == false) // only in metadata offset and payload offset
+ {
+ WriteCharacteristicRecord(characteristic_offset, stats.Offset,
+ buffer, characteristicsCounter);
+ WriteCharacteristicRecord(characteristic_payload_offset,
+ stats.PayloadOffset, buffer,
+ characteristicsCounter);
+ }
+ // END OF CHARACTERISTICS
+
+ // Back to characteristics count and length
+ CopyToBuffer(buffer, characteristicsCountPosition,
+ &characteristicsCounter); // count (1)
+ const std::uint32_t characteristicsLength =
+ buffer.size() - characteristicsCountPosition - 4 -
+ 1; // remove its own length (4 bytes) + characteristic counter (
+ // 1 byte
+ // )
+ CopyToBuffer(buffer, characteristicsCountPosition + 1,
+ &characteristicsLength); // length
}
- return stats;
- }
-
- /**
- * GetStats for std::complex<T> types
- * @param variable
- * @return stats
- */
- template <class T>
- Stats<T> GetStats(const Variable<std::complex<T>> &variable) const noexcept
- {
- Stats<T> stats;
- const std::size_t valuesSize = variable.TotalSize();
-
- if (m_Verbosity == 0)
+
+ /**
+ * Writes from &buffer[position]: [2
+ * bytes:string.length()][string.length():
+ * string.c_str()]
+ * @param name
+ * @param buffer
+ * @param position
+ */
+ void WriteNameRecord(const std::string name,
+ std::vector<char> &buffer) const noexcept;
+
+ /**
+ * Write a dimension record for a global variable used by
+ * WriteVariableCommon
+ * @param buffer
+ * @param position
+ * @param localDimensions
+ * @param globalDimensions
+ * @param globalOffsets
+ * @param addType true: for data buffers, false: for metadata buffer and
+ * data
+ * characteristic
+ */
+ void WriteDimensionsRecord(std::vector<char> &buffer,
+ const std::vector<std::size_t> &localDimensions,
+ const std::vector<std::size_t> &globalDimensions,
+ const std::vector<std::size_t> &globalOffsets,
+ const unsigned int skip,
+ const bool addType = false) const noexcept;
+
+ /**
+ * GetStats for primitive types except std::complex<T> types
+ * @param variable
+ * @return stats
+ */
+ template <class T>
+ Stats<T> GetStats(const Variable<T> &variable) const noexcept
{
- if (valuesSize >= 10000000) // ten million? this needs actual results
- // //here we can make decisions for threads
- // based on valuesSize
- GetMinMax(variable.m_AppValues, valuesSize, stats.Min, stats.Max,
- m_Threads); // here we can add cores from constructor
- else
- GetMinMax(variable.m_AppValues, valuesSize, stats.Min, stats.Max);
+ Stats<T> stats;
+ const std::size_t valuesSize = variable.TotalSize();
+
+ if (m_Verbosity == 0)
+ {
+ if (valuesSize >=
+ 10000000) // ten million? this needs actual results
+ // //here we can make decisions for threads
+ // based on valuesSize
+ GetMinMax(variable.m_AppValues, valuesSize, stats.Min,
+ stats.Max,
+ m_Threads); // here we can add cores from constructor
+ else
+ GetMinMax(variable.m_AppValues, valuesSize, stats.Min,
+ stats.Max);
+ }
+ return stats;
}
- return stats;
- }
-
- template <class T>
- void WriteBoundsRecord(const bool isScalar, const Stats<T> &stats,
- std::vector<char> &buffer,
- std::uint8_t &characteristicsCounter,
- const bool addLength) const noexcept
- {
- if (isScalar == true)
+
+ /**
+ * GetStats for std::complex<T> types
+ * @param variable
+ * @return stats
+ */
+ template <class T>
+ Stats<T> GetStats(const Variable<std::complex<T>> &variable) const noexcept
{
- WriteCharacteristicRecord(characteristic_value, stats.Min, buffer,
- characteristicsCounter,
- addLength); // stats.min = stats.max = value
- return;
+ Stats<T> stats;
+ const std::size_t valuesSize = variable.TotalSize();
+
+ if (m_Verbosity == 0)
+ {
+ if (valuesSize >=
+ 10000000) // ten million? this needs actual results
+ // //here we can make decisions for threads
+ // based on valuesSize
+ GetMinMax(variable.m_AppValues, valuesSize, stats.Min,
+ stats.Max,
+ m_Threads); // here we can add cores from constructor
+ else
+ GetMinMax(variable.m_AppValues, valuesSize, stats.Min,
+ stats.Max);
+ }
+ return stats;
}
- if (m_Verbosity == 0) // default verbose
+ template <class T>
+ void WriteBoundsRecord(const bool isScalar, const Stats<T> &stats,
+ std::vector<char> &buffer,
+ std::uint8_t &characteristicsCounter,
+ const bool addLength) const noexcept
{
- WriteCharacteristicRecord(characteristic_min, stats.Min, buffer,
- characteristicsCounter, addLength);
- WriteCharacteristicRecord(characteristic_max, stats.Max, buffer,
- characteristicsCounter, addLength);
+ if (isScalar == true)
+ {
+ WriteCharacteristicRecord(
+ characteristic_value, stats.Min, buffer, characteristicsCounter,
+ addLength); // stats.min = stats.max = value
+ return;
+ }
+
+ if (m_Verbosity == 0) // default verbose
+ {
+ WriteCharacteristicRecord(characteristic_min, stats.Min, buffer,
+ characteristicsCounter, addLength);
+ WriteCharacteristicRecord(characteristic_max, stats.Max, buffer,
+ characteristicsCounter, addLength);
+ }
}
- }
-
- /**
- * Write a characteristic value record to buffer
- * @param id
- * @param value
- * @param buffers
- * @param positions
- * @param characvteristicsCounter to be updated by 1
- * @param addLength true for data, false for metadata
- */
- template <class T>
- void WriteCharacteristicRecord(const std::uint8_t characteristicID,
- const T &value, std::vector<char> &buffer,
- std::uint8_t &characteristicsCounter,
- const bool addLength = false) const noexcept
- {
- const std::uint8_t id = characteristicID;
- CopyToBuffer(buffer, &id);
-
- if (addLength == true)
+
+ /**
+ * Write a characteristic value record to buffer
+ * @param id
+ * @param value
+ * @param buffers
+ * @param positions
+ * @param characvteristicsCounter to be updated by 1
+ * @param addLength true for data, false for metadata
+ */
+ template <class T>
+ void WriteCharacteristicRecord(const std::uint8_t characteristicID,
+ const T &value, std::vector<char> &buffer,
+ std::uint8_t &characteristicsCounter,
+ const bool addLength = false) const noexcept
{
- const std::uint16_t lengthOfCharacteristic = sizeof(T); // id
- CopyToBuffer(buffer, &lengthOfCharacteristic);
+ const std::uint8_t id = characteristicID;
+ CopyToBuffer(buffer, &id);
+
+ if (addLength == true)
+ {
+ const std::uint16_t lengthOfCharacteristic = sizeof(T); // id
+ CopyToBuffer(buffer, &lengthOfCharacteristic);
+ }
+
+ CopyToBuffer(buffer, &value);
+ ++characteristicsCounter;
}
- CopyToBuffer(buffer, &value);
- ++characteristicsCounter;
- }
-
- /**
- * Returns corresponding index of type BP1Index, if doesn't exists creates a
- * new one.
- * Used for variables and attributes
- * @param name variable or attribute name to look for index
- * @param indices look up hash table of indices
- * @param isNew true: index is newly created, false: index already exists in
- * indices
- * @return reference to BP1Index in indices
- */
- BP1Index &GetBP1Index(const std::string name,
- std::unordered_map<std::string, BP1Index> &indices,
- bool &isNew) const noexcept;
-
- /**
- * Flattens the data and fills the pg length, vars count, vars length and
- * attributes
- * @param metadataSet
- * @param buffer
- */
- void FlattenData(BP1MetadataSet &metadataSet,
- capsule::STLVector &buffer) const noexcept;
-
- /**
- * Flattens the metadata indices into a single metadata buffer in capsule
- * @param metadataSet
- * @param buffer
- */
- void FlattenMetadata(BP1MetadataSet &metadataSet,
- capsule::STLVector &buffer) const
- noexcept; ///< sets the metadata buffer in capsule with indices and
- /// minifooter
+ /**
+ * Returns corresponding index of type BP1Index, if doesn't exists creates a
+ * new one.
+ * Used for variables and attributes
+ * @param name variable or attribute name to look for index
+ * @param indices look up hash table of indices
+ * @param isNew true: index is newly created, false: index already exists in
+ * indices
+ * @return reference to BP1Index in indices
+ */
+ BP1Index &GetBP1Index(const std::string name,
+ std::unordered_map<std::string, BP1Index> &indices,
+ bool &isNew) const noexcept;
+
+ /**
+ * Flattens the data and fills the pg length, vars count, vars length and
+ * attributes
+ * @param metadataSet
+ * @param buffer
+ */
+ void FlattenData(BP1MetadataSet &metadataSet,
+ capsule::STLVector &buffer) const noexcept;
+
+ /**
+ * Flattens the metadata indices into a single metadata buffer in capsule
+ * @param metadataSet
+ * @param buffer
+ */
+ void FlattenMetadata(BP1MetadataSet &metadataSet,
+ capsule::STLVector &buffer) const
+ noexcept; ///< sets the metadata buffer in capsule with indices and
+ /// minifooter
};
} // end namespace format
diff --git a/include/functions/adiosTemplates.h b/include/functions/adiosTemplates.h
index 249bebf32393497319372466611b0347b6b40839..7266a6b213978bde383267ca8d2ac565ec4d01ee 100644
--- a/include/functions/adiosTemplates.h
+++ b/include/functions/adiosTemplates.h
@@ -32,51 +32,51 @@ template <> inline std::string GetType<void>() noexcept { return "unknown"; }
template <> inline std::string GetType<char>() noexcept { return "char"; }
template <> inline std::string GetType<unsigned char>() noexcept
{
- return "unsigned char";
+ return "unsigned char";
}
template <> inline std::string GetType<short>() noexcept { return "short"; }
template <> inline std::string GetType<unsigned short>() noexcept
{
- return "unsigned short";
+ return "unsigned short";
}
template <> inline std::string GetType<int>() noexcept { return "int"; }
template <> inline std::string GetType<unsigned int>() noexcept
{
- return "unsigned int";
+ return "unsigned int";
}
template <> inline std::string GetType<long int>() noexcept
{
- return "long int";
+ return "long int";
}
template <> inline std::string GetType<unsigned long int>() noexcept
{
- return "unsigned long int";
+ return "unsigned long int";
}
template <> inline std::string GetType<long long int>() noexcept
{
- return "long long int";
+ return "long long int";
}
template <> inline std::string GetType<unsigned long long int>() noexcept
{
- return "unsigned long long int";
+ return "unsigned long long int";
}
template <> inline std::string GetType<float>() noexcept { return "float"; }
template <> inline std::string GetType<double>() noexcept { return "double"; }
template <> inline std::string GetType<long double>() noexcept
{
- return "long double";
+ return "long double";
}
template <> inline std::string GetType<std::complex<float>>() noexcept
{
- return "float complex";
+ return "float complex";
}
template <> inline std::string GetType<std::complex<double>>() noexcept
{
- return "double complex";
+ return "double complex";
}
template <> inline std::string GetType<std::complex<long double>>() noexcept
{
- return "long double complex";
+ return "long double complex";
}
/**
@@ -92,15 +92,15 @@ bool IsTypeAlias(
const std::string type,
const std::map<std::string, std::set<std::string>> &aliases) noexcept
{
- if (type == GetType<T>()) // most of the time we will pass the same type,
- // which is a key in aliases
- return true;
+ if (type == GetType<T>()) // most of the time we will pass the same type,
+ // which is a key in aliases
+ return true;
- bool isAlias = false;
- if (aliases.at(GetType<T>()).count(type) == 1)
- isAlias = true;
+ bool isAlias = false;
+ if (aliases.at(GetType<T>()).count(type) == 1)
+ isAlias = true;
- return isAlias;
+ return isAlias;
}
/**
@@ -115,20 +115,20 @@ template <class T>
inline void GetMinMax(const T *values, const std::size_t size, T &min, T &max,
const unsigned int nthreads = 1) noexcept
{
- min = values[0];
- max = min;
+ min = values[0];
+ max = min;
- for (std::size_t i = 1; i < size; ++i)
- {
- if (values[i] < min)
+ for (std::size_t i = 1; i < size; ++i)
{
- min = values[i];
- continue;
- }
+ if (values[i] < min)
+ {
+ min = values[i];
+ continue;
+ }
- if (values[i] > max)
- max = values[i];
- }
+ if (values[i] > max)
+ max = values[i];
+ }
}
/**
@@ -145,27 +145,27 @@ inline void GetMinMax(const std::complex<T> *values, const std::size_t size,
T &min, T &max, const unsigned int nthreads = 1) noexcept
{
- min = std::norm(values[0]);
- max = min;
-
- for (std::size_t i = 1; i < size; ++i)
- {
- T norm = std::norm(values[i]);
+ min = std::norm(values[0]);
+ max = min;
- if (norm < min)
+ for (std::size_t i = 1; i < size; ++i)
{
- min = norm;
- continue;
- }
+ T norm = std::norm(values[i]);
- if (norm > max)
- {
- max = norm;
+ if (norm < min)
+ {
+ min = norm;
+ continue;
+ }
+
+ if (norm > max)
+ {
+ max = norm;
+ }
}
- }
- min = std::sqrt(min);
- max = std::sqrt(max);
+ min = std::sqrt(min);
+ max = std::sqrt(max);
}
/**
@@ -179,49 +179,49 @@ template <class T, class U>
void MemcpyThreads(T *destination, const U *source, std::size_t count,
const unsigned int nthreads = 1)
{
- // do not decompose tasks to less than 4MB pieces
- const std::size_t minBlockSize = 4194304;
- const std::size_t maxNThreads =
- std::max((std::size_t)nthreads, count / minBlockSize);
+ // do not decompose tasks to less than 4MB pieces
+ const std::size_t minBlockSize = 4194304;
+ const std::size_t maxNThreads =
+ std::max((std::size_t)nthreads, count / minBlockSize);
- if (maxNThreads == 1)
- {
- std::memcpy(destination, source, count);
- return;
- }
+ if (maxNThreads == 1)
+ {
+ std::memcpy(destination, source, count);
+ return;
+ }
- const std::size_t stride = count / maxNThreads;
- const std::size_t remainder = count % maxNThreads;
- const std::size_t last = stride + remainder;
+ const std::size_t stride = count / maxNThreads;
+ const std::size_t remainder = count % maxNThreads;
+ const std::size_t last = stride + remainder;
- std::vector<std::thread> memcpyThreads;
- memcpyThreads.reserve(maxNThreads);
+ std::vector<std::thread> memcpyThreads;
+ memcpyThreads.reserve(maxNThreads);
- for (unsigned int t = 0; t < maxNThreads; ++t)
- {
- const size_t initialDestination = stride * t / sizeof(T);
- const size_t initialSource = stride * t / sizeof(U);
+ for (unsigned int t = 0; t < maxNThreads; ++t)
+ {
+ const size_t initialDestination = stride * t / sizeof(T);
+ const size_t initialSource = stride * t / sizeof(U);
- if (t == maxNThreads - 1)
- memcpyThreads.push_back(std::thread(std::memcpy,
- &destination[initialDestination],
- &source[initialSource], last));
- else
- memcpyThreads.push_back(std::thread(std::memcpy,
- &destination[initialDestination],
- &source[initialSource], stride));
- }
- // Now join the threads (is this really needed?)
- for (auto &thread : memcpyThreads)
- thread.join();
+ if (t == maxNThreads - 1)
+ memcpyThreads.push_back(
+ std::thread(std::memcpy, &destination[initialDestination],
+ &source[initialSource], last));
+ else
+ memcpyThreads.push_back(
+ std::thread(std::memcpy, &destination[initialDestination],
+ &source[initialSource], stride));
+ }
+ // Now join the threads (is this really needed?)
+ for (auto &thread : memcpyThreads)
+ thread.join();
}
template <class T>
void MemcpyToBuffer(std::vector<char> &raw, std::size_t &position,
const T *source, std::size_t size) noexcept
{
- std::memcpy(&raw[position], source, size);
- position += size;
+ std::memcpy(&raw[position], source, size);
+ position += size;
}
/**
@@ -235,8 +235,8 @@ template <class T>
void CopyToBuffer(std::vector<char> &buffer, const T *source,
const std::size_t elements = 1) noexcept
{
- const char *src = reinterpret_cast<const char *>(source);
- buffer.insert(buffer.end(), src, src + elements * sizeof(T));
+ const char *src = reinterpret_cast<const char *>(source);
+ buffer.insert(buffer.end(), src, src + elements * sizeof(T));
}
/**
@@ -251,8 +251,8 @@ template <class T>
void CopyToBuffer(std::vector<char> &buffer, const std::size_t position,
const T *source, const std::size_t elements = 1) noexcept
{
- const char *src = reinterpret_cast<const char *>(source);
- std::copy(src, src + elements * sizeof(T), buffer.begin() + position);
+ const char *src = reinterpret_cast<const char *>(source);
+ std::copy(src, src + elements * sizeof(T), buffer.begin() + position);
}
template <class T>
@@ -260,24 +260,24 @@ void CopyFromBuffer(T *destination, std::size_t elements,
const std::vector<char> &raw,
std::size_t &position) noexcept
{
- std::copy(raw.begin() + position,
- raw.begin() + position + sizeof(T) * elements,
- reinterpret_cast<char *>(destination));
- position += elements * sizeof(T);
+ std::copy(raw.begin() + position,
+ raw.begin() + position + sizeof(T) * elements,
+ reinterpret_cast<char *>(destination));
+ position += elements * sizeof(T);
}
template <class T>
void PrintValues(const std::string name, const char *buffer,
const std::size_t position, const std::size_t elements)
{
- std::vector<T> values(elements);
- std::memcpy(values.data(), &buffer[position], elements * sizeof(T));
+ std::vector<T> values(elements);
+ std::memcpy(values.data(), &buffer[position], elements * sizeof(T));
- std::cout << "Read " << name << "\n";
- for (const auto value : values)
- std::cout << value << " ";
+ std::cout << "Read " << name << "\n";
+ for (const auto value : values)
+ std::cout << value << " ";
- std::cout << "\n";
+ std::cout << "\n";
}
} // end namespace
diff --git a/include/transform/BZip2.h b/include/transform/BZip2.h
index 755b6453c2631db0fb5207ce06e3abbd0b3dd477..0735ae2c711eec9d6774da0066192108567728e4 100644
--- a/include/transform/BZip2.h
+++ b/include/transform/BZip2.h
@@ -22,20 +22,20 @@ class BZIP2 : public Transform
{
public:
- /**
- * Initialize parent method
- * @param compressionLevel
- * @param variable
- */
- BZIP2();
+ /**
+ * Initialize parent method
+ * @param compressionLevel
+ * @param variable
+ */
+ BZIP2();
- ~BZIP2();
+ ~BZIP2();
- void Compress(const std::vector<char> &bufferIn,
- std::vector<char> &bufferOut);
-
- void Decompress(const std::vector<char> &bufferIn,
+ void Compress(const std::vector<char> &bufferIn,
std::vector<char> &bufferOut);
+
+ void Decompress(const std::vector<char> &bufferIn,
+ std::vector<char> &bufferOut);
};
} // end namespace transform
diff --git a/include/transport/file/FStream.h b/include/transport/file/FStream.h
index 8553c35981ebdb87048631033f293404f3774f88..7a54d040b7fd46b61bcdb890ef281e0bb749e39d 100644
--- a/include/transport/file/FStream.h
+++ b/include/transport/file/FStream.h
@@ -29,22 +29,22 @@ class FStream : public Transport
{
public:
- FStream(MPI_Comm mpiComm, const bool debugMode);
+ FStream(MPI_Comm mpiComm, const bool debugMode);
- virtual ~FStream() = default;
+ virtual ~FStream() = default;
- void Open(const std::string name, const std::string accessMode);
+ void Open(const std::string name, const std::string accessMode);
- void SetBuffer(char *buffer, std::size_t size);
+ void SetBuffer(char *buffer, std::size_t size);
- void Write(const char *buffer, std::size_t size);
+ void Write(const char *buffer, std::size_t size);
- void Flush();
+ void Flush();
- void Close();
+ void Close();
private:
- std::fstream m_FStream; ///< file stream under name.bp.dir/name.bp.rank
+ std::fstream m_FStream; ///< file stream under name.bp.dir/name.bp.rank
};
} // end namespace transport
diff --git a/include/transport/file/FileDescriptor.h b/include/transport/file/FileDescriptor.h
index 98d17dfb86d77303588b398a4363fe3c68e2d2ab..63d7a672114aa11e0968ca8a4355ec838fd011d0 100644
--- a/include/transport/file/FileDescriptor.h
+++ b/include/transport/file/FileDescriptor.h
@@ -25,18 +25,18 @@ class FileDescriptor : public Transport
{
public:
- FileDescriptor(MPI_Comm mpiComm, const bool debugMode);
+ FileDescriptor(MPI_Comm mpiComm, const bool debugMode);
- ~FileDescriptor();
+ ~FileDescriptor();
- void Open(const std::string name, const std::string accessMode);
+ void Open(const std::string name, const std::string accessMode);
- void Write(const char *buffer, std::size_t size);
+ void Write(const char *buffer, std::size_t size);
- void Close();
+ void Close();
private:
- int m_FileDescriptor = -1; ///< file descriptor returned by POSIX open
+ int m_FileDescriptor = -1; ///< file descriptor returned by POSIX open
};
} // end namespace transport
diff --git a/include/transport/file/FilePointer.h b/include/transport/file/FilePointer.h
index 439bffebebf6ce3bcfb520b05bb4603c2759ee6e..c1de95056ff85e0886d7d7aa0ed7e9f1707e42d7 100644
--- a/include/transport/file/FilePointer.h
+++ b/include/transport/file/FilePointer.h
@@ -30,22 +30,22 @@ class FilePointer : public Transport
{
public:
- FilePointer(MPI_Comm mpiComm, const bool debugMode);
+ FilePointer(MPI_Comm mpiComm, const bool debugMode);
- ~FilePointer();
+ ~FilePointer();
- void Open(const std::string name, const std::string accessMode);
+ void Open(const std::string name, const std::string accessMode);
- void SetBuffer(char *buffer, std::size_t size);
+ void SetBuffer(char *buffer, std::size_t size);
- void Write(const char *buffer, std::size_t size);
+ void Write(const char *buffer, std::size_t size);
- void Flush();
+ void Flush();
- void Close();
+ void Close();
private:
- FILE *m_File = NULL; ///< C file pointer
+ FILE *m_File = NULL; ///< C file pointer
};
} // end namespace transport
diff --git a/include/transport/file/MPI_File.h b/include/transport/file/MPI_File.h
index 5966cc531da35b6e991cd6fe47189a569fb6e5ec..10685e8cea3d2f9a90f12b9ee1d020a384511725 100644
--- a/include/transport/file/MPI_File.h
+++ b/include/transport/file/MPI_File.h
@@ -27,22 +27,22 @@ class MPI_File : public Transport
{
public:
- MPI_File(MPI_Comm mpiComm, const bool debugMode);
+ MPI_File(MPI_Comm mpiComm, const bool debugMode);
- ~MPI_File();
+ ~MPI_File();
- void Open(const std::string streamName, const std::string accessMode);
+ void Open(const std::string streamName, const std::string accessMode);
- void SetBuffer(char *buffer, std::size_t size);
+ void SetBuffer(char *buffer, std::size_t size);
- void Write(const char *buffer, std::size_t size);
+ void Write(const char *buffer, std::size_t size);
- void Flush();
+ void Flush();
- void Close();
+ void Close();
private:
- MPI_File m_MPIFile; ///< MPI File
+ MPI_File m_MPIFile; ///< MPI File
};
} // end namespace transport
diff --git a/include/transport/wan/MdtmMan.h b/include/transport/wan/MdtmMan.h
index 84a71156e560909da7b31b7c087337de2bdf1bce..7ddd162acc11beb73abedab6f43aad5c9dd0b7ae 100644
--- a/include/transport/wan/MdtmMan.h
+++ b/include/transport/wan/MdtmMan.h
@@ -25,112 +25,113 @@ class MdtmMan : public Transport
{
public:
- /**
- *
- * @param localIP
- * @param remoteIP
- * @param mode
- * @param prefix
- * @param numberOfPipes
- * @param tolerances
- * @param priorities
- * @param mpiComm
- * @param debugMode
- */
- MdtmMan(const std::string localIP, const std::string remoteIP,
- const std::string mode, const std::string prefix,
- const int numberOfPipes, const std::vector<int> tolerances,
- const std::vector<int> priorities, MPI_Comm mpiComm,
- const bool debugMode);
-
- ~MdtmMan();
-
- void Open(const std::string name, const std::string accessMode);
-
- void SetBuffer(char *buffer, std::size_t size);
-
- /**
- * We can always overload this function in the base class and accept other
- * types of data pointers, e.g. Write( json* );
- * I'm sticking with char* as it's more general (only C++ libraries, e.g.
- * boost understand std::std::vector, MPI, POSIX, Infiniband use pointer*)
- * @param buffer
- * @param size
- */
- void Write(const char *buffer, std::size_t size);
-
- void Flush(); ///< not sure if this one is needed...
-
- void Close();
+ /**
+ *
+ * @param localIP
+ * @param remoteIP
+ * @param mode
+ * @param prefix
+ * @param numberOfPipes
+ * @param tolerances
+ * @param priorities
+ * @param mpiComm
+ * @param debugMode
+ */
+ MdtmMan(const std::string localIP, const std::string remoteIP,
+ const std::string mode, const std::string prefix,
+ const int numberOfPipes, const std::vector<int> tolerances,
+ const std::vector<int> priorities, MPI_Comm mpiComm,
+ const bool debugMode);
+
+ ~MdtmMan();
+
+ void Open(const std::string name, const std::string accessMode);
+
+ void SetBuffer(char *buffer, std::size_t size);
+
+ /**
+ * We can always overload this function in the base class and accept other
+ * types of data pointers, e.g. Write( json* );
+ * I'm sticking with char* as it's more general (only C++ libraries, e.g.
+ * boost understand std::std::vector, MPI, POSIX, Infiniband use pointer*)
+ * @param buffer
+ * @param size
+ */
+ void Write(const char *buffer, std::size_t size);
+
+ void Flush(); ///< not sure if this one is needed...
+
+ void Close();
private:
- std::string m_LocalIP; ///< local ip address, can change over time
- std::string m_RemoteIP; ///< remote ip address, can change over time
- std::string m_Mode; ///< send/write, receive/read
- std::string m_Prefix; ///< prefix given to message
- int m_NumberOfPipes = -1; ///< should it be unsigned int?
- std::vector<int> m_Tolerances;
- std::vector<int> m_Priorities;
-
- /**
- * Should we change data to char* ?
- * @param data
- * @param doid
- * @param variable
- * @param dType
- * @param putShape
- * @param varShape
- * @param offset
- * @param timestep
- * @param tolerance
- * @param priority
- * @return
- */
- int Put(const void *data, const std::string doid, const std::string variable,
- const std::string dType, const std::vector<std::uint64_t> &putShape,
- const std::vector<uint64_t> &varShape,
- const std::vector<uint64_t> &offset, const std::uint64_t timestep,
- const int tolerance, const int priority);
-
- /**
- *
- * @param data
- * @param doid
- * @param variable
- * @param dType
- * @param putShape
- * @param varShape
- * @param offset
- * @param timestep
- * @param tolerance
- * @param priority
- * @return
- */
- int Get(void *data, const std::string doid, const std::string variable,
- const std::string dType, const std::vector<std::uint64_t> &putShape,
- const std::vector<uint64_t> &varShape,
- const std::vector<uint64_t> &offset, const std::uint64_t timestep,
- const int tolerance, const int priority);
-
- /**
- *
- * @param data
- * @param doid
- * @param variable
- * @param dType
- * @param varShape
- * @param timestep
- * @return
- */
- int Get(void *data, const std::string doid, const std::string variable,
- const std::string dType, std::vector<std::uint64_t> &varShape,
- const std::uint64_t timestep);
-
- /**
- *
- * @param jData
- */
- void OnReceive(nlohmann::json &jData);
+ std::string m_LocalIP; ///< local ip address, can change over time
+ std::string m_RemoteIP; ///< remote ip address, can change over time
+ std::string m_Mode; ///< send/write, receive/read
+ std::string m_Prefix; ///< prefix given to message
+ int m_NumberOfPipes = -1; ///< should it be unsigned int?
+ std::vector<int> m_Tolerances;
+ std::vector<int> m_Priorities;
+
+ /**
+ * Should we change data to char* ?
