diff --git a/doc/API_design/API_example_use.cpp b/doc/API_design/API_example_use.cpp
index cdac31541c54370a9a9982b41224cf53b1049dd8..a35146935cf564dea610accee6ad67efdfbe6ce6 100644
--- a/doc/API_design/API_example_use.cpp
+++ b/doc/API_design/API_example_use.cpp
@@ -6,8 +6,8 @@
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)
@@ -73,9 +73,9 @@ int main(int argc, char *argv[])
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
+ "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
@@ -215,8 +215,9 @@ int main(int argc, char *argv[])
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
+ struct adios::Statistics stats =
+ reader.InquiryVariableStat(reader, var2D, perstepstat,
+ perblockstat); // get min/max statistics
// this is adios1 ADIOS_VARSTAT
while (true)
@@ -242,9 +243,9 @@ int main(int argc, char *argv[])
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
+ reader->Advance(adios::NEXT_AVAILABLE); // default
+ reader->Advance(adios::LATEST_AVAILABLE); // interested only in the
+ // latest data
}
// Close file/stream
reader->Close();
diff --git a/examples/groupless/basic/reader.cpp b/examples/groupless/basic/reader.cpp
index 8ffdbf3e309ca7e7d8f0aa8bd4fa99a2bca70712..1e91476b27d48444819de5f303b1f1dcdf82f576 100644
--- a/examples/groupless/basic/reader.cpp
+++ b/examples/groupless/basic/reader.cpp
@@ -89,9 +89,9 @@ int main(int argc, char *argv[])
// selection => read whole array
std::vector<int> partsV;
- bpReader->Read<int>(
- "Nparts",
- partsV); // read with string name, no selection => read whole array
+ bpReader->Read<int>("Nparts",
+ partsV); // read with string name, no selection =>
+ // read whole array
(Nwriters == partsV.size())
/* Nice */
@@ -100,8 +100,8 @@ int main(int argc, char *argv[])
varNice = bpReader.InquiryVariable("Nice");
if (varNice == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to find variable 'myDoubles' in input file\n");
+ 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 =
diff --git a/examples/groupless/basic/writer.cpp b/examples/groupless/basic/writer.cpp
index e5e2d620cde5ff20add6f42f2b9df2c70cade226..cbd556ccc1cabf313b470b22fd84da2ca8ca9409 100644
--- a/examples/groupless/basic/writer.cpp
+++ b/examples/groupless/basic/writer.cpp
@@ -54,9 +54,11 @@ int main(int argc, char *argv[])
"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<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>(
@@ -74,8 +76,9 @@ int main(int argc, char *argv[])
// 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
+ "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
diff --git a/examples/groupless/compound/reader.cpp b/examples/groupless/compound/reader.cpp
index 31cb19c29ac8d380f06fd350c01f67e327d84802..58a0e1fd69bb18293f1445ab082d2631683132b1 100644
--- a/examples/groupless/compound/reader.cpp
+++ b/examples/groupless/compound/reader.cpp
@@ -96,9 +96,9 @@ int main(int argc, char *argv[])
// selection => read whole array
std::vector<int> partsV;
- bpReader->Read<int>(
- "Nparts",
- partsV); // read with string name, no selection => read whole array
+ bpReader->Read<int>("Nparts",
+ partsV); // read with string name, no selection =>
+ // read whole array
(Nwriters == partsV.size())
/* Nice */
@@ -123,8 +123,8 @@ int main(int argc, char *argv[])
bpReader.InquiryVariable("Nice", mtype);
if (varNice == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to find variable 'myDoubles' in input file\n");
+ 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 =
diff --git a/examples/groupless/compound/writer.cpp b/examples/groupless/compound/writer.cpp
index ae128de75cb2fcd2cca690560c36d982972973cb..f8c105e2f0508cccdf3d5322342afe0dc50c4286 100644
--- a/examples/groupless/compound/writer.cpp
+++ b/examples/groupless/compound/writer.cpp
@@ -64,9 +64,11 @@ int main(int argc, char *argv[])
"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<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 */
@@ -85,8 +87,9 @@ int main(int argc, char *argv[])
// 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
+ "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
diff --git a/examples/groupless/multistep/reader_allsteps.cpp b/examples/groupless/multistep/reader_allsteps.cpp
index 94e1d7cc970e19a98c87e4c4cd7b095c00c352a3..1b28a82c72d71e1438c077f6b00ae88aa837a1f6 100644
--- a/examples/groupless/multistep/reader_allsteps.cpp
+++ b/examples/groupless/multistep/reader_allsteps.cpp
@@ -118,8 +118,8 @@ int main(int argc, char *argv[])
bpReader.InquiryVariable("Nice");
if (varNice == nullptr)
- throw std::ios_base::failure(
- "ERROR: failed to find variable 'myDoubles' in input file\n");
+ 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 =
diff --git a/examples/groupless/multistep/reader_stepping.cpp b/examples/groupless/multistep/reader_stepping.cpp
index 36f4f7b6bb395a4f3486e677ea301d5f29665993..5328408da4249e62be66d2157a3cdb43a57ae703 100644
--- a/examples/groupless/multistep/reader_stepping.cpp
+++ b/examples/groupless/multistep/reader_stepping.cpp
@@ -85,8 +85,8 @@ int main(int argc, char *argv[])
// ? 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?
