diff --git a/CMakeLists.txt b/CMakeLists.txt
index 874ef37fbc5ff05792703b722f2e87bd76922c3a..bbf244496dd5c2b5cba43cd19fc2f001e3e9872f 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -38,6 +38,11 @@ endif()
# Top level options
#------------------------------------------------------------------------------#
+# Default to a debug build if not specified
+if(NOT CMAKE_BUILD_TYPE)
+ set(CMAKE_BUILD_TYPE "Debug" CACHE STRING "Choose the type of build." FORCE)
+endif()
+
# Force C++11
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED True)
@@ -61,6 +66,10 @@ if(ADIOS_ENABLE_PIC)
endif()
option(ADIOS_USE_MPI "Enable the MPI version of ADIOS" ON)
+if(ADIOS_USE_MPI)
+ # Workaround for OpenMPI forcing th elink of C++ bindings
+ add_definitions(-DOMPI_SKIP_MPICXX)
+endif()
option(ADIOS_USE_BZip2 "Enable support for BZip2 transforms" ON)
option(ADIOS_USE_ADIOS1 "Enable support for the ADIOS 1 engine" OFF)
option(ADIOS_USE_DataMan "Enable support for the DataMan engine" OFF)
@@ -68,8 +77,9 @@ option(ADIOS_USE_DataMan "Enable support for the DataMan engine" OFF)
#------------------------------------------------------------------------------#
# Third party libraries
#------------------------------------------------------------------------------#
-option(ADIOS_BUILD_TESTING "Build ADIOS tests" OFF)
-set(BUILD_TESTING ${ADIOS_BUILD_TESTING} CACHE INTERNAL "")
+option(ADIOS_BUILD_TESTING "Build ADIOS tests" ON)
+set(BUILD_TESTING ${ADIOS_BUILD_TESTING})
+mark_as_advanced(BUILD_TESTING)
include(CTest)
add_subdirectory(thirdparty)
@@ -113,10 +123,11 @@ message("")
message(" Installation prefix: ${CMAKE_INSTALL_PREFIX}")
message(" Features:")
if(BUILD_SHARED_LIBS)
- message(" Type: shared")
+ message(" Library Type: shared")
else()
- message(" Type: static")
+ message(" Library Type: static")
endif()
+message(" Build Type: ${CMAKE_BUILD_TYPE}")
message(" Testing: ${BUILD_TESTING}")
message(" MPI: ${ADIOS_USE_MPI}")
message(" BZip2: ${ADIOS_USE_BZip2}")
diff --git a/examples/heatTransfer/IO_adios2.cpp b/examples/heatTransfer/IO_adios2.cpp
index 49e9c58602b8dd5bcf05d4c2502746af42b14e54..5cfb9ae8807c611cc8c81836b012cddef763acd2 100644
--- a/examples/heatTransfer/IO_adios2.cpp
+++ b/examples/heatTransfer/IO_adios2.cpp
@@ -28,7 +28,7 @@ IO::IO(const Settings &s, MPI_Comm comm)
// 1. Get method def from config file or define new one
adios::Method &bpWriterSettings = ad->DeclareMethod("output");
- if (!bpWriterSettings.isUserDefined())
+ if (!bpWriterSettings.IsUserDefined())
{
// if not defined by user, we can change the default settings
bpWriterSettings.SetEngine("BP"); // BP is the default engine
@@ -37,8 +37,8 @@ IO::IO(const Settings &s, MPI_Comm comm)
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(
+ "have_metadata_file=yes"); // Passing parameters to the engine
bpWriterSettings.SetParameters(
"Aggregation",
std::to_string((s.nproc + 1) / 2)); // number of aggregators
@@ -56,8 +56,7 @@ IO::IO(const Settings &s, MPI_Comm comm)
// 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);
if (bpWriter == nullptr)
throw std::ios_base::failure("ERROR: failed to open ADIOS bpWriter\n");
diff --git a/examples/hello/bpWriter/CMakeLists.txt b/examples/hello/bpWriter/CMakeLists.txt
index 3518b42787191b823fce4f840f9275693867b8f3..67e193342b05fe0c7d99881038a69e5233706fda 100644
--- a/examples/hello/bpWriter/CMakeLists.txt
+++ b/examples/hello/bpWriter/CMakeLists.txt
@@ -8,7 +8,16 @@ if(ADIOS_USE_MPI)
add_executable(hello_bpWriter helloBPWriter.cpp)
target_include_directories(hello_bpWriter PRIVATE ${MPI_C_INCLUDE_PATH})
target_link_libraries(hello_bpWriter adios2 ${MPI_C_LIBRARIES})
+
+ if(ADIOS_BUILD_TESTING)
+ add_test( NAME Example::hello::bpWriter COMMAND hello_bpWriter)
+ endif()
+else()
+ add_executable(hello_bpWriter_nompi helloBPWriter_nompi.cpp)
+ target_link_libraries(hello_bpWriter_nompi adios2)
+
+ if(ADIOS_BUILD_TESTING)
+ add_test( NAME Example::hello::bpWriter_nompi COMMAND hello_bpWriter_nompi)
+ endif()
endif()
-add_executable(hello_bpWriter_nompi helloBPWriter_nompi.cpp)
-target_link_libraries(hello_bpWriter_nompi adios2)
diff --git a/examples/hello/bpWriter/helloBPWriter.cpp b/examples/hello/bpWriter/helloBPWriter.cpp
index 1be2cececb66a16a6c09d2b5b050bc019f53fe05..7281aca901c1522f18b1aa074ea98e50cd006e53 100644
--- a/examples/hello/bpWriter/helloBPWriter.cpp
+++ b/examples/hello/bpWriter/helloBPWriter.cpp
@@ -11,9 +11,7 @@
#include <iostream>
#include <vector>
-#define OMPI_SKIP_MPICXX 1 // workaround for OpenMPI forcing C++ bindings
#include <mpi.h>
-#undef OMPI_SKIP_MPICXX
#include "ADIOS_CPP.h"
@@ -68,8 +66,7 @@ int main(int argc, char *argv[])
// 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);
+ auto bpWriter = adios.Open("myDoubles.bp", "w", bpWriterSettings);
if (bpWriter == nullptr)
throw std::ios_base::failure("ERROR: couldn't create bpWriter at Open\n");