+ * @param data
+ * @param doid
+ * @param variable
+ * @param dType
+ * @param putShape
+ * @param varShape
+ * @param offset
+ * @param timestep
+ * @param tolerance
+ * @param priority
+ * @return
+ */
+ int Put(const void *data, const std::string doid,
+ const std::string variable, const std::string dType,
+ const std::vector<std::uint64_t> &putShape,
+ const std::vector<uint64_t> &varShape,
+ const std::vector<uint64_t> &offset, const std::uint64_t timestep,
+ const int tolerance, const int priority);
+
+ /**
+ *
+ * @param data
+ * @param doid
+ * @param variable
+ * @param dType
+ * @param putShape
+ * @param varShape
+ * @param offset
+ * @param timestep
+ * @param tolerance
+ * @param priority
+ * @return
+ */
+ int Get(void *data, const std::string doid, const std::string variable,
+ const std::string dType, const std::vector<std::uint64_t> &putShape,
+ const std::vector<uint64_t> &varShape,
+ const std::vector<uint64_t> &offset, const std::uint64_t timestep,
+ const int tolerance, const int priority);
+
+ /**
+ *
+ * @param data
+ * @param doid
+ * @param variable
+ * @param dType
+ * @param varShape
+ * @param timestep
+ * @return
+ */
+ int Get(void *data, const std::string doid, const std::string variable,
+ const std::string dType, std::vector<std::uint64_t> &varShape,
+ const std::uint64_t timestep);
+
+ /**
+ *
+ * @param jData
+ */
+ void OnReceive(nlohmann::json &jData);
};
} // end namespace transport
diff --git a/source/ADIOS.cpp b/source/ADIOS.cpp
index d752a127d699ea3726e0db798976356f1eff62e6..0f26439d810c1a641dde3d89cf58d7cc1ea92b91 100644
--- a/source/ADIOS.cpp
+++ b/source/ADIOS.cpp
@@ -40,62 +40,63 @@ namespace adios
ADIOS::ADIOS(const Verbose /*verbose*/, const bool debugMode)
: m_DebugMode{debugMode}
{
- InitMPI();
+ InitMPI();
}
ADIOS::ADIOS(std::string config, const Verbose /*verbose*/,
const bool debugMode)
: m_ConfigFile{std::move(config)}, m_DebugMode{debugMode}
{
- InitMPI();
- // InitXML( m_ConfigFile, m_MPIComm, m_DebugMode, m_Transforms );
+ InitMPI();
+ // InitXML( m_ConfigFile, m_MPIComm, m_DebugMode, m_Transforms );
}
ADIOS::ADIOS(std::string config, MPI_Comm mpiComm, const Verbose /*verbose*/,
const bool debugMode)
: m_MPIComm{mpiComm}, m_ConfigFile{std::move(config)}, m_DebugMode{debugMode}
{
- InitMPI();
- // InitXML( m_XMLConfigFile, m_MPIComm, m_DebugMode, m_HostLanguage,
- // m_Transforms, m_Groups );
+ InitMPI();
+ // InitXML( m_XMLConfigFile, m_MPIComm, m_DebugMode, m_HostLanguage,
+ // m_Transforms, m_Groups );
}
ADIOS::ADIOS(MPI_Comm mpiComm, const Verbose /*verbose*/, const bool debugMode)
: m_MPIComm{mpiComm}, m_DebugMode{debugMode}
{
- InitMPI();
+ InitMPI();
}
// ADIOS::~ADIOS() {}
void ADIOS::InitMPI()
{
- if (m_DebugMode == true)
- {
- if (m_MPIComm == MPI_COMM_NULL)
+ if (m_DebugMode == true)
{
- throw std::ios_base::failure(
- "ERROR: engine communicator is MPI_COMM_NULL,"
- " in call to ADIOS Open or Constructor\n");
+ if (m_MPIComm == MPI_COMM_NULL)
+ {
+ throw std::ios_base::failure(
+ "ERROR: engine communicator is MPI_COMM_NULL,"
+ " in call to ADIOS Open or Constructor\n");
+ }
}
- }
- MPI_Comm_rank(m_MPIComm, &m_RankMPI);
- MPI_Comm_size(m_MPIComm, &m_SizeMPI);
+ MPI_Comm_rank(m_MPIComm, &m_RankMPI);
+ MPI_Comm_size(m_MPIComm, &m_SizeMPI);
}
Method &ADIOS::DeclareMethod(const std::string &methodName)
{
- if (m_DebugMode == true)
- {
- if (m_Methods.count(methodName) == 1)
+ if (m_DebugMode == true)
{
- throw std::invalid_argument("ERROR: method " + methodName +
- " already declared, from DeclareMethod\n");
+ if (m_Methods.count(methodName) == 1)
+ {
+ throw std::invalid_argument(
+ "ERROR: method " + methodName +
+ " already declared, from DeclareMethod\n");
+ }
}
- }
- m_Methods.emplace(methodName, Method(methodName, m_DebugMode));
- return m_Methods.at(methodName);
+ m_Methods.emplace(methodName, Method(methodName, m_DebugMode));
+ return m_Methods.at(methodName);
}
std::shared_ptr<Engine> ADIOS::Open(const std::string &name,
@@ -104,97 +105,103 @@ std::shared_ptr<Engine> ADIOS::Open(const std::string &name,
const IOMode iomode,
const float timeout_sec)
{
- if (m_DebugMode == true)
- {
- if (m_EngineNames.count(name) == 1) // Check if Engine already exists
+ if (m_DebugMode == true)
{
- throw std::invalid_argument(
- "ERROR: engine name " + name +
- " already created by Open, in call from Open.\n");
+ if (m_EngineNames.count(name) == 1) // Check if Engine already exists
+ {
+ throw std::invalid_argument(
+ "ERROR: engine name " + name +
+ " already created by Open, in call from Open.\n");
+ }
}
- }
-
- m_EngineNames.insert(name);
-
- const std::string type(method.m_Type);
-
- const bool isDefaultWriter = (accessMode == "w" || accessMode == "write" ||
- accessMode == "a" || accessMode == "append") &&
- type.empty()
- ? true
- : false;
-
- const bool isDefaultReader =
- (accessMode == "r" || accessMode == "read") && type.empty() ? true
- : false;
-
- if (isDefaultWriter || type == "BPFileWriter" || type == "bpfilewriter")
- {
- return std::make_shared<BPFileWriter>(*this, name, accessMode, mpiComm,
- method, iomode, timeout_sec,
- m_DebugMode, method.m_nThreads);
- }
- else if (isDefaultReader || type == "BPReader" || type == "bpreader")
- {
- return std::make_shared<BPFileReader>(*this, name, accessMode, mpiComm,
- method, iomode, timeout_sec,
- m_DebugMode, method.m_nThreads);
- }
- else if (type == "SIRIUS" || type == "sirius" || type == "Sirius")
- {
- // not yet supported
- // return std::make_shared<engine::DataMan>( *this, name, accessMode,
- // mpiComm, method, iomode, timeout_sec, m_DebugMode, method.m_nThreads );
- }
- else if (type == "DataManWriter")
- {
+
+ m_EngineNames.insert(name);
+
+ const std::string type(method.m_Type);
+
+ const bool isDefaultWriter =
+ (accessMode == "w" || accessMode == "write" || accessMode == "a" ||
+ accessMode == "append") &&
+ type.empty()
+ ? true
+ : false;
+
+ const bool isDefaultReader =
+ (accessMode == "r" || accessMode == "read") && type.empty() ? true
+ : false;
+
+ if (isDefaultWriter || type == "BPFileWriter" || type == "bpfilewriter")
+ {
+ return std::make_shared<BPFileWriter>(*this, name, accessMode, mpiComm,
+ method, iomode, timeout_sec,
+ m_DebugMode, method.m_nThreads);
+ }
+ else if (isDefaultReader || type == "BPReader" || type == "bpreader")
+ {
+ return std::make_shared<BPFileReader>(*this, name, accessMode, mpiComm,
+ method, iomode, timeout_sec,
+ m_DebugMode, method.m_nThreads);
+ }
+ else if (type == "SIRIUS" || type == "sirius" || type == "Sirius")
+ {
+ // not yet supported
+ // return std::make_shared<engine::DataMan>( *this, name, accessMode,
+ // mpiComm, method, iomode, timeout_sec, m_DebugMode, method.m_nThreads
+ // );
+ }
+ else if (type == "DataManWriter")
+ {
#ifdef HAVE_DATAMAN
- return std::make_shared<DataManWriter>(*this, name, accessMode, mpiComm,
- method, iomode, timeout_sec,
- m_DebugMode, method.m_nThreads);
+ return std::make_shared<DataManWriter>(*this, name, accessMode, mpiComm,
+ method, iomode, timeout_sec,
+ m_DebugMode, method.m_nThreads);
#else
- throw std::invalid_argument("ERROR: this version didn't compile with "
- "Dataman library, can't Open DataManWriter\n");
+ throw std::invalid_argument(
+ "ERROR: this version didn't compile with "
+ "Dataman library, can't Open DataManWriter\n");
#endif
- }
- else if (type == "DataManReader")
- {
+ }
+ else if (type == "DataManReader")
+ {
#ifdef HAVE_DATAMAN
- return std::make_shared<DataManReader>(*this, name, accessMode, mpiComm,
- method, iomode, timeout_sec,
- m_DebugMode, method.m_nThreads);
+ return std::make_shared<DataManReader>(*this, name, accessMode, mpiComm,
+ method, iomode, timeout_sec,
+ m_DebugMode, method.m_nThreads);
#else
- throw std::invalid_argument("ERROR: this version didn't compile with "
- "Dataman library, can't Open DataManReader\n");
+ throw std::invalid_argument(
+ "ERROR: this version didn't compile with "
+ "Dataman library, can't Open DataManReader\n");
#endif
- }
- else if (type == "ADIOS1Writer")
- {
+ }
+ else if (type == "ADIOS1Writer")
+ {
#ifdef HAVE_ADIOS1
- return std::make_shared<ADIOS1Writer>(*this, name, accessMode, mpiComm,
- method, iomode, timeout_sec,
- m_DebugMode, method.m_nThreads);
+ return std::make_shared<ADIOS1Writer>(*this, name, accessMode, mpiComm,
+ method, iomode, timeout_sec,
+ m_DebugMode, method.m_nThreads);
#else
- throw std::invalid_argument("ERROR: this version didn't compile with ADIOS "
- "1.x library, can't Open ADIOS1Writer\n");
+ throw std::invalid_argument(
+ "ERROR: this version didn't compile with ADIOS "
+ "1.x library, can't Open ADIOS1Writer\n");
#endif
- }
- else if (type == "Vis")
- {
- // return std::make_shared<Vis>( *this, name, accessMode, mpiComm, method,
- // iomode, timeout_sec, m_DebugMode, method.m_nThreads );
- }
- else
- {
- if (m_DebugMode == true)
+ }
+ else if (type == "Vis")
{
- throw std::invalid_argument("ERROR: method type " + type +
- " not supported for " + name +
- ", in call to Open\n");
+ // return std::make_shared<Vis>( *this, name, accessMode, mpiComm,
+ // method,
+ // iomode, timeout_sec, m_DebugMode, method.m_nThreads );
+ }
+ else
+ {
+ if (m_DebugMode == true)
+ {
+ throw std::invalid_argument("ERROR: method type " + type +
+ " not supported for " + name +
+ ", in call to Open\n");
+ }
}
- }
- return nullptr; // if debug mode is off
+ return nullptr; // if debug mode is off
}
std::shared_ptr<Engine> ADIOS::Open(const std::string &streamName,
@@ -202,7 +209,7 @@ std::shared_ptr<Engine> ADIOS::Open(const std::string &streamName,
const Method &method, const IOMode iomode,
const float timeout_sec)
{
- return Open(streamName, accessMode, m_MPIComm, method, iomode, timeout_sec);
+ return Open(streamName, accessMode, m_MPIComm, method, iomode, timeout_sec);
}
std::shared_ptr<Engine>
@@ -210,14 +217,15 @@ ADIOS::Open(const std::string &name, const std::string &accessMode,
MPI_Comm mpiComm, const std::string &methodName,
const IOMode iomode, const float timeout_sec)
{
- auto itMethod = m_Methods.find(methodName);
+ auto itMethod = m_Methods.find(methodName);
- if (m_DebugMode == true)
- {
- CheckMethod(itMethod, methodName, " in call to Open\n");
- }
+ if (m_DebugMode == true)
+ {
+ CheckMethod(itMethod, methodName, " in call to Open\n");
+ }
- return Open(name, accessMode, mpiComm, itMethod->second, iomode, timeout_sec);
+ return Open(name, accessMode, mpiComm, itMethod->second, iomode,
+ timeout_sec);
}
std::shared_ptr<Engine> ADIOS::Open(const std::string &name,
@@ -226,7 +234,7 @@ std::shared_ptr<Engine> ADIOS::Open(const std::string &name,
const IOMode iomode,
const float timeout_sec)
{
- return Open(name, accessMode, m_MPIComm, methodName, iomode, timeout_sec);
+ return Open(name, accessMode, m_MPIComm, methodName, iomode, timeout_sec);
}
std::shared_ptr<Engine> ADIOS::OpenFileReader(const std::string &name,
@@ -234,7 +242,7 @@ std::shared_ptr<Engine> ADIOS::OpenFileReader(const std::string &name,
const Method &method,
const IOMode iomode)
{
- return Open(name, "r", m_MPIComm, method, iomode);
+ return Open(name, "r", m_MPIComm, method, iomode);
}
std::shared_ptr<Engine> ADIOS::OpenFileReader(const std::string &name,
@@ -242,117 +250,117 @@ std::shared_ptr<Engine> ADIOS::OpenFileReader(const std::string &name,
const std::string &methodName,
const IOMode iomode)
{
- auto itMethod = m_Methods.find(methodName);
+ auto itMethod = m_Methods.find(methodName);
- if (m_DebugMode == true)
- {
- CheckMethod(itMethod, methodName, " in call to Open\n");
- }
+ if (m_DebugMode == true)
+ {
+ CheckMethod(itMethod, methodName, " in call to Open\n");
+ }
- return Open(name, "r", m_MPIComm, itMethod->second, iomode);
+ return Open(name, "r", m_MPIComm, itMethod->second, iomode);
}
VariableCompound &ADIOS::GetVariableCompound(const std::string &name)
{
- return m_Compound.at(GetVariableIndex<void>(name));
+ return m_Compound.at(GetVariableIndex<void>(name));
}
void ADIOS::MonitorVariables(std::ostream &logStream)
{
- logStream << "\tVariable \t Type\n";
-
- for (auto &variablePair : m_Variables)
- {
- const std::string name(variablePair.first);
- const std::string type(variablePair.second.first);
+ logStream << "\tVariable \t Type\n";
- if (type == GetType<char>())
- {
- GetVariable<char>(name).Monitor(logStream);
- }
- else if (type == GetType<unsigned char>())
- {
- GetVariable<unsigned char>(name).Monitor(logStream);
- }
- else if (type == GetType<short>())
+ for (auto &variablePair : m_Variables)
{
- GetVariable<short>(name).Monitor(logStream);
+ const std::string name(variablePair.first);
+ const std::string type(variablePair.second.first);
+
+ if (type == GetType<char>())
+ {
+ GetVariable<char>(name).Monitor(logStream);
+ }
+ else if (type == GetType<unsigned char>())
+ {
+ GetVariable<unsigned char>(name).Monitor(logStream);
+ }
+ else if (type == GetType<short>())
+ {
+ GetVariable<short>(name).Monitor(logStream);
+ }
+ else if (type == GetType<unsigned short>())
+ {
+ GetVariable<unsigned short>(name).Monitor(logStream);
+ }
+ else if (type == GetType<int>())
+ {
+ GetVariable<int>(name).Monitor(logStream);
+ }
+ else if (type == GetType<unsigned int>())
+ {
+ GetVariable<unsigned int>(name).Monitor(logStream);
+ }
+ else if (type == GetType<long int>())
+ {
+ GetVariable<long int>(name).Monitor(logStream);
+ }
+ else if (type == GetType<unsigned long int>())
+ {
+ GetVariable<unsigned long int>(name).Monitor(logStream);
+ }
+ else if (type == GetType<long long int>())
+ {
+ GetVariable<long long int>(name).Monitor(logStream);
+ }
+ else if (type == GetType<unsigned long long int>())
+ {
+ GetVariable<unsigned long long int>(name).Monitor(logStream);
+ }
+ else if (type == GetType<float>())
+ {
+ GetVariable<float>(name).Monitor(logStream);
+ }
+ else if (type == GetType<double>())
+ {
+ GetVariable<double>(name).Monitor(logStream);
+ }
+ else if (type == GetType<long double>())
+ {
+ GetVariable<long double>(name).Monitor(logStream);
+ }
+ else if (type == GetType<std::complex<float>>())
+ {
+ GetVariable<std::complex<float>>(name).Monitor(logStream);
+ }
+ else if (type == GetType<std::complex<double>>())
+ {
+ GetVariable<std::complex<double>>(name).Monitor(logStream);
+ }
+ else if (type == GetType<std::complex<long double>>())
+ {
+ GetVariable<std::complex<long double>>(name).Monitor(logStream);
+ }
}
- else if (type == GetType<unsigned short>())
- {
- GetVariable<unsigned short>(name).Monitor(logStream);
- }
- else if (type == GetType<int>())
- {
- GetVariable<int>(name).Monitor(logStream);
- }
- else if (type == GetType<unsigned int>())
- {
- GetVariable<unsigned int>(name).Monitor(logStream);
- }
- else if (type == GetType<long int>())
- {
- GetVariable<long int>(name).Monitor(logStream);
- }
- else if (type == GetType<unsigned long int>())
- {
- GetVariable<unsigned long int>(name).Monitor(logStream);
- }
- else if (type == GetType<long long int>())
- {
- GetVariable<long long int>(name).Monitor(logStream);
- }
- else if (type == GetType<unsigned long long int>())
- {
- GetVariable<unsigned long long int>(name).Monitor(logStream);
- }
- else if (type == GetType<float>())
- {
- GetVariable<float>(name).Monitor(logStream);
- }
- else if (type == GetType<double>())
- {
- GetVariable<double>(name).Monitor(logStream);
- }
- else if (type == GetType<long double>())
- {
- GetVariable<long double>(name).Monitor(logStream);
- }
- else if (type == GetType<std::complex<float>>())
- {
- GetVariable<std::complex<float>>(name).Monitor(logStream);
- }
- else if (type == GetType<std::complex<double>>())
- {
- GetVariable<std::complex<double>>(name).Monitor(logStream);
- }
- else if (type == GetType<std::complex<long double>>())
- {
- GetVariable<std::complex<long double>>(name).Monitor(logStream);
- }
- }
}
// PRIVATE FUNCTIONS BELOW
void ADIOS::CheckVariableInput(const std::string &name,
const Dims &dimensions) const
{
- if (m_DebugMode == true)
- {
- if (m_Variables.count(name) == 1)
- {
- throw std::invalid_argument(
- "ERROR: variable " + name +
- " already exists, in call to DefineVariable\n");
- }
-
- if (dimensions.empty() == true)
+ if (m_DebugMode == true)
{
- throw std::invalid_argument(
- "ERROR: variable " + name +
- " dimensions can't be empty, in call to DefineVariable\n");
+ if (m_Variables.count(name) == 1)
+ {
+ throw std::invalid_argument(
+ "ERROR: variable " + name +
+ " already exists, in call to DefineVariable\n");
+ }
+
+ if (dimensions.empty() == true)
+ {
+ throw std::invalid_argument(
+ "ERROR: variable " + name +
+ " dimensions can't be empty, in call to DefineVariable\n");
+ }
}
- }
}
void ADIOS::CheckVariableName(
@@ -360,25 +368,25 @@ void ADIOS::CheckVariableName(
itVariable,
const std::string &name, const std::string &hint) const
{
- if (m_DebugMode == true)
- {
- if (itVariable == m_Variables.end())
+ if (m_DebugMode == true)
{
- throw std::invalid_argument("ERROR: variable " + name +
- " does not exist " + hint + "\n");
+ if (itVariable == m_Variables.end())
+ {
+ throw std::invalid_argument("ERROR: variable " + name +
+ " does not exist " + hint + "\n");
+ }
}
- }
}
void ADIOS::CheckMethod(std::map<std::string, Method>::const_iterator itMethod,
const std::string &methodName,
const std::string &hint) const
{
- if (itMethod == m_Methods.end())
- {
- throw std::invalid_argument("ERROR: method " + methodName + " not found " +
- hint + "\n");
- }
+ if (itMethod == m_Methods.end())
+ {
+ throw std::invalid_argument("ERROR: method " + methodName +
+ " not found " + hint + "\n");
+ }
}
} // end namespace adios
diff --git a/source/ADIOS_C.cpp b/source/ADIOS_C.cpp
index d6f30da48a55cf7fae051d584852fb289c0abbd2..a3306931e5ad22e80525160466606e0013f453bb 100644
--- a/source/ADIOS_C.cpp
+++ b/source/ADIOS_C.cpp
@@ -25,227 +25,227 @@ extern "C" {
void adios_init(const char *xmlConfigFile, const MPI_Comm mpiComm)
{
- int rank;
- MPI_Comm_rank(mpiComm, &rank);
-
- try
- {
- adios = new adios::ADIOS(std::string(xmlConfigFile), mpiComm);
- }
- catch (std::bad_alloc &e)
- {
- if (rank == 0)
- std::cout << "Bad allocation exception, STOPPING PROGRAM\n"
- << e.what() << "\n";
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n"
- << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- std::cout << "Exception, STOPPING PROGRAM\n" << e.what() << "\n";
- }
-
- // return ( ADIOS* ) ( adios );
+ int rank;
+ MPI_Comm_rank(mpiComm, &rank);
+
+ try
+ {
+ adios = new adios::ADIOS(std::string(xmlConfigFile), mpiComm);
+ }
+ catch (std::bad_alloc &e)
+ {
+ if (rank == 0)
+ std::cout << "Bad allocation exception, STOPPING PROGRAM\n"
+ << e.what() << "\n";
+ }
+ catch (std::invalid_argument &e)
+ {
+ if (rank == 0)
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n"
+ << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ if (rank == 0)
+ std::cout << "Exception, STOPPING PROGRAM\n" << e.what() << "\n";
+ }
+
+ // return ( ADIOS* ) ( adios );
}
ADIOS *adios_init_debug(const char *xmlConfigFile, const MPI_Comm mpiComm)
{
- adios::ADIOS *adios;
- int rank;
- MPI_Comm_rank(mpiComm, &rank);
-
- try
- {
- adios = new adios::ADIOS(std::string(xmlConfigFile), mpiComm, true);
- }
- catch (std::bad_alloc &e)
- {
- if (rank == 0)
- std::cout << "Bad allocation exception, STOPPING PROGRAM\n"
- << e.what() << "\n";
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n"
- << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- std::cout << "Exception, STOPPING PROGRAM\n" << e.what() << "\n";
- }
-
- return (ADIOS *)(adios);
+ adios::ADIOS *adios;
+ int rank;
+ MPI_Comm_rank(mpiComm, &rank);
+
+ try
+ {
+ adios = new adios::ADIOS(std::string(xmlConfigFile), mpiComm, true);
+ }
+ catch (std::bad_alloc &e)
+ {
+ if (rank == 0)
+ std::cout << "Bad allocation exception, STOPPING PROGRAM\n"
+ << e.what() << "\n";
+ }
+ catch (std::invalid_argument &e)
+ {
+ if (rank == 0)
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n"
+ << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ if (rank == 0)
+ std::cout << "Exception, STOPPING PROGRAM\n" << e.what() << "\n";
+ }
+
+ return (ADIOS *)(adios);
}
void adios_open(const ADIOS *adiosC, const char *groupName,
const char *fileName, const char *accessMode)
{
- adios::ADIOS *adios = (adios::ADIOS *)adiosC;
- int rank;
- MPI_Comm_rank(adios->m_MPIComm, &rank);
-
- try
- {
adios::ADIOS *adios = (adios::ADIOS *)adiosC;
- adios->Open(std::string(groupName), std::string(fileName),
- std::string(accessMode));
- }
- catch (std::bad_alloc &e)
- {
- if (rank == 0)
- std::cout << "Bad allocation exception, STOPPING PROGRAM\n"
- << e.what() << "\n";
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n"
- << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- std::cout << "Exception, STOPPING PROGRAM\n" << e.what() << "\n";
- }
+ int rank;
+ MPI_Comm_rank(adios->m_MPIComm, &rank);
+
+ try
+ {
+ adios::ADIOS *adios = (adios::ADIOS *)adiosC;
+ adios->Open(std::string(groupName), std::string(fileName),
+ std::string(accessMode));
+ }
+ catch (std::bad_alloc &e)
+ {
+ if (rank == 0)
+ std::cout << "Bad allocation exception, STOPPING PROGRAM\n"
+ << e.what() << "\n";
+ }
+ catch (std::invalid_argument &e)
+ {
+ if (rank == 0)
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n"
+ << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ if (rank == 0)
+ std::cout << "Exception, STOPPING PROGRAM\n" << e.what() << "\n";
+ }
}
void adios_write(const ADIOS *adiosC, const char *groupName,
const char *variableName, const void *values)
{
- adios::ADIOS *adios = (adios::ADIOS *)adiosC;
- int rank;
- MPI_Comm_rank(adios->m_MPIComm, &rank);
-
- try
- {
- adios->Write(const std::string(groupName), const std::string(variableName),
- values);
- }
- catch (std::bad_alloc &e)
- {
- if (rank == 0)
- std::cout << "Bad allocation exception, STOPPING PROGRAM\n"
- << e.what() << "\n";
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n"
- << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- std::cout << "Exception, STOPPING PROGRAM\n" << e.what() << "\n";
- }
+ adios::ADIOS *adios = (adios::ADIOS *)adiosC;
+ int rank;
+ MPI_Comm_rank(adios->m_MPIComm, &rank);
+
+ try
+ {
+ adios->Write(const std::string(groupName),
+ const std::string(variableName), values);
+ }
+ catch (std::bad_alloc &e)
+ {
+ if (rank == 0)
+ std::cout << "Bad allocation exception, STOPPING PROGRAM\n"
+ << e.what() << "\n";
+ }
+ catch (std::invalid_argument &e)
+ {
+ if (rank == 0)
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n"
+ << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ if (rank == 0)
+ std::cout << "Exception, STOPPING PROGRAM\n" << e.what() << "\n";
+ }
}
void adios_close(const ADIOS *adiosC, const char *groupName)
{
- adios::ADIOS *adios = (adios::ADIOS *)adiosC;
- int rank;
- MPI_Comm_rank(adios->m_MPIComm, &rank);
-
- try
- {
- adios->Close(std::string(groupName));
- }
- catch (std::bad_alloc &e)
- {
- if (rank == 0)
- std::cout << "Bad allocation exception, STOPPING PROGRAM\n"
- << e.what() << "\n";
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n"
- << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- std::cout << "Exception, STOPPING PROGRAM\n" << e.what() << "\n";
- }
+ adios::ADIOS *adios = (adios::ADIOS *)adiosC;
+ int rank;
+ MPI_Comm_rank(adios->m_MPIComm, &rank);
+
+ try
+ {
+ adios->Close(std::string(groupName));
+ }
+ catch (std::bad_alloc &e)
+ {
+ if (rank == 0)
+ std::cout << "Bad allocation exception, STOPPING PROGRAM\n"
+ << e.what() << "\n";
+ }
+ catch (std::invalid_argument &e)
+ {
+ if (rank == 0)
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n"
+ << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ if (rank == 0)
+ std::cout << "Exception, STOPPING PROGRAM\n" << e.what() << "\n";
+ }
}
void adios_free(const ADIOS *adiosC)
{
- adios::ADIOS *adios = (adios::ADIOS *)adiosC;
- delete adios;
+ adios::ADIOS *adios = (adios::ADIOS *)adiosC;
+ delete adios;
}
void adios_monitor_groups(const ADIOS *adiosC)
{
- adios::ADIOS *adios = (adios::ADIOS *)adiosC;
- int rank;
- MPI_Comm_rank(adios->m_MPIComm, &rank);
-
- try
- {
- adios->MonitorGroups(std::cout);
- }
- catch (std::bad_alloc &e)
- {
- if (rank == 0)
- std::cout << "Bad allocation exception, STOPPING PROGRAM\n"
- << e.what() << "\n";
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n"
- << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- std::cout << "Exception, STOPPING PROGRAM\n" << e.what() << "\n";
- }
+ adios::ADIOS *adios = (adios::ADIOS *)adiosC;
+ int rank;
+ MPI_Comm_rank(adios->m_MPIComm, &rank);
+
+ try
+ {
+ adios->MonitorGroups(std::cout);
+ }
+ catch (std::bad_alloc &e)
+ {
+ if (rank == 0)
+ std::cout << "Bad allocation exception, STOPPING PROGRAM\n"
+ << e.what() << "\n";
+ }
+ catch (std::invalid_argument &e)
+ {
+ if (rank == 0)
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n"
+ << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ if (rank == 0)
+ std::cout << "Exception, STOPPING PROGRAM\n" << e.what() << "\n";
+ }
}
void adios_monitor_groups_file(const ADIOS *adiosC, const char *fileName,
const char *mode)
{
- adios::ADIOS *adios = (adios::ADIOS *)adiosC;
- int rank;
- MPI_Comm_rank(adios->m_MPIComm, &rank);
-
- try
- {
- std::ofstream fileStream;
-
- if (strcmp(mode, "a") == 0 || strcmp(mode, "append") == 0)
- fileStream.open(fileName, std::ostream::app);
- else if (strcmp(mode, "w") == 0 || strcmp(mode, "write") == 0)
- fileStream.open(fileName);
-
- adios->MonitorGroups(fileStream);
- }
- catch (std::bad_alloc &e)
- {
- if (rank == 0)
- std::cout << "Bad allocation exception, STOPPING PROGRAM\n"
- << e.what() << "\n";
- }
- catch (std::invalid_argument &e)
- {
- if (rank == 0)
- std::cout << "Invalid argument exception, STOPPING PROGRAM\n"
- << e.what() << "\n";
- }
- catch (std::exception &e)
- {
- if (rank == 0)
- std::cout << "Exception, STOPPING PROGRAM\n" << e.what() << "\n";
- }
+ adios::ADIOS *adios = (adios::ADIOS *)adiosC;
+ int rank;
+ MPI_Comm_rank(adios->m_MPIComm, &rank);
+
+ try
+ {
+ std::ofstream fileStream;
+
+ if (strcmp(mode, "a") == 0 || strcmp(mode, "append") == 0)
+ fileStream.open(fileName, std::ostream::app);
+ else if (strcmp(mode, "w") == 0 || strcmp(mode, "write") == 0)
+ fileStream.open(fileName);
+
+ adios->MonitorGroups(fileStream);
+ }
+ catch (std::bad_alloc &e)
+ {
+ if (rank == 0)
+ std::cout << "Bad allocation exception, STOPPING PROGRAM\n"
+ << e.what() << "\n";
+ }
+ catch (std::invalid_argument &e)
+ {
+ if (rank == 0)
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n"
+ << e.what() << "\n";
+ }
+ catch (std::exception &e)
+ {
+ if (rank == 0)
+ std::cout << "Exception, STOPPING PROGRAM\n" << e.what() << "\n";
+ }
}
#ifdef __cplusplus
diff --git a/source/capsule/heap/STLVector.cpp b/source/capsule/heap/STLVector.cpp
index 03564095e71fbbcbe560ef293d89d8038c86e699..99d9971e873dd2dedc614525b69b352e9b03101c 100644
--- a/source/capsule/heap/STLVector.cpp
+++ b/source/capsule/heap/STLVector.cpp
@@ -23,7 +23,7 @@ namespace capsule
STLVector::STLVector(std::string accessMode, int rankMPI, bool debugMode)
: Capsule{"Heap", std::move(accessMode), rankMPI, debugMode}
{
- m_Data.reserve(16777216);
+ m_Data.reserve(16777216);
}
char *STLVector::GetData() { return m_Data.data(); }
@@ -36,44 +36,44 @@ std::size_t STLVector::GetMetadataSize() const { return m_Metadata.size(); }
void STLVector::ResizeData(const std::size_t size)
{
- if (m_DebugMode == true)
- {
- try
+ if (m_DebugMode == true)
{
- m_Data.resize(size);
+ try
+ {
+ m_Data.resize(size);
+ }
+ catch (std::bad_alloc &e)
+ {
+ throw std::runtime_error("ERROR: bad_alloc detected when resizing "
+ "data buffer with size " +
+ std::to_string(size) + "\n");
+ }
}
- catch (std::bad_alloc &e)
+ else
{
- throw std::runtime_error(
- "ERROR: bad_alloc detected when resizing data buffer with size " +
- std::to_string(size) + "\n");
+ m_Data.resize(size);
}
- }
- else
- {
- m_Data.resize(size);
- }
}
void STLVector::ResizeMetadata(const std::size_t size)
{
- if (m_DebugMode == true)
- {
- try
+ if (m_DebugMode == true)
{
- m_Metadata.resize(size);
+ try
+ {
+ m_Metadata.resize(size);
+ }
+ catch (std::bad_alloc &e)
+ {
+ throw std::runtime_error("ERROR: bad_alloc detected when resizing "
+ "metadata buffer with size " +
+ std::to_string(size) + "\n");
+ }
}
- catch (std::bad_alloc &e)
+ else
{
- throw std::runtime_error(
- "ERROR: bad_alloc detected when resizing metadata buffer with size " +
- std::to_string(size) + "\n");
+ m_Metadata.resize(size);
}
- }
- else
- {
- m_Metadata.resize(size);
- }
}
} // end namespace capsule
diff --git a/source/capsule/shmem/ShmSystemV.cpp b/source/capsule/shmem/ShmSystemV.cpp
index 8c3e14dd10ef1481d2f160a93c9d984672e37374..b26868c46640c317c9ca77f0b7479379267b0bd9 100644
--- a/source/capsule/shmem/ShmSystemV.cpp
+++ b/source/capsule/shmem/ShmSystemV.cpp
@@ -25,26 +25,26 @@ ShmSystemV::ShmSystemV(std::string accessMode, int rankMPI,
: Capsule{"ShmSystemV", std::move(accessMode), rankMPI, debugMode},
m_DataSize{dataSize}, m_MetadataSize{metadataSize}
{
- // Data Shared memory sector
- const std::string dataPath(pathName + "/adios.shm.data." +
- std::to_string(m_RankMPI));
- m_DataKey = ftok(dataPath.c_str(), m_RankMPI + 1);
- m_DataShmID = shmget(m_DataKey, m_DataSize, IPC_CREAT | 0666);
- m_Data = static_cast<char *>(shmat(m_DataShmID, nullptr, 0));
+ // Data Shared memory sector
+ const std::string dataPath(pathName + "/adios.shm.data." +
+ std::to_string(m_RankMPI));
+ m_DataKey = ftok(dataPath.c_str(), m_RankMPI + 1);
+ m_DataShmID = shmget(m_DataKey, m_DataSize, IPC_CREAT | 0666);
+ m_Data = static_cast<char *>(shmat(m_DataShmID, nullptr, 0));
- // Metadata Shared memory sector
- const std::string metadataPath(pathName + "/adios.shm.metadata." +
- std::to_string(m_RankMPI));
- m_MetadataKey =
- ftok(metadataPath.c_str(),
- m_RankMPI + 1); // 2nd field must be greater than zero and unique
- m_MetadataShmID = shmget(m_MetadataKey, m_MetadataSize, IPC_CREAT | 0666);
- m_Metadata = static_cast<char *>(shmat(m_MetadataShmID, nullptr, 0));
+ // Metadata Shared memory sector
+ const std::string metadataPath(pathName + "/adios.shm.metadata." +
+ std::to_string(m_RankMPI));
+ m_MetadataKey =
+ ftok(metadataPath.c_str(),
+ m_RankMPI + 1); // 2nd field must be greater than zero and unique
+ m_MetadataShmID = shmget(m_MetadataKey, m_MetadataSize, IPC_CREAT | 0666);
+ m_Metadata = static_cast<char *>(shmat(m_MetadataShmID, nullptr, 0));
- if (m_DebugMode == true)
- {
- CheckShm();
- }
+ if (m_DebugMode == true)
+ {
+ CheckShm();
+ }
}
char *ShmSystemV::GetData() { return m_Data; }
@@ -57,37 +57,39 @@ size_t ShmSystemV::GetMetadataSize() const { return m_MetadataSize; }
void ShmSystemV::CheckShm() const
{
- if (m_DataShmID < 0)
- {
- throw std::ios_base::failure(
- "ERROR: Failed to create data shm segment of size " +
- std::to_string(m_DataSize) + " from call to ShmSystemV constructor\n");
- }
+ if (m_DataShmID < 0)
+ {
+ throw std::ios_base::failure(
+ "ERROR: Failed to create data shm segment of size " +
+ std::to_string(m_DataSize) +
+ " from call to ShmSystemV constructor\n");
+ }
- if (m_Data == nullptr)
- {
- throw std::ios_base::failure(
- "ERROR: Failed to attach to data shm segment of size " +
- std::to_string(m_DataSize) + " and id " + std::to_string(m_DataShmID) +
- ", from call to ShmSystemV constructor\n");
- }
+ if (m_Data == nullptr)
+ {
+ throw std::ios_base::failure(
+ "ERROR: Failed to attach to data shm segment of size " +
+ std::to_string(m_DataSize) + " and id " +
+ std::to_string(m_DataShmID) +
+ ", from call to ShmSystemV constructor\n");
+ }
- if (m_DataShmID < 0)
- {
- throw std::ios_base::failure(
- "ERROR: Failed to create metadata shm segment of size " +
- std::to_string(m_MetadataSize) +
- " from call to ShmSystemV constructor\n");
- }
+ if (m_DataShmID < 0)
+ {
+ throw std::ios_base::failure(
+ "ERROR: Failed to create metadata shm segment of size " +
+ std::to_string(m_MetadataSize) +
+ " from call to ShmSystemV constructor\n");
+ }
- if (m_Metadata == nullptr)
- {
- throw std::ios_base::failure(
- "ERROR: Failed to attach to metadata shm segment of size " +
- std::to_string(m_MetadataSize) + " and id " +
- std::to_string(m_MetadataShmID) +
- " from call to ShmSystemV constructor\n");
- }
+ if (m_Metadata == nullptr)
+ {
+ throw std::ios_base::failure(
+ "ERROR: Failed to attach to metadata shm segment of size " +
+ std::to_string(m_MetadataSize) + " and id " +
+ std::to_string(m_MetadataShmID) +
+ " from call to ShmSystemV constructor\n");
+ }
}
} // end namespace adios
diff --git a/source/core/Engine.cpp b/source/core/Engine.cpp
index 31497911e9f7ad729d17d17a66a87efc8675fd5b..ad23b38f143866f8f97cc1710b22e21e3f4cb59d 100644
--- a/source/core/Engine.cpp
+++ b/source/core/Engine.cpp
@@ -25,18 +25,18 @@ Engine::Engine(ADIOS &adios, std::string engineType, std::string name,