+ 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)
@@ -114,14 +114,14 @@ int main(int argc, char *argv[])
adios::VARYING_DIMENSION)
{
throw std::ios_base::failure(
- "Unexpected condition: Ragged array's fast dimension "
+ "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
+ if (rank < varRagged->nblocks[0]) // same as rank < Nwriters in
+ // this example
{
// get per-writer size information
varRagged->InquiryBlocks();
@@ -148,7 +148,8 @@ int main(int argc, char *argv[])
1); // contains the largest
std::vector<int> raggedDims =
varRagged->GetVaryingGlobalDimensions(
- 1); // contains all individual sizes in that dimension
+ 1); // contains all individual sizes in that
+ // dimension
// promise to not read more from this step
bpReader->Release();
diff --git a/examples/groupless/multistep/writer_multistep.cpp b/examples/groupless/multistep/writer_multistep.cpp
index 00b4da5da2142803b0eb0cd9f762f294e536074f..696d4bdb636ed422d4872ae043505551a84e05a9 100644
--- a/examples/groupless/multistep/writer_multistep.cpp
+++ b/examples/groupless/multistep/writer_multistep.cpp
@@ -51,9 +51,11 @@ int main(int argc, char *argv[])
"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<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>(
@@ -71,8 +73,9 @@ int main(int argc, char *argv[])
// 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
+ "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
diff --git a/examples/heatTransfer/IO_adios2.cpp b/examples/heatTransfer/IO_adios2.cpp
index 846dc912390a5da78f753a9ebca74e18bf7f76ed..ac0567820549d3300ca410c9686fe8552fb9578f 100644
--- a/examples/heatTransfer/IO_adios2.cpp
+++ b/examples/heatTransfer/IO_adios2.cpp
@@ -71,17 +71,13 @@ IO::~IO()
delete ad;
}
-#if 1
-
-void IO::write(int step, const HeatTransfer &ht, const Settings &s,
- MPI_Comm comm)
+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();
}
-#else
-
void IO::write(int step, const HeatTransfer &ht, const Settings &s,
MPI_Comm comm)
{
@@ -116,5 +112,3 @@ void IO::write(int step, const HeatTransfer &ht, const Settings &s,
bpWriter->Write<double>(*varT, ht.data());
bpWriter->Advance();
}
-
-#endif // 1
diff --git a/include/ADIOS.h b/include/ADIOS.h
index 5086153a2b98aab533e0d8515afcb42d5779cc88..be624488c96a3fb1c8baf00abf41dcbd2d0eecef 100644
--- a/include/ADIOS.h
+++ b/include/ADIOS.h
@@ -307,8 +307,9 @@ protected: // no const to allow default empty and copy constructors
// 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
+ 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>>
@@ -324,7 +325,7 @@ protected: // no const to allow default empty and copy constructors
*/
std::map<std::string, Method> m_Methods;
std::set<std::string> m_EngineNames; ///< set used to check Engine name
- ///uniqueness in debug mode
+ /// uniqueness in debug mode
/**
* @brief Checks for group existence in m_Groups, if failed throws
@@ -362,10 +363,10 @@ protected: // no const to allow default empty and copy constructors
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");
+ CheckVariableName(itVariable, name,
+ "in call to GetVariable<" + GetType<T>() +
+ ">, or call to GetVariableCompound if <T> = "
+ "<compound>\n");
return itVariable->second.second;
}
};
diff --git a/include/capsule/shmem/ShmSystemV.h b/include/capsule/shmem/ShmSystemV.h
index 3122ae783559c5ec23063463342b1d3e60fbef78..2e3a14c5b804736b5c2f8d4d5890bc49efde2eba 100644
--- a/include/capsule/shmem/ShmSystemV.h
+++ b/include/capsule/shmem/ShmSystemV.h
@@ -39,7 +39,7 @@ public:
private:
char *m_Data = nullptr; ///< reference to a shared memory data buffer
- ///created with shmget
+ /// 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
diff --git a/include/core/Method.h b/include/core/Method.h
index 58a67348b1e51b73869be3dd4a5239545d486f9d..0576703b6999fed3eea947642f614297c9d8771c 100644
--- a/include/core/Method.h
+++ b/include/core/Method.h
@@ -51,7 +51,7 @@ public:
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
+ /// their
/// own parameters
/**
diff --git a/include/core/Support.h b/include/core/Support.h
index 321f96641e3a3da6c1de5b57d664339898e49f5d..a36476660fb7bf34603aab6d907957ebdf606e32 100644
--- a/include/core/Support.h
+++ b/include/core/Support.h
@@ -23,9 +23,10 @@ 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::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
@@ -35,7 +36,8 @@ struct Support
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.
+ DatatypesAliases; ///< all supported int aliases, key: C++ type
+ ///(e.g.