diff --git a/examples/hello/bpWriter/helloBPWriter_nompi.cpp b/examples/hello/bpWriter/helloBPWriter_nompi.cpp
index edb09e086fd8a8d9b20c8b3a04ea51070e5135d8..6c62e53b0aed54f866a7a5040cc2abe131d20765 100644
--- a/examples/hello/bpWriter/helloBPWriter_nompi.cpp
+++ b/examples/hello/bpWriter/helloBPWriter_nompi.cpp
@@ -8,12 +8,14 @@
* Author: wfg
*/
+#include <ios>
#include <iostream>
+#include <stdexcept>
#include <vector>
#include "ADIOS_CPP.h"
-int main(int argc, char *argv[])
+int main(int /*argc*/, char ** /*argv*/)
{
const bool adiosDebug = true;
adios::ADIOS adios(adios::Verbose::WARN, adiosDebug);
@@ -25,7 +27,6 @@ int main(int argc, char *argv[])
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};
try
@@ -51,11 +52,12 @@ int main(int argc, char *argv[])
// 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);
+ auto bpFileWriter = adios.Open("myDoubles_nompi.bp", "w", bpWriterSettings);
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>
diff --git a/examples/hello/datamanReader/CMakeLists.txt b/examples/hello/datamanReader/CMakeLists.txt
index f32a2283869203b1157cdb67dc540fe19b7ef90d..3aa3e264ad829cf697e9cd91a6336d6fcf8b668d 100644
--- a/examples/hello/datamanReader/CMakeLists.txt
+++ b/examples/hello/datamanReader/CMakeLists.txt
@@ -3,8 +3,26 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
-add_executable(hello_datamanReader helloDataManReader.cpp)
-target_link_libraries(hello_datamanReader adios2)
+if(ADIOS_USE_MPI)
+ find_package(MPI COMPONENTS C REQUIRED)
-add_executable(hello_datamanReader_nompi helloDataManReader_nompi.cpp)
-target_link_libraries(hello_datamanReader_nompi adios2)
+ add_executable(hello_datamanReader helloDataManReader.cpp)
+ target_link_libraries(hello_datamanReader adios2)
+ target_include_directories(hello_datamanReader PRIVATE ${MPI_C_INCLUDE_PATH})
+ target_link_libraries(hello_datamanReader adios2 ${MPI_C_LIBRARIES})
+
+ if(ADIOS_BUILD_TESTING)
+ add_test(NAME Example::hello::datamanReader COMMAND hello_datamanReader)
+ endif()
+else()
+ add_executable(hello_datamanReader_nompi helloDataManReader_nompi.cpp)
+ target_link_libraries(hello_datamanReader_nompi adios2)
+
+ if(ADIOS_BUILD_TESTING)
+ add_test(
+ NAME Example::hello::datamanReader_nompi
+ COMMAND hello_datamanReader_nompi
+ )
+ endif()
+endif()
+
diff --git a/examples/hello/datamanWriter/CMakeLists.txt b/examples/hello/datamanWriter/CMakeLists.txt
index dee5f38e1823c4a55f22d53954d09c440e1c6ff4..7defd6c40b3bd2eba1802a4e6e99dd41f5de1697 100644
--- a/examples/hello/datamanWriter/CMakeLists.txt
+++ b/examples/hello/datamanWriter/CMakeLists.txt
@@ -3,8 +3,26 @@
# accompanying file Copyright.txt for details.
#------------------------------------------------------------------------------#
-add_executable(hello_datamanWriter helloDataManWriter.cpp)
-target_link_libraries(hello_datamanWriter adios2)
+if(ADIOS_USE_MPI)
+ find_package(MPI COMPONENTS C REQUIRED)
+
+ add_executable(hello_datamanWriter helloDataManWriter.cpp)
+ target_link_libraries(hello_datamanWriter adios2)
+ target_include_directories(hello_datamanWriter PRIVATE ${MPI_C_INCLUDE_PATH})
+ target_link_libraries(hello_datamanWriter adios2 ${MPI_C_LIBRARIES})
+
+ if(ADIOS_BUILD_TESTING)
+ add_test(NAME Example::hello::datamanWriter COMMAND hello_datamanWriter)
+ endif()
+else()
+ add_executable(hello_datamanWriter_nompi helloDataManWriter_nompi.cpp)
+ target_link_libraries(hello_datamanWriter_nompi adios2)
+
+ if(ADIOS_BUILD_TESTING)
+ add_test(
+ NAME Example::hello::datamanWriter_nompi
+ COMMAND hello_datamanWriter_nompi
+ )
+ endif()
+endif()
-add_executable(hello_datamanWriter_nompi helloDataManWriter_nompi.cpp)
-target_link_libraries(hello_datamanWriter_nompi adios2)
diff --git a/examples/hello/timeBP/CMakeLists.txt b/examples/hello/timeBP/CMakeLists.txt
index a0e38282532c2bf6cd2c2c726a809e2dd2ea2cac..d86828c90625a3a4e34952730fcd6ed9631c2949 100644
--- a/examples/hello/timeBP/CMakeLists.txt
+++ b/examples/hello/timeBP/CMakeLists.txt
@@ -9,8 +9,18 @@ if(ADIOS_USE_MPI)
target_link_libraries(hello_timeBPWriter adios2)
target_include_directories(hello_timeBPWriter PRIVATE ${MPI_C_INCLUDE_PATH})
target_link_libraries(hello_timeBPWriter adios2 ${MPI_C_LIBRARIES})
-endif()
+ if(ADIOS_BUILD_TESTING)
+ add_test(NAME Example::hello::timeBPWriter COMMAND hello_timeBPWriter)
+ endif()
+else()
+ add_executable(hello_timeBPWriter_nompi timeBPWriter_nompi.cpp)
+ target_link_libraries(hello_timeBPWriter_nompi adios2)
-add_executable(hello_timeBPWriter_nompi timeBPWriter_nompi.cpp)
-target_link_libraries(hello_timeBPWriter_nompi adios2)
+ if(ADIOS_BUILD_TESTING)
+ add_test(
+ NAME Example::hello::timeBPWriter_nompi
+ COMMAND hello_timeBPWriter_nompi
+ )
+ endif()
+endif()
diff --git a/examples/hello/timeBP/timeBPWriter.cpp b/examples/hello/timeBP/timeBPWriter.cpp