m_Method(method), m_ADIOS(adios), m_DebugMode(debugMode),
m_nThreads(nthreads), m_EndMessage(std::move(endMessage))
{
- if (m_DebugMode == true)
- {
- if (m_MPIComm == MPI_COMM_NULL)
+ if (m_DebugMode == true)
{
- throw std::ios_base::failure(
- "ERROR: engine communicator is MPI_COMM_NULL,"
- " in call to ADIOS Open or Constructor\n");
+ if (m_MPIComm == MPI_COMM_NULL)
+ {
+ throw std::ios_base::failure(
+ "ERROR: engine communicator is MPI_COMM_NULL,"
+ " in call to ADIOS Open or Constructor\n");
+ }
}
- }
- MPI_Comm_rank(m_MPIComm, &m_RankMPI);
- MPI_Comm_size(m_MPIComm, &m_SizeMPI);
+ MPI_Comm_rank(m_MPIComm, &m_RankMPI);
+ MPI_Comm_size(m_MPIComm, &m_SizeMPI);
}
void Engine::SetCallBack(std::function<void(const void *, std::string,
@@ -181,95 +181,95 @@ void Engine::Close(const int /*transportIndex*/) {}
Variable<void> *Engine::InquireVariable(const std::string /*name*/,
const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<char> *Engine::InquireVariableChar(const std::string /*name*/,
const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<unsigned char> *
Engine::InquireVariableUChar(const std::string /*name*/, const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<short> *Engine::InquireVariableShort(const std::string /*name*/,
const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<unsigned short> *
Engine::InquireVariableUShort(const std::string /*name*/, const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<int> *Engine::InquireVariableInt(const std::string /*name*/,
const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<unsigned int> *Engine::InquireVariableUInt(const std::string /*name*/,
const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<long int> *Engine::InquireVariableLInt(const std::string /*name*/,
const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<unsigned long int> *
Engine::InquireVariableULInt(const std::string /*name*/, const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<long long int> *
Engine::InquireVariableLLInt(const std::string /*name*/, const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<unsigned long long int> *
Engine::InquireVariableULLInt(const std::string /*name*/, const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<float> *Engine::InquireVariableFloat(const std::string /*name*/,
const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<double> *Engine::InquireVariableDouble(const std::string /*name*/,
const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<long double> *
Engine::InquireVariableLDouble(const std::string /*name*/,
const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<std::complex<float>> *
Engine::InquireVariableCFloat(const std::string /*name*/, const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<std::complex<double>> *
Engine::InquireVariableCDouble(const std::string /*name*/,
const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
Variable<std::complex<long double>> *
Engine::InquireVariableCLDouble(const std::string /*name*/,
const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
VariableCompound *Engine::InquireVariableCompound(const std::string /*name*/,
const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
void Engine::Read(Variable<double> & /*variable*/, const double * /*values*/) {}
@@ -291,72 +291,72 @@ void Engine::CheckParameter(
const std::map<std::string, std::string> ¶meters,
const std::string parameterName, const std::string hint) const
{
- if (itParam == parameters.end())
- {
+ if (itParam == parameters.end())
{
- throw std::invalid_argument("ERROR: parameter name " + parameterName +
- " not found " + hint);
+ {
+ throw std::invalid_argument("ERROR: parameter name " +
+ parameterName + " not found " + hint);
+ }
}
- }
}
bool Engine::TransportNamesUniqueness() const
{
- auto lf_CheckTransportsType =
- [&](const std::set<std::string> &specificType) -> bool {
- std::set<std::string> transportNames;
+ auto lf_CheckTransportsType =
+ [&](const std::set<std::string> &specificType) -> bool {
+ std::set<std::string> transportNames;
- for (const auto ¶meters : m_Method.m_TransportParameters)
- {
- auto itTransport = parameters.find("transport");
- if (m_DebugMode == true)
- {
- if (itTransport == parameters.end())
+ for (const auto ¶meters : m_Method.m_TransportParameters)
{
- throw std::invalid_argument(
- "ERROR: transport not defined in Method input to Engine " +
- m_Name);
- }
- }
+ auto itTransport = parameters.find("transport");
+ if (m_DebugMode == true)
+ {
+ if (itTransport == parameters.end())
+ {
+ throw std::invalid_argument("ERROR: transport not defined "
+ "in Method input to Engine " +
+ m_Name);
+ }
+ }
- const std::string type(itTransport->second);
- if (specificType.count(type) == 1) // file transports type
- {
- std::string name(m_Name);
- auto itName = parameters.find("name");
- if (itName != parameters.end())
- {
- name = itName->second;
- }
+ const std::string type(itTransport->second);
+ if (specificType.count(type) == 1) // file transports type
+ {
+ std::string name(m_Name);
+ auto itName = parameters.find("name");
+ if (itName != parameters.end())
+ {
+ name = itName->second;
+ }
- if (transportNames.count(name) == 0)
- {
- transportNames.insert(name);
- }
- else
- {
- return false;
+ if (transportNames.count(name) == 0)
+ {
+ transportNames.insert(name);
+ }
+ else
+ {
+ return false;
+ }
+ }
}
- }
- }
- return true;
- };
+ return true;
+ };
- return lf_CheckTransportsType(Support::FileTransports);
+ return lf_CheckTransportsType(Support::FileTransports);
}
void Engine::CheckTransportIndex(const int transportIndex)
{
- if (m_DebugMode == true)
- {
- if (transportIndex >= static_cast<int>(m_Transports.size()) ||
- transportIndex < -1)
+ if (m_DebugMode == true)
{
- throw std::invalid_argument(
- "ERROR: transport index " + std::to_string(transportIndex) +
- " is out of range, in call to " + m_Name + "Close \n");
+ if (transportIndex >= static_cast<int>(m_Transports.size()) ||
+ transportIndex < -1)
+ {
+ throw std::invalid_argument(
+ "ERROR: transport index " + std::to_string(transportIndex) +
+ " is out of range, in call to " + m_Name + "Close \n");
+ }
}
- }
}
} // end namespace adios
diff --git a/source/core/Method.cpp b/source/core/Method.cpp
index 905b04f9e4c50d6b172c20cfaee909be7309dcb9..02d1750344feb7fa6b2a5154394a7cb08cb396fd 100644
--- a/source/core/Method.cpp
+++ b/source/core/Method.cpp
@@ -19,56 +19,57 @@ namespace adios
Method::Method(std::string name, bool debugMode)
: m_Name{std::move(name)}, m_DebugMode{debugMode}
{
- // m_Type can stay empty (forcing the choice of the default engine)
- m_nThreads = 1;
+ // m_Type can stay empty (forcing the choice of the default engine)
+ m_nThreads = 1;
}
bool Method::isUserDefined()
{
- return false; // TODO(wfg): check if XML has the method defined
+ return false; // TODO(wfg): check if XML has the method defined
}
void Method::SetEngine(const std::string type) { m_Type = type; }
void Method::AllowThreads(const int nThreads)
{
- if (nThreads > 1)
- {
- m_nThreads = nThreads;
- }
- else
- {
- m_nThreads = 1;
- }
+ if (nThreads > 1)
+ {
+ m_nThreads = nThreads;
+ }
+ else
+ {
+ m_nThreads = 1;
+ }
}
// PRIVATE Functions
void Method::AddTransportParameters(const std::string type,
const std::vector<std::string> ¶meters)
{
- if (m_DebugMode == true)
- {
- if (type.empty() || type.find("=") != type.npos)
+ if (m_DebugMode == true)
{
- throw std::invalid_argument("ERROR: first argument in AddTransport must "
- "be a single word for transport\n");
+ if (type.empty() || type.find("=") != type.npos)
+ {
+ throw std::invalid_argument(
+ "ERROR: first argument in AddTransport must "
+ "be a single word for transport\n");
+ }
}
- }
- std::map<std::string, std::string> mapParameters =
- BuildParametersMap(parameters, m_DebugMode);
- if (m_DebugMode == true)
- {
- if (mapParameters.count("transport") == 1)
+ std::map<std::string, std::string> mapParameters =
+ BuildParametersMap(parameters, m_DebugMode);
+ if (m_DebugMode == true)
{
- std::invalid_argument(
- "ERROR: transport can't be redefined with \"transport=type\", "
- "type must be the first argument\n");
+ if (mapParameters.count("transport") == 1)
+ {
+ std::invalid_argument("ERROR: transport can't be redefined with "
+ "\"transport=type\", "
+ "type must be the first argument\n");
+ }
}
- }
- mapParameters["transport"] = type;
- m_TransportParameters.push_back(mapParameters);
+ mapParameters["transport"] = type;
+ m_TransportParameters.push_back(mapParameters);
}
} // end namespace adios
diff --git a/source/core/Transport.cpp b/source/core/Transport.cpp
index 29fbc773e19e3ecd398f6d4bd79fcae8fe185cda..a3a3e2505be5df43a9345377994ca2446bf175cc 100644
--- a/source/core/Transport.cpp
+++ b/source/core/Transport.cpp
@@ -18,8 +18,8 @@ namespace adios
Transport::Transport(std::string type, MPI_Comm mpiComm, bool debugMode)
: m_Type{std::move(type)}, m_MPIComm{mpiComm}, m_DebugMode{debugMode}
{
- MPI_Comm_rank(m_MPIComm, &m_RankMPI);
- MPI_Comm_size(m_MPIComm, &m_SizeMPI);
+ MPI_Comm_rank(m_MPIComm, &m_RankMPI);
+ MPI_Comm_size(m_MPIComm, &m_SizeMPI);
}
void Transport::SetBuffer(char * /*buffer*/, size_t /*size*/) {}
@@ -31,27 +31,27 @@ void Transport::Close() {}
void Transport::InitProfiler(const std::string accessMode,
const Support::Resolutions resolution)
{
- m_Profiler.m_Timers.emplace_back("open", Support::Resolutions::mus);
+ m_Profiler.m_Timers.emplace_back("open", Support::Resolutions::mus);
- if (accessMode == "w" || accessMode == "write")
- {
- m_Profiler.m_Timers.emplace_back("write", resolution);
- }
+ if (accessMode == "w" || accessMode == "write")
+ {
+ m_Profiler.m_Timers.emplace_back("write", resolution);
+ }
- else if (accessMode == "a" || accessMode == "append")
- {
- m_Profiler.m_Timers.emplace_back("append", resolution);
- }
+ else if (accessMode == "a" || accessMode == "append")
+ {
+ m_Profiler.m_Timers.emplace_back("append", resolution);
+ }
- else if (accessMode == "r" || accessMode == "read")
- {
- m_Profiler.m_Timers.emplace_back("read", resolution);
- }
+ else if (accessMode == "r" || accessMode == "read")
+ {
+ m_Profiler.m_Timers.emplace_back("read", resolution);
+ }
- m_Profiler.m_Timers.emplace_back("close", Support::Resolutions::mus);
+ m_Profiler.m_Timers.emplace_back("close", Support::Resolutions::mus);
- m_Profiler.m_TotalBytes.push_back(0);
- m_Profiler.m_IsActive = true;
+ m_Profiler.m_TotalBytes.push_back(0);
+ m_Profiler.m_IsActive = true;
}
} // end namespace adios
diff --git a/source/engine/adios1/ADIOS1Reader.cpp b/source/engine/adios1/ADIOS1Reader.cpp
index 406c752d39d2e8357c1a0a008c2d2a975cf80425..e3ff93ec01d049bebf8e00c5a03485cc85ef5c2a 100644
--- a/source/engine/adios1/ADIOS1Reader.cpp
+++ b/source/engine/adios1/ADIOS1Reader.cpp
@@ -30,7 +30,7 @@ BPFileReader::BPFileReader(ADIOS &adios, const std::string name,
nthreads, " BPFileReader constructor (or call to ADIOS Open).\n"),
m_Buffer(accessMode, m_RankMPI, m_DebugMode)
{
- Init();
+ Init();
}
BPFileReader::~BPFileReader() {}
@@ -39,109 +39,109 @@ Variable<void> *
BPFileReader::InquireVariable(const std::string name,
const bool readIn) // not yet implemented
{
- return nullptr;
+ return nullptr;
}
Variable<char> *BPFileReader::InquireVariableChar(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<char>(name, readIn);
+ return InquireVariableCommon<char>(name, readIn);
}
Variable<unsigned char> *
BPFileReader::InquireVariableUChar(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned char>(name, readIn);
+ return InquireVariableCommon<unsigned char>(name, readIn);
}
Variable<short> *BPFileReader::InquireVariableShort(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<short>(name, readIn);
+ return InquireVariableCommon<short>(name, readIn);
}
Variable<unsigned short> *
BPFileReader::InquireVariableUShort(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned short>(name, readIn);
+ return InquireVariableCommon<unsigned short>(name, readIn);
}
Variable<int> *BPFileReader::InquireVariableInt(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<int>(name, readIn);
+ return InquireVariableCommon<int>(name, readIn);
}
Variable<unsigned int> *
BPFileReader::InquireVariableUInt(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned int>(name, readIn);
+ return InquireVariableCommon<unsigned int>(name, readIn);
}
Variable<long int> *BPFileReader::InquireVariableLInt(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<long int>(name, readIn);
+ return InquireVariableCommon<long int>(name, readIn);
}
Variable<unsigned long int> *
BPFileReader::InquireVariableULInt(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned long int>(name, readIn);
+ return InquireVariableCommon<unsigned long int>(name, readIn);
}
Variable<long long int> *
BPFileReader::InquireVariableLLInt(const std::string name, const bool readIn)
{
- return InquireVariableCommon<long long int>(name, readIn);
+ return InquireVariableCommon<long long int>(name, readIn);
}
Variable<unsigned long long int> *
BPFileReader::InquireVariableULLInt(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned long long int>(name, readIn);
+ return InquireVariableCommon<unsigned long long int>(name, readIn);
}
Variable<float> *BPFileReader::InquireVariableFloat(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<float>(name, readIn);
+ return InquireVariableCommon<float>(name, readIn);
}
Variable<double> *BPFileReader::InquireVariableDouble(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<double>(name, readIn);
+ return InquireVariableCommon<double>(name, readIn);
}
Variable<long double> *
BPFileReader::InquireVariableLDouble(const std::string name, const bool readIn)
{
- return InquireVariableCommon<long double>(name, readIn);
+ return InquireVariableCommon<long double>(name, readIn);
}
Variable<std::complex<float>> *
BPFileReader::InquireVariableCFloat(const std::string name, const bool readIn)
{
- return InquireVariableCommon<std::complex<float>>(name, readIn);
+ return InquireVariableCommon<std::complex<float>>(name, readIn);
}
Variable<std::complex<double>> *
BPFileReader::InquireVariableCDouble(const std::string name, const bool readIn)
{
- return InquireVariableCommon<std::complex<double>>(name, readIn);
+ return InquireVariableCommon<std::complex<double>>(name, readIn);
}
Variable<std::complex<long double>> *
BPFileReader::InquireVariableCLDouble(const std::string name, const bool readIn)
{
- return InquireVariableCommon<std::complex<long double>>(name, readIn);
+ return InquireVariableCommon<std::complex<long double>>(name, readIn);
}
VariableCompound *BPFileReader::InquireVariableCompound(const std::string name,
const bool readIn)
{
- return nullptr;
+ return nullptr;
}
void BPFileReader::Close(const int transportIndex) {}
@@ -149,84 +149,87 @@ void BPFileReader::Close(const int transportIndex) {}
// PRIVATE
void BPFileReader::Init()
{
- if (m_DebugMode == true)
- {
- if (m_AccessMode != "r" && m_AccessMode != "read")
- throw std::invalid_argument(
- "ERROR: BPFileReader doesn't support access mode " + m_AccessMode +
- ", in call to ADIOS Open or BPFileReader constructor\n");
- }
+ if (m_DebugMode == true)
+ {
+ if (m_AccessMode != "r" && m_AccessMode != "read")
+ throw std::invalid_argument(
+ "ERROR: BPFileReader doesn't support access mode " +
+ m_AccessMode +
+ ", in call to ADIOS Open or BPFileReader constructor\n");
+ }
- InitCapsules();
- InitTransports();
+ InitCapsules();
+ InitTransports();
}
void BPFileReader::InitCapsules()
{
- // here init memory capsules
+ // here init memory capsules
}
void BPFileReader::InitTransports() // maybe move this?
{
- if (m_DebugMode == true)
- {
- if (TransportNamesUniqueness() == false)
+ if (m_DebugMode == true)
{
- throw std::invalid_argument(
- "ERROR: two transports of the same kind (e.g file IO) "
- "can't have the same name, modify with name= in Method "
- "AddTransport\n");
+ if (TransportNamesUniqueness() == false)
+ {
+ throw std::invalid_argument(
+ "ERROR: two transports of the same kind (e.g file IO) "
+ "can't have the same name, modify with name= in Method "
+ "AddTransport\n");
+ }
}
- }
- for (const auto ¶meters : m_Method.m_TransportParameters)
- {
- auto itTransport = parameters.find("transport");
- if (itTransport->second == "file" || itTransport->second == "File")
- {
- auto itLibrary = parameters.find("library");
- if (itLibrary == parameters.end() ||
- itLibrary->second == "POSIX") // use default POSIX
- {
- auto file =
- std::make_shared<transport::FileDescriptor>(m_MPIComm, m_DebugMode);
- // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "FILE*" || itLibrary->second == "stdio.h")
- {
- auto file =
- std::make_shared<transport::FilePointer>(m_MPIComm, m_DebugMode);
- // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "fstream" ||
- itLibrary->second == "std::fstream")
- {
- auto file =
- std::make_shared<transport::FStream>(m_MPIComm, m_DebugMode);
- // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "MPI-IO")
- {
- }
- else
- {
- if (m_DebugMode == true)
- throw std::invalid_argument(
- "ERROR: file transport library " + itLibrary->second +
- " not supported, in " + m_Name + m_EndMessage);
- }
- }
- else
+ for (const auto ¶meters : m_Method.m_TransportParameters)
{
- if (m_DebugMode == true)
- throw std::invalid_argument("ERROR: transport " + itTransport->second +
- " (you mean File?) not supported, in " +
- m_Name + m_EndMessage);
+ auto itTransport = parameters.find("transport");
+ if (itTransport->second == "file" || itTransport->second == "File")
+ {
+ auto itLibrary = parameters.find("library");
+ if (itLibrary == parameters.end() ||
+ itLibrary->second == "POSIX") // use default POSIX
+ {
+ auto file = std::make_shared<transport::FileDescriptor>(
+ m_MPIComm, m_DebugMode);
+ // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
+ m_Transports.push_back(std::move(file));
+ }
+ else if (itLibrary->second == "FILE*" ||
+ itLibrary->second == "stdio.h")
+ {
+ auto file = std::make_shared<transport::FilePointer>(
+ m_MPIComm, m_DebugMode);
+ // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
+ m_Transports.push_back(std::move(file));
+ }
+ else if (itLibrary->second == "fstream" ||
+ itLibrary->second == "std::fstream")
+ {
+ auto file = std::make_shared<transport::FStream>(m_MPIComm,
+ m_DebugMode);
+ // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
+ m_Transports.push_back(std::move(file));
+ }
+ else if (itLibrary->second == "MPI-IO")
+ {
+ }
+ else
+ {
+ if (m_DebugMode == true)
+ throw std::invalid_argument(
+ "ERROR: file transport library " + itLibrary->second +
+ " not supported, in " + m_Name + m_EndMessage);
+ }
+ }
+ else
+ {
+ if (m_DebugMode == true)
+ throw std::invalid_argument(
+ "ERROR: transport " + itTransport->second +
+ " (you mean File?) not supported, in " + m_Name +
+ m_EndMessage);
+ }
}
- }
}
} // end namespace
diff --git a/source/engine/adios1/ADIOS1Writer.cpp b/source/engine/adios1/ADIOS1Writer.cpp
index dc45da793801236e09720ba4a5626067a9fe7290..81813dc63f759ec71aeebc70c13e1968f1b57aba 100644
--- a/source/engine/adios1/ADIOS1Writer.cpp
+++ b/source/engine/adios1/ADIOS1Writer.cpp
@@ -28,49 +28,49 @@ ADIOS1Writer::ADIOS1Writer(ADIOS &adios, const std::string name,
nthreads, " ADIOS1Writer constructor (or call to ADIOS Open).\n"),
m_groupname{method.m_Name.c_str()}, m_filename{name.c_str()}, m_comm{mpiComm}
{
- Init();
- adios_open(&m_adios_file, m_groupname, m_filename, accessMode.c_str(),
- m_comm);
- if (adios_errno == err_no_error)
- {
- m_IsFileOpen = true;
- }
+ Init();
+ adios_open(&m_adios_file, m_groupname, m_filename, accessMode.c_str(),
+ m_comm);
+ if (adios_errno == err_no_error)
+ {
+ m_IsFileOpen = true;
+ }
}
ADIOS1Writer::~ADIOS1Writer()
{
- if (m_IsFileOpen)
- {
- adios_close(m_adios_file);
- m_IsFileOpen = false;
- }
+ if (m_IsFileOpen)
+ {
+ adios_close(m_adios_file);
+ m_IsFileOpen = false;
+ }
}
void ADIOS1Writer::Init()
{
- if (!m_initialized)
- {
- adios_init_noxml(m_comm);
- m_initialized = true;
- }
- adios_declare_group(&m_adios_group, m_groupname, "", adios_stat_default);
+ if (!m_initialized)
+ {
+ adios_init_noxml(m_comm);
+ m_initialized = true;
+ }
+ adios_declare_group(&m_adios_group, m_groupname, "", adios_stat_default);
- InitParameters();
- InitTransports();
+ InitParameters();
+ InitTransports();
}
bool ADIOS1Writer::ReOpenAsNeeded()
{
- if (!m_IsFileOpen)
- {
- adios_open(&m_adios_file, m_groupname, m_filename, "a", m_comm);
- if (adios_errno == err_no_error)
+ if (!m_IsFileOpen)
{
- m_IsFileOpen = true;
- adios_delete_vardefs(m_adios_group);
+ adios_open(&m_adios_file, m_groupname, m_filename, "a", m_comm);
+ if (adios_errno == err_no_error)
+ {
+ m_IsFileOpen = true;
+ adios_delete_vardefs(m_adios_group);
+ }
}
- }
- return m_IsFileOpen;
+ return m_IsFileOpen;
}
void ADIOS1Writer::DefineVariable(std::string name, bool isScalar,
@@ -78,15 +78,15 @@ void ADIOS1Writer::DefineVariable(std::string name, bool isScalar,
std::string ldims, std::string gdims,
std::string offs)
{
- if (isScalar)
- {
- adios_define_var(m_adios_group, name.c_str(), "", vartype, "", "", "");
- }
- else
- {
- adios_define_var(m_adios_group, name.c_str(), "", vartype, ldims.c_str(),
- gdims.c_str(), offs.c_str());
- }
+ if (isScalar)
+ {
+ adios_define_var(m_adios_group, name.c_str(), "", vartype, "", "", "");
+ }
+ else
+ {
+ adios_define_var(m_adios_group, name.c_str(), "", vartype,
+ ldims.c_str(), gdims.c_str(), offs.c_str());
+ }
}
void ADIOS1Writer::WriteVariable(std::string name, bool isScalar,
@@ -94,357 +94,362 @@ void ADIOS1Writer::WriteVariable(std::string name, bool isScalar,
std::string ldims, std::string gdims,
std::string offs, const void *values)
{
- if (ReOpenAsNeeded())
- {
- DefineVariable(name, isScalar, vartype, ldims, gdims, offs);
- adios_write(m_adios_file, name.c_str(), values);
- }
+ if (ReOpenAsNeeded())
+ {
+ DefineVariable(name, isScalar, vartype, ldims, gdims, offs);
+ adios_write(m_adios_file, name.c_str(), values);
+ }
}
void ADIOS1Writer::Write(Variable<char> &variable, const char *values)
{
- WriteVariable(variable.m_Name, variable.m_IsScalar, adios_byte,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ WriteVariable(variable.m_Name, variable.m_IsScalar, adios_byte,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<unsigned char> &variable,
const unsigned char *values)
{
- WriteVariable(variable.m_Name, variable.m_IsScalar, adios_unsigned_byte,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ WriteVariable(variable.m_Name, variable.m_IsScalar, adios_unsigned_byte,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<short> &variable, const short *values)
{
- WriteVariable(variable.m_Name, variable.m_IsScalar, adios_short,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ WriteVariable(variable.m_Name, variable.m_IsScalar, adios_short,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<unsigned short> &variable,
const unsigned short *values)
{
- WriteVariable(variable.m_Name, variable.m_IsScalar, adios_unsigned_short,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ WriteVariable(variable.m_Name, variable.m_IsScalar, adios_unsigned_short,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<int> &variable, const int *values)
{
- WriteVariable(variable.m_Name, variable.m_IsScalar, adios_integer,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ WriteVariable(variable.m_Name, variable.m_IsScalar, adios_integer,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<unsigned int> &variable,
const unsigned int *values)
{
- WriteVariable(variable.m_Name, variable.m_IsScalar, adios_unsigned_integer,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ WriteVariable(variable.m_Name, variable.m_IsScalar, adios_unsigned_integer,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<long int> &variable, const long int *values)
{
- enum ADIOS_DATATYPES type =
- adios_integer; // long int is usually 4 bytes which is adios_integer
- if (sizeof(long int) == 8)
- {
- type = adios_long;
- }
- WriteVariable(variable.m_Name, variable.m_IsScalar, type,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ enum ADIOS_DATATYPES type =
+ adios_integer; // long int is usually 4 bytes which is adios_integer
+ if (sizeof(long int) == 8)
+ {
+ type = adios_long;
+ }
+ WriteVariable(variable.m_Name, variable.m_IsScalar, type,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<unsigned long int> &variable,
const unsigned long int *values)
{
- enum ADIOS_DATATYPES type =
- adios_unsigned_integer; // long int is usually 4 bytes
- if (sizeof(long int) == 8)
- {
- type = adios_unsigned_long;
- }
- WriteVariable(variable.m_Name, variable.m_IsScalar, type,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ enum ADIOS_DATATYPES type =
+ adios_unsigned_integer; // long int is usually 4 bytes
+ if (sizeof(long int) == 8)
+ {
+ type = adios_unsigned_long;
+ }
+ WriteVariable(variable.m_Name, variable.m_IsScalar, type,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<long long int> &variable,
const long long int *values)
{
- WriteVariable(variable.m_Name, variable.m_IsScalar, adios_long,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ WriteVariable(variable.m_Name, variable.m_IsScalar, adios_long,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<unsigned long long int> &variable,
const unsigned long long int *values)
{
- WriteVariable(variable.m_Name, variable.m_IsScalar, adios_unsigned_long,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ WriteVariable(variable.m_Name, variable.m_IsScalar, adios_unsigned_long,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<float> &variable, const float *values)
{
- WriteVariable(variable.m_Name, variable.m_IsScalar, adios_real,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ WriteVariable(variable.m_Name, variable.m_IsScalar, adios_real,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<double> &variable, const double *values)
{
- WriteVariable(variable.m_Name, variable.m_IsScalar, adios_double,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ WriteVariable(variable.m_Name, variable.m_IsScalar, adios_double,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<long double> &variable,
const long double *values)
{
- /* TODO: This is faulty: adios_long_double expects 16 bytes per elements, but
- * long double is compiler dependent */
- WriteVariable(variable.m_Name, variable.m_IsScalar, adios_long_double,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ /* TODO: This is faulty: adios_long_double expects 16 bytes per elements,
+ * but
+ * long double is compiler dependent */
+ WriteVariable(variable.m_Name, variable.m_IsScalar, adios_long_double,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<std::complex<float>> &variable,
const std::complex<float> *values)
{
- WriteVariable(variable.m_Name, variable.m_IsScalar, adios_complex,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ WriteVariable(variable.m_Name, variable.m_IsScalar, adios_complex,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<std::complex<double>> &variable,
const std::complex<double> *values)
{
- WriteVariable(variable.m_Name, variable.m_IsScalar, adios_double_complex,
- variable.GetDimensionAsString(),
- variable.GetGlobalDimensionAsString(),
- variable.GetOffsetsAsString(), values);
+ WriteVariable(variable.m_Name, variable.m_IsScalar, adios_double_complex,
+ variable.GetDimensionAsString(),
+ variable.GetGlobalDimensionAsString(),
+ variable.GetOffsetsAsString(), values);
}
void ADIOS1Writer::Write(Variable<std::complex<long double>> &variable,
const std::complex<long double> *values)
{
- throw std::invalid_argument("ERROR: Adios 1.x does not support complex<long "
- "double> type, so it cannot write variable " +
- variable.m_Name + "\n");
+ throw std::invalid_argument(
+ "ERROR: Adios 1.x does not support complex<long "
+ "double> type, so it cannot write variable " +
+ variable.m_Name + "\n");
}
void ADIOS1Writer::Write(VariableCompound &variable, const void *values)
{
- throw std::invalid_argument("ERROR: Adios 1.x does not support compound "
- "types, so it cannot write variable " +
- variable.m_Name + "\n");
+ throw std::invalid_argument("ERROR: Adios 1.x does not support compound "
+ "types, so it cannot write variable " +
+ variable.m_Name + "\n");
}
// String version
void ADIOS1Writer::Write(const std::string variableName, const char *values)
{
- Write(m_ADIOS.GetVariable<char>(variableName), values);
+ Write(m_ADIOS.GetVariable<char>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName,
const unsigned char *values)
{
- Write(m_ADIOS.GetVariable<unsigned char>(variableName), values);
+ Write(m_ADIOS.GetVariable<unsigned char>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName, const short *values)
{
- Write(m_ADIOS.GetVariable<short>(variableName), values);
+ Write(m_ADIOS.GetVariable<short>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName,
const unsigned short *values)
{
- Write(m_ADIOS.GetVariable<unsigned short>(variableName), values);
+ Write(m_ADIOS.GetVariable<unsigned short>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName, const int *values)
{
- Write(m_ADIOS.GetVariable<int>(variableName), values);
+ Write(m_ADIOS.GetVariable<int>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName,
const unsigned int *values)
{
- Write(m_ADIOS.GetVariable<unsigned int>(variableName), values);
+ Write(m_ADIOS.GetVariable<unsigned int>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName, const long int *values)
{
- Write(m_ADIOS.GetVariable<long int>(variableName), values);
+ Write(m_ADIOS.GetVariable<long int>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName,
const unsigned long int *values)
{
- Write(m_ADIOS.GetVariable<unsigned long int>(variableName), values);
+ Write(m_ADIOS.GetVariable<unsigned long int>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName,
const long long int *values)
{
- Write(m_ADIOS.GetVariable<long long int>(variableName), values);
+ Write(m_ADIOS.GetVariable<long long int>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName,
const unsigned long long int *values)
{
- Write(m_ADIOS.GetVariable<unsigned long long int>(variableName), values);
+ Write(m_ADIOS.GetVariable<unsigned long long int>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName, const float *values)
{
- Write(m_ADIOS.GetVariable<float>(variableName), values);
+ Write(m_ADIOS.GetVariable<float>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName, const double *values)
{
- Write(m_ADIOS.GetVariable<double>(variableName), values);
+ Write(m_ADIOS.GetVariable<double>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName,
const long double *values)
{
- Write(m_ADIOS.GetVariable<long double>(variableName), values);
+ Write(m_ADIOS.GetVariable<long double>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName,
const std::complex<float> *values)
{
- Write(m_ADIOS.GetVariable<std::complex<float>>(variableName), values);
+ Write(m_ADIOS.GetVariable<std::complex<float>>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName,
const std::complex<double> *values)
{
- Write(m_ADIOS.GetVariable<std::complex<double>>(variableName), values);
+ Write(m_ADIOS.GetVariable<std::complex<double>>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName,
const std::complex<long double> *values)
{
- Write(m_ADIOS.GetVariable<std::complex<long double>>(variableName), values);
+ Write(m_ADIOS.GetVariable<std::complex<long double>>(variableName), values);
}
void ADIOS1Writer::Write(const std::string variableName,
const void *values) // Compound type
{
- throw std::invalid_argument("ERROR: Adios 1.x does not support compound "
- "types, so it cannot write variable " +
- variableName + "\n");
+ throw std::invalid_argument("ERROR: Adios 1.x does not support compound "
+ "types, so it cannot write variable " +
+ variableName + "\n");
}
void ADIOS1Writer::Advance()
{
- if (m_IsFileOpen)
- {
- adios_close(m_adios_file);
- m_IsFileOpen = false;
- }
+ if (m_IsFileOpen)
+ {
+ adios_close(m_adios_file);
+ m_IsFileOpen = false;
+ }
}
void ADIOS1Writer::Close(const int transportIndex)
{
- if (m_IsFileOpen)
- {
- adios_close(m_adios_file);
- m_IsFileOpen = false;
- }
+ if (m_IsFileOpen)
+ {
+ adios_close(m_adios_file);
+ m_IsFileOpen = false;
+ }
}
// PRIVATE FUNCTIONS
void ADIOS1Writer::InitParameters()
{
- auto itMaxBufferSize = m_Method.m_Parameters.find("max_size_MB");
- if (itMaxBufferSize != m_Method.m_Parameters.end())
- {
- adios_set_max_buffer_size(std::stoul(itMaxBufferSize->second));
- }
+ auto itMaxBufferSize = m_Method.m_Parameters.find("max_size_MB");
+ if (itMaxBufferSize != m_Method.m_Parameters.end())
+ {
+ adios_set_max_buffer_size(std::stoul(itMaxBufferSize->second));
+ }