/// int), value: aliases to type in key (e.g. int,
/// integer)
diff --git a/include/core/Variable.h b/include/core/Variable.h
index 212dc0da48436fa9e53451d28465634e86cad48f..93acbfc9fe94a05bef0ecc607efad4272fc50f58 100644
--- a/include/core/Variable.h
+++ b/include/core/Variable.h
@@ -29,7 +29,7 @@ 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
+ /// transformation is applied
};
/**
diff --git a/include/engine/adios1/ADIOS1Writer.h b/include/engine/adios1/ADIOS1Writer.h
index 04d70cf5806b4150b03b3e7217076987cca3e5a5..8f41ed432d566e370110775b13e90c051f51a531 100644
--- a/include/engine/adios1/ADIOS1Writer.h
+++ b/include/engine/adios1/ADIOS1Writer.h
@@ -110,9 +110,9 @@ private:
/// 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
+ 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();
diff --git a/include/format/BP1.h b/include/format/BP1.h
index 78f67cc056fe7633028ea46e11f9af1487314426..518325ecdbabfa44403bb3306853a101fccdaa82 100644
--- a/include/format/BP1.h
+++ b/include/format/BP1.h
@@ -36,8 +36,8 @@ 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)
+ 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}
@@ -59,8 +59,10 @@ struct BP1MetadataSet
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> VarsIndices; ///< key: variable
+ /// name, value: bp
+ /// metadata variable
+ /// index
std::unordered_map<std::string, BP1Index> AttributesIndices; ///< key:
/// attribute
/// name, value:
diff --git a/include/format/BP1Writer.h b/include/format/BP1Writer.h
index 3deb008cefe81facf48e7f4925a55eb68727567b..765961978bcb4c5a15040981e342b87ac865e996 100644
--- a/include/format/BP1Writer.h
+++ b/include/format/BP1Writer.h
@@ -34,12 +34,12 @@ 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.
+ 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.
+ /// redefined in Engine method.
const std::uint8_t m_Version = 3; ///< BP format version
/**
@@ -306,7 +306,8 @@ private:
noexcept
{
const std::size_t characteristicsCountPosition =
- buffer.size(); // very important to track as writer is going back to
+ 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)
@@ -355,8 +356,8 @@ private:
&characteristicsCounter); // count (1)
const std::uint32_t characteristicsLength =
buffer.size() - characteristicsCountPosition - 4 -
- 1; // remove its own length (4 bytes) + characteristic counter ( 1
- // byte
+ 1; // remove its own length (4 bytes) + characteristic counter (
+ // 1 byte
// )
CopyToBuffer(buffer, characteristicsCountPosition + 1,
&characteristicsLength); // length
diff --git a/source/core/Method.cpp b/source/core/Method.cpp
index 1bcd3893358e321ba4706372ea23697642185387..02d1750344feb7fa6b2a5154394a7cb08cb396fd 100644
--- a/source/core/Method.cpp
+++ b/source/core/Method.cpp
@@ -62,9 +62,9 @@ void Method::AddTransportParameters(const std::string type,
{
if (mapParameters.count("transport") == 1)
{
- std::invalid_argument(
- "ERROR: transport can't be redefined with \"transport=type\", "
- "type must be the first argument\n");
+ std::invalid_argument("ERROR: transport can't be redefined with "
+ "\"transport=type\", "
+ "type must be the first argument\n");
}
}
diff --git a/source/engine/adios1/ADIOS1Reader.cpp b/source/engine/adios1/ADIOS1Reader.cpp
index 6f8fd564a959a147fe436a0f888651fe0ba8bac8..817b1467cd20482bfc81aca0862f3b71c4600140 100644
--- a/source/engine/adios1/ADIOS1Reader.cpp
+++ b/source/engine/adios1/ADIOS1Reader.cpp
@@ -27,6 +27,7 @@ ADIOS1Reader::ADIOS1Reader(ADIOS &adios, const std::string name,
{
Init();
adios_read_init_method(read_method, m_MPIComm, "");
+
}
ADIOS1Reader::~ADIOS1Reader() { adios_read_finalize_method(read_method); }
@@ -173,4 +174,5 @@ void ADIOS1Reader::Init()
}
}
+
} // end namespace
diff --git a/source/transport/file/FileDescriptor.cpp b/source/transport/file/FileDescriptor.cpp
index b95896c93725ee4ca845bb5c6331a5fbfc5f257b..e1c3df9ab69d0ecd027a9ea3af072674e084e5ec 100644
--- a/source/transport/file/FileDescriptor.cpp
+++ b/source/transport/file/FileDescriptor.cpp
@@ -63,8 +63,8 @@ void FileDescriptor::Open(const std::string name, const std::string accessMode)
m_Profiler.m_Timers[0].SetInitialTime();
}
- m_FileDescriptor =
- open(m_Name.c_str(), O_WRONLY | O_APPEND); // we need to change this
+ m_FileDescriptor = open(m_Name.c_str(),
+ O_WRONLY | O_APPEND); // we need to change this
if (m_Profiler.m_IsActive == true)
{