index 846151357b20798aa26070aa8e6044267558bb30..280e97e1e7eb08761a1b7ce5f0eba11bb4ed66e6 100644
--- a/examples/hello/timeBP/timeBPWriter.cpp
+++ b/examples/hello/timeBP/timeBPWriter.cpp
@@ -11,9 +11,7 @@
#include <iostream>
#include <vector>
-#define OMPI_SKIP_MPICXX 1 // workaround for OpenMPI forcing C++ bindings
#include <mpi.h>
-#undef OMPI_SKIP_MPICXX
#include "ADIOS_CPP.h"
diff --git a/examples/hello/timeBP/timeBPWriter_nompi.cpp b/examples/hello/timeBP/timeBPWriter_nompi.cpp
index dc4135216764e46c753656f5cac4a3f4a1fdc4d9..48fdd2bbf3111f3c36b550c927d03b475893bf4e 100644
--- a/examples/hello/timeBP/timeBPWriter_nompi.cpp
+++ b/examples/hello/timeBP/timeBPWriter_nompi.cpp
@@ -13,7 +13,7 @@
#include "ADIOS_CPP.h"
-int main(int argc, char *argv[])
+int main(int /*argc*/, char ** /*argv*/)
{
const bool adiosDebug = true;
adios::ADIOS adios(adios::Verbose::ERROR, adiosDebug);
diff --git a/include/ADIOS.h b/include/ADIOS.h
index 85bd4825950c9fceb4865a906c5bdd4cea3d48a5..e0a42c05aa45d8d21add357ae69d5c5aace3e38f 100644
--- a/include/ADIOS.h
+++ b/include/ADIOS.h
@@ -60,11 +60,11 @@ public:
/**
* @brief Serial constructor for config file, only allowed and compiled in
* libadios_nompi.a
- * @param config XML config file
+ * @param config XML config file name
* @param debugMode true: on throws exceptions and do additional checks,
* false: off (faster, but unsafe)
*/
- ADIOS(std::string config, const Verbose verbose = Verbose::WARN,
+ ADIOS(const std::string config, const Verbose verbose = Verbose::WARN,
const bool debugMode = false);
/**
@@ -74,7 +74,7 @@ public:
* @param debugMode true: on, false: off (faster, but unsafe)
*/
- ADIOS(std::string config, MPI_Comm mpiComm,
+ ADIOS(const std::string config, MPI_Comm mpiComm,
const Verbose verbose = Verbose::WARN, const bool debugMode = false);
/**
@@ -98,7 +98,7 @@ public:
* @return
*/
template <class T>
- inline Variable<T> &DefineVariable(const std::string &name,
+ inline Variable<T> &DefineVariable(const std::string name,
const Dims dimensions = Dims{1},
const Dims globalDimensions = Dims(),
const Dims globalOffsets = Dims())
@@ -107,14 +107,14 @@ public:
name + " in call to DefineVariable\n");
}
- template <class T> inline Variable<T> &GetVariable(const std::string &name)
+ 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,
+ VariableCompound &DefineVariableCompound(const std::string name,
const Dims dimensions = Dims{1},
const Dims globalDimensions = Dims(),
const Dims globalOffsets = Dims())
@@ -128,7 +128,7 @@ public:
return m_Compound.at(size);
}
- VariableCompound &GetVariableCompound(const std::string &name);
+ VariableCompound &GetVariableCompound(const std::string name);
/**
* Declares a new method. If the method is defined in the user config file,
@@ -139,7 +139,7 @@ public:
* Use method.isUserDefined() to distinguish between the two cases.
* @param methodName must be unique
*/
- Method &DeclareMethod(const std::string &methodName);
+ Method &DeclareMethod(const std::string methodName);
/**
* @brief Open to Write, Read. Creates a new engine from previously defined
@@ -157,11 +157,9 @@ public:
* @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);
+ std::shared_ptr<Engine> Open(const std::string streamName,
+ const std::string accessMode, MPI_Comm mpiComm,
+ const Method &method);
/**
* @brief Open to Write, Read. Creates a new engine from previously defined
@@ -178,11 +176,9 @@ public:
* @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);
+ std::shared_ptr<Engine> Open(std::string streamName,
+ const std::string accessMode,
+ const Method &method);
/**
* Version required by the XML config file implementation, searches method
@@ -198,11 +194,9 @@ public:
* @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);
+ std::shared_ptr<Engine> Open(const std::string streamName,
+ const std::string accessMode, MPI_Comm mpiComm,
+ const std::string methodName);
/**
* Version required by the XML config file implementation, searches method
@@ -218,11 +212,9 @@ public:
* @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);
+ std::shared_ptr<Engine> Open(const std::string streamName,
+ const std::string accessMode,
+ const std::string methodName);
/**
* @brief Open to Read all steps from a file. No streaming, advancing is
@@ -238,10 +230,9 @@ public:
* @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);
+ std::shared_ptr<Engine> OpenFileReader(const std::string fileName,
+ MPI_Comm mpiComm,
+ const Method &method);
/**
* @brief Open to Read all steps from a file. No streaming, advancing is
@@ -258,10 +249,9 @@ public:
* @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);
+ std::shared_ptr<Engine> OpenFileReader(const std::string fileName,
+ MPI_Comm mpiComm,
+ const std::string methodName);
/**
* @brief Dumps groups information to a file stream or standard output.