- auto itVerbosity = m_Method.m_Parameters.find("verbose");
- if (itVerbosity != m_Method.m_Parameters.end())
- {
- int verbosity = std::stoi(itVerbosity->second);
- if (m_DebugMode == true)
+ auto itVerbosity = m_Method.m_Parameters.find("verbose");
+ if (itVerbosity != m_Method.m_Parameters.end())
{
- if (verbosity < 0 || verbosity > 5)
- throw std::invalid_argument("ERROR: Method verbose argument must be an "
- "integer in the range [0,5], in call to "
- "Open or Engine constructor\n");
+ int verbosity = std::stoi(itVerbosity->second);
+ if (m_DebugMode == true)
+ {
+ if (verbosity < 0 || verbosity > 5)
+ throw std::invalid_argument(
+ "ERROR: Method verbose argument must be an "
+ "integer in the range [0,5], in call to "
+ "Open or Engine constructor\n");
+ }
+ adios_verbose_level = verbosity;
}
- adios_verbose_level = verbosity;
- }
}
void ADIOS1Writer::InitTransports()
{
- if (m_DebugMode == true)
- {
- if (TransportNamesUniqueness() == false)
+ if (m_DebugMode == true)
{
- throw std::invalid_argument(
- "ERROR: two transports of the same kind (e.g file IO) "
- "can't have the same name, modify with name= in Method "
- "AddTransport\n");
+ if (TransportNamesUniqueness() == false)
+ {
+ throw std::invalid_argument(
+ "ERROR: two transports of the same kind (e.g file IO) "
+ "can't have the same name, modify with name= in Method "
+ "AddTransport\n");
+ }
}
- }
-
- for (const auto ¶meters : m_Method.m_TransportParameters)
- {
- auto itTransport = parameters.find("transport");
- if (itTransport->second == "file" || itTransport->second == "File")
- {
- auto itLibrary = parameters.find("library");
- if (itLibrary == parameters.end() ||
- itLibrary->second == "POSIX") // use default POSIX
- {
- adios_select_method(m_adios_group, "POSIX", "", "");
- }
- else if (itLibrary->second == "MPI_File" || itLibrary->second == "MPI-IO")
- {
- adios_select_method(m_adios_group, "MPI", "", "");
- }
- else
- {
- if (m_DebugMode == true)
- throw std::invalid_argument(
- "ERROR: file transport library " + itLibrary->second +
- " not supported, in " + m_Name + m_EndMessage);
- }
- }
- else
+ for (const auto ¶meters : m_Method.m_TransportParameters)
{
- if (m_DebugMode == true)
- throw std::invalid_argument("ERROR: transport " + itTransport->second +
- " (you mean File?) not supported, in " +
- m_Name + m_EndMessage);
+ auto itTransport = parameters.find("transport");
+
+ if (itTransport->second == "file" || itTransport->second == "File")
+ {
+ auto itLibrary = parameters.find("library");
+ if (itLibrary == parameters.end() ||
+ itLibrary->second == "POSIX") // use default POSIX
+ {
+ adios_select_method(m_adios_group, "POSIX", "", "");
+ }
+ else if (itLibrary->second == "MPI_File" ||
+ itLibrary->second == "MPI-IO")
+ {
+ adios_select_method(m_adios_group, "MPI", "", "");
+ }
+ else
+ {
+ if (m_DebugMode == true)
+ throw std::invalid_argument(
+ "ERROR: file transport library " + itLibrary->second +
+ " not supported, in " + m_Name + m_EndMessage);
+ }
+ }
+ else
+ {
+ if (m_DebugMode == true)
+ throw std::invalid_argument(
+ "ERROR: transport " + itTransport->second +
+ " (you mean File?) not supported, in " + m_Name +
+ m_EndMessage);
+ }
}
- }
}
} // end namespace adios
diff --git a/source/engine/bp/BPFileReader.cpp b/source/engine/bp/BPFileReader.cpp
index e658e5580d3046b6cde1847a09c65f2d71d5de4e..b12b655e0f6327c094c9757f3cf255408db3ddfe 100644
--- a/source/engine/bp/BPFileReader.cpp
+++ b/source/engine/bp/BPFileReader.cpp
@@ -31,117 +31,117 @@ BPFileReader::BPFileReader(ADIOS &adios, std::string name,
" BPFileReader constructor (or call to ADIOS Open).\n"),
m_Buffer(accessMode, m_RankMPI, m_DebugMode)
{
- Init();
+ Init();
}
Variable<void> *BPFileReader::InquireVariable(const std::string /*name*/,
const bool /*readIn*/)
{
- // not yet implemented
- return nullptr;
+ // not yet implemented
+ return nullptr;
}
Variable<char> *BPFileReader::InquireVariableChar(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<char>(name, readIn);
+ return InquireVariableCommon<char>(name, readIn);
}
Variable<unsigned char> *
BPFileReader::InquireVariableUChar(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned char>(name, readIn);
+ return InquireVariableCommon<unsigned char>(name, readIn);
}
Variable<short> *BPFileReader::InquireVariableShort(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<short>(name, readIn);
+ return InquireVariableCommon<short>(name, readIn);
}
Variable<unsigned short> *
BPFileReader::InquireVariableUShort(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned short>(name, readIn);
+ return InquireVariableCommon<unsigned short>(name, readIn);
}
Variable<int> *BPFileReader::InquireVariableInt(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<int>(name, readIn);
+ return InquireVariableCommon<int>(name, readIn);
}
Variable<unsigned int> *
BPFileReader::InquireVariableUInt(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned int>(name, readIn);
+ return InquireVariableCommon<unsigned int>(name, readIn);
}
Variable<long int> *BPFileReader::InquireVariableLInt(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<long int>(name, readIn);
+ return InquireVariableCommon<long int>(name, readIn);
}
Variable<unsigned long int> *
BPFileReader::InquireVariableULInt(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned long int>(name, readIn);
+ return InquireVariableCommon<unsigned long int>(name, readIn);
}
Variable<long long int> *
BPFileReader::InquireVariableLLInt(const std::string name, const bool readIn)
{
- return InquireVariableCommon<long long int>(name, readIn);
+ return InquireVariableCommon<long long int>(name, readIn);
}
Variable<unsigned long long int> *
BPFileReader::InquireVariableULLInt(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned long long int>(name, readIn);
+ return InquireVariableCommon<unsigned long long int>(name, readIn);
}
Variable<float> *BPFileReader::InquireVariableFloat(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<float>(name, readIn);
+ return InquireVariableCommon<float>(name, readIn);
}
Variable<double> *BPFileReader::InquireVariableDouble(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<double>(name, readIn);
+ return InquireVariableCommon<double>(name, readIn);
}
Variable<long double> *
BPFileReader::InquireVariableLDouble(const std::string name, const bool readIn)
{
- return InquireVariableCommon<long double>(name, readIn);
+ return InquireVariableCommon<long double>(name, readIn);
}
Variable<std::complex<float>> *
BPFileReader::InquireVariableCFloat(const std::string name, const bool readIn)
{
- return InquireVariableCommon<std::complex<float>>(name, readIn);
+ return InquireVariableCommon<std::complex<float>>(name, readIn);
}
Variable<std::complex<double>> *
BPFileReader::InquireVariableCDouble(const std::string name, const bool readIn)
{
- return InquireVariableCommon<std::complex<double>>(name, readIn);
+ return InquireVariableCommon<std::complex<double>>(name, readIn);
}
Variable<std::complex<long double>> *
BPFileReader::InquireVariableCLDouble(const std::string name, const bool readIn)
{
- return InquireVariableCommon<std::complex<long double>>(name, readIn);
+ return InquireVariableCommon<std::complex<long double>>(name, readIn);
}
VariableCompound *
BPFileReader::InquireVariableCompound(const std::string /*name*/,
const bool /*readIn*/)
{
- return nullptr;
+ return nullptr;
}
void BPFileReader::Close(const int /*transportIndex*/) {}
@@ -149,90 +149,93 @@ void BPFileReader::Close(const int /*transportIndex*/) {}
// PRIVATE
void BPFileReader::Init()
{
- if (m_DebugMode == true)
- {
- if (m_AccessMode != "r" && m_AccessMode != "read")
+ if (m_DebugMode == true)
{
- throw std::invalid_argument(
- "ERROR: BPFileReader doesn't support access mode " + m_AccessMode +
- ", in call to ADIOS Open or BPFileReader constructor\n");
+ if (m_AccessMode != "r" && m_AccessMode != "read")
+ {
+ throw std::invalid_argument(
+ "ERROR: BPFileReader doesn't support access mode " +
+ m_AccessMode +
+ ", in call to ADIOS Open or BPFileReader constructor\n");
+ }
}
- }
- InitCapsules();
- InitTransports();
+ InitCapsules();
+ InitTransports();
}
void BPFileReader::InitCapsules()
{
- // here init memory capsules
+ // here init memory capsules
}
void BPFileReader::InitTransports() // maybe move this?
{
- if (m_DebugMode == true)
- {
- if (TransportNamesUniqueness() == false)
+ if (m_DebugMode == true)
{
- throw std::invalid_argument(
- "ERROR: two transports of the same kind (e.g file IO) "
- "can't have the same name, modify with name= in Method "
- "AddTransport\n");
+ if (TransportNamesUniqueness() == false)
+ {
+ throw std::invalid_argument(
+ "ERROR: two transports of the same kind (e.g file IO) "
+ "can't have the same name, modify with name= in Method "
+ "AddTransport\n");
+ }
}
- }
- for (const auto ¶meters : m_Method.m_TransportParameters)
- {
- auto itTransport = parameters.find("transport");
- if (itTransport->second == "file" || itTransport->second == "File")
+ for (const auto ¶meters : m_Method.m_TransportParameters)
{
- auto itLibrary = parameters.find("library");
- if (itLibrary == parameters.end() ||
- itLibrary->second == "POSIX") // use default POSIX
- {
- auto file =
- std::make_shared<transport::FileDescriptor>(m_MPIComm, m_DebugMode);
- // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "FILE*" || itLibrary->second == "stdio.h")
- {
- auto file =
- std::make_shared<transport::FilePointer>(m_MPIComm, m_DebugMode);
- // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "fstream" ||
- itLibrary->second == "std::fstream")
- {
- auto file =
- std::make_shared<transport::FStream>(m_MPIComm, m_DebugMode);
- // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "MPI-IO")
- {
- }
- else
- {
- if (m_DebugMode == true)
+ auto itTransport = parameters.find("transport");
+ if (itTransport->second == "file" || itTransport->second == "File")
{
- throw std::invalid_argument(
- "ERROR: file transport library " + itLibrary->second +
- " not supported, in " + m_Name + m_EndMessage);
+ auto itLibrary = parameters.find("library");
+ if (itLibrary == parameters.end() ||
+ itLibrary->second == "POSIX") // use default POSIX
+ {
+ auto file = std::make_shared<transport::FileDescriptor>(
+ m_MPIComm, m_DebugMode);
+ // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
+ m_Transports.push_back(std::move(file));
+ }
+ else if (itLibrary->second == "FILE*" ||
+ itLibrary->second == "stdio.h")
+ {
+ auto file = std::make_shared<transport::FilePointer>(
+ m_MPIComm, m_DebugMode);
+ // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
+ m_Transports.push_back(std::move(file));
+ }
+ else if (itLibrary->second == "fstream" ||
+ itLibrary->second == "std::fstream")
+ {
+ auto file = std::make_shared<transport::FStream>(m_MPIComm,
+ m_DebugMode);
+ // m_BP1Reader.OpenRankFiles( m_Name, m_AccessMode, *file );
+ m_Transports.push_back(std::move(file));
+ }
+ else if (itLibrary->second == "MPI-IO")
+ {
+ }
+ else
+ {
+ if (m_DebugMode == true)
+ {
+ throw std::invalid_argument(
+ "ERROR: file transport library " + itLibrary->second +
+ " not supported, in " + m_Name + m_EndMessage);
+ }
+ }
+ }
+ else
+ {
+ if (m_DebugMode == true)
+ {
+ throw std::invalid_argument(
+ "ERROR: transport " + itTransport->second +
+ " (you mean File?) not supported, in " + m_Name +
+ m_EndMessage);
+ }
}
- }
- }
- else
- {
- if (m_DebugMode == true)
- {
- throw std::invalid_argument("ERROR: transport " + itTransport->second +
- " (you mean File?) not supported, in " +
- m_Name + m_EndMessage);
- }
}
- }
}
} // end namespace adios
diff --git a/source/engine/bp/BPFileWriter.cpp b/source/engine/bp/BPFileWriter.cpp
index eb85db8e5b70c4dace2d7e30874b0d715f967fe7..62f6c4d72c34678fcb987787d58b23b8568dadb9 100644
--- a/source/engine/bp/BPFileWriter.cpp
+++ b/source/engine/bp/BPFileWriter.cpp
@@ -32,107 +32,108 @@ BPFileWriter::BPFileWriter(ADIOS &adios, std::string name,
m_BP1Aggregator(m_MPIComm, debugMode),
m_MaxBufferSize(m_Buffer.m_Data.max_size())
{
- m_MetadataSet.TimeStep = 1; // starting at one to be compatible with ADIOS1.x
- Init();
+ m_MetadataSet.TimeStep =
+ 1; // starting at one to be compatible with ADIOS1.x
+ Init();
}
BPFileWriter::~BPFileWriter() = default;
void BPFileWriter::Init()
{
- InitParameters();
- InitTransports();
- InitProcessGroup();
+ InitParameters();
+ InitTransports();
+ InitProcessGroup();
}
void BPFileWriter::Write(Variable<char> &variable, const char *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<unsigned char> &variable,
const unsigned char *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<short> &variable, const short *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<unsigned short> &variable,
const unsigned short *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<int> &variable, const int *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<unsigned int> &variable,
const unsigned int *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<long int> &variable, const long int *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<unsigned long int> &variable,
const unsigned long int *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<long long int> &variable,
const long long int *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<unsigned long long int> &variable,
const unsigned long long int *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<float> &variable, const float *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<double> &variable, const double *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<long double> &variable,
const long double *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<std::complex<float>> &variable,
const std::complex<float> *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<std::complex<double>> &variable,
const std::complex<double> *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(Variable<std::complex<long double>> &variable,
const std::complex<long double> *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void BPFileWriter::Write(VariableCompound & /*variable*/,
@@ -143,98 +144,101 @@ void BPFileWriter::Write(VariableCompound & /*variable*/,
// String version
void BPFileWriter::Write(const std::string variableName, const char *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<char>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<char>(variableName), values);
}
void BPFileWriter::Write(const std::string variableName,
const unsigned char *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<unsigned char>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<unsigned char>(variableName),
+ values);
}
void BPFileWriter::Write(const std::string variableName, const short *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<short>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<short>(variableName), values);
}
void BPFileWriter::Write(const std::string variableName,
const unsigned short *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<unsigned short>(variableName),
- values);
+ WriteVariableCommon(m_ADIOS.GetVariable<unsigned short>(variableName),
+ values);
}
void BPFileWriter::Write(const std::string variableName, const int *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<int>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<int>(variableName), values);
}
void BPFileWriter::Write(const std::string variableName,
const unsigned int *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<unsigned int>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<unsigned int>(variableName),
+ values);
}
void BPFileWriter::Write(const std::string variableName, const long int *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<long int>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<long int>(variableName), values);
}
void BPFileWriter::Write(const std::string variableName,
const unsigned long int *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<unsigned long int>(variableName),
- values);
+ WriteVariableCommon(m_ADIOS.GetVariable<unsigned long int>(variableName),
+ values);
}
void BPFileWriter::Write(const std::string variableName,
const long long int *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<long long int>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<long long int>(variableName),
+ values);
}
void BPFileWriter::Write(const std::string variableName,
const unsigned long long int *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<unsigned long long int>(variableName),
- values);
+ WriteVariableCommon(
+ m_ADIOS.GetVariable<unsigned long long int>(variableName), values);
}
void BPFileWriter::Write(const std::string variableName, const float *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<float>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<float>(variableName), values);
}
void BPFileWriter::Write(const std::string variableName, const double *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<double>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<double>(variableName), values);
}
void BPFileWriter::Write(const std::string variableName,
const long double *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<long double>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<long double>(variableName), values);
}
void BPFileWriter::Write(const std::string variableName,
const std::complex<float> *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<std::complex<float>>(variableName),
- values);
+ WriteVariableCommon(m_ADIOS.GetVariable<std::complex<float>>(variableName),
+ values);
}
void BPFileWriter::Write(const std::string variableName,
const std::complex<double> *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<std::complex<double>>(variableName),
- values);
+ WriteVariableCommon(m_ADIOS.GetVariable<std::complex<double>>(variableName),
+ values);
}
void BPFileWriter::Write(const std::string variableName,
const std::complex<long double> *values)
{
- WriteVariableCommon(
- m_ADIOS.GetVariable<std::complex<long double>>(variableName), values);
+ WriteVariableCommon(
+ m_ADIOS.GetVariable<std::complex<long double>>(variableName), values);
}
void BPFileWriter::Write(const std::string /*variableName*/,
@@ -244,308 +248,326 @@ void BPFileWriter::Write(const std::string /*variableName*/,
void BPFileWriter::Advance(float /*timeout_sec*/)
{
- m_BP1Writer.Advance(m_MetadataSet, m_Buffer);
+ m_BP1Writer.Advance(m_MetadataSet, m_Buffer);
}
void BPFileWriter::Close(const int transportIndex)
{
- CheckTransportIndex(transportIndex);
- if (transportIndex == -1)
- {
- for (auto &transport : m_Transports)
- { // by reference or value or it doesn't matter?
- m_BP1Writer.Close(m_MetadataSet, m_Buffer, *transport, m_IsFirstClose,
- false); // false: not using aggregation for now
+ CheckTransportIndex(transportIndex);
+ if (transportIndex == -1)
+ {
+ for (auto &transport : m_Transports)
+ { // by reference or value or it doesn't matter?
+ m_BP1Writer.Close(m_MetadataSet, m_Buffer, *transport,
+ m_IsFirstClose,
+ false); // false: not using aggregation for now
+ }
}
- }
- else
- {
- m_BP1Writer.Close(m_MetadataSet, m_Buffer, *m_Transports[transportIndex],
- m_IsFirstClose,
- false); // false: not using aggregation for now
- }
-
- if (m_MetadataSet.Log.m_IsActive == true)
- {
- bool allClose = true;
- for (auto &transport : m_Transports)
+ else
{
- if (transport->m_IsOpen == true)
- {
- allClose = false;
- break;
- }
+ m_BP1Writer.Close(m_MetadataSet, m_Buffer,
+ *m_Transports[transportIndex], m_IsFirstClose,
+ false); // false: not using aggregation for now
}
- if (allClose == true) // aggregate and write profiling.log
+
+ if (m_MetadataSet.Log.m_IsActive == true)
{
- const std::string rankLog = m_BP1Writer.GetRankProfilingLog(
- m_RankMPI, m_MetadataSet, m_Transports);
+ bool allClose = true;
+ for (auto &transport : m_Transports)
+ {
+ if (transport->m_IsOpen == true)
+ {
+ allClose = false;
+ break;
+ }
+ }
+ if (allClose == true) // aggregate and write profiling.log
+ {
+ const std::string rankLog = m_BP1Writer.GetRankProfilingLog(
+ m_RankMPI, m_MetadataSet, m_Transports);
- const std::string fileName(m_BP1Writer.GetDirectoryName(m_Name) +
- "/profiling.log");
- m_BP1Aggregator.WriteProfilingLog(fileName, rankLog);
+ const std::string fileName(m_BP1Writer.GetDirectoryName(m_Name) +
+ "/profiling.log");
+ m_BP1Aggregator.WriteProfilingLog(fileName, rankLog);
+ }
}
- }
}
// PRIVATE FUNCTIONS
void BPFileWriter::InitParameters()
{
- auto itGrowthFactor = m_Method.m_Parameters.find("buffer_growth");
- if (itGrowthFactor != m_Method.m_Parameters.end())
- {
- const float growthFactor = std::stof(itGrowthFactor->second);
- if (m_DebugMode == true)
+ auto itGrowthFactor = m_Method.m_Parameters.find("buffer_growth");
+ if (itGrowthFactor != m_Method.m_Parameters.end())
{
- if (growthFactor == 1.f)
- {
- throw std::invalid_argument(
- "ERROR: buffer_growth argument can't be less of equal than 1, in " +
- m_EndMessage + "\n");
- }
- }
-
- m_BP1Writer.m_GrowthFactor = growthFactor;
- m_GrowthFactor = growthFactor; // float
- }
+ const float growthFactor = std::stof(itGrowthFactor->second);
+ if (m_DebugMode == true)
+ {
+ if (growthFactor == 1.f)
+ {
+ throw std::invalid_argument("ERROR: buffer_growth argument "
+ "can't be less of equal than 1, "
+ "in " +
+ m_EndMessage + "\n");
+ }
+ }
- auto itMaxBufferSize = m_Method.m_Parameters.find("max_size_MB");
- if (itMaxBufferSize != m_Method.m_Parameters.end())
- {
- if (m_DebugMode == true)
- {
- if (m_GrowthFactor <= 1.f)
- {
- throw std::invalid_argument("ERROR: Method buffer_growth argument "
- "can't be less of equal than 1, in " +
- m_EndMessage + "\n");
- }
+ m_BP1Writer.m_GrowthFactor = growthFactor;
+ m_GrowthFactor = growthFactor; // float
}
- m_MaxBufferSize = std::stoul(itMaxBufferSize->second) *
- 1048576; // convert from MB to bytes
- }
-
- auto itVerbosity = m_Method.m_Parameters.find("verbose");
- if (itVerbosity != m_Method.m_Parameters.end())
- {
- int verbosity = std::stoi(itVerbosity->second);
- if (m_DebugMode == true)
+ auto itMaxBufferSize = m_Method.m_Parameters.find("max_size_MB");
+ if (itMaxBufferSize != m_Method.m_Parameters.end())
{
- if (verbosity < 0 || verbosity > 5)
- {
- throw std::invalid_argument("ERROR: Method verbose argument must be an "
- "integer in the range [0,5], in call to "
- "Open or Engine constructor\n");
- }
- }
- m_BP1Writer.m_Verbosity = verbosity;
- }
-
- auto itProfile = m_Method.m_Parameters.find("profile_units");
- if (itProfile != m_Method.m_Parameters.end())
- {
- auto &profiler = m_MetadataSet.Log;
+ if (m_DebugMode == true)
+ {
+ if (m_GrowthFactor <= 1.f)
+ {
+ throw std::invalid_argument(
+ "ERROR: Method buffer_growth argument "
+ "can't be less of equal than 1, in " +
+ m_EndMessage + "\n");
+ }
+ }
- if (itProfile->second == "mus" || itProfile->second == "microseconds")
- {
- profiler.m_Timers.emplace_back("buffering", Support::Resolutions::mus);
- }
- else if (itProfile->second == "ms" || itProfile->second == "milliseconds")
- {
- profiler.m_Timers.emplace_back("buffering", Support::Resolutions::ms);
+ m_MaxBufferSize = std::stoul(itMaxBufferSize->second) *
+ 1048576; // convert from MB to bytes
}
- else if (itProfile->second == "s" || itProfile->second == "seconds")
- {
- profiler.m_Timers.emplace_back("buffering", Support::Resolutions::s);
- }
- else if (itProfile->second == "min" || itProfile->second == "minutes")
- {
- profiler.m_Timers.emplace_back("buffering", Support::Resolutions::m);
- }
- else if (itProfile->second == "h" || itProfile->second == "hours")
+
+ auto itVerbosity = m_Method.m_Parameters.find("verbose");
+ if (itVerbosity != m_Method.m_Parameters.end())
{
- profiler.m_Timers.emplace_back("buffering", Support::Resolutions::h);
+ int verbosity = std::stoi(itVerbosity->second);
+ if (m_DebugMode == true)
+ {
+ if (verbosity < 0 || verbosity > 5)
+ {
+ throw std::invalid_argument(
+ "ERROR: Method verbose argument must be an "
+ "integer in the range [0,5], in call to "
+ "Open or Engine constructor\n");
+ }
+ }
+ m_BP1Writer.m_Verbosity = verbosity;
}
- else
+
+ auto itProfile = m_Method.m_Parameters.find("profile_units");
+ if (itProfile != m_Method.m_Parameters.end())
{
- if (m_DebugMode == true)
- {
- throw std::invalid_argument("ERROR: Method profile_buffering_units "
- "argument must be mus, ms, s, min or h, in "
- "call to Open or Engine constructor\n");
- }
- }
+ auto &profiler = m_MetadataSet.Log;
+
+ if (itProfile->second == "mus" || itProfile->second == "microseconds")
+ {
+ profiler.m_Timers.emplace_back("buffering",
+ Support::Resolutions::mus);
+ }
+ else if (itProfile->second == "ms" ||
+ itProfile->second == "milliseconds")
+ {
+ profiler.m_Timers.emplace_back("buffering",
+ Support::Resolutions::ms);
+ }
+ else if (itProfile->second == "s" || itProfile->second == "seconds")
+ {
+ profiler.m_Timers.emplace_back("buffering",
+ Support::Resolutions::s);
+ }
+ else if (itProfile->second == "min" || itProfile->second == "minutes")
+ {
+ profiler.m_Timers.emplace_back("buffering",
+ Support::Resolutions::m);
+ }
+ else if (itProfile->second == "h" || itProfile->second == "hours")
+ {
+ profiler.m_Timers.emplace_back("buffering",
+ Support::Resolutions::h);
+ }
+ else
+ {
+ if (m_DebugMode == true)
+ {
+ throw std::invalid_argument(
+ "ERROR: Method profile_buffering_units "
+ "argument must be mus, ms, s, min or h, in "
+ "call to Open or Engine constructor\n");
+ }
+ }
- profiler.m_IsActive = true;
- }
+ profiler.m_IsActive = true;
+ }
}
void BPFileWriter::InitTransports()
{
- if (m_DebugMode == true)
- {
- if (TransportNamesUniqueness() == false)
- {
- throw std::invalid_argument(
- "ERROR: two transports of the same kind (e.g file IO) "
- "can't have the same name, modify with name= in Method "
- "AddTransport\n");
- }
- }
-
- for (const auto ¶meters : m_Method.m_TransportParameters)
- {
- auto itProfile = parameters.find("profile_units");
- bool doProfiling = false;
- Support::Resolutions resolution =
- Support::Resolutions::s; // default is seconds
- if (itProfile != parameters.end())
+ if (m_DebugMode == true)
{
- if (itProfile->second == "mus" || itProfile->second == "microseconds")
- {
- resolution = Support::Resolutions::mus;
- }
- else if (itProfile->second == "ms" || itProfile->second == "milliseconds")
- {
- resolution = Support::Resolutions::ms;
- }
- else if (itProfile->second == "s" || itProfile->second == "seconds")
- {
- resolution = Support::Resolutions::s;
- }
- else if (itProfile->second == "min" || itProfile->second == "minutes")
- {
- resolution = Support::Resolutions::m;
- }
- else if (itProfile->second == "h" || itProfile->second == "hours")
- {
- resolution = Support::Resolutions::h;
- }
- else
- {
- if (m_DebugMode == true)
+ if (TransportNamesUniqueness() == false)
{
- throw std::invalid_argument("ERROR: Transport profile_units argument "
- "must be mus, ms, s, min or h " +
- m_EndMessage);
+ throw std::invalid_argument(
+ "ERROR: two transports of the same kind (e.g file IO) "
+ "can't have the same name, modify with name= in Method "
+ "AddTransport\n");
}
- }
- doProfiling = true;
}
- auto itTransport = parameters.find("transport");
-
- if (itTransport->second == "file" || itTransport->second == "File")
+ for (const auto ¶meters : m_Method.m_TransportParameters)
{
- auto itLibrary = parameters.find("library");
- if (itLibrary == parameters.end() ||
- itLibrary->second == "POSIX") // use default POSIX
- {
- auto file =
- std::make_shared<transport::FileDescriptor>(m_MPIComm, m_DebugMode);
- if (doProfiling == true)
+ auto itProfile = parameters.find("profile_units");
+ bool doProfiling = false;
+ Support::Resolutions resolution =
+ Support::Resolutions::s; // default is seconds
+ if (itProfile != parameters.end())
{
- file->InitProfiler(m_AccessMode, resolution);
+ if (itProfile->second == "mus" ||
+ itProfile->second == "microseconds")
+ {
+ resolution = Support::Resolutions::mus;
+ }
+ else if (itProfile->second == "ms" ||
+ itProfile->second == "milliseconds")
+ {
+ resolution = Support::Resolutions::ms;
+ }
+ else if (itProfile->second == "s" || itProfile->second == "seconds")
+ {
+ resolution = Support::Resolutions::s;
+ }
+ else if (itProfile->second == "min" ||
+ itProfile->second == "minutes")
+ {
+ resolution = Support::Resolutions::m;
+ }
+ else if (itProfile->second == "h" || itProfile->second == "hours")
+ {
+ resolution = Support::Resolutions::h;
+ }
+ else
+ {
+ if (m_DebugMode == true)
+ {
+ throw std::invalid_argument(
+ "ERROR: Transport profile_units argument "
+ "must be mus, ms, s, min or h " +
+ m_EndMessage);
+ }
+ }
+ doProfiling = true;
}
- m_BP1Writer.OpenRankFiles(m_Name, m_AccessMode, *file);
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "FILE*" || itLibrary->second == "stdio")
- {
- auto file =
- std::make_shared<transport::FilePointer>(m_MPIComm, m_DebugMode);
- if (doProfiling == true)
- {
- file->InitProfiler(m_AccessMode, resolution);
- }
+ auto itTransport = parameters.find("transport");
- m_BP1Writer.OpenRankFiles(m_Name, m_AccessMode, *file);
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "fstream" ||
- itLibrary->second == "std::fstream")
- {
- auto file =
- std::make_shared<transport::FStream>(m_MPIComm, m_DebugMode);
-
- if (doProfiling == true)
+ if (itTransport->second == "file" || itTransport->second == "File")
{
- file->InitProfiler(m_AccessMode, resolution);
+ auto itLibrary = parameters.find("library");
+ if (itLibrary == parameters.end() ||
+ itLibrary->second == "POSIX") // use default POSIX
+ {
+ auto file = std::make_shared<transport::FileDescriptor>(
+ m_MPIComm, m_DebugMode);
+ if (doProfiling == true)
+ {
+ file->InitProfiler(m_AccessMode, resolution);
+ }
+
+ m_BP1Writer.OpenRankFiles(m_Name, m_AccessMode, *file);
+ m_Transports.push_back(std::move(file));
+ }
+ else if (itLibrary->second == "FILE*" ||
+ itLibrary->second == "stdio")
+ {
+ auto file = std::make_shared<transport::FilePointer>(
+ m_MPIComm, m_DebugMode);
+ if (doProfiling == true)
+ {
+ file->InitProfiler(m_AccessMode, resolution);
+ }
+
+ m_BP1Writer.OpenRankFiles(m_Name, m_AccessMode, *file);
+ m_Transports.push_back(std::move(file));
+ }
+ else if (itLibrary->second == "fstream" ||
+ itLibrary->second == "std::fstream")
+ {
+ auto file = std::make_shared<transport::FStream>(m_MPIComm,
+ m_DebugMode);
+
+ if (doProfiling == true)
+ {
+ file->InitProfiler(m_AccessMode, resolution);
+ }
+
+ m_BP1Writer.OpenRankFiles(m_Name, m_AccessMode, *file);
+ m_Transports.push_back(std::move(file));
+ }
+ else if (itLibrary->second == "MPI_File" ||
+ itLibrary->second == "MPI-IO")
+ {
+ }
+ else
+ {
+ if (m_DebugMode == true)
+ {
+ throw std::invalid_argument(
+ "ERROR: file transport library " + itLibrary->second +
+ " not supported, in " + m_Name + m_EndMessage);
+ }
+ }
}
-
- m_BP1Writer.OpenRankFiles(m_Name, m_AccessMode, *file);
- m_Transports.push_back(std::move(file));
- }
- else if (itLibrary->second == "MPI_File" || itLibrary->second == "MPI-IO")
- {
- }
- else
- {
- if (m_DebugMode == true)
+ else
{
- throw std::invalid_argument(
- "ERROR: file transport library " + itLibrary->second +
- " not supported, in " + m_Name + m_EndMessage);
+ if (m_DebugMode == true)
+ {
+ throw std::invalid_argument(
+ "ERROR: transport " + itTransport->second +
+ " (you mean File?) not supported, in " + m_Name +
+ m_EndMessage);
+ }
}
- }
}
- else
- {
- if (m_DebugMode == true)
- {
- throw std::invalid_argument("ERROR: transport " + itTransport->second +
- " (you mean File?) not supported, in " +
- m_Name + m_EndMessage);
- }
- }
- }
}
void BPFileWriter::InitProcessGroup()
{
- if (m_MetadataSet.Log.m_IsActive == true)
- {
- m_MetadataSet.Log.m_Timers[0].SetInitialTime();
- }
+ if (m_MetadataSet.Log.m_IsActive == true)
+ {
+ m_MetadataSet.Log.m_Timers[0].SetInitialTime();
+ }
- if (m_AccessMode == "a")
- {
- // Get last pg timestep and update timestep counter in
- // format::BP1MetadataSet
- }
+ if (m_AccessMode == "a")
+ {
+ // Get last pg timestep and update timestep counter in
+ // format::BP1MetadataSet
+ }
- WriteProcessGroupIndex();
+ WriteProcessGroupIndex();
- if (m_MetadataSet.Log.m_IsActive == true)
- {
- m_MetadataSet.Log.m_Timers[0].SetTime();
- }
+ if (m_MetadataSet.Log.m_IsActive == true)
+ {
+ m_MetadataSet.Log.m_Timers[0].SetTime();
+ }
}
void BPFileWriter::WriteProcessGroupIndex()
{
- // pg = process group
- // const std::size_t pgIndexSize = m_BP1Writer.GetProcessGroupIndexSize(
- // std::to_string( m_RankMPI ),
- // std::to_string(
- // m_MetadataSet.TimeStep
- // ),
- // m_Transports.size()
- // );
- // metadata
- // GrowBuffer( pgIndexSize, m_GrowthFactor, m_MetadataSet.PGIndex );
-
- // data? Need to be careful, maybe add some trailing tolerance in variable
- // ????
- // GrowBuffer( pgIndexSize, m_GrowthFactor, m_Buffer.m_Data );
-
- const bool isFortran = (m_HostLanguage == "Fortran") ? true : false;
-
- m_BP1Writer.WriteProcessGroupIndex(isFortran, std::to_string(m_RankMPI),
- static_cast<std::uint32_t>(m_RankMPI),
- m_Transports, m_Buffer, m_MetadataSet);
+ // pg = process group
+ // const std::size_t pgIndexSize = m_BP1Writer.GetProcessGroupIndexSize(
+ // std::to_string( m_RankMPI ),
+ // std::to_string(
+ // m_MetadataSet.TimeStep
+ // ),
+ // m_Transports.size()
+ // );
+ // metadata
+ // GrowBuffer( pgIndexSize, m_GrowthFactor, m_MetadataSet.PGIndex );
+
+ // data? Need to be careful, maybe add some trailing tolerance in variable
+ // ????
+ // GrowBuffer( pgIndexSize, m_GrowthFactor, m_Buffer.m_Data );
+
+ const bool isFortran = (m_HostLanguage == "Fortran") ? true : false;
+
+ m_BP1Writer.WriteProcessGroupIndex(isFortran, std::to_string(m_RankMPI),
+ static_cast<std::uint32_t>(m_RankMPI),
+ m_Transports, m_Buffer, m_MetadataSet);
}
} // end namespace adios
diff --git a/source/engine/dataman/DataManReader.cpp b/source/engine/dataman/DataManReader.cpp
index 941fe8f6065d6e112a26e29c72d2ef626e8b0492..9de0149532e6302aa7ceb7133260d044f7804c8f 100644
--- a/source/engine/dataman/DataManReader.cpp
+++ b/source/engine/dataman/DataManReader.cpp
@@ -33,7 +33,7 @@ DataManReader::DataManReader(ADIOS &adios, const std::string name,
nthreads, " DataManReader constructor (or call to ADIOS Open).\n"),
m_Buffer(accessMode, m_RankMPI, m_DebugMode)
{
- Init();
+ Init();
}
DataManReader::~DataManReader() {}
@@ -43,118 +43,118 @@ void DataManReader::SetCallBack(
Dims)>
callback)
{
- m_CallBack = callback;
- m_Man.reg_callback(callback);
+ m_CallBack = callback;
+ m_Man.reg_callback(callback);
}
Variable<void> *
DataManReader::InquireVariable(const std::string name,
const bool readIn) // not yet implemented
{
- return nullptr;
+ return nullptr;
}
Variable<char> *DataManReader::InquireVariableChar(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<char>(name, readIn);
+ return InquireVariableCommon<char>(name, readIn);
}
Variable<unsigned char> *
DataManReader::InquireVariableUChar(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned char>(name, readIn);
+ return InquireVariableCommon<unsigned char>(name, readIn);
}
Variable<short> *DataManReader::InquireVariableShort(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<short>(name, readIn);
+ return InquireVariableCommon<short>(name, readIn);
}
Variable<unsigned short> *
DataManReader::InquireVariableUShort(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned short>(name, readIn);
+ return InquireVariableCommon<unsigned short>(name, readIn);
}
Variable<int> *DataManReader::InquireVariableInt(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<int>(name, readIn);
+ return InquireVariableCommon<int>(name, readIn);
}
Variable<unsigned int> *
DataManReader::InquireVariableUInt(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned int>(name, readIn);
+ return InquireVariableCommon<unsigned int>(name, readIn);
}
Variable<long int> *DataManReader::InquireVariableLInt(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<long int>(name, readIn);
+ return InquireVariableCommon<long int>(name, readIn);
}
Variable<unsigned long int> *
DataManReader::InquireVariableULInt(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned long int>(name, readIn);
+ return InquireVariableCommon<unsigned long int>(name, readIn);
}
Variable<long long int> *
DataManReader::InquireVariableLLInt(const std::string name, const bool readIn)
{
- return InquireVariableCommon<long long int>(name, readIn);
+ return InquireVariableCommon<long long int>(name, readIn);
}
Variable<unsigned long long int> *
DataManReader::InquireVariableULLInt(const std::string name, const bool readIn)
{
- return InquireVariableCommon<unsigned long long int>(name, readIn);
+ return InquireVariableCommon<unsigned long long int>(name, readIn);
}
Variable<float> *DataManReader::InquireVariableFloat(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<float>(name, readIn);
+ return InquireVariableCommon<float>(name, readIn);
}
Variable<double> *DataManReader::InquireVariableDouble(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<double>(name, readIn);
+ return InquireVariableCommon<double>(name, readIn);
}
Variable<long double> *
DataManReader::InquireVariableLDouble(const std::string name, const bool readIn)
{
- return InquireVariableCommon<long double>(name, readIn);
+ return InquireVariableCommon<long double>(name, readIn);
}
Variable<std::complex<float>> *
DataManReader::InquireVariableCFloat(const std::string name, const bool readIn)
{
- return InquireVariableCommon<std::complex<float>>(name, readIn);
+ return InquireVariableCommon<std::complex<float>>(name, readIn);
}
Variable<std::complex<double>> *
DataManReader::InquireVariableCDouble(const std::string name, const bool readIn)
{
- return InquireVariableCommon<std::complex<double>>(name, readIn);
+ return InquireVariableCommon<std::complex<double>>(name, readIn);
}
Variable<std::complex<long double>> *
DataManReader::InquireVariableCLDouble(const std::string name,
const bool readIn)
{
- return InquireVariableCommon<std::complex<long double>>(name, readIn);
+ return InquireVariableCommon<std::complex<long double>>(name, readIn);
}
VariableCompound *DataManReader::InquireVariableCompound(const std::string name,
const bool readIn)
{
- return nullptr;
+ return nullptr;
}
void DataManReader::Close(const int transportIndex) {}
@@ -162,159 +162,163 @@ void DataManReader::Close(const int transportIndex) {}
// PRIVATE
void DataManReader::Init()
{
- if (m_DebugMode == true)
- {
- if (m_AccessMode != "r" && m_AccessMode != "read")
- throw std::invalid_argument(
- "ERROR: DataManReader doesn't support access mode " + m_AccessMode +
- ", in call to ADIOS Open or DataManReader constructor\n");
- }
-
- auto itRealTime = m_Method.m_Parameters.find("real_time");
- if (itRealTime != m_Method.m_Parameters.end())
- {
- if (itRealTime->second == "yes" || itRealTime->second == "true")
- m_DoRealTime = true;
- }
-
- if (m_DoRealTime)
- {
- /**
- * Lambda function that assigns a parameter in m_Method to a localVariable
- * of type std::string
- */
- auto lf_AssignString = [this](const std::string parameter,
- std::string &localVariable) {
- auto it = m_Method.m_Parameters.find(parameter);
- if (it != m_Method.m_Parameters.end())
- {
- localVariable = it->second;
- }
- };
-
- /**
- * Lambda function that assigns a parameter in m_Method to a localVariable
- * of type int
- */
- auto lf_AssignInt = [this](const std::string parameter,
- int &localVariable) {
- auto it = m_Method.m_Parameters.find(parameter);
- if (it != m_Method.m_Parameters.end())
- {
- localVariable = std::stoi(it->second);
- }
- };
-
- auto is_number = [](const std::string &s) {
- return !s.empty() && std::find_if(s.begin(), s.end(), [](char c) {
- return !std::isdigit(c);
- }) == s.end();
- };
-
- json jmsg;
- for (auto &i : m_Method.m_Parameters)
+ if (m_DebugMode == true)
+ {
+ if (m_AccessMode != "r" && m_AccessMode != "read")
+ throw std::invalid_argument(
+ "ERROR: DataManReader doesn't support access mode " +
+ m_AccessMode +
+ ", in call to ADIOS Open or DataManReader constructor\n");
+ }
+
+ auto itRealTime = m_Method.m_Parameters.find("real_time");
+ if (itRealTime != m_Method.m_Parameters.end())
{
- if (is_number(i.second))
- {
- jmsg[i.first] = std::stoi(i.second);
- }
- else
- {
- jmsg[i.first] = i.second;
- }
+ if (itRealTime->second == "yes" || itRealTime->second == "true")
+ m_DoRealTime = true;
+ }
+
+ if (m_DoRealTime)
+ {
+ /**
+ * Lambda function that assigns a parameter in m_Method to a
+ * localVariable
+ * of type std::string
+ */
+ auto lf_AssignString = [this](const std::string parameter,
+ std::string &localVariable) {
+ auto it = m_Method.m_Parameters.find(parameter);
+ if (it != m_Method.m_Parameters.end())
+ {
+ localVariable = it->second;
+ }
+ };
+
+ /**
+ * Lambda function that assigns a parameter in m_Method to a
+ * localVariable
+ * of type int
+ */
+ auto lf_AssignInt = [this](const std::string parameter,
+ int &localVariable) {
+ auto it = m_Method.m_Parameters.find(parameter);
+ if (it != m_Method.m_Parameters.end())
+ {
+ localVariable = std::stoi(it->second);
+ }
+ };
+
+ auto is_number = [](const std::string &s) {
+ return !s.empty() && std::find_if(s.begin(), s.end(), [](char c) {
+ return !std::isdigit(c);
+ }) == s.end();
+ };
+
+ json jmsg;
+ for (auto &i : m_Method.m_Parameters)
+ {
+ if (is_number(i.second))
+ {
+ jmsg[i.first] = std::stoi(i.second);
+ }
+ else
+ {
+ jmsg[i.first] = i.second;
+ }
+ }
+ jmsg["stream_mode"] = "receiver";
+ m_Man.add_stream(jmsg);
+
+ std::string method_type;
+ int num_channels = 0;
+ lf_AssignString("method_type", method_type);
+ lf_AssignInt("num_channels", num_channels);
+ }
+ else
+ {
+ InitCapsules();
+ InitTransports();
}
- jmsg["stream_mode"] = "receiver";
- m_Man.add_stream(jmsg);
-
- std::string method_type;
- int num_channels = 0;
- lf_AssignString("method_type", method_type);
- lf_AssignInt("num_channels", num_channels);
- }
- else
- {
- InitCapsules();
- InitTransports();
- }
}
void DataManReader::InitCapsules()
{
- // here init memory capsules
+ // here init memory capsules
}
void DataManReader::InitTransports() // maybe move this?
{
- TransportNamesUniqueness();
+ TransportNamesUniqueness();
- for (const auto ¶meters : m_Method.m_TransportParameters)
- {
- auto itTransport = parameters.find("transport");
-
- if (itTransport->second == "Mdtm" || itTransport->second == "MdtmMan")
- {
- const std::string localIP(
- GetMdtmParameter("localIP", parameters)); // mandatory
- const std::string remoteIP(
- GetMdtmParameter("remoteIP", parameters)); // mandatory
- const std::string prefix(GetMdtmParameter("prefix", parameters));
- const int numberOfPipes =
- std::stoi(GetMdtmParameter("pipes", parameters));
- const std::vector<int> tolerances =
- CSVToVectorInt(GetMdtmParameter("tolerances", parameters));
- const std::vector<int> priorities =
- CSVToVectorInt(GetMdtmParameter("priorities", parameters));
-
- m_Transports.push_back(std::make_shared<transport::MdtmMan>(
- localIP, remoteIP, m_AccessMode, prefix, numberOfPipes, tolerances,
- priorities, m_MPIComm, m_DebugMode));
- }
- else if (itTransport->second == "Zmq")
- {
- }
- else
+ for (const auto ¶meters : m_Method.m_TransportParameters)
{
- if (m_DebugMode == true)
- throw std::invalid_argument(
- "ERROR: transport + " + itTransport->second +
- " not supported, in " + m_Name + m_EndMessage);
+ auto itTransport = parameters.find("transport");
+
+ if (itTransport->second == "Mdtm" || itTransport->second == "MdtmMan")
+ {
+ const std::string localIP(
+ GetMdtmParameter("localIP", parameters)); // mandatory
+ const std::string remoteIP(
+ GetMdtmParameter("remoteIP", parameters)); // mandatory
+ const std::string prefix(GetMdtmParameter("prefix", parameters));
+ const int numberOfPipes =
+ std::stoi(GetMdtmParameter("pipes", parameters));
+ const std::vector<int> tolerances =
+ CSVToVectorInt(GetMdtmParameter("tolerances", parameters));
+ const std::vector<int> priorities =
+ CSVToVectorInt(GetMdtmParameter("priorities", parameters));
+
+ m_Transports.push_back(std::make_shared<transport::MdtmMan>(
+ localIP, remoteIP, m_AccessMode, prefix, numberOfPipes,
+ tolerances, priorities, m_MPIComm, m_DebugMode));
+ }
+ else if (itTransport->second == "Zmq")
+ {
+ }
+ else
+ {
+ if (m_DebugMode == true)
+ throw std::invalid_argument(
+ "ERROR: transport + " + itTransport->second +
+ " not supported, in " + m_Name + m_EndMessage);
+ }
}
- }
}
std::string DataManReader::GetMdtmParameter(
const std::string parameter,
const std::map<std::string, std::string> &mdtmParameters)
{
- auto itParam = mdtmParameters.find(parameter);
- if (itParam != mdtmParameters.end()) // found
- {
- return itParam->second; // return value
- }
- // if not found
- // mandatory ones
- if (parameter == "localIP" || parameter == "remoteIP")
- {
- if (m_DebugMode == true)
- throw std::invalid_argument("ERROR: " + parameter +
- " parameter not found in Method, in call to "
- "DataManWriter constructor\n");
- }
- else if (parameter == "prefix")
- {
- return "";
- }
- else if (parameter == "pipes")
- {
- return "0"; // or 1?
- }
- else if (parameter == "tolerances") // so far empty string
- {
- }
- else if (parameter == "priority")
- {
- }
-
- return ""; // return empty string
+ auto itParam = mdtmParameters.find(parameter);
+ if (itParam != mdtmParameters.end()) // found
+ {
+ return itParam->second; // return value
+ }
+ // if not found
+ // mandatory ones
+ if (parameter == "localIP" || parameter == "remoteIP")
+ {
+ if (m_DebugMode == true)
+ throw std::invalid_argument(
+ "ERROR: " + parameter +
+ " parameter not found in Method, in call to "
+ "DataManWriter constructor\n");
+ }
+ else if (parameter == "prefix")
+ {
+ return "";
+ }
+ else if (parameter == "pipes")
+ {
+ return "0"; // or 1?
+ }
+ else if (parameter == "tolerances") // so far empty string
+ {
+ }
+ else if (parameter == "priority")
+ {
+ }
+
+ return ""; // return empty string
}
}
diff --git a/source/engine/dataman/DataManWriter.cpp b/source/engine/dataman/DataManWriter.cpp
index edb5275795a7bf872220c8c8ea49cd4954457a1a..2aa7aaac8bd393d59c6ec923e990ccdc77bccb7c 100644
--- a/source/engine/dataman/DataManWriter.cpp
+++ b/source/engine/dataman/DataManWriter.cpp
@@ -31,7 +31,7 @@ DataManWriter::DataManWriter(ADIOS &adios, const std::string name,
nthreads, " DataManWriter constructor (or call to ADIOS Open).\n"),
m_Buffer(accessMode, m_RankMPI, m_DebugMode)
{
- Init();
+ Init();
}
DataManWriter::~DataManWriter() {}
@@ -41,370 +41,378 @@ void DataManWriter::SetCallBack(
Dims)>
callback)
{
- m_CallBack = callback;
- m_Man.reg_callback(callback);
+ m_CallBack = callback;
+ m_Man.reg_callback(callback);
}
void DataManWriter::Write(Variable<char> &variable, const char *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<unsigned char> &variable,
const unsigned char *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<short> &variable, const short *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<unsigned short> &variable,
const unsigned short *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<int> &variable, const int *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<unsigned int> &variable,
const unsigned int *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<long int> &variable, const long int *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<unsigned long int> &variable,
const unsigned long int *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<long long int> &variable,
const long long int *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<unsigned long long int> &variable,
const unsigned long long int *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<float> &variable, const float *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<double> &variable, const double *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<long double> &variable,
const long double *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<std::complex<float>> &variable,
const std::complex<float> *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<std::complex<double>> &variable,
const std::complex<double> *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
void DataManWriter::Write(Variable<std::complex<long double>> &variable,
const std::complex<long double> *values)
{
- WriteVariableCommon(variable, values);
+ WriteVariableCommon(variable, values);
}
// String version
void DataManWriter::Write(const std::string variableName, const char *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<char>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<char>(variableName), values);
}
void DataManWriter::Write(const std::string variableName,
const unsigned char *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<unsigned char>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<unsigned char>(variableName),
+ values);
}
void DataManWriter::Write(const std::string variableName, const short *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<short>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<short>(variableName), values);
}
void DataManWriter::Write(const std::string variableName,
const unsigned short *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<unsigned short>(variableName),
- values);
+ WriteVariableCommon(m_ADIOS.GetVariable<unsigned short>(variableName),
+ values);
}
void DataManWriter::Write(const std::string variableName, const int *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<int>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<int>(variableName), values);
}
void DataManWriter::Write(const std::string variableName,
const unsigned int *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<unsigned int>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<unsigned int>(variableName),
+ values);
}
void DataManWriter::Write(const std::string variableName,
const long int *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<long int>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<long int>(variableName), values);
}
void DataManWriter::Write(const std::string variableName,
const unsigned long int *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<unsigned long int>(variableName),
- values);
+ WriteVariableCommon(m_ADIOS.GetVariable<unsigned long int>(variableName),
+ values);
}
void DataManWriter::Write(const std::string variableName,
const long long int *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<long long int>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<long long int>(variableName),
+ values);
}
void DataManWriter::Write(const std::string variableName,
const unsigned long long int *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<unsigned long long int>(variableName),
- values);
+ WriteVariableCommon(
+ m_ADIOS.GetVariable<unsigned long long int>(variableName), values);
}
void DataManWriter::Write(const std::string variableName, const float *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<float>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<float>(variableName), values);
}
void DataManWriter::Write(const std::string variableName, const double *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<double>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<double>(variableName), values);
}
void DataManWriter::Write(const std::string variableName,
const long double *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<long double>(variableName), values);
+ WriteVariableCommon(m_ADIOS.GetVariable<long double>(variableName), values);
}
void DataManWriter::Write(const std::string variableName,
const std::complex<float> *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<std::complex<float>>(variableName),
- values);
+ WriteVariableCommon(m_ADIOS.GetVariable<std::complex<float>>(variableName),
+ values);
}
void DataManWriter::Write(const std::string variableName,
const std::complex<double> *values)
{
- WriteVariableCommon(m_ADIOS.GetVariable<std::complex<double>>(variableName),
- values);
+ WriteVariableCommon(m_ADIOS.GetVariable<std::complex<double>>(variableName),
+ values);
}
void DataManWriter::Write(const std::string variableName,
const std::complex<long double> *values)
{
- WriteVariableCommon(
- m_ADIOS.GetVariable<std::complex<long double>>(variableName), values);
+ WriteVariableCommon(
+ m_ADIOS.GetVariable<std::complex<long double>>(variableName), values);
}
void DataManWriter::Close(const int transportIndex)
{
- m_Man.flush();
- // here close IPs and deallocate or free/close resources (if using STL no need
- // for memory deallocation)
+ m_Man.flush();
+ // here close IPs and deallocate or free/close resources (if using STL no
+ // need
+ // for memory deallocation)
}
// PRIVATE functions below
void DataManWriter::Init()
{
- if (m_DebugMode == true)
- {
- if (m_AccessMode != "w" && m_AccessMode != "write" && m_AccessMode != "a" &&
- m_AccessMode != "append")
- throw std::invalid_argument(
- "ERROR: DataManWriter doesn't support access mode " + m_AccessMode +
- ", in call to ADIOS Open or DataManWriter constructor\n");
- }
-
- auto itRealTime = m_Method.m_Parameters.find("real_time");
- if (itRealTime != m_Method.m_Parameters.end())
- {
- if (itRealTime->second == "yes" || itRealTime->second == "true")
- m_DoRealTime = true;
- }
-
- itRealTime = m_Method.m_Parameters.find("monitoring");
- if (itRealTime != m_Method.m_Parameters.end())
- {
- if (itRealTime->second == "yes" || itRealTime->second == "true")
- m_DoMonitor = true;
- }
-
- if (m_DoRealTime)
- {
- /**
- * Lambda function that assigns a parameter in m_Method to a localVariable
- * of type std::string
- */
- auto lf_AssignString = [this](const std::string parameter,
- std::string &localVariable) {
- auto it = m_Method.m_Parameters.find(parameter);
- if (it != m_Method.m_Parameters.end())
- {
- localVariable = it->second;
- }
- };
-
- /**
- * Lambda function that assigns a parameter in m_Method to a localVariable
- * of type int
- */
- auto lf_AssignInt = [this](const std::string parameter,
- int &localVariable) {
- auto it = m_Method.m_Parameters.find(parameter);
- if (it != m_Method.m_Parameters.end())
- {
- localVariable = std::stoi(it->second);
- }
- };
-
- auto is_number = [](const std::string &s) {
- return !s.empty() && std::find_if(s.begin(), s.end(), [](char c) {
- return !std::isdigit(c);
- }) == s.end();
- };
-
- json jmsg;
- for (auto &i : m_Method.m_Parameters)
+ if (m_DebugMode == true)
+ {
+ if (m_AccessMode != "w" && m_AccessMode != "write" &&
+ m_AccessMode != "a" && m_AccessMode != "append")
+ throw std::invalid_argument(
+ "ERROR: DataManWriter doesn't support access mode " +
+ m_AccessMode +
+ ", in call to ADIOS Open or DataManWriter constructor\n");
+ }
+
+ auto itRealTime = m_Method.m_Parameters.find("real_time");
+ if (itRealTime != m_Method.m_Parameters.end())
{
- if (is_number(i.second))
- {
- jmsg[i.first] = std::stoi(i.second);
- }
- else
- {
- jmsg[i.first] = i.second;
- }
+ if (itRealTime->second == "yes" || itRealTime->second == "true")
+ m_DoRealTime = true;
}
- jmsg["stream_mode"] = "sender";
- m_Man.add_stream(jmsg);
- std::string method_type;
- int num_channels = 0;
- lf_AssignString("method_type", method_type);
- lf_AssignInt("num_channels", num_channels);
- }
- else
- {
- InitCapsules();
- InitTransports();
- }
+ itRealTime = m_Method.m_Parameters.find("monitoring");
+ if (itRealTime != m_Method.m_Parameters.end())
+ {
+ if (itRealTime->second == "yes" || itRealTime->second == "true")
+ m_DoMonitor = true;
+ }
+
+ if (m_DoRealTime)
+ {
+ /**
+ * Lambda function that assigns a parameter in m_Method to a
+ * localVariable
+ * of type std::string
+ */
+ auto lf_AssignString = [this](const std::string parameter,
+ std::string &localVariable) {
+ auto it = m_Method.m_Parameters.find(parameter);
+ if (it != m_Method.m_Parameters.end())
+ {
+ localVariable = it->second;
+ }
+ };
+
+ /**
+ * Lambda function that assigns a parameter in m_Method to a
+ * localVariable
+ * of type int
+ */
+ auto lf_AssignInt = [this](const std::string parameter,
+ int &localVariable) {
+ auto it = m_Method.m_Parameters.find(parameter);
+ if (it != m_Method.m_Parameters.end())
+ {
+ localVariable = std::stoi(it->second);
+ }
+ };
+
+ auto is_number = [](const std::string &s) {
+ return !s.empty() && std::find_if(s.begin(), s.end(), [](char c) {
+ return !std::isdigit(c);
+ }) == s.end();
+ };
+
+ json jmsg;
+ for (auto &i : m_Method.m_Parameters)
+ {
+ if (is_number(i.second))
+ {
+ jmsg[i.first] = std::stoi(i.second);
+ }
+ else
+ {
+ jmsg[i.first] = i.second;
+ }
+ }
+ jmsg["stream_mode"] = "sender";
+ m_Man.add_stream(jmsg);
+
+ std::string method_type;
+ int num_channels = 0;
+ lf_AssignString("method_type", method_type);
+ lf_AssignInt("num_channels", num_channels);
+ }
+ else
+ {
+ InitCapsules();
+ InitTransports();
+ }
}
void DataManWriter::InitCapsules()
{
- // here init memory capsules
+ // here init memory capsules
}
void DataManWriter::InitTransports() // maybe move this?