@@ -322,8 +312,7 @@ protected: // no const to allow default empty and copy constructors
* @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;
+ void CheckVariableInput(const std::string name, const Dims &dimensions) const;
/**
* Checks for variable name, if not found throws an invalid exception
@@ -334,7 +323,7 @@ protected: // no const to allow default empty and copy constructors
void CheckVariableName(
std::map<std::string,
std::pair<std::string, unsigned int>>::const_iterator itVariable,
- const std::string &name, const std::string &hint) const;
+ const std::string name, const std::string hint) const;
/**
* @brief Checks for method existence in m_Methods, if failed throws
@@ -344,10 +333,9 @@ protected: // no const to allow default empty and copy constructors
* @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;
+ const std::string methodName, const std::string hint) const;
- template <class T> unsigned int GetVariableIndex(const std::string &name)
+ template <class T> unsigned int GetVariableIndex(const std::string name)
{
auto itVariable = m_Variables.find(name);
CheckVariableName(
@@ -361,7 +349,7 @@ protected: // no const to allow default empty and copy constructors
// template specializations of DefineVariable:
template <>
inline Variable<char> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -374,7 +362,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<unsigned char> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -388,7 +376,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<short> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -401,7 +389,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<unsigned short> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -415,7 +403,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<int> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -428,7 +416,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<unsigned int> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -442,7 +430,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<long int> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -455,7 +443,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<unsigned long int> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -469,7 +457,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<long long int> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -483,7 +471,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<unsigned long long int> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -498,7 +486,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<float> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -511,7 +499,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<double> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -524,7 +512,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<long double> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -538,7 +526,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<std::complex<float>> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -546,6 +534,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
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);
@@ -553,7 +542,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<std::complex<double>> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -568,7 +557,7 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
template <>
inline Variable<std::complex<long double>> &
-ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
+ADIOS::DefineVariable(const std::string name, const Dims dimensions,
const Dims globalDimensions, const Dims globalOffsets)
{
CheckVariableInput(name, dimensions);
@@ -582,97 +571,96 @@ ADIOS::DefineVariable(const std::string &name, const Dims dimensions,
}
// Get template specialization
-template <> inline Variable<char> &ADIOS::GetVariable(const std::string &name)
+template <> inline Variable<char> &ADIOS::GetVariable(const std::string name)
{
return m_Char.at(GetVariableIndex<char>(name));
}
template <>
-inline Variable<unsigned char> &ADIOS::GetVariable(const std::string &name)
+inline Variable<unsigned char> &ADIOS::GetVariable(const std::string name)
{
return m_UChar.at(GetVariableIndex<unsigned char>(name));
}
-template <> inline Variable<short> &ADIOS::GetVariable(const std::string &name)
+template <> inline Variable<short> &ADIOS::GetVariable(const std::string name)
{
return m_Short.at(GetVariableIndex<short>(name));
}
template <>
-inline Variable<unsigned short> &ADIOS::GetVariable(const std::string &name)
+inline Variable<unsigned short> &ADIOS::GetVariable(const std::string name)
{
return m_UShort.at(GetVariableIndex<unsigned short>(name));
}
-template <> inline Variable<int> &ADIOS::GetVariable(const std::string &name)
+template <> inline Variable<int> &ADIOS::GetVariable(const std::string name)
{
return m_Int.at(GetVariableIndex<int>(name));
}
template <>
-inline Variable<unsigned int> &ADIOS::GetVariable(const std::string &name)
+inline Variable<unsigned int> &ADIOS::GetVariable(const std::string name)
{
return m_UInt.at(GetVariableIndex<unsigned int>(name));
}
template <>
-inline Variable<long int> &ADIOS::GetVariable(const std::string &name)
+inline Variable<long int> &ADIOS::GetVariable(const std::string name)
{
return m_LInt.at(GetVariableIndex<unsigned int>(name));
}
template <>
-inline Variable<unsigned long int> &ADIOS::GetVariable(const std::string &name)
+inline Variable<unsigned long int> &ADIOS::GetVariable(const std::string name)
{
return m_ULInt.at(GetVariableIndex<unsigned long int>(name));
}
template <>
-inline Variable<long long int> &ADIOS::GetVariable(const std::string &name)
+inline Variable<long long int> &ADIOS::GetVariable(const std::string name)