{
- TransportNamesUniqueness();
+ TransportNamesUniqueness();
- for (const auto ¶meters : m_Method.m_TransportParameters)
- {
- auto itTransport = parameters.find("transport");
-
- if (itTransport->second == "Mdtm" || itTransport->second == "MdtmMan")
- {
- const std::string localIP(
- GetMdtmParameter("localIP", parameters)); // mandatory
- const std::string remoteIP(
- GetMdtmParameter("remoteIP", parameters)); // mandatory
- const std::string prefix(GetMdtmParameter("prefix", parameters));
- const int numberOfPipes =
- std::stoi(GetMdtmParameter("pipes", parameters));
- const std::vector<int> tolerances =
- CSVToVectorInt(GetMdtmParameter("tolerances", parameters));
- const std::vector<int> priorities =
- CSVToVectorInt(GetMdtmParameter("priorities", parameters));
-
- m_Transports.push_back(std::make_shared<transport::MdtmMan>(
- localIP, remoteIP, m_AccessMode, prefix, numberOfPipes, tolerances,
- priorities, m_MPIComm, m_DebugMode));
- }
- else if (itTransport->second == "Zmq")
- {
- }
- else
+ for (const auto ¶meters : m_Method.m_TransportParameters)
{
- if (m_DebugMode == true)
- throw std::invalid_argument(
- "ERROR: transport + " + itTransport->second +
- " not supported, in " + m_Name + m_EndMessage);
+ auto itTransport = parameters.find("transport");
+
+ if (itTransport->second == "Mdtm" || itTransport->second == "MdtmMan")
+ {
+ const std::string localIP(
+ GetMdtmParameter("localIP", parameters)); // mandatory
+ const std::string remoteIP(
+ GetMdtmParameter("remoteIP", parameters)); // mandatory
+ const std::string prefix(GetMdtmParameter("prefix", parameters));
+ const int numberOfPipes =
+ std::stoi(GetMdtmParameter("pipes", parameters));
+ const std::vector<int> tolerances =
+ CSVToVectorInt(GetMdtmParameter("tolerances", parameters));
+ const std::vector<int> priorities =
+ CSVToVectorInt(GetMdtmParameter("priorities", parameters));
+
+ m_Transports.push_back(std::make_shared<transport::MdtmMan>(
+ localIP, remoteIP, m_AccessMode, prefix, numberOfPipes,
+ tolerances, priorities, m_MPIComm, m_DebugMode));
+ }
+ else if (itTransport->second == "Zmq")
+ {
+ }
+ else
+ {
+ if (m_DebugMode == true)
+ throw std::invalid_argument(
+ "ERROR: transport + " + itTransport->second +
+ " not supported, in " + m_Name + m_EndMessage);
+ }
}
- }
}
std::string DataManWriter::GetMdtmParameter(
const std::string parameter,
const std::map<std::string, std::string> &mdtmParameters)
{
- auto itParam = mdtmParameters.find(parameter);
- if (itParam != mdtmParameters.end()) // found
- {
- return itParam->second; // return value
- }
- // if not found
- // mandatory ones
- if (parameter == "localIP" || parameter == "remoteIP")
- {
- if (m_DebugMode == true)
- throw std::invalid_argument("ERROR: " + parameter +
- " parameter not found in Method, in call to "
- "DataManWriter constructor\n");
- }
- else if (parameter == "prefix")
- {
- return "";
- }
- else if (parameter == "pipes")
- {
- return "0"; // or 1?
- }
- else if (parameter == "tolerances") // so far empty string
- {
- }
- else if (parameter == "priority")
- {
- }
-
- return ""; // return empty string
+ auto itParam = mdtmParameters.find(parameter);
+ if (itParam != mdtmParameters.end()) // found
+ {
+ return itParam->second; // return value
+ }
+ // if not found
+ // mandatory ones
+ if (parameter == "localIP" || parameter == "remoteIP")
+ {
+ if (m_DebugMode == true)
+ throw std::invalid_argument(
+ "ERROR: " + parameter +
+ " parameter not found in Method, in call to "
+ "DataManWriter constructor\n");
+ }
+ else if (parameter == "prefix")
+ {
+ return "";
+ }
+ else if (parameter == "pipes")
+ {
+ return "0"; // or 1?
+ }
+ else if (parameter == "tolerances") // so far empty string
+ {
+ }
+ else if (parameter == "priority")
+ {
+ }
+
+ return ""; // return empty string
}
} // end namespace adios
diff --git a/source/format/BP1.cpp b/source/format/BP1.cpp
index e9ec112c5753ab5e7905a016cf17815ad7daa1bc..ef69751b1918312def11a2b3005594abf9afd829 100644
--- a/source/format/BP1.cpp
+++ b/source/format/BP1.cpp
@@ -18,71 +18,71 @@ namespace format
std::string BP1::GetDirectoryName(const std::string name) const noexcept
{
- std::string directory;
+ std::string directory;
- if (name.find(".bp") == name.size() - 3)
- {
- directory = name;
- }
- else
- {
- directory = name + ".bp";
- }
- return directory;
+ if (name.find(".bp") == name.size() - 3)
+ {
+ directory = name;
+ }
+ else
+ {
+ directory = name + ".bp";
+ }
+ return directory;
}
void BP1::OpenRankFiles(const std::string name, const std::string accessMode,
Transport &file) const
{
- const std::string directory = GetDirectoryName(name);
- CreateDirectory(
- directory); // creates a directory and sub-directories recursively
+ const std::string directory = GetDirectoryName(name);
+ CreateDirectory(
+ directory); // creates a directory and sub-directories recursively
- std::string fileName(directory + "/" + directory + "." +
- std::to_string(file.m_RankMPI));
- file.Open(fileName, accessMode); // opens a file transport under
- // name.bp.dir/name.bp.rank reserve that
- // location fro writing
+ std::string fileName(directory + "/" + directory + "." +
+ std::to_string(file.m_RankMPI));
+ file.Open(fileName, accessMode); // opens a file transport under
+ // name.bp.dir/name.bp.rank reserve that
+ // location fro writing
}
std::vector<std::uint8_t> BP1::GetMethodIDs(
const std::vector<std::shared_ptr<Transport>> &transports) const noexcept
{
- auto lf_GetMethodID = [](const std::string method) -> std::uint8_t {
- int id = METHOD_UNKNOWN;
- if (method == "NULL")
- {
- id = METHOD_NULL;
- }
- else if (method == "POSIX")
- {
- id = METHOD_POSIX;
- }
- else if (method == "FStream")
- {
- id = METHOD_FSTREAM;
- }
- else if (method == "File")
- {
- id = METHOD_FILE;
- }
- else if (method == "MPI")
- {
- id = METHOD_MPI;
- }
+ auto lf_GetMethodID = [](const std::string method) -> std::uint8_t {
+ int id = METHOD_UNKNOWN;
+ if (method == "NULL")
+ {
+ id = METHOD_NULL;
+ }
+ else if (method == "POSIX")
+ {
+ id = METHOD_POSIX;
+ }
+ else if (method == "FStream")
+ {
+ id = METHOD_FSTREAM;
+ }
+ else if (method == "File")
+ {
+ id = METHOD_FILE;
+ }
+ else if (method == "MPI")
+ {
+ id = METHOD_MPI;
+ }
- return id;
- };
+ return id;
+ };
- std::vector<std::uint8_t> methodIDs;
- methodIDs.reserve(transports.size());
+ std::vector<std::uint8_t> methodIDs;
+ methodIDs.reserve(transports.size());
- for (const auto &transport : transports)
- {
- methodIDs.push_back(lf_GetMethodID(transport->m_Type));
- }
+ for (const auto &transport : transports)
+ {
+ methodIDs.push_back(lf_GetMethodID(transport->m_Type));
+ }
- return methodIDs;
+ return methodIDs;
}
} // end namespace format
diff --git a/source/format/BP1Aggregator.cpp b/source/format/BP1Aggregator.cpp
index f0de393a3ef307ed0b1c4959301ca0b3d0b18677..7b095cb112fa0bb3c54c788e4b731db1f75ba2a7 100644
--- a/source/format/BP1Aggregator.cpp
+++ b/source/format/BP1Aggregator.cpp
@@ -24,8 +24,8 @@ namespace format
BP1Aggregator::BP1Aggregator(MPI_Comm mpiComm, const bool debugMode)
: m_MPIComm{mpiComm}, m_DebugMode{debugMode}
{
- MPI_Comm_rank(m_MPIComm, &m_RankMPI);
- MPI_Comm_size(m_MPIComm, &m_SizeMPI);
+ MPI_Comm_rank(m_MPIComm, &m_RankMPI);
+ MPI_Comm_size(m_MPIComm, &m_SizeMPI);
}
BP1Aggregator::~BP1Aggregator() = default;
@@ -33,74 +33,75 @@ BP1Aggregator::~BP1Aggregator() = default;
void BP1Aggregator::WriteProfilingLog(const std::string fileName,
const std::string &rankLog)
{
- if (m_RankMPI == 0)
- {
- unsigned int sizeMPI = static_cast<unsigned int>(m_SizeMPI);
- std::vector<std::vector<char>> rankLogs(sizeMPI -
- 1); // rankLogs from other processes
- std::vector<int> rankLogsSizes(sizeMPI - 1, -1); // init with -1
- std::vector<MPI_Request> requests(sizeMPI);
- std::vector<MPI_Status> statuses(sizeMPI);
-
- // first receive sizes
- for (unsigned int i = 1; i < sizeMPI; ++i)
+ if (m_RankMPI == 0)
{
- MPI_Irecv(&rankLogsSizes[i - 1], 1, MPI_INT, i, 0, m_MPIComm,
- &requests[i]);
- }
+ unsigned int sizeMPI = static_cast<unsigned int>(m_SizeMPI);
+ std::vector<std::vector<char>> rankLogs(
+ sizeMPI - 1); // rankLogs from other processes
+ std::vector<int> rankLogsSizes(sizeMPI - 1, -1); // init with -1
+ std::vector<MPI_Request> requests(sizeMPI);
+ std::vector<MPI_Status> statuses(sizeMPI);
- for (unsigned int i = 1; i < sizeMPI; ++i)
- {
- MPI_Wait(&requests[i], &statuses[i]);
- if (m_DebugMode == true)
- {
- if (rankLogsSizes[i - 1] == -1)
+ // first receive sizes
+ for (unsigned int i = 1; i < sizeMPI; ++i)
{
- throw std::runtime_error("ERROR: couldn't get size from rank " +
- std::to_string(i) +
- ", in ADIOS aggregator for Profiling.log\n");
+ MPI_Irecv(&rankLogsSizes[i - 1], 1, MPI_INT, i, 0, m_MPIComm,
+ &requests[i]);
}
- }
- rankLogs[i - 1].resize(rankLogsSizes[i - 1]); // allocate with zeros
- }
- // receive rankLog from other ranks
- for (unsigned int i = 1; i < sizeMPI; ++i)
- {
- MPI_Irecv(rankLogs[i - 1].data(), rankLogsSizes[i - 1], MPI_CHAR, i, 1,
- m_MPIComm, &requests[i]);
- }
+ for (unsigned int i = 1; i < sizeMPI; ++i)
+ {
+ MPI_Wait(&requests[i], &statuses[i]);
+ if (m_DebugMode == true)
+ {
+ if (rankLogsSizes[i - 1] == -1)
+ {
+ throw std::runtime_error(
+ "ERROR: couldn't get size from rank " +
+ std::to_string(i) +
+ ", in ADIOS aggregator for Profiling.log\n");
+ }
+ }
+ rankLogs[i - 1].resize(rankLogsSizes[i - 1]); // allocate with zeros
+ }
- for (unsigned int i = 1; i < sizeMPI; ++i)
- {
- MPI_Wait(&requests[i], &statuses[i]);
- }
+ // receive rankLog from other ranks
+ for (unsigned int i = 1; i < sizeMPI; ++i)
+ {
+ MPI_Irecv(rankLogs[i - 1].data(), rankLogsSizes[i - 1], MPI_CHAR, i,
+ 1, m_MPIComm, &requests[i]);
+ }
- // write file
- std::string logFile("log = { \n");
- logFile += rankLog + "\n";
- for (unsigned int i = 1; i < sizeMPI; ++i)
- {
- const std::string rankLogStr(rankLogs[i - 1].data(),
- rankLogs[i - 1].size());
- logFile += rankLogStr + "\n";
- }
- logFile += " }\n";
+ for (unsigned int i = 1; i < sizeMPI; ++i)
+ {
+ MPI_Wait(&requests[i], &statuses[i]);
+ }
- std::ofstream logStream(fileName);
- logStream.write(logFile.c_str(), logFile.size());
- logStream.close();
- }
- else
- {
- int rankLogSize = static_cast<int>(rankLog.size());
- MPI_Request requestSize;
- MPI_Isend(&rankLogSize, 1, MPI_INT, 0, 0, m_MPIComm, &requestSize);
+ // write file
+ std::string logFile("log = { \n");
+ logFile += rankLog + "\n";
+ for (unsigned int i = 1; i < sizeMPI; ++i)
+ {
+ const std::string rankLogStr(rankLogs[i - 1].data(),
+ rankLogs[i - 1].size());
+ logFile += rankLogStr + "\n";
+ }
+ logFile += " }\n";
- MPI_Request requestRankLog;
- MPI_Isend(rankLog.data(), rankLogSize, MPI_CHAR, 0, 1, m_MPIComm,
- &requestRankLog);
- }
+ std::ofstream logStream(fileName);
+ logStream.write(logFile.c_str(), logFile.size());
+ logStream.close();
+ }
+ else
+ {
+ int rankLogSize = static_cast<int>(rankLog.size());
+ MPI_Request requestSize;
+ MPI_Isend(&rankLogSize, 1, MPI_INT, 0, 0, m_MPIComm, &requestSize);
+
+ MPI_Request requestRankLog;
+ MPI_Isend(rankLog.data(), rankLogSize, MPI_CHAR, 0, 1, m_MPIComm,
+ &requestRankLog);
+ }
}
} // end namespace format
diff --git a/source/format/BP1Writer.cpp b/source/format/BP1Writer.cpp
index 97b717eebf8846f119326761578b14fb988ce6c9..caafd8e86d7c3e111c7caf98daf7ae9d35ca9377 100644
--- a/source/format/BP1Writer.cpp
+++ b/source/format/BP1Writer.cpp
@@ -25,10 +25,11 @@ std::size_t BP1Writer::GetProcessGroupIndexSize(
const std::string name, const std::string timeStepName,
const std::size_t numberOfTransports) const noexcept
{
- // pgIndex + list of methods (transports)
- return (name.length() + timeStepName.length() + 23) +
- (3 + numberOfTransports); // should be sufficient for data and metadata
- // pgindices
+ // pgIndex + list of methods (transports)
+ return (name.length() + timeStepName.length() + 23) +
+ (3 +
+ numberOfTransports); // should be sufficient for data and metadata
+ // pgindices
}
void BP1Writer::WriteProcessGroupIndex(
@@ -36,162 +37,163 @@ void BP1Writer::WriteProcessGroupIndex(
const std::vector<std::shared_ptr<Transport>> &transports,
capsule::STLVector &heap, BP1MetadataSet &metadataSet) const noexcept
{
- std::vector<char> &metadataBuffer = metadataSet.PGIndex.Buffer;
- std::vector<char> &dataBuffer = heap.m_Data;
-
- metadataSet.DataPGLengthPosition = dataBuffer.size();
- dataBuffer.insert(dataBuffer.end(), 8, 0); // skip pg length (8)
-
- const std::size_t metadataPGLengthPosition = metadataBuffer.size();
- metadataBuffer.insert(metadataBuffer.end(), 2, 0); // skip pg length (2)
-
- // write name to metadata
- WriteNameRecord(name, metadataBuffer);
- // write if host language Fortran in metadata and data
- const char hostFortran =
- (isFortran) ? 'y' : 'n'; // if host language is fortran
- CopyToBuffer(metadataBuffer, &hostFortran);
- CopyToBuffer(dataBuffer, &hostFortran);
- // write name in data
- WriteNameRecord(name, dataBuffer);
-
- // processID in metadata,
- CopyToBuffer(metadataBuffer, &processID);
- // skip coordination var in data ....what is coordination var?
- dataBuffer.insert(dataBuffer.end(), 4, 0);
-
- // time step name to metadata and data
- const std::string timeStepName(std::to_string(metadataSet.TimeStep));
- WriteNameRecord(timeStepName, metadataBuffer);
- WriteNameRecord(timeStepName, dataBuffer);
-
- // time step to metadata and data
- CopyToBuffer(metadataBuffer, &metadataSet.TimeStep);
- CopyToBuffer(dataBuffer, &metadataSet.TimeStep);
-
- // offset to pg in data in metadata which is the current absolute position
- CopyToBuffer(metadataBuffer,
- static_cast<uint64_t *>(&heap.m_DataAbsolutePosition));
-
- // Back to writing metadata pg index length (length of group)
- const std::uint16_t metadataPGIndexLength =
- metadataBuffer.size() - metadataPGLengthPosition -
- 2; // without length of group record
- CopyToBuffer(metadataBuffer, metadataPGLengthPosition,
- &metadataPGIndexLength);
- // DONE With metadataBuffer
-
- // here write method in data
- const std::vector<std::uint8_t> methodIDs = GetMethodIDs(transports);
- const std::uint8_t methodsCount = methodIDs.size();
- CopyToBuffer(dataBuffer, &methodsCount); // count
- const std::uint16_t methodsLength =
- methodIDs.size() *
- 3; // methodID (1) + method params length(2), no parameters for now
- CopyToBuffer(dataBuffer, &methodsLength); // length
-
- for (const auto methodID : methodIDs)
- {
- CopyToBuffer(dataBuffer, &methodID); // method ID,
- dataBuffer.insert(dataBuffer.end(), 2,
- 0); // skip method params length = 0 (2 bytes) for now
- }
-
- // update absolute position
- heap.m_DataAbsolutePosition +=
- dataBuffer.size() - metadataSet.DataPGLengthPosition;
- // pg vars count and position
- metadataSet.DataPGVarsCount = 0;
- metadataSet.DataPGVarsCountPosition = dataBuffer.size();
- // add vars count and length
- dataBuffer.insert(dataBuffer.end(), 12, 0);
- heap.m_DataAbsolutePosition += 12; // add vars count and length
-
- ++metadataSet.DataPGCount;
- metadataSet.DataPGIsOpen = true;
+ std::vector<char> &metadataBuffer = metadataSet.PGIndex.Buffer;
+ std::vector<char> &dataBuffer = heap.m_Data;
+
+ metadataSet.DataPGLengthPosition = dataBuffer.size();
+ dataBuffer.insert(dataBuffer.end(), 8, 0); // skip pg length (8)
+
+ const std::size_t metadataPGLengthPosition = metadataBuffer.size();
+ metadataBuffer.insert(metadataBuffer.end(), 2, 0); // skip pg length (2)
+
+ // write name to metadata
+ WriteNameRecord(name, metadataBuffer);
+ // write if host language Fortran in metadata and data
+ const char hostFortran =
+ (isFortran) ? 'y' : 'n'; // if host language is fortran
+ CopyToBuffer(metadataBuffer, &hostFortran);
+ CopyToBuffer(dataBuffer, &hostFortran);
+ // write name in data
+ WriteNameRecord(name, dataBuffer);
+
+ // processID in metadata,
+ CopyToBuffer(metadataBuffer, &processID);
+ // skip coordination var in data ....what is coordination var?
+ dataBuffer.insert(dataBuffer.end(), 4, 0);
+
+ // time step name to metadata and data
+ const std::string timeStepName(std::to_string(metadataSet.TimeStep));
+ WriteNameRecord(timeStepName, metadataBuffer);
+ WriteNameRecord(timeStepName, dataBuffer);
+
+ // time step to metadata and data
+ CopyToBuffer(metadataBuffer, &metadataSet.TimeStep);
+ CopyToBuffer(dataBuffer, &metadataSet.TimeStep);
+
+ // offset to pg in data in metadata which is the current absolute position
+ CopyToBuffer(metadataBuffer,
+ static_cast<uint64_t *>(&heap.m_DataAbsolutePosition));
+
+ // Back to writing metadata pg index length (length of group)
+ const std::uint16_t metadataPGIndexLength =
+ metadataBuffer.size() - metadataPGLengthPosition -
+ 2; // without length of group record
+ CopyToBuffer(metadataBuffer, metadataPGLengthPosition,
+ &metadataPGIndexLength);
+ // DONE With metadataBuffer
+
+ // here write method in data
+ const std::vector<std::uint8_t> methodIDs = GetMethodIDs(transports);
+ const std::uint8_t methodsCount = methodIDs.size();
+ CopyToBuffer(dataBuffer, &methodsCount); // count
+ const std::uint16_t methodsLength =
+ methodIDs.size() *
+ 3; // methodID (1) + method params length(2), no parameters for now
+ CopyToBuffer(dataBuffer, &methodsLength); // length
+
+ for (const auto methodID : methodIDs)
+ {
+ CopyToBuffer(dataBuffer, &methodID); // method ID,
+ dataBuffer.insert(dataBuffer.end(), 2,
+ 0); // skip method params length = 0 (2 bytes) for now
+ }
+
+ // update absolute position
+ heap.m_DataAbsolutePosition +=
+ dataBuffer.size() - metadataSet.DataPGLengthPosition;
+ // pg vars count and position
+ metadataSet.DataPGVarsCount = 0;
+ metadataSet.DataPGVarsCountPosition = dataBuffer.size();
+ // add vars count and length
+ dataBuffer.insert(dataBuffer.end(), 12, 0);
+ heap.m_DataAbsolutePosition += 12; // add vars count and length
+
+ ++metadataSet.DataPGCount;
+ metadataSet.DataPGIsOpen = true;
}
void BP1Writer::Advance(BP1MetadataSet &metadataSet, capsule::STLVector &buffer)
{
- FlattenData(metadataSet, buffer);
+ FlattenData(metadataSet, buffer);
}
void BP1Writer::Close(BP1MetadataSet &metadataSet, capsule::STLVector &heap,
Transport &transport, bool &isFirstClose,
const bool doAggregation) const noexcept
{
- if (metadataSet.Log.m_IsActive == true)
- {
- metadataSet.Log.m_Timers[0].SetInitialTime();
- }
-
- if (isFirstClose == true)
- {
- if (metadataSet.DataPGIsOpen == true)
+ if (metadataSet.Log.m_IsActive == true)
{
- FlattenData(metadataSet, heap);
+ metadataSet.Log.m_Timers[0].SetInitialTime();
}
- FlattenMetadata(metadataSet, heap);
-
- if (metadataSet.Log.m_IsActive == true)
+ if (isFirstClose == true)
{
- metadataSet.Log.m_Timers[0].SetInitialTime();
+ if (metadataSet.DataPGIsOpen == true)
+ {
+ FlattenData(metadataSet, heap);
+ }
+
+ FlattenMetadata(metadataSet, heap);
+
+ if (metadataSet.Log.m_IsActive == true)
+ {
+ metadataSet.Log.m_Timers[0].SetInitialTime();
+ }
+
+ if (doAggregation ==
+ true) // N-to-M where 1 <= M <= N-1, might need a new
+ // Log metadataSet.Log.m_Timers just for
+ // aggregation
+ {
+ // here call aggregator
+ }
+ isFirstClose = false;
}
- if (doAggregation == true) // N-to-M where 1 <= M <= N-1, might need a new
- // Log metadataSet.Log.m_Timers just for
- // aggregation
+ if (doAggregation == true) // N-to-M where 1 <= M <= N-1
+ {
+ // here call aggregator to select transports for Write and Close
+ }
+ else // N-to-N
{
- // here call aggregator
+ transport.Write(heap.m_Data.data(), heap.m_Data.size()); // single write
+ transport.Close();
}
- isFirstClose = false;
- }
-
- if (doAggregation == true) // N-to-M where 1 <= M <= N-1
- {
- // here call aggregator to select transports for Write and Close
- }
- else // N-to-N
- {
- transport.Write(heap.m_Data.data(), heap.m_Data.size()); // single write
- transport.Close();
- }
}
std::string BP1Writer::GetRankProfilingLog(
const int rank, const BP1MetadataSet &metadataSet,
const std::vector<std::shared_ptr<Transport>> &transports) const noexcept
{
- auto lf_WriterTimer = [](std::string &rankLog, const Timer &timer) {
- rankLog += "'" + timer.Process + "_" + timer.GetUnits() + "': " +
- std::to_string(timer.ProcessTime) + ", ";
- };
+ auto lf_WriterTimer = [](std::string &rankLog, const Timer &timer) {
+ rankLog += "'" + timer.Process + "_" + timer.GetUnits() + "': " +
+ std::to_string(timer.ProcessTime) + ", ";
+ };
- // prepare string dictionary per rank
- std::string rankLog("'rank_" + std::to_string(rank) + "': { ");
+ // prepare string dictionary per rank
+ std::string rankLog("'rank_" + std::to_string(rank) + "': { ");
- auto &profiler = metadataSet.Log;
- rankLog += "'bytes': " + std::to_string(profiler.m_TotalBytes[0]) + ", ";
- lf_WriterTimer(rankLog, profiler.m_Timers[0]);
+ auto &profiler = metadataSet.Log;
+ rankLog += "'bytes': " + std::to_string(profiler.m_TotalBytes[0]) + ", ";
+ lf_WriterTimer(rankLog, profiler.m_Timers[0]);
- for (unsigned int t = 0; t < transports.size(); ++t)
- {
- auto &timers = transports[t]->m_Profiler.m_Timers;
+ for (unsigned int t = 0; t < transports.size(); ++t)
+ {
+ auto &timers = transports[t]->m_Profiler.m_Timers;
- rankLog += "'transport_" + std::to_string(t) + "': { ";
- rankLog += "'lib': " + transports[t]->m_Type + ", ";
+ rankLog += "'transport_" + std::to_string(t) + "': { ";
+ rankLog += "'lib': " + transports[t]->m_Type + ", ";
- for (unsigned int i = 0; i < 3; ++i)
- {
- lf_WriterTimer(rankLog, timers[i]);
- }
+ for (unsigned int i = 0; i < 3; ++i)
+ {
+ lf_WriterTimer(rankLog, timers[i]);
+ }
+ rankLog += "}, ";
+ }
rankLog += "}, ";
- }
- rankLog += "}, ";
- return rankLog;
+ return rankLog;
}
// PRIVATE FUNCTIONS
@@ -201,66 +203,70 @@ void BP1Writer::WriteDimensionsRecord(
const std::vector<std::size_t> &globalOffsets, const unsigned int skip,
const bool addType) const noexcept
{
- auto lf_WriteFlaggedDim = [](std::vector<char> &buffer, const char no,
- const std::size_t dimension) {
- CopyToBuffer(buffer, &no);
- CopyToBuffer(buffer, static_cast<const uint64_t *>(&dimension));
- };
-
- // BODY Starts here
- if (globalDimensions.empty())
- {
- if (addType == true)
- {
- constexpr char no = 'n'; // dimension format unsigned int value (not using
- // memberID for now)
- for (const auto &localDimension : localDimensions)
- {
- lf_WriteFlaggedDim(buffer, no, localDimension);
- buffer.insert(buffer.end(), skip, 0);
- }
- }
- else
+ auto lf_WriteFlaggedDim = [](std::vector<char> &buffer, const char no,
+ const std::size_t dimension) {
+ CopyToBuffer(buffer, &no);
+ CopyToBuffer(buffer, static_cast<const uint64_t *>(&dimension));
+ };
+
+ // BODY Starts here
+ if (globalDimensions.empty())
{
- for (const auto &localDimension : localDimensions)
- {
- CopyToBuffer(buffer, static_cast<const uint64_t *>(&localDimension));
- buffer.insert(buffer.end(), skip, 0);
- }
- }
- }
- else
- {
- if (addType == true)
- {
- constexpr char no = 'n'; // dimension format unsigned int value for now
- for (unsigned int d = 0; d < localDimensions.size(); ++d)
- {
- lf_WriteFlaggedDim(buffer, no, localDimensions[d]);
- lf_WriteFlaggedDim(buffer, no, globalDimensions[d]);
- lf_WriteFlaggedDim(buffer, no, globalOffsets[d]);
- }
+ if (addType == true)
+ {
+ constexpr char no =
+ 'n'; // dimension format unsigned int value (not using
+ // memberID for now)
+ for (const auto &localDimension : localDimensions)
+ {
+ lf_WriteFlaggedDim(buffer, no, localDimension);
+ buffer.insert(buffer.end(), skip, 0);
+ }
+ }
+ else
+ {
+ for (const auto &localDimension : localDimensions)
+ {
+ CopyToBuffer(buffer,
+ static_cast<const uint64_t *>(&localDimension));
+ buffer.insert(buffer.end(), skip, 0);
+ }
+ }
}
else
{
- for (unsigned int d = 0; d < localDimensions.size(); ++d)
- {
- CopyToBuffer(buffer,
- static_cast<const uint64_t *>(&localDimensions[d]));
- CopyToBuffer(buffer,
- static_cast<const uint64_t *>(&globalDimensions[d]));
- CopyToBuffer(buffer, static_cast<const uint64_t *>(&globalOffsets[d]));
- }
+ if (addType == true)
+ {
+ constexpr char no =
+ 'n'; // dimension format unsigned int value for now
+ for (unsigned int d = 0; d < localDimensions.size(); ++d)
+ {
+ lf_WriteFlaggedDim(buffer, no, localDimensions[d]);
+ lf_WriteFlaggedDim(buffer, no, globalDimensions[d]);
+ lf_WriteFlaggedDim(buffer, no, globalOffsets[d]);
+ }
+ }
+ else
+ {
+ for (unsigned int d = 0; d < localDimensions.size(); ++d)
+ {
+ CopyToBuffer(
+ buffer, static_cast<const uint64_t *>(&localDimensions[d]));
+ CopyToBuffer(buffer, static_cast<const uint64_t *>(
+ &globalDimensions[d]));
+ CopyToBuffer(buffer,
+ static_cast<const uint64_t *>(&globalOffsets[d]));
+ }
+ }
}
- }
}
void BP1Writer::WriteNameRecord(const std::string name,
std::vector<char> &buffer) const noexcept
{
- const std::uint16_t length = name.length();
- CopyToBuffer(buffer, &length);
- CopyToBuffer(buffer, name.c_str(), length);
+ const std::uint16_t length = name.length();
+ CopyToBuffer(buffer, &length);
+ CopyToBuffer(buffer, name.c_str(), length);
}
BP1Index &
@@ -268,138 +274,138 @@ BP1Writer::GetBP1Index(const std::string name,
std::unordered_map<std::string, BP1Index> &indices,
bool &isNew) const noexcept
{
- auto itName = indices.find(name);
- if (itName == indices.end())
- {
- indices.emplace(name, BP1Index(indices.size()));
- isNew = true;
- return indices.at(name);
- }
-
- isNew = false;
- return itName->second;
+ auto itName = indices.find(name);
+ if (itName == indices.end())
+ {
+ indices.emplace(name, BP1Index(indices.size()));
+ isNew = true;
+ return indices.at(name);
+ }
+
+ isNew = false;
+ return itName->second;
}
void BP1Writer::FlattenData(BP1MetadataSet &metadataSet,
capsule::STLVector &heap) const noexcept
{
- auto &buffer = heap.m_Data;
- // vars count and Length (only for PG)
- CopyToBuffer(buffer, metadataSet.DataPGVarsCountPosition,
- &metadataSet.DataPGVarsCount);
- const std::uint64_t varsLength = buffer.size() -
- metadataSet.DataPGVarsCountPosition - 8 -
- 4; // without record itself and vars count
- CopyToBuffer(buffer, metadataSet.DataPGVarsCountPosition + 4, &varsLength);
-
- // attributes (empty for now) count (4) and length (8) are zero by moving
- // positions in time step zero
- buffer.insert(buffer.end(), 12, 0);
- heap.m_DataAbsolutePosition += 12;
-
- // Finish writing pg group length
- const std::uint64_t dataPGLength =
- buffer.size() - metadataSet.DataPGLengthPosition -
- 8; // without record itself, 12 due to empty attributes
- CopyToBuffer(buffer, metadataSet.DataPGLengthPosition, &dataPGLength);
-
- ++metadataSet.TimeStep;
- metadataSet.DataPGIsOpen = false;
+ auto &buffer = heap.m_Data;
+ // vars count and Length (only for PG)
+ CopyToBuffer(buffer, metadataSet.DataPGVarsCountPosition,
+ &metadataSet.DataPGVarsCount);
+ const std::uint64_t varsLength = buffer.size() -
+ metadataSet.DataPGVarsCountPosition - 8 -
+ 4; // without record itself and vars count
+ CopyToBuffer(buffer, metadataSet.DataPGVarsCountPosition + 4, &varsLength);
+
+ // attributes (empty for now) count (4) and length (8) are zero by moving
+ // positions in time step zero
+ buffer.insert(buffer.end(), 12, 0);
+ heap.m_DataAbsolutePosition += 12;
+
+ // Finish writing pg group length
+ const std::uint64_t dataPGLength =
+ buffer.size() - metadataSet.DataPGLengthPosition -
+ 8; // without record itself, 12 due to empty attributes
+ CopyToBuffer(buffer, metadataSet.DataPGLengthPosition, &dataPGLength);
+
+ ++metadataSet.TimeStep;
+ metadataSet.DataPGIsOpen = false;
}
void BP1Writer::FlattenMetadata(BP1MetadataSet &metadataSet,
capsule::STLVector &heap) const noexcept
{
- auto lf_IndexCountLength =
- [](std::unordered_map<std::string, BP1Index> &indices,
- std::uint32_t &count, std::uint64_t &length) {
- count = indices.size();
- length = 0;
- for (auto &indexPair : indices) // set each index length
- {
- auto &indexBuffer = indexPair.second.Buffer;
- const std::uint32_t indexLength = indexBuffer.size() - 4;
- CopyToBuffer(indexBuffer, 0, &indexLength);
-
- length += indexBuffer.size(); // overall length
- }
- };
+ auto lf_IndexCountLength =
+ [](std::unordered_map<std::string, BP1Index> &indices,
+ std::uint32_t &count, std::uint64_t &length) {
+ count = indices.size();
+ length = 0;
+ for (auto &indexPair : indices) // set each index length
+ {
+ auto &indexBuffer = indexPair.second.Buffer;
+ const std::uint32_t indexLength = indexBuffer.size() - 4;
+ CopyToBuffer(indexBuffer, 0, &indexLength);
+
+ length += indexBuffer.size(); // overall length
+ }
+ };
+
+ auto lf_FlattenIndices =
+ [](const std::uint32_t count, const std::uint64_t length,
+ const std::unordered_map<std::string, BP1Index> &indices,
+ std::vector<char> &buffer) {
+ CopyToBuffer(buffer, &count);
+ CopyToBuffer(buffer, &length);
+
+ for (const auto &indexPair : indices) // set each index length
+ {
+ const auto &indexBuffer = indexPair.second.Buffer;
+ CopyToBuffer(buffer, indexBuffer.data(), indexBuffer.size());
+ }
+ };
+
+ // Finish writing metadata counts and lengths
+ // PG Index
+ const std::uint64_t pgCount = metadataSet.DataPGCount;
+ const std::uint64_t pgLength = metadataSet.PGIndex.Buffer.size();
+
+ // var index count and length (total), and each index length
+ std::uint32_t varsCount;
+ std::uint64_t varsLength;
+ lf_IndexCountLength(metadataSet.VarsIndices, varsCount, varsLength);
+ // attribute index count and length, and each index length
+ std::uint32_t attributesCount;
+ std::uint64_t attributesLength;
+ lf_IndexCountLength(metadataSet.AttributesIndices, attributesCount,
+ attributesLength);
+
+ const std::size_t footerSize = (pgLength + 16) + (varsLength + 12) +
+ (attributesLength + 12) +
+ metadataSet.MiniFooterSize;
+ auto &buffer = heap.m_Data;
+ buffer.reserve(buffer.size() + footerSize); // reserve data to fit metadata,
+ // must replace with growth buffer
+ // strategy
+
+ // write pg index
+ CopyToBuffer(buffer, &pgCount);
+ CopyToBuffer(buffer, &pgLength);
+ CopyToBuffer(buffer, metadataSet.PGIndex.Buffer.data(), pgLength);
+ // Vars indices
+ lf_FlattenIndices(varsCount, varsLength, metadataSet.VarsIndices, buffer);
+ // Attribute indices
+ lf_FlattenIndices(attributesCount, attributesLength,
+ metadataSet.AttributesIndices, buffer);
+
+ // getting absolute offsets, minifooter is 28 bytes for now
+ const std::uint64_t offsetPGIndex = heap.m_DataAbsolutePosition;
+ const std::uint64_t offsetVarsIndex = offsetPGIndex + (pgLength + 16);
+ const std::uint64_t offsetAttributeIndex =
+ offsetVarsIndex + (varsLength + 12);
+
+ CopyToBuffer(buffer, &offsetPGIndex);
+ CopyToBuffer(buffer, &offsetVarsIndex);
+ CopyToBuffer(buffer, &offsetAttributeIndex);
+
+ // version
+ if (IsLittleEndian())
+ {
+ const std::uint8_t endian = 0;
+ CopyToBuffer(buffer, &endian);
+ buffer.insert(buffer.end(), 2, 0);
+ CopyToBuffer(buffer, &m_Version);
+ }
+ else
+ {
+ }
- auto lf_FlattenIndices =
- [](const std::uint32_t count, const std::uint64_t length,
- const std::unordered_map<std::string, BP1Index> &indices,
- std::vector<char> &buffer) {
- CopyToBuffer(buffer, &count);
- CopyToBuffer(buffer, &length);
+ heap.m_DataAbsolutePosition += footerSize;
- for (const auto &indexPair : indices) // set each index length
- {
- const auto &indexBuffer = indexPair.second.Buffer;
- CopyToBuffer(buffer, indexBuffer.data(), indexBuffer.size());
- }
- };
-
- // Finish writing metadata counts and lengths
- // PG Index
- const std::uint64_t pgCount = metadataSet.DataPGCount;
- const std::uint64_t pgLength = metadataSet.PGIndex.Buffer.size();
-
- // var index count and length (total), and each index length
- std::uint32_t varsCount;
- std::uint64_t varsLength;
- lf_IndexCountLength(metadataSet.VarsIndices, varsCount, varsLength);
- // attribute index count and length, and each index length
- std::uint32_t attributesCount;
- std::uint64_t attributesLength;
- lf_IndexCountLength(metadataSet.AttributesIndices, attributesCount,
- attributesLength);
-
- const std::size_t footerSize = (pgLength + 16) + (varsLength + 12) +
- (attributesLength + 12) +
- metadataSet.MiniFooterSize;
- auto &buffer = heap.m_Data;
- buffer.reserve(buffer.size() + footerSize); // reserve data to fit metadata,
- // must replace with growth buffer
- // strategy
-
- // write pg index
- CopyToBuffer(buffer, &pgCount);
- CopyToBuffer(buffer, &pgLength);
- CopyToBuffer(buffer, metadataSet.PGIndex.Buffer.data(), pgLength);
- // Vars indices
- lf_FlattenIndices(varsCount, varsLength, metadataSet.VarsIndices, buffer);
- // Attribute indices
- lf_FlattenIndices(attributesCount, attributesLength,
- metadataSet.AttributesIndices, buffer);
-
- // getting absolute offsets, minifooter is 28 bytes for now
- const std::uint64_t offsetPGIndex = heap.m_DataAbsolutePosition;
- const std::uint64_t offsetVarsIndex = offsetPGIndex + (pgLength + 16);
- const std::uint64_t offsetAttributeIndex =
- offsetVarsIndex + (varsLength + 12);
-
- CopyToBuffer(buffer, &offsetPGIndex);
- CopyToBuffer(buffer, &offsetVarsIndex);
- CopyToBuffer(buffer, &offsetAttributeIndex);
-
- // version
- if (IsLittleEndian())
- {
- const std::uint8_t endian = 0;
- CopyToBuffer(buffer, &endian);
- buffer.insert(buffer.end(), 2, 0);
- CopyToBuffer(buffer, &m_Version);
- }
- else
- {
- }
-
- heap.m_DataAbsolutePosition += footerSize;
-
- if (metadataSet.Log.m_IsActive == true)
- {
- metadataSet.Log.m_TotalBytes.push_back(heap.m_DataAbsolutePosition);
- }
+ if (metadataSet.Log.m_IsActive == true)
+ {
+ metadataSet.Log.m_TotalBytes.push_back(heap.m_DataAbsolutePosition);
+ }
}
} // end namespace format
diff --git a/source/functions/adiosFunctions.cpp b/source/functions/adiosFunctions.cpp
index 78393c641f2c502c35728c46e590252ff8580749..0946dc0d6efa6d79860a595f0ff0be85ad84d8f4 100644
--- a/source/functions/adiosFunctions.cpp
+++ b/source/functions/adiosFunctions.cpp
@@ -35,197 +35,202 @@ namespace adios
void DumpFileToString(const std::string fileName, std::string &fileContent)
{
- std::ifstream fileStream(fileName);
-
- if (fileStream.good() == false)
- { // check file
- throw std::ios_base::failure(
- "ERROR: file " + fileName +
- " could not be opened. Check permissions or file existence\n");
- }
-
- std::ostringstream fileSS;
- fileSS << fileStream.rdbuf();
- fileStream.close();
- fileContent = fileSS.str(); // convert to string and check
-
- if (fileContent.empty())
- {
- throw std::invalid_argument("ERROR: file " + fileName + " is empty\n");
- }
+ std::ifstream fileStream(fileName);
+
+ if (fileStream.good() == false)
+ { // check file
+ throw std::ios_base::failure(
+ "ERROR: file " + fileName +
+ " could not be opened. Check permissions or file existence\n");
+ }
+
+ std::ostringstream fileSS;
+ fileSS << fileStream.rdbuf();
+ fileStream.close();
+ fileContent = fileSS.str(); // convert to string and check
+
+ if (fileContent.empty())
+ {
+ throw std::invalid_argument("ERROR: file " + fileName + " is empty\n");
+ }
}
void GetSubString(const std::string initialTag, const std::string finalTag,
const std::string content, std::string &subString,
std::string::size_type ¤tPosition)
{
- auto lf_Wipe = [](std::string &subString,
- std::string::size_type ¤tPosition) {
- subString.clear();
- currentPosition = std::string::npos;
- };
-
- auto lf_SetPositions =
- [](const char quote, const std::string::size_type quotePosition,
- const std::string &content, std::string::size_type ¤tPosition,
- std::string::size_type &closingQuotePosition) {
- currentPosition = quotePosition;
- closingQuotePosition = content.find(quote, currentPosition + 1);
- };
-
- // BODY OF FUNCTION STARTS HERE
- std::string::size_type start(content.find(initialTag, currentPosition));
- if (start == content.npos)
- {
- lf_Wipe(subString, currentPosition);
- return;
- }
- currentPosition = start;
-
- std::string::size_type end(content.find(finalTag, currentPosition));
- if (end == content.npos)
- {
- lf_Wipe(subString, currentPosition);
- return;
- }
-
- // here make sure the finalTag is not a value surrounded by " " or ' ', if so
- // find next
- bool isValue = true;
-
- while (isValue == true)
- {
- std::string::size_type singleQuotePosition =
- content.find('\'', currentPosition);
- std::string::size_type doubleQuotePosition =
- content.find('\"', currentPosition);
-
- if ((singleQuotePosition == content.npos &&
- doubleQuotePosition == content.npos) ||
- (singleQuotePosition == content.npos && end < doubleQuotePosition) ||
- (doubleQuotePosition == content.npos && end < singleQuotePosition) ||
- (end < singleQuotePosition && end < doubleQuotePosition))
+ auto lf_Wipe = [](std::string &subString,
+ std::string::size_type ¤tPosition) {
+ subString.clear();
+ currentPosition = std::string::npos;
+ };
+
+ auto lf_SetPositions =
+ [](const char quote, const std::string::size_type quotePosition,
+ const std::string &content, std::string::size_type ¤tPosition,
+ std::string::size_type &closingQuotePosition) {
+ currentPosition = quotePosition;
+ closingQuotePosition = content.find(quote, currentPosition + 1);
+ };
+
+ // BODY OF FUNCTION STARTS HERE
+ std::string::size_type start(content.find(initialTag, currentPosition));
+ if (start == content.npos)
{
- break;
+ lf_Wipe(subString, currentPosition);
+ return;
}
+ currentPosition = start;
- // find the closing corresponding quote
- std::string::size_type closingQuotePosition;
-
- if (singleQuotePosition == content.npos)
- { // no ' anywhere
- lf_SetPositions('\"', doubleQuotePosition, content, currentPosition,
- closingQuotePosition);
- }
- else if (doubleQuotePosition == content.npos)
- { // no " anywhere
- lf_SetPositions('\'', singleQuotePosition, content, currentPosition,
- closingQuotePosition);
- }
- else
+ std::string::size_type end(content.find(finalTag, currentPosition));
+ if (end == content.npos)
{
- if (singleQuotePosition < doubleQuotePosition)
- {
- lf_SetPositions('\'', singleQuotePosition, content, currentPosition,
- closingQuotePosition);
- }
- else
- { // find the closing "
- lf_SetPositions('\"', doubleQuotePosition, content, currentPosition,
- closingQuotePosition);
- }
+ lf_Wipe(subString, currentPosition);
+ return;
}
- if (closingQuotePosition ==
- content.npos) // if can't find closing it's open until the end
+ // here make sure the finalTag is not a value surrounded by " " or ' ', if
+ // so
+ // find next
+ bool isValue = true;
+
+ while (isValue == true)
{
- lf_Wipe(subString, currentPosition);
- return;
- }
+ std::string::size_type singleQuotePosition =
+ content.find('\'', currentPosition);
+ std::string::size_type doubleQuotePosition =
+ content.find('\"', currentPosition);
+
+ if ((singleQuotePosition == content.npos &&
+ doubleQuotePosition == content.npos) ||
+ (singleQuotePosition == content.npos &&
+ end < doubleQuotePosition) ||
+ (doubleQuotePosition == content.npos &&
+ end < singleQuotePosition) ||
+ (end < singleQuotePosition && end < doubleQuotePosition))
+ {
+ break;
+ }
- currentPosition = closingQuotePosition + 1;
+ // find the closing corresponding quote
+ std::string::size_type closingQuotePosition;
- if (closingQuotePosition < end)
- {
- continue;
- }
+ if (singleQuotePosition == content.npos)
+ { // no ' anywhere
+ lf_SetPositions('\"', doubleQuotePosition, content, currentPosition,
+ closingQuotePosition);
+ }
+ else if (doubleQuotePosition == content.npos)
+ { // no " anywhere
+ lf_SetPositions('\'', singleQuotePosition, content, currentPosition,
+ closingQuotePosition);
+ }
+ else
+ {
+ if (singleQuotePosition < doubleQuotePosition)
+ {
+ lf_SetPositions('\'', singleQuotePosition, content,
+ currentPosition, closingQuotePosition);
+ }
+ else
+ { // find the closing "
+ lf_SetPositions('\"', doubleQuotePosition, content,
+ currentPosition, closingQuotePosition);
+ }
+ }
+
+ if (closingQuotePosition ==
+ content.npos) // if can't find closing it's open until the end
+ {
+ lf_Wipe(subString, currentPosition);
+ return;
+ }
+
+ currentPosition = closingQuotePosition + 1;
+
+ if (closingQuotePosition < end)
+ {
+ continue;
+ }
- // if this point is reached it means it's a value inside " " or ' ', move to
- // the next end
- end = content.find(finalTag, currentPosition);
- }
+ // if this point is reached it means it's a value inside " " or ' ',
+ // move to
+ // the next end
+ end = content.find(finalTag, currentPosition);
+ }
- subString = content.substr(start, end - start + finalTag.size());
- currentPosition = end;
+ subString = content.substr(start, end - start + finalTag.size());
+ currentPosition = end;
}
void GetQuotedValue(const char quote,
const std::string::size_type "ePosition,
std::string ¤tTag, std::string &value)
{
- currentTag = currentTag.substr(quotePosition + 1);
- auto nextQuotePosition = currentTag.find(quote);
+ currentTag = currentTag.substr(quotePosition + 1);
+ auto nextQuotePosition = currentTag.find(quote);
- if (nextQuotePosition == currentTag.npos)
- {
- throw std::invalid_argument("ERROR: Invalid attribute in..." + currentTag +
- "...check XML file\n");
- }
+ if (nextQuotePosition == currentTag.npos)
+ {
+ throw std::invalid_argument("ERROR: Invalid attribute in..." +
+ currentTag + "...check XML file\n");
+ }
- value = currentTag.substr(0, nextQuotePosition);
- currentTag = currentTag.substr(nextQuotePosition + 1);
+ value = currentTag.substr(0, nextQuotePosition);
+ currentTag = currentTag.substr(nextQuotePosition + 1);
}
void GetPairs(const std::string tag,
std::vector<std::pair<const std::string, const std::string>>
&pairs) noexcept
{
- std::string currentTag(
- tag.substr(tag.find_first_of(" \t\n"))); // initialize current tag
-
- while (currentTag.find('=') != currentTag.npos) // equalPosition
- {
- currentTag = currentTag.substr(currentTag.find_first_not_of(" \t\n"));
- auto equalPosition = currentTag.find('=');
- const std::string field(currentTag.substr(0, equalPosition)); // get field
- std::string value;
-
- const char quote = currentTag[equalPosition + 1];
- if (quote == '\'' || quote == '"') // single quotes
+ std::string currentTag(
+ tag.substr(tag.find_first_of(" \t\n"))); // initialize current tag
+
+ while (currentTag.find('=') != currentTag.npos) // equalPosition
{
- GetQuotedValue(quote, equalPosition + 1, currentTag, value);
- }
+ currentTag = currentTag.substr(currentTag.find_first_not_of(" \t\n"));
+ auto equalPosition = currentTag.find('=');
+ const std::string field(
+ currentTag.substr(0, equalPosition)); // get field
+ std::string value;
+
+ const char quote = currentTag[equalPosition + 1];
+ if (quote == '\'' || quote == '"') // single quotes
+ {
+ GetQuotedValue(quote, equalPosition + 1, currentTag, value);
+ }
- pairs.push_back(
- std::pair<const std::string, const std::string>(field, value));
- }
+ pairs.push_back(
+ std::pair<const std::string, const std::string>(field, value));
+ }
}
void GetPairsFromTag(
const std::string &fileContent, const std::string tag,
std::vector<std::pair<const std::string, const std::string>> &pairs)
{
- if (tag.back() == '/') // last char is / --> "XML empty tag"
- {
- GetPairs(tag, pairs);
- }
- else if (tag[0] == '/') // first char is / ---> closing tag
- {
- }
- else // opening tag
- {
- const std::string tagName(tag.substr(0, tag.find_first_of(" \t\n\r")));
- const std::string closingTagName("</" + tagName +
- ">"); // check for closing tagName
-
- if (fileContent.find(closingTagName) == fileContent.npos)
+ if (tag.back() == '/') // last char is / --> "XML empty tag"
{
- throw std::invalid_argument("ERROR: closing tag " + closingTagName +
- " missing, check XML file\n");
+ GetPairs(tag, pairs);
}
+ else if (tag[0] == '/') // first char is / ---> closing tag
+ {
+ }
+ else // opening tag
+ {
+ const std::string tagName(tag.substr(0, tag.find_first_of(" \t\n\r")));
+ const std::string closingTagName("</" + tagName +
+ ">"); // check for closing tagName
- GetPairs(tag, pairs);
- }
+ if (fileContent.find(closingTagName) == fileContent.npos)
+ {
+ throw std::invalid_argument("ERROR: closing tag " + closingTagName +
+ " missing, check XML file\n");
+ }
+
+ GetPairs(tag, pairs);
+ }
}
// void SetMembers( const std::string& fileContent, const MPI_Comm mpiComm,
@@ -428,48 +433,48 @@ void GetPairsFromTag(
std::size_t GetTotalSize(const std::vector<std::size_t> &dimensions)
{
- std::size_t product = 1;
+ std::size_t product = 1;
- for (const auto dimension : dimensions)
- {
- product *= dimension;
- }
+ for (const auto dimension : dimensions)
+ {
+ product *= dimension;
+ }
- return product;
+ return product;
}
void CreateDirectory(const std::string fullPath) noexcept
{
- auto lf_Mkdir = [](const std::string directory, struct stat &st) {
- if (stat(directory.c_str(), &st) == -1)
- {
- mkdir(directory.c_str(), 0777);
- }
- };
-
- auto directoryPosition = fullPath.find("/");
+ auto lf_Mkdir = [](const std::string directory, struct stat &st) {
+ if (stat(directory.c_str(), &st) == -1)
+ {
+ mkdir(directory.c_str(), 0777);
+ }
+ };
- if (fullPath[0] == '/' || fullPath[0] == '.')
- { // find the second '/'
- directoryPosition = fullPath.find("/", directoryPosition + 1);
- }
+ auto directoryPosition = fullPath.find("/");
- struct stat st = {0};
- if (directoryPosition == fullPath.npos) // no subdirectories
- {
- lf_Mkdir(fullPath.c_str(), st);
- return;
- }
+ if (fullPath[0] == '/' || fullPath[0] == '.')
+ { // find the second '/'
+ directoryPosition = fullPath.find("/", directoryPosition + 1);
+ }
- std::string directory(fullPath.substr(0, directoryPosition));
- lf_Mkdir(directory.c_str(), st);
+ struct stat st = {0};
+ if (directoryPosition == fullPath.npos) // no subdirectories
+ {
+ lf_Mkdir(fullPath.c_str(), st);
+ return;
+ }
- while (directoryPosition != fullPath.npos)
- {
- directoryPosition = fullPath.find("/", directoryPosition + 1);
- directory = fullPath.substr(0, directoryPosition);
+ std::string directory(fullPath.substr(0, directoryPosition));
lf_Mkdir(directory.c_str(), st);
- }
+
+ while (directoryPosition != fullPath.npos)
+ {
+ directoryPosition = fullPath.find("/", directoryPosition + 1);
+ directory = fullPath.substr(0, directoryPosition);
+ lf_Mkdir(directory.c_str(), st);
+ }
}
void SetTransformsHelper(const std::vector<std::string> &transformNames,
@@ -478,207 +483,209 @@ void SetTransformsHelper(const std::vector<std::string> &transformNames,
std::vector<short> &transformIndices,
std::vector<short> ¶meters)
{
- // function to get a parameter from "method:parameter"
- auto lf_GetParameter = [](const std::string transformName,
- std::string &transformMethod,
- const bool debugMode) -> short {
- short parameter = -1;
- auto colonPosition = transformName.find(":");
-
- if (colonPosition != transformName.npos)
- {
- if (debugMode == true)
- {
- if (colonPosition == transformName.size() - 1)
+ // function to get a parameter from "method:parameter"
+ auto lf_GetParameter = [](const std::string transformName,
+ std::string &transformMethod,
+ const bool debugMode) -> short {
+ short parameter = -1;
+ auto colonPosition = transformName.find(":");
+
+ if (colonPosition != transformName.npos)
{
- throw std::invalid_argument("ERROR: wrong format for transform " +
- transformName +
- ", in call to SetTransform\n");
+ if (debugMode == true)
+ {
+ if (colonPosition == transformName.size() - 1)
+ {
+ throw std::invalid_argument(
+ "ERROR: wrong format for transform " + transformName +
+ ", in call to SetTransform\n");
+ }
+ }
+
+ transformMethod = transformName.substr(0, colonPosition);
+ parameter = std::stoi(
+ transformName.substr(colonPosition + 1)); // need to test
}
- }
+ return parameter;
+ };
+
+ // Get transform index from transforms, if not found return -1
+ auto lf_GetTransformIndex =
+ [](const std::string transformMethod,
+ const std::vector<std::shared_ptr<Transform>> &transforms) -> short {
+ short transformIndex = -1;
+ for (unsigned int i = 0; i < transforms.size(); ++i)
+ {
+ if (transforms[i]->m_Method == transformMethod)
+ {
+ transformIndex = i;
+ break;
+ }
+ }
+ return transformIndex;
+ };
- transformMethod = transformName.substr(0, colonPosition);
- parameter =
- std::stoi(transformName.substr(colonPosition + 1)); // need to test
- }
- return parameter;
- };
-
- // Get transform index from transforms, if not found return -1
- auto lf_GetTransformIndex =
- [](const std::string transformMethod,
- const std::vector<std::shared_ptr<Transform>> &transforms) -> short {
- short transformIndex = -1;
- for (unsigned int i = 0; i < transforms.size(); ++i)
- {
- if (transforms[i]->m_Method == transformMethod)
- {
- transformIndex = i;
- break;
- }
- }
- return transformIndex;
- };
-
- // BODY of FUNCTION STARTS HERE
- for (const std::string transformName : transformNames)
- {
- std::string transformMethod(transformName);
- short parameter =
- lf_GetParameter(transformName, transformMethod,
- debugMode); // from transform = "method:parameter"
- short transformIndex = lf_GetTransformIndex(transformMethod, transforms);
-
- if (transformIndex == -1) // not found, then create a new transform
+ // BODY of FUNCTION STARTS HERE
+ for (const std::string transformName : transformNames)
{
- if (transformMethod == "bzip2")
- {
+ std::string transformMethod(transformName);
+ short parameter =
+ lf_GetParameter(transformName, transformMethod,
+ debugMode); // from transform = "method:parameter"
+ short transformIndex =
+ lf_GetTransformIndex(transformMethod, transforms);
+
+ if (transformIndex == -1) // not found, then create a new transform
+ {
+ if (transformMethod == "bzip2")
+ {
#ifdef HAVE_BZIP2
- transforms.push_back(std::make_shared<CBZIP2>());
+ transforms.push_back(std::make_shared<CBZIP2>());
#endif
- }
+ }
- transformIndex = static_cast<short>(transforms.size() - 1);
+ transformIndex = static_cast<short>(transforms.size() - 1);
+ }
+ transformIndices.push_back(transformIndex);
+ parameters.push_back(parameter);
}
- transformIndices.push_back(transformIndex);
- parameters.push_back(parameter);
- }
}
std::map<std::string, std::string>
BuildParametersMap(const std::vector<std::string> ¶meters,
const bool debugMode)
{
- auto lf_GetFieldValue = [](const std::string parameter, std::string &field,
- std::string &value, const bool debugMode) {
- auto equalPosition = parameter.find("=");
+ auto lf_GetFieldValue = [](const std::string parameter, std::string &field,
+ std::string &value, const bool debugMode) {
+ auto equalPosition = parameter.find("=");
- if (debugMode == true)
- {
- if (equalPosition == parameter.npos)
- {
- throw std::invalid_argument("ERROR: wrong format for parameter " +
- parameter +
- ", format must be field=value \n");
- }
-
- if (equalPosition == parameter.size() - 1)
- {
- throw std::invalid_argument("ERROR: empty value in parameter " +
- parameter +
- ", format must be field=value \n");
- }
- }
-
- field = parameter.substr(0, equalPosition);
- value = parameter.substr(equalPosition + 1); // need to test
- };
+ if (debugMode == true)
+ {
+ if (equalPosition == parameter.npos)
+ {
+ throw std::invalid_argument(
+ "ERROR: wrong format for parameter " + parameter +
+ ", format must be field=value \n");
+ }
+
+ if (equalPosition == parameter.size() - 1)
+ {
+ throw std::invalid_argument("ERROR: empty value in parameter " +
+ parameter +
+ ", format must be field=value \n");
+ }
+ }
- // BODY OF FUNCTION STARTS HERE
- std::map<std::string, std::string> parametersOutput;
+ field = parameter.substr(0, equalPosition);
+ value = parameter.substr(equalPosition + 1); // need to test
+ };
- for (const auto parameter : parameters)
- {
- std::string field, value;
- lf_GetFieldValue(parameter, field, value, debugMode);
+ // BODY OF FUNCTION STARTS HERE
+ std::map<std::string, std::string> parametersOutput;
- if (debugMode == true)
+ for (const auto parameter : parameters)
{
- if (parametersOutput.count(field) == 1)
- {
- throw std::invalid_argument("ERROR: parameter " + field +
- " already exists, must be unique\n");
- }
- }
+ std::string field, value;
+ lf_GetFieldValue(parameter, field, value, debugMode);
- parametersOutput[field] = value;
- }
+ if (debugMode == true)
+ {
+ if (parametersOutput.count(field) == 1)
+ {
+ throw std::invalid_argument(
+ "ERROR: parameter " + field +