{
return m_LLInt.at(GetVariableIndex<long long int>(name));
}
template <>
inline Variable<unsigned long long int> &
-ADIOS::GetVariable(const std::string &name)
+ADIOS::GetVariable(const std::string name)
{
return m_ULLInt.at(GetVariableIndex<unsigned long long int>(name));
}
-template <> inline Variable<float> &ADIOS::GetVariable(const std::string &name)
+template <> inline Variable<float> &ADIOS::GetVariable(const std::string name)
{
return m_Float.at(GetVariableIndex<float>(name));
}
-template <> inline Variable<double> &ADIOS::GetVariable(const std::string &name)
+template <> inline Variable<double> &ADIOS::GetVariable(const std::string name)
{
return m_Double.at(GetVariableIndex<double>(name));
}
template <>
-inline Variable<long double> &ADIOS::GetVariable(const std::string &name)
+inline Variable<long double> &ADIOS::GetVariable(const std::string name)
{
return m_LDouble.at(GetVariableIndex<long double>(name));
}
template <>
-inline Variable<std::complex<float>> &
-ADIOS::GetVariable(const std::string &name)
+inline Variable<std::complex<float>> &ADIOS::GetVariable(const std::string name)
{
return m_CFloat.at(GetVariableIndex<std::complex<float>>(name));
}
template <>
inline Variable<std::complex<double>> &
-ADIOS::GetVariable(const std::string &name)
+ADIOS::GetVariable(const std::string name)
{
return m_CDouble.at(GetVariableIndex<std::complex<double>>(name));
}
template <>
inline Variable<std::complex<long double>> &
-ADIOS::GetVariable(const std::string &name)
+ADIOS::GetVariable(const std::string name)
{
return m_CLDouble.at(GetVariableIndex<std::complex<long double>>(name));
}
diff --git a/include/capsule/heap/STLVector.h b/include/capsule/heap/STLVector.h
index b548a64d640a3072d55b9d923174df62fc845eb7..7e83a09d9a5ee4b7ff9177895746fca683f97719 100644
--- a/include/capsule/heap/STLVector.h
+++ b/include/capsule/heap/STLVector.h
@@ -40,7 +40,8 @@ public:
* @param rankMPI MPI rank
* @param debugMode true: extra checks, slower
*/
- STLVector(std::string accessMode, int rankMPI, bool debugMode = false);
+ STLVector(const std::string accessMode, const int rankMPI,
+ const bool debugMode = false);
~STLVector() = default;
diff --git a/include/core/Capsule.h b/include/core/Capsule.h
index 815c8542363f614be1c61e4023b7a9d8ffa779af..715cdc1cbc9279b6188d77d074d46d9614de49d3 100644
--- a/include/core/Capsule.h
+++ b/include/core/Capsule.h
@@ -30,12 +30,11 @@ public:
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
+ std::size_t m_DataPosition = 0; ///< position in current data buffer (not
+ /// included data flushed to transports)
+ std::size_t m_DataAbsolutePosition = 0; ///< include bytes flushed
- size_t m_MetadataPosition = 0; ///< position in metadata buffer
+ std::size_t m_MetadataPosition = 0; ///< position in metadata buffer
/**
* Base class constructor providing type from derived class and accessMode
@@ -44,8 +43,8 @@ public:
* @param rankMPI current MPI rank
* @param debugMode
*/
- Capsule(std::string type, std::string accessMode, int rankMPI,
- bool debugMode);
+ Capsule(const std::string type, const std::string accessMode,
+ const int rankMPI, const bool debugMode);
virtual ~Capsule() = default;
@@ -53,12 +52,11 @@ public:
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 std::size_t GetDataSize() const = 0; ///< data buffer size
+ virtual std::size_t GetMetadataSize() const = 0; ///< metadata buffer size
- virtual void ResizeData(size_t size); ///< resize data buffer
- virtual void ResizeMetadata(size_t size); ///< resize metadata buffer
+ virtual void ResizeData(std::size_t size); ///< resize data buffer
+ virtual void ResizeMetadata(std::size_t size); ///< resize metadata buffer
protected:
const int m_RankMPI = 0; ///< current MPI rank
diff --git a/include/core/Engine.h b/include/core/Engine.h
index eb943b0707acd31adf47120b3ca6a126480198ae..f6c714aebab39ef520693f1c24f8b2bc7202b3fe 100644
--- a/include/core/Engine.h
+++ b/include/core/Engine.h
@@ -75,7 +75,7 @@ public:
*/
Engine(ADIOS &adios, const std::string engineType, const std::string name,
const std::string accessMode, MPI_Comm mpiComm, const Method &method,
- std::string endMessage);
+ const std::string endMessage);
virtual ~Engine() = default;
diff --git a/include/core/Method.h b/include/core/Method.h
index 37eae8f741836215e8970854e010d5c7cbfa3067..96f2862bb7e7a6df35542a902d06fdb6d0390f98 100644
--- a/include/core/Method.h
+++ b/include/core/Method.h
@@ -44,10 +44,12 @@ 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
+ /// additional checks, false: off, faster
/// unsafe
std::string m_Type; ///< Method's engine type
- unsigned int m_nThreads;
+ unsigned int m_nThreads = 1;
+ adios::IOMode m_IOMode = adios::IOMode::INDEPENDENT;
+
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
@@ -60,13 +62,13 @@ public:
*/
Method(const std::string name, const bool debugMode = false);
- ~Method();
+ ~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();
+ bool IsUserDefined();
/**
* Define the engine type
@@ -135,6 +137,6 @@ private:
const std::vector<std::string> ¶meters);
};
-} // end namespace
+} // end namespace adios
#endif /* METHOD_H_ */
diff --git a/include/core/Support.h b/include/core/Support.h
index 481f8fb4185ec57f73c60369a1fc8a019152d1af..bb9b451e842f07afbe38d9d3b36da864594e0c65 100644
--- a/include/core/Support.h
+++ b/include/core/Support.h
@@ -51,6 +51,6 @@ struct Support
};
};
-} // end namespace
+} // end namespace adios
#endif /* SUPPORT_H_ */
diff --git a/include/core/Transform.h b/include/core/Transform.h
index 190541dac62c8c84f93abf05eb20d9a6e65194fd..a6a6dc75ab80f232f8f08e724837d6b83655b7e2 100644
--- a/include/core/Transform.h
+++ b/include/core/Transform.h
@@ -33,9 +33,9 @@ public:
* Initialize parent method
* @param method zlib, bzip2, szip
*/
- Transform(const std::string method);
+ Transform(std::string method);
- virtual ~Transform();
+ virtual ~Transform() = default;
virtual void Compress(const std::vector<char> &bufferIn,
std::vector<char> &bufferOut);
@@ -44,5 +44,5 @@ public:
std::vector<char> &bufferOut);
};
-} // end namespace
+} // end namespace adios
#endif /* TRANSFORM_H_ */
diff --git a/include/core/Transport.h b/include/core/Transport.h
index cc803a6da687cc32801bbe1a9db02323d00cef00..12bbb6ae22aa5156c9ec6f4a1e17f3afd1a57d40 100644
--- a/include/core/Transport.h
+++ b/include/core/Transport.h
@@ -14,11 +14,12 @@
/// \cond EXCLUDE_FROM_DOXYGEN
#include <string>
#include <vector>
+
+#include "../utilities/profiling/iochrono/IOChrono.h"
/// \endcond
#include "ADIOS_MPI.h"
-#include "packages/profiling/iochrono/IOChrono.h"
namespace adios
{
@@ -44,9 +45,9 @@ public:
* @param mpiComm passed to m_MPIComm
* @param debugMode passed to m_DebugMode
*/
- Transport(const std::string type, MPI_Comm mpiComm, const bool debugMode);
+ Transport(std::string type, MPI_Comm mpiComm, bool debugMode);
- virtual ~Transport(); ///< empty destructor, using STL for memory management
+ virtual ~Transport() = default;
/**
* Open Output file accesing a mode
@@ -87,6 +88,6 @@ protected:
const bool m_DebugMode = false; ///< if true: additional checks and exceptions
};
-} // end namespace
+} // end namespace adios
#endif /* TRANSPORT_H_ */
diff --git a/include/engine/bp/BPFileReader.h b/include/engine/bp/BPFileReader.h
index 2b4f756af68c3deb2c373d98a6d9b7e964fd302d..0d975e859c2fa58cd5c0a9197a551ca6168c2dbc 100644
--- a/include/engine/bp/BPFileReader.h
+++ b/include/engine/bp/BPFileReader.h
@@ -15,7 +15,6 @@
#include "core/Engine.h"
-// supported capsules
#include "capsule/heap/STLVector.h"
namespace adios
@@ -39,7 +38,7 @@ public:
const std::string accessMode, MPI_Comm mpiComm,
const Method &method);
- ~BPFileReader();
+ virtual ~BPFileReader() = default;
Variable<void> *InquireVariable(const std::string name,
const bool readIn = true);
diff --git a/include/engine/bp/BPFileWriter.h b/include/engine/bp/BPFileWriter.h
index 3f04ee7be44e98bdfd5bf98644fb4033b0825759..ca0353cad321d41f37dafffc7ccf95180fa1bcfa 100644
--- a/include/engine/bp/BPFileWriter.h
+++ b/include/engine/bp/BPFileWriter.h
@@ -11,11 +11,9 @@
#ifndef BPFILEWRITER_H_
#define BPFILEWRITER_H_
-#include "core/Engine.h"
-#include "packages/format/bp1/BP1.h"
-
-// supported capsules
#include "capsule/heap/STLVector.h"
+#include "core/Engine.h"
+#include "utilities/format/bp1/BP1.h"
namespace adios
{
diff --git a/include/engine/dataman/DataManWriter.h b/include/engine/dataman/DataManWriter.h
index 8245c00a4cab1816e0f64d21b905c4876fec0c88..5eafb3e7ec4247ada6ff60a94691b838ee3c3f17 100644
--- a/include/engine/dataman/DataManWriter.h
+++ b/include/engine/dataman/DataManWriter.h
@@ -14,10 +14,8 @@
#include <iostream> //std::cout must be removed, only used for hello example
#include <unistd.h> //sleep must be removed
+#include "../../utilities/format/bp1/BP1Writer.h"
#include "core/Engine.h"
-#include "packages/format/bp1/BP1Writer.h"
-
-// supported capsules
#include "capsule/heap/STLVector.h"
#include "DataManager.h" //here comes your DataMan header
diff --git a/include/mpidummy.h b/include/mpidummy.h
index 65b380f5cd4a229e87ddffad8bb24c806bf452a6..86122ede8af34481a719166a9df32f9cddacd835 100644
--- a/include/mpidummy.h
+++ b/include/mpidummy.h
@@ -73,34 +73,35 @@ int MPI_Comm_size(MPI_Comm comm, int *size);
int MPI_Comm_free(MPI_Comm *comm);
MPI_Comm MPI_Comm_f2c(MPI_Fint comm);
-int MPI_Gather(void *sendbuf, int sendcnt, MPI_Datatype sendtype, void *recvbuf,
- int recvcnt, MPI_Datatype recvtype, int root, MPI_Comm comm);
-int MPI_Gatherv(void *sendbuf, int sendcnt, MPI_Datatype sendtype,
- void *recvbuf, int *recvcnts, int *displs,
+int MPI_Gather(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
+ void *recvbuf, int recvcount, MPI_Datatype recvtype, int root,
+ MPI_Comm comm);
+int MPI_Gatherv(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
+ void *recvbuf, const int *recvcounts, const int *displs,
MPI_Datatype recvtype, int root, MPI_Comm comm);
-int MPI_Allgather(void *sendbuf, int sendcount, MPI_Datatype sendtype,
+int MPI_Allgather(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
void *recvbuf, int recvcount, MPI_Datatype recvtype,
MPI_Comm comm);
-int MPI_Scatter(void *sendbuf, int sendcnt, MPI_Datatype sendtype,
- void *recvbuf, int recvcnt, MPI_Datatype recvtype, int root,
+int MPI_Scatter(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
+ void *recvbuf, int recvcount, MPI_Datatype recvtype, int root,
MPI_Comm comm);
-int MPI_Scatterv(void *sendbuf, int *sendcnts, int *displs,
- MPI_Datatype sendtype, void *recvbuf, int recvcnt,
+int MPI_Scatterv(const void *sendbuf, const int *sendcounts, const int *displs,
+ MPI_Datatype sendtype, void *recvbuf, int recvcount,
MPI_Datatype recvtype, int root, MPI_Comm comm);
-int MPI_Recv(void *recvbuffer, int count, MPI_Datatype type, int source,
- int tag, MPI_Comm comm, MPI_Status *status);
-int MPI_Irecv(void *recvbuffer, int count, MPI_Datatype type, int source,
- int tag, MPI_Comm comm, MPI_Request *request);
-int MPI_Send(void *sendbuffer, int count, MPI_Datatype type, int destination,
+int MPI_Recv(void *buf, int count, MPI_Datatype datatype, int source, int tag,
+ MPI_Comm comm, MPI_Status *status);
+int MPI_Irecv(void *buf, int count, MPI_Datatype datatype, int source, int tag,
+ MPI_Comm comm, MPI_Request *request);
+int MPI_Send(const void *buf, int count, MPI_Datatype datatype, int dest,
int tag, MPI_Comm comm);
-int MPI_Isend(void *recvbuffer, int count, MPI_Datatype type, int source,
+int MPI_Isend(const void *buf, int count, MPI_Datatype datatype, int dest,
int tag, MPI_Comm comm, MPI_Request *request);
int MPI_Wait(MPI_Request *request, MPI_Status *status);
-int MPI_File_open(MPI_Comm comm, char *filename, int amode, MPI_Info info,
+int MPI_File_open(MPI_Comm comm, const char *filename, int amode, MPI_Info info,
MPI_File *fh);
int MPI_File_close(MPI_File *fh);
int MPI_File_get_size(MPI_File fh, MPI_Offset *size);
@@ -108,7 +109,7 @@ int MPI_File_read(MPI_File fh, void *buf, int count, MPI_Datatype datatype,
MPI_Status *status);
int MPI_File_seek(MPI_File fh, MPI_Offset offset, int whence);
-int MPI_Get_count(MPI_Status *status, MPI_Datatype datatype, int *count);
+int MPI_Get_count(const MPI_Status *status, MPI_Datatype datatype, int *count);
int MPI_Error_string(int errorcode, char *string, int *resultlen);
int MPI_Comm_split(MPI_Comm comm, int color, int key, MPI_Comm *comm_out);
diff --git a/include/transport/file/FStream.h b/include/transport/file/FStream.h
index 163b96478e23334fcf2fc0ab8afe1b824789d9f2..8553c35981ebdb87048631033f293404f3774f88 100644
--- a/include/transport/file/FStream.h
+++ b/include/transport/file/FStream.h
@@ -31,7 +31,7 @@ class FStream : public Transport
public:
FStream(MPI_Comm mpiComm, const bool debugMode);
- ~FStream();
+ virtual ~FStream() = default;
void Open(const std::string name, const std::string accessMode);
@@ -48,6 +48,6 @@ private:
};
} // end namespace transport
-} // end namespace
+} // end namespace adios
#endif /* FSTREAM_H_ */
diff --git a/include/packages/format/bp1/BP1.h b/include/utilities/format/bp1/BP1.h
similarity index 60%
rename from include/packages/format/bp1/BP1.h
rename to include/utilities/format/bp1/BP1.h
index 1e0aebd1ba2dc6692912742d08707598fadbc1e4..d1b394088ed27a85e9d7a9cd2a448a9cbd986146 100644
--- a/include/packages/format/bp1/BP1.h
+++ b/include/utilities/format/bp1/BP1.h
@@ -11,9 +11,8 @@
#ifndef BP1_H_
#define BP1_H_
-#include "packages/format/bp1/BP1Structs.h"
-#include "packages/format/bp1/BP1Writer.h"
-// will add Reader later
-#include "packages/format/bp1/BP1Aggregator.h"
+#include "utilities/format/bp1/BP1Aggregator.h"
+#include "utilities/format/bp1/BP1Structs.h"
+#include "utilities/format/bp1/BP1Writer.h"
#endif /* BP1_H_ */
diff --git a/include/packages/format/bp1/BP1Aggregator.h b/include/utilities/format/bp1/BP1Aggregator.h
similarity index 100%
rename from include/packages/format/bp1/BP1Aggregator.h
rename to include/utilities/format/bp1/BP1Aggregator.h
diff --git a/include/packages/format/bp1/BP1Base.h b/include/utilities/format/bp1/BP1Base.h
similarity index 100%
rename from include/packages/format/bp1/BP1Base.h
rename to include/utilities/format/bp1/BP1Base.h
diff --git a/include/packages/format/bp1/BP1Structs.h b/include/utilities/format/bp1/BP1Structs.h
similarity index 87%
rename from include/packages/format/bp1/BP1Structs.h
rename to include/utilities/format/bp1/BP1Structs.h
index 8c6365933f69cefa5877db519d565b27a9051ec1..10ca50eaee4cc189962c1655780a33c228c1bc3c 100644
--- a/include/packages/format/bp1/BP1Structs.h
+++ b/include/utilities/format/bp1/BP1Structs.h
@@ -18,7 +18,7 @@
#include <vector>
/// \endcond
-#include "packages/profiling/iochrono/IOChrono.h"
+#include "utilities/profiling/iochrono/IOChrono.h"
namespace adios
{
@@ -54,8 +54,8 @@ 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
+ /** @brief key: variable name, value: bp metadata variable index */
+ std::unordered_map<std::string, BP1Index> VarsIndices;
std::unordered_map<std::string, BP1Index>
AttributesIndices; ///< key: name, value: attribute bp index
@@ -68,9 +68,13 @@ struct BP1MetadataSet
/// position, needs to be updated in
/// every advance step or init
std::uint32_t DataPGVarsCount = 0; ///< variables in current PG
+
+ /**
+ * current PG variable count ( relative ) position, needs to be
+ * updated in very Advance
+ */
std::size_t DataPGVarsCountPosition = 0;
- ///< current PG variable count ( relative ) position, needs to be
- /// updated in every advance step or init
+
bool DataPGIsOpen = false;
profiling::IOChrono Log; ///< object that takes buffering profiling info
diff --git a/include/packages/format/bp1/BP1Writer.h b/include/utilities/format/bp1/BP1Writer.h
similarity index 99%
rename from include/packages/format/bp1/BP1Writer.h
rename to include/utilities/format/bp1/BP1Writer.h
index 9295251dbf7372a6c4fbf7794390be8e2f5adcf9..fa4382cf9c19fa0b850a4e72d4ac26f1cd882d4c 100644
--- a/include/packages/format/bp1/BP1Writer.h
+++ b/include/utilities/format/bp1/BP1Writer.h
@@ -15,14 +15,15 @@
#include <algorithm> //std::count, std::copy, std::for_each
#include <cmath> //std::ceil
#include <cstring> //std::memcpy
+
+#include "utilities/format/bp1/BP1Base.h"
+#include "utilities/format/bp1/BP1Structs.h"
/// \endcond
#include "capsule/heap/STLVector.h"
#include "core/Variable.h"
#include "functions/adiosFunctions.h"
#include "functions/adiosTemplates.h"
-#include "packages/format/bp1/BP1Base.h"
-#include "packages/format/bp1/BP1Structs.h"
namespace adios
{
diff --git a/include/packages/profiling/iochrono/IOChrono.h b/include/utilities/profiling/iochrono/IOChrono.h
similarity index 93%
rename from include/packages/profiling/iochrono/IOChrono.h
rename to include/utilities/profiling/iochrono/IOChrono.h
index 442a8df8ca5eaadcfb8c6088c08e731316e62793..fed27a79a6cb3ee0486ebff2cf2169765634e80d 100644
--- a/include/packages/profiling/iochrono/IOChrono.h
+++ b/include/utilities/profiling/iochrono/IOChrono.h
@@ -15,7 +15,7 @@
#include <vector>
/// \endcond
-#include "packages/profiling/iochrono/Timer.h"
+#include "profiling/iochrono/Timer.h"
namespace adios
{
diff --git a/include/packages/profiling/iochrono/Timer.h b/include/utilities/profiling/iochrono/Timer.h
similarity index 100%
rename from include/packages/profiling/iochrono/Timer.h
rename to include/utilities/profiling/iochrono/Timer.h
diff --git a/source/ADIOS.cpp b/source/ADIOS.cpp
index efd3e2eac459425b04661ada7f740ee910e1b5ad..5fd0fbf366ae0ae74958ad7ea65c3d78f1dc9e5d 100644
--- a/source/ADIOS.cpp
+++ b/source/ADIOS.cpp
@@ -10,12 +10,14 @@
/// \cond EXCLUDE_FROM_DOXYGEN
#include <fstream>
+#include <ios> //std::ios_base::failure
#include <iostream>
#include <sstream>
#include <utility>
/// \endcond
#include "ADIOS.h"
+
#include "functions/adiosFunctions.h"
// Engines
@@ -41,17 +43,17 @@ ADIOS::ADIOS(const Verbose /*verbose*/, const bool debugMode)
InitMPI();
}
-ADIOS::ADIOS(std::string config, const Verbose /*verbose*/,
+ADIOS::ADIOS(const std::string config, const Verbose /*verbose*/,
const bool debugMode)
-: m_ConfigFile{std::move(config)}, m_DebugMode{debugMode}
+: m_ConfigFile{config}, m_DebugMode{debugMode}
{
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}
+ADIOS::ADIOS(const std::string config, MPI_Comm mpiComm,
+ const Verbose /*verbose*/, const bool debugMode)
+: m_MPIComm{mpiComm}, m_ConfigFile{config}, m_DebugMode{debugMode}
{
InitMPI();
// InitXML( m_XMLConfigFile, m_MPIComm, m_DebugMode, m_HostLanguage,
@@ -82,7 +84,7 @@ void ADIOS::InitMPI()
MPI_Comm_size(m_MPIComm, &m_SizeMPI);
}
-Method &ADIOS::DeclareMethod(const std::string &methodName)
+Method &ADIOS::DeclareMethod(const std::string methodName)
{
if (m_DebugMode == true)
{
@@ -96,11 +98,9 @@ Method &ADIOS::DeclareMethod(const std::string &methodName)
return m_Methods.at(methodName);
}
-std::shared_ptr<Engine> ADIOS::Open(const std::string &name,
- const std::string &accessMode,
- MPI_Comm mpiComm, const Method &method,
- const IOMode iomode,
- const float timeout_sec)
+std::shared_ptr<Engine> ADIOS::Open(const std::string name,
+ const std::string accessMode,
+ MPI_Comm mpiComm, const Method &method)
{
if (m_DebugMode == true)
{
@@ -190,18 +190,17 @@ std::shared_ptr<Engine> ADIOS::Open(const std::string &name,
return nullptr; // if debug mode is off
}
-std::shared_ptr<Engine> ADIOS::Open(const std::string &streamName,
- const std::string &accessMode,
- const Method &method, const IOMode iomode,
- const float timeout_sec)
+std::shared_ptr<Engine> ADIOS::Open(const std::string name,
+ const std::string accessMode,
+ const Method &method)
{
- return Open(streamName, accessMode, m_MPIComm, method, iomode, timeout_sec);
+ return Open(name, accessMode, m_MPIComm, method);
}
-std::shared_ptr<Engine>
-ADIOS::Open(const std::string &name, const std::string &accessMode,
- MPI_Comm mpiComm, const std::string &methodName,
- const IOMode iomode, const float timeout_sec)
+std::shared_ptr<Engine> ADIOS::Open(const std::string name,
+ const std::string accessMode,
+ MPI_Comm mpiComm,
+ const std::string methodName)
{
auto itMethod = m_Methods.find(methodName);
@@ -210,30 +209,26 @@ ADIOS::Open(const std::string &name, const std::string &accessMode,
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);
}
-std::shared_ptr<Engine> ADIOS::Open(const std::string &name,
- const std::string &accessMode,
- const std::string &methodName,
- const IOMode iomode,
- const float timeout_sec)
+std::shared_ptr<Engine> ADIOS::Open(const std::string name,
+ const std::string accessMode,
+ const std::string methodName)
{
- return Open(name, accessMode, m_MPIComm, methodName, iomode, timeout_sec);
+ return Open(name, accessMode, m_MPIComm, methodName);
}
-std::shared_ptr<Engine> ADIOS::OpenFileReader(const std::string &name,
- MPI_Comm /*mpiComm*/,
- const Method &method,
- const IOMode iomode)
+std::shared_ptr<Engine> ADIOS::OpenFileReader(const std::string name,
+ MPI_Comm mpiComm,
+ const Method &method)
{
- return Open(name, "r", m_MPIComm, method, iomode);
+ return Open(name, "r", mpiComm, method);
}
-std::shared_ptr<Engine> ADIOS::OpenFileReader(const std::string &name,
- MPI_Comm /*mpiComm*/,
- const std::string &methodName,
- const IOMode iomode)
+std::shared_ptr<Engine> ADIOS::OpenFileReader(const std::string name,
+ MPI_Comm mpiComm,
+ const std::string methodName)
{
auto itMethod = m_Methods.find(methodName);
@@ -242,10 +237,10 @@ std::shared_ptr<Engine> ADIOS::OpenFileReader(const std::string &name,
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);
}
-VariableCompound &ADIOS::GetVariableCompound(const std::string &name)
+VariableCompound &ADIOS::GetVariableCompound(const std::string name)
{
return m_Compound.at(GetVariableIndex<void>(name));
}
@@ -327,7 +322,7 @@ void ADIOS::MonitorVariables(std::ostream &logStream)
}
// PRIVATE FUNCTIONS BELOW
-void ADIOS::CheckVariableInput(const std::string &name,
+void ADIOS::CheckVariableInput(const std::string name,
const Dims &dimensions) const
{
if (m_DebugMode == true)
@@ -351,7 +346,7 @@ void ADIOS::CheckVariableInput(const std::string &name,
void ADIOS::CheckVariableName(
std::map<std::string, std::pair<std::string, unsigned int>>::const_iterator
itVariable,
- const std::string &name, const std::string &hint) const
+ const std::string name, const std::string hint) const
{
if (m_DebugMode == true)
{
@@ -364,8 +359,8 @@ void ADIOS::CheckVariableName(
}
void ADIOS::CheckMethod(std::map<std::string, Method>::const_iterator itMethod,
- const std::string &methodName,
- const std::string &hint) const
+ const std::string methodName,
+ const std::string hint) const
{
if (itMethod == m_Methods.end())
{
diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt
index 731a1153f54c68bdecd076b3db6a54d5a3e183ff..e6f56432a41ceaec549dc5a37ed582ec1559e907 100644
--- a/source/CMakeLists.txt
+++ b/source/CMakeLists.txt
@@ -20,11 +20,11 @@ add_library(adios2
engine/bp/BPFileReader.cpp