+ " already exists, must be unique\n");
+ }
+ }
+
+ parametersOutput[field] = value;
+ }
- return parametersOutput;
+ return parametersOutput;
}
std::vector<int> CSVToVectorInt(const std::string csv)
{
- std::vector<int> numbers;
- if (csv.empty())
- {
- return numbers;
- }
-
- if (csv.find(",") == csv.npos) // check if no commas, one int
- {
- numbers.push_back(std::stoi(csv)); // might need to be checked
- }
- else
- {
- int count = std::count(csv.begin(), csv.end(), ',');
- numbers.reserve(count);
-
- std::istringstream csvSS(csv);
- std::string value;
- while (std::getline(csvSS, value, ',')) // need to test
+ std::vector<int> numbers;
+ if (csv.empty())
{
- numbers.push_back(std::stoi(csv));
+ return numbers;
}
- }
- return numbers;
+ if (csv.find(",") == csv.npos) // check if no commas, one int
+ {
+ numbers.push_back(std::stoi(csv)); // might need to be checked
+ }
+ else
+ {
+ int count = std::count(csv.begin(), csv.end(), ',');
+ numbers.reserve(count);
+
+ std::istringstream csvSS(csv);
+ std::string value;
+ while (std::getline(csvSS, value, ',')) // need to test
+ {
+ numbers.push_back(std::stoi(csv));
+ }
+ }
+
+ return numbers;
}
bool CheckBufferAllocation(const std::size_t newSize, const float growthFactor,
const std::size_t maxBufferSize,
std::vector<char> &buffer)
{
- // Check if data in buffer needs to be reallocated
- const std::size_t requiredDataSize =
- buffer.size() + newSize + 100; // adding some bytes for tolerance
- // might need to write payload in batches
- bool doTransportsFlush = (requiredDataSize > maxBufferSize) ? true : false;
-
- if (GrowBuffer(requiredDataSize, growthFactor, buffer) == -1)
- {
- doTransportsFlush = true;
- }
-
- return doTransportsFlush;
+ // Check if data in buffer needs to be reallocated
+ const std::size_t requiredDataSize =
+ buffer.size() + newSize + 100; // adding some bytes for tolerance
+ // might need to write payload in batches
+ bool doTransportsFlush = (requiredDataSize > maxBufferSize) ? true : false;
+
+ if (GrowBuffer(requiredDataSize, growthFactor, buffer) == -1)
+ {
+ doTransportsFlush = true;
+ }
+
+ return doTransportsFlush;
}
int GrowBuffer(const std::size_t incomingDataSize, const float growthFactor,
std::vector<char> &buffer)
{
- const std::size_t currentCapacity = buffer.capacity();
- const std::size_t availableSpace = currentCapacity - buffer.size();
- const double gf = static_cast<double>(growthFactor);
-
- if (incomingDataSize > availableSpace)
- {
- const std::size_t neededCapacity = incomingDataSize + buffer.size();
- const double numerator = std::log(static_cast<double>(neededCapacity) /
- static_cast<double>(currentCapacity));
- const double denominator = std::log(gf);
-
- double n = std::ceil(numerator / denominator);
- const std::size_t newSize =
- static_cast<std::size_t>(std::ceil(std::pow(gf, n) * currentCapacity));
-
- try
- {
- buffer.reserve(newSize);
- }
- catch (std::bad_alloc &e)
+ const std::size_t currentCapacity = buffer.capacity();
+ const std::size_t availableSpace = currentCapacity - buffer.size();
+ const double gf = static_cast<double>(growthFactor);
+
+ if (incomingDataSize > availableSpace)
{
- return -1;
- }
+ const std::size_t neededCapacity = incomingDataSize + buffer.size();
+ const double numerator = std::log(static_cast<double>(neededCapacity) /
+ static_cast<double>(currentCapacity));
+ const double denominator = std::log(gf);
+
+ double n = std::ceil(numerator / denominator);
+ const std::size_t newSize = static_cast<std::size_t>(
+ std::ceil(std::pow(gf, n) * currentCapacity));
- return 1;
- }
- return 0;
+ try
+ {
+ buffer.reserve(newSize);
+ }
+ catch (std::bad_alloc &e)
+ {
+ return -1;
+ }
+
+ return 1;
+ }
+ return 0;
}
bool IsLittleEndian() noexcept
{
- uint16_t hexa = 0x1234;
- return *reinterpret_cast<uint8_t *>(&hexa) != 0x12; // NOLINT
+ uint16_t hexa = 0x1234;
+ return *reinterpret_cast<uint8_t *>(&hexa) != 0x12; // NOLINT
}
} // namespace adios
diff --git a/source/mpidummy.cpp b/source/mpidummy.cpp
index f85e40a44a64c84718691452db59a420e1b8f369..c70ae74e0d74dd3a1215427e8d82e1ab36d55b5e 100644
--- a/source/mpidummy.cpp
+++ b/source/mpidummy.cpp
@@ -40,26 +40,26 @@ static char mpierrmsg[MPI_MAX_ERROR_STRING];
int MPI_Init(int * /*argc*/, char *** /*argv*/)
{
- mpierrmsg[0] = '\0';
- return MPI_SUCCESS;
+ mpierrmsg[0] = '\0';
+ return MPI_SUCCESS;
}
int MPI_Finalize()
{
- mpierrmsg[0] = '\0';
- return MPI_SUCCESS;
+ mpierrmsg[0] = '\0';
+ return MPI_SUCCESS;
}
int MPI_Initialized(int *flag)
{
- *flag = 1;
- return MPI_SUCCESS;
+ *flag = 1;
+ return MPI_SUCCESS;
}
int MPI_Comm_split(MPI_Comm /*comm*/, int /*color*/, int /*key*/,
MPI_Comm * /*comm_out*/)
{
- return MPI_SUCCESS;
+ return MPI_SUCCESS;
}
int MPI_Barrier(MPI_Comm /*comm*/) { return MPI_SUCCESS; }
@@ -67,31 +67,31 @@ int MPI_Barrier(MPI_Comm /*comm*/) { return MPI_SUCCESS; }
int MPI_Bcast(void * /*buffer*/, int /*count*/, MPI_Datatype /*datatype*/,
int /*root*/, MPI_Comm /*comm*/)
{
- return MPI_SUCCESS;
+ return MPI_SUCCESS;
}
int MPI_Comm_dup(MPI_Comm comm, MPI_Comm *newcomm)
{
- *newcomm = comm;
- return MPI_SUCCESS;
+ *newcomm = comm;
+ return MPI_SUCCESS;
}
int MPI_Comm_rank(MPI_Comm /*comm*/, int *rank)
{
- *rank = 0;
- return MPI_SUCCESS;
+ *rank = 0;
+ return MPI_SUCCESS;
}
int MPI_Comm_size(MPI_Comm /*comm*/, int *size)
{
- *size = 1;
- return MPI_SUCCESS;
+ *size = 1;
+ return MPI_SUCCESS;
}
int MPI_Comm_free(MPI_Comm *comm)
{
- *comm = 0;
- return MPI_SUCCESS;
+ *comm = 0;
+ return MPI_SUCCESS;
}
MPI_Comm MPI_Comm_f2c(MPI_Fint comm) { return comm; }
@@ -100,158 +100,158 @@ int MPI_Gather(const void *sendbuf, int sendcnt, MPI_Datatype sendtype,
void *recvbuf, int recvcnt, MPI_Datatype recvtype, int root,
MPI_Comm comm)
{
- int ier = MPI_SUCCESS;
- size_t n = 0, nsent = 0, nrecv = 0;
- if (!sendbuf || !recvbuf)
- {
- ier = MPI_ERR_BUFFER;
- }
- if (comm == MPI_COMM_NULL || root)
- {
- ier = MPI_ERR_COMM;
- }
-
- switch (sendtype)
- {
+ int ier = MPI_SUCCESS;
+ size_t n = 0, nsent = 0, nrecv = 0;
+ if (!sendbuf || !recvbuf)
+ {
+ ier = MPI_ERR_BUFFER;
+ }
+ if (comm == MPI_COMM_NULL || root)
+ {
+ ier = MPI_ERR_COMM;
+ }
+
+ switch (sendtype)
+ {
case MPI_INT:
- n = sizeof(int);
- break;
+ n = sizeof(int);
+ break;
default:
- return MPI_ERR_TYPE;
- }
- nsent = n * sendcnt;
+ return MPI_ERR_TYPE;
+ }
+ nsent = n * sendcnt;
- switch (recvtype)
- {
+ switch (recvtype)
+ {
case MPI_INT:
- nrecv = sizeof(int);
- break;
+ nrecv = sizeof(int);
+ break;
default:
- return MPI_ERR_TYPE;
- }
- nrecv = n * recvcnt;
-
- if (nrecv != nsent)
- {
- ier = MPI_ERR_COUNT;
- }
-
- if (ier == MPI_SUCCESS)
- {
- memcpy(recvbuf, sendbuf, nsent);
- }
- else
- {
- snprintf(mpierrmsg, ier, "could not gather data\n");
- }
-
- return ier;
+ return MPI_ERR_TYPE;
+ }
+ nrecv = n * recvcnt;
+
+ if (nrecv != nsent)
+ {
+ ier = MPI_ERR_COUNT;
+ }
+
+ if (ier == MPI_SUCCESS)
+ {
+ memcpy(recvbuf, sendbuf, nsent);
+ }
+ else
+ {
+ snprintf(mpierrmsg, ier, "could not gather data\n");
+ }
+
+ return ier;
}
int MPI_Gatherv(const void *sendbuf, int sendcnt, MPI_Datatype sendtype,
void *recvbuf, const int *recvcnts, const int *displs,
MPI_Datatype recvtype, int root, MPI_Comm comm)
{
- int ier = MPI_SUCCESS;
- if (!recvcnts || !displs)
- {
- ier = MPI_ERR_BUFFER;
- }
-
- if (ier == MPI_SUCCESS)
- {
- ier = MPI_Gather(sendbuf, sendcnt, sendtype, recvbuf, *recvcnts, recvtype,
- root, comm);
- }
-
- return ier;
+ int ier = MPI_SUCCESS;
+ if (!recvcnts || !displs)
+ {
+ ier = MPI_ERR_BUFFER;
+ }
+
+ if (ier == MPI_SUCCESS)
+ {
+ ier = MPI_Gather(sendbuf, sendcnt, sendtype, recvbuf, *recvcnts,
+ recvtype, root, comm);
+ }
+
+ return ier;
}
int MPI_Allgather(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
void *recvbuf, int recvcount, MPI_Datatype recvtype,
MPI_Comm comm)
{
- return MPI_Gather(sendbuf, sendcount, sendtype, recvbuf, recvcount, recvtype,
- 0, comm);
+ return MPI_Gather(sendbuf, sendcount, sendtype, recvbuf, recvcount,
+ recvtype, 0, comm);
}
int MPI_Scatter(const void *sendbuf, int sendcnt, MPI_Datatype sendtype,
void *recvbuf, int recvcnt, MPI_Datatype recvtype, int root,
MPI_Comm comm)
{
- int ier = MPI_SUCCESS;
- size_t n = 0, nsent = 0, nrecv = 0;
- if (!sendbuf || !recvbuf)
- {
- ier = MPI_ERR_BUFFER;
- }
-
- if (comm == MPI_COMM_NULL || root)
- {
- ier = MPI_ERR_COMM;
- }
-
- switch (sendtype)
- {
+ int ier = MPI_SUCCESS;
+ size_t n = 0, nsent = 0, nrecv = 0;
+ if (!sendbuf || !recvbuf)
+ {
+ ier = MPI_ERR_BUFFER;
+ }
+
+ if (comm == MPI_COMM_NULL || root)
+ {
+ ier = MPI_ERR_COMM;
+ }
+
+ switch (sendtype)
+ {
case MPI_INT:
- n = sizeof(int);
- break;
+ n = sizeof(int);
+ break;
default:
- return MPI_ERR_TYPE;
- }
- nsent = n * sendcnt;
+ return MPI_ERR_TYPE;
+ }
+ nsent = n * sendcnt;
- switch (recvtype)
- {
+ switch (recvtype)
+ {
case MPI_INT:
- nrecv = sizeof(int);
- break;
+ nrecv = sizeof(int);
+ break;
default:
- return MPI_ERR_TYPE;
- }
- nrecv = n * recvcnt;
-
- if (nrecv != nsent)
- {
- ier = MPI_ERR_COUNT;
- }
-
- if (ier == MPI_SUCCESS)
- {
- memcpy(recvbuf, sendbuf, nsent);
- }
- else
- {
- snprintf(mpierrmsg, ier, "could not scatter data\n");
- }
-
- return ier;
+ return MPI_ERR_TYPE;
+ }
+ nrecv = n * recvcnt;
+
+ if (nrecv != nsent)
+ {
+ ier = MPI_ERR_COUNT;
+ }
+
+ if (ier == MPI_SUCCESS)
+ {
+ memcpy(recvbuf, sendbuf, nsent);
+ }
+ else
+ {
+ snprintf(mpierrmsg, ier, "could not scatter data\n");
+ }
+
+ return ier;
}
int MPI_Scatterv(const void *sendbuf, const int *sendcnts, const int *displs,
MPI_Datatype sendtype, void *recvbuf, int recvcnt,
MPI_Datatype recvtype, int root, MPI_Comm comm)
{
- int ier = MPI_SUCCESS;
- if (!sendcnts || !displs)
- {
- ier = MPI_ERR_BUFFER;
- }
-
- if (ier == MPI_SUCCESS)
- {
- ier = MPI_Scatter(sendbuf, *sendcnts, sendtype, recvbuf, recvcnt, recvtype,
- root, comm);
- }
-
- return ier;
+ int ier = MPI_SUCCESS;
+ if (!sendcnts || !displs)
+ {
+ ier = MPI_ERR_BUFFER;
+ }
+
+ if (ier == MPI_SUCCESS)
+ {
+ ier = MPI_Scatter(sendbuf, *sendcnts, sendtype, recvbuf, recvcnt,
+ recvtype, root, comm);
+ }
+
+ return ier;
}
int MPI_Recv(void * /*recvbuffer*/, int /*count*/, MPI_Datatype /*type*/,
int /*source*/, int /*tag*/, MPI_Comm /*comm*/,
MPI_Status * /*status*/)
{
- return 0;
+ return 0;
}
int MPI_Irecv(void * /*recvbuffer*/, int /*count*/, MPI_Datatype /*type*/,
@@ -259,20 +259,20 @@ int MPI_Irecv(void * /*recvbuffer*/, int /*count*/, MPI_Datatype /*type*/,
MPI_Request * /*request*/)
{
- return 0;
+ return 0;
}
int MPI_Send(const void * /*sendbuffer*/, int /*count*/, MPI_Datatype /*type*/,
int /*destination*/, int /*tag*/, MPI_Comm /*comm*/)
{
- return 0;
+ return 0;
}
int MPI_Isend(const void * /*recvbuffer*/, int /*count*/, MPI_Datatype /*type*/,
int /*source*/, int /*tag*/, MPI_Comm /*comm*/,
MPI_Request * /*request*/)
{
- return 0;
+ return 0;
}
int MPI_Wait(MPI_Request * /*request*/, MPI_Status * /*status*/) { return 0; }
@@ -280,83 +280,85 @@ int MPI_Wait(MPI_Request * /*request*/, MPI_Status * /*status*/) { return 0; }
int MPI_File_open(MPI_Comm /*comm*/, const char *filename, int amode,
MPI_Info /*info*/, MPI_File *fh)
{
- *fh = open64(filename, amode);
- if (*fh == -1)
- {
- snprintf(mpierrmsg, MPI_MAX_ERROR_STRING, "File not found: %s", filename);
- return -1;
- }
- return MPI_SUCCESS;
+ *fh = open64(filename, amode);
+ if (*fh == -1)
+ {
+ snprintf(mpierrmsg, MPI_MAX_ERROR_STRING, "File not found: %s",
+ filename);
+ return -1;
+ }
+ return MPI_SUCCESS;
}
int MPI_File_close(MPI_File *fh) { return close(*fh); }
int MPI_File_get_size(MPI_File fh, MPI_Offset *size)
{
- uint64_t curpos = lseek64(fh, 0, SEEK_CUR); // get the current seek pos
- uint64_t endpos =
- lseek64(fh, 0, SEEK_END); // go to end, returned is the size in bytes
- lseek64(fh, curpos, SEEK_SET); // go back where we were
- *size = static_cast<MPI_Offset>(endpos);
- // printf("MPI_File_get_size: fh=%d, size=%lld\n", fh, *size);
- return MPI_SUCCESS;
+ uint64_t curpos = lseek64(fh, 0, SEEK_CUR); // get the current seek pos
+ uint64_t endpos =
+ lseek64(fh, 0, SEEK_END); // go to end, returned is the size in bytes
+ lseek64(fh, curpos, SEEK_SET); // go back where we were
+ *size = static_cast<MPI_Offset>(endpos);
+ // printf("MPI_File_get_size: fh=%d, size=%lld\n", fh, *size);
+ return MPI_SUCCESS;
}
int MPI_File_read(MPI_File fh, void *buf, int count, MPI_Datatype datatype,
MPI_Status *status)
{
- // FIXME: int count can read only 2GB (*datatype size) array at max
- uint64_t bytes_to_read = static_cast<uint64_t>(count) * datatype;
- uint64_t bytes_read;
- bytes_read = read(fh, buf, bytes_to_read);
- if (bytes_read != bytes_to_read)
- {
- snprintf(mpierrmsg, MPI_MAX_ERROR_STRING,
- "could not read %" PRId64 " bytes. read only: %" PRId64 "\n",
- bytes_to_read, bytes_read);
- return -2;
- }
- *status = bytes_read;
- // printf("MPI_File_read: fh=%d, count=%d, typesize=%d, bytes read=%lld\n",
- // fh, count, datatype, *status);
- return MPI_SUCCESS;
+ // FIXME: int count can read only 2GB (*datatype size) array at max
+ uint64_t bytes_to_read = static_cast<uint64_t>(count) * datatype;
+ uint64_t bytes_read;
+ bytes_read = read(fh, buf, bytes_to_read);
+ if (bytes_read != bytes_to_read)
+ {
+ snprintf(mpierrmsg, MPI_MAX_ERROR_STRING,
+ "could not read %" PRId64 " bytes. read only: %" PRId64 "\n",
+ bytes_to_read, bytes_read);
+ return -2;
+ }
+ *status = bytes_read;
+ // printf("MPI_File_read: fh=%d, count=%d, typesize=%d, bytes read=%lld\n",
+ // fh, count, datatype, *status);
+ return MPI_SUCCESS;
}
int MPI_File_seek(MPI_File fh, MPI_Offset offset, int whence)
{
- lseek64(fh, offset, whence);
- // printf("MPI_File_seek: fh=%d, offset=%lld, whence=%d\n", fh, off, whence);
- return MPI_SUCCESS;
+ lseek64(fh, offset, whence);
+ // printf("MPI_File_seek: fh=%d, offset=%lld, whence=%d\n", fh, off,
+ // whence);
+ return MPI_SUCCESS;
}
int MPI_Get_count(const MPI_Status *status, MPI_Datatype, int *count)
{
- *count = static_cast<int>(*status);
- return MPI_SUCCESS;
+ *count = static_cast<int>(*status);
+ return MPI_SUCCESS;
}
int MPI_Error_string(int /*errorcode*/, char *string, int *resultlen)
{
- // sprintf(string, "Dummy lib does not know error strings.
- // Code=%d\n",errorcode);
- strcpy(string, mpierrmsg);
- *resultlen = strlen(string);
- return MPI_SUCCESS;
+ // sprintf(string, "Dummy lib does not know error strings.
+ // Code=%d\n",errorcode);
+ strcpy(string, mpierrmsg);
+ *resultlen = strlen(string);
+ return MPI_SUCCESS;
}
double MPI_Wtime()
{
- // Implementation not tested
- timeval tv = {0, 0};
- gettimeofday(&tv, nullptr);
- return tv.tv_sec + tv.tv_usec * 1e-6;
+ // Implementation not tested
+ timeval tv = {0, 0};
+ gettimeofday(&tv, nullptr);
+ return tv.tv_sec + tv.tv_usec * 1e-6;
}
int MPI_Get_processor_name(char *name, int *resultlen)
{
- sprintf(name, "0");
- *resultlen = 1;
- return 0;
+ sprintf(name, "0");
+ *resultlen = 1;
+ return 0;
}
} // end namespace adios
diff --git a/source/transport/file/FStream.cpp b/source/transport/file/FStream.cpp
index 2a404ae6a96a10471e5ccd97acd547617a73fdb0..b516de8b067f6b6d373ba237965999e3c72b62d6 100644
--- a/source/transport/file/FStream.cpp
+++ b/source/transport/file/FStream.cpp
@@ -27,50 +27,51 @@ FStream::FStream(MPI_Comm mpiComm, bool debugMode)
void FStream::Open(const std::string name, const std::string accessMode)
{
- m_Name = name;
- m_AccessMode = accessMode;
+ m_Name = name;
+ m_AccessMode = accessMode;
- if (accessMode == "w" || accessMode == "write")
- {
- m_FStream.open(name, std::fstream::out);
- }
- else if (accessMode == "a" || accessMode == "append")
- {
- m_FStream.open(name, std::fstream::out | std::fstream::app);
- }
- else if (accessMode == "r" || accessMode == "read")
- {
- m_FStream.open(name, std::fstream::in);
- }
+ if (accessMode == "w" || accessMode == "write")
+ {
+ m_FStream.open(name, std::fstream::out);
+ }
+ else if (accessMode == "a" || accessMode == "append")
+ {
+ m_FStream.open(name, std::fstream::out | std::fstream::app);
+ }
+ else if (accessMode == "r" || accessMode == "read")
+ {
+ m_FStream.open(name, std::fstream::in);
+ }
- if (m_DebugMode == true)
- {
- if (!m_FStream)
+ if (m_DebugMode == true)
{
- throw std::ios_base::failure(
- "ERROR: couldn't open file " + name +
- ", in call to Open from FStream transport\n");
+ if (!m_FStream)
+ {
+ throw std::ios_base::failure(
+ "ERROR: couldn't open file " + name +
+ ", in call to Open from FStream transport\n");
+ }
}
- }
}
void FStream::SetBuffer(char *buffer, std::size_t size)
{
- m_FStream.rdbuf()->pubsetbuf(buffer, size);
+ m_FStream.rdbuf()->pubsetbuf(buffer, size);
}
void FStream::Write(const char *buffer, std::size_t size)
{
- m_FStream.write(buffer, size);
+ m_FStream.write(buffer, size);
- if (m_DebugMode == true)
- {
- if (!m_FStream)
+ if (m_DebugMode == true)
{
- throw std::ios_base::failure("ERROR: couldn't write to file " + m_Name +
- ", in call to FStream write\n");
+ if (!m_FStream)
+ {
+ throw std::ios_base::failure("ERROR: couldn't write to file " +
+ m_Name +
+ ", in call to FStream write\n");
+ }
}
- }
}
void FStream::Flush() { m_FStream.flush(); }
diff --git a/source/transport/file/FileDescriptor.cpp b/source/transport/file/FileDescriptor.cpp
index 0d6a87c96826042d79581ec356b9c96d796a85cf..e1c3df9ab69d0ecd027a9ea3af072674e084e5ec 100644
--- a/source/transport/file/FileDescriptor.cpp
+++ b/source/transport/file/FileDescriptor.cpp
@@ -31,128 +31,129 @@ FileDescriptor::FileDescriptor(MPI_Comm mpiComm, const bool debugMode)
FileDescriptor::~FileDescriptor()
{
- if (m_FileDescriptor != -1)
- {
- close(m_FileDescriptor);
- }
+ if (m_FileDescriptor != -1)
+ {
+ close(m_FileDescriptor);
+ }
}
void FileDescriptor::Open(const std::string name, const std::string accessMode)
{
- m_Name = name;
- m_AccessMode = accessMode;
+ m_Name = name;
+ m_AccessMode = accessMode;
- if (accessMode == "w" || accessMode == "write")
- {
- if (m_Profiler.m_IsActive == true)
+ if (accessMode == "w" || accessMode == "write")
{
- m_Profiler.m_Timers[0].SetInitialTime();
- }
+ if (m_Profiler.m_IsActive == true)
+ {
+ m_Profiler.m_Timers[0].SetInitialTime();
+ }
- m_FileDescriptor = open(m_Name.c_str(), O_WRONLY | O_CREAT, 0777);
+ m_FileDescriptor = open(m_Name.c_str(), O_WRONLY | O_CREAT, 0777);
- if (m_Profiler.m_IsActive == true)
- {
- m_Profiler.m_Timers[0].SetTime();
- }
- }
- else if (accessMode == "a" || accessMode == "append")
- {
- if (m_Profiler.m_IsActive == true)
- {
- m_Profiler.m_Timers[0].SetInitialTime();
+ if (m_Profiler.m_IsActive == true)
+ {
+ m_Profiler.m_Timers[0].SetTime();
+ }
}
-
- m_FileDescriptor =
- open(m_Name.c_str(), O_WRONLY | O_APPEND); // we need to change this
-
- if (m_Profiler.m_IsActive == true)
+ else if (accessMode == "a" || accessMode == "append")
{
- m_Profiler.m_Timers[0].SetTime();
+ if (m_Profiler.m_IsActive == true)
+ {
+ m_Profiler.m_Timers[0].SetInitialTime();
+ }
+
+ m_FileDescriptor = open(m_Name.c_str(),
+ O_WRONLY | O_APPEND); // we need to change this
+
+ if (m_Profiler.m_IsActive == true)
+ {
+ m_Profiler.m_Timers[0].SetTime();
+ }
}
- }
- else if (accessMode == "r" || accessMode == "read")
- {
- if (m_Profiler.m_IsActive == true)
+ else if (accessMode == "r" || accessMode == "read")
{
- m_Profiler.m_Timers[0].SetInitialTime();
- }
+ if (m_Profiler.m_IsActive == true)
+ {
+ m_Profiler.m_Timers[0].SetInitialTime();
+ }
- m_FileDescriptor = open(m_Name.c_str(), O_RDONLY);
+ m_FileDescriptor = open(m_Name.c_str(), O_RDONLY);
- if (m_Profiler.m_IsActive == true)
- {
- m_Profiler.m_Timers[0].SetTime();
+ if (m_Profiler.m_IsActive == true)
+ {
+ m_Profiler.m_Timers[0].SetTime();
+ }
}
- }
- if (m_DebugMode == true)
- {
- if (m_FileDescriptor == -1)
+ if (m_DebugMode == true)
{
- throw std::ios_base::failure("ERROR: couldn't open file " + m_Name +
- ", from call to Open in FD transport using "
- "POSIX open. Does file exists?\n");
+ if (m_FileDescriptor == -1)
+ {
+ throw std::ios_base::failure(
+ "ERROR: couldn't open file " + m_Name +
+ ", from call to Open in FD transport using "
+ "POSIX open. Does file exists?\n");
+ }
}
- }
}
void FileDescriptor::Write(const char *buffer, std::size_t size)
{
- if (m_Profiler.m_IsActive == true)
- {
- m_Profiler.m_Timers[1].SetInitialTime();
- }
-
- auto writtenSize = write(m_FileDescriptor, buffer, size);
+ if (m_Profiler.m_IsActive == true)
+ {
+ m_Profiler.m_Timers[1].SetInitialTime();
+ }
- if (m_Profiler.m_IsActive == true)
- {
- m_Profiler.m_Timers[1].SetTime();
- }
+ auto writtenSize = write(m_FileDescriptor, buffer, size);
- if (m_DebugMode == true)
- {
- if (writtenSize == -1)
+ if (m_Profiler.m_IsActive == true)
{
- throw std::ios_base::failure("ERROR: couldn't write to file " + m_Name +
- ", in call to POSIX write\n");
+ m_Profiler.m_Timers[1].SetTime();
}
- if (static_cast<std::size_t>(writtenSize) != size)
+ if (m_DebugMode == true)
{
- throw std::ios_base::failure(
- "ERROR: written size + " + std::to_string(writtenSize) +
- " is not equal to intended size " + std::to_string(size) +
- " in file " + m_Name + ", in call to POSIX write\n");
+ if (writtenSize == -1)
+ {
+ throw std::ios_base::failure("ERROR: couldn't write to file " +
+ m_Name + ", in call to POSIX write\n");
+ }
+
+ if (static_cast<std::size_t>(writtenSize) != size)
+ {
+ throw std::ios_base::failure(
+ "ERROR: written size + " + std::to_string(writtenSize) +
+ " is not equal to intended size " + std::to_string(size) +
+ " in file " + m_Name + ", in call to POSIX write\n");
+ }
}
- }
}
void FileDescriptor::Close()
{
- if (m_Profiler.m_IsActive == true)
- {
- m_Profiler.m_Timers[2].SetInitialTime();
- }
+ if (m_Profiler.m_IsActive == true)
+ {
+ m_Profiler.m_Timers[2].SetInitialTime();
+ }
- int status = close(m_FileDescriptor);
+ int status = close(m_FileDescriptor);
- if (m_Profiler.m_IsActive == true)
- {
- m_Profiler.m_Timers[2].SetTime();
- }
+ if (m_Profiler.m_IsActive == true)
+ {
+ m_Profiler.m_Timers[2].SetTime();
+ }
- if (m_DebugMode == true)
- {
- if (status == -1)
+ if (m_DebugMode == true)
{
- throw std::ios_base::failure("ERROR: couldn't close file " + m_Name +
- ", in call to POSIX write\n");
+ if (status == -1)
+ {
+ throw std::ios_base::failure("ERROR: couldn't close file " +
+ m_Name + ", in call to POSIX write\n");
+ }
}
- }
- m_IsOpen = false;
+ m_IsOpen = false;
}
} // end namespace transport
diff --git a/source/transport/file/FilePointer.cpp b/source/transport/file/FilePointer.cpp
index 1ba57204e6a6827c7454c688b37b8e2f1d62e2c9..4cbe9a8918f4c8a2fcae03543460292e2a22648b 100644
--- a/source/transport/file/FilePointer.cpp
+++ b/source/transport/file/FilePointer.cpp
@@ -26,76 +26,78 @@ FilePointer::FilePointer(MPI_Comm mpiComm, const bool debugMode)
FilePointer::~FilePointer()
{
- if (m_File != nullptr)
- {
- fclose(m_File);
- }
+ if (m_File != nullptr)
+ {
+ fclose(m_File);
+ }
}
void FilePointer::Open(const std::string name, const std::string accessMode)
{
- m_Name = name;
- m_AccessMode = accessMode;
-
- if (accessMode == "w" || accessMode == "write")
- {
- m_File = fopen(name.c_str(), "w");
- }
- else if (accessMode == "a" || accessMode == "append")
- {
- m_File = fopen(name.c_str(), "a");
- }
- else if (accessMode == "r" || accessMode == "read")
- {
- m_File = fopen(name.c_str(), "r");
- }
-
- if (m_DebugMode == true)
- {
- if (m_File == nullptr)
+ m_Name = name;
+ m_AccessMode = accessMode;
+
+ if (accessMode == "w" || accessMode == "write")
+ {
+ m_File = fopen(name.c_str(), "w");
+ }
+ else if (accessMode == "a" || accessMode == "append")
{
- throw std::ios_base::failure("ERROR: couldn't open file " + name +
- ", "
- "in call to Open from File* transport\n");
+ m_File = fopen(name.c_str(), "a");
+ }
+ else if (accessMode == "r" || accessMode == "read")
+ {
+ m_File = fopen(name.c_str(), "r");
+ }
+
+ if (m_DebugMode == true)
+ {
+ if (m_File == nullptr)
+ {
+ throw std::ios_base::failure(
+ "ERROR: couldn't open file " + name +
+ ", "
+ "in call to Open from File* transport\n");
+ }
}
- }
}
void FilePointer::SetBuffer(char *buffer, std::size_t size)
{
- int status = setvbuf(m_File, buffer, _IOFBF, size);
+ int status = setvbuf(m_File, buffer, _IOFBF, size);
- if (m_DebugMode == true)
- {
- if (status == 1)
+ if (m_DebugMode == true)
{
- throw std::ios_base::failure("ERROR: could not set buffer in rank " +
- std::to_string(m_RankMPI) + "\n");
+ if (status == 1)
+ {
+ throw std::ios_base::failure(
+ "ERROR: could not set buffer in rank " +
+ std::to_string(m_RankMPI) + "\n");
+ }
}
- }
}
void FilePointer::Write(const char *buffer, std::size_t size)
{
- fwrite(buffer, sizeof(char), size, m_File);
+ fwrite(buffer, sizeof(char), size, m_File);
- if (m_DebugMode == true)
- {
- if (ferror(m_File))
+ if (m_DebugMode == true)
{
- throw std::ios_base::failure("ERROR: couldn't write to file " + m_Name +
- ", in call to File* write\n");
+ if (ferror(m_File))
+ {
+ throw std::ios_base::failure("ERROR: couldn't write to file " +
+ m_Name + ", in call to File* write\n");
+ }
}
- }
}
void FilePointer::Flush() { fflush(m_File); }
void FilePointer::Close()
{
- fclose(m_File);
+ fclose(m_File);
- m_IsOpen = false;
+ m_IsOpen = false;
}
} // end namespace transport
diff --git a/source/transport/wan/MdtmMan.cpp b/source/transport/wan/MdtmMan.cpp
index 55324e0c2f23d9f2ba33f5b1a43584becda3bac8..cdece2ecbfa5270b2e36eedb07af430319056cb1 100644
--- a/source/transport/wan/MdtmMan.cpp
+++ b/source/transport/wan/MdtmMan.cpp
@@ -49,7 +49,7 @@ int MdtmMan::Put(const void *data, const std::string doid,
const int priority)
{
- return 0;
+ return 0;
}
int MdtmMan::Get(void *data, const std::string doid, const std::string variable,
@@ -61,7 +61,7 @@ int MdtmMan::Get(void *data, const std::string doid, const std::string variable,
const int priority)
{
- return 0;
+ return 0;
}
int MdtmMan::Get(void *data, const std::string doid, const std::string variable,
@@ -69,7 +69,7 @@ int MdtmMan::Get(void *data, const std::string doid, const std::string variable,
const std::uint64_t timestep)
{
- return 0;
+ return 0;
}
void MdtmMan::OnReceive(nlohmann::json &jData) {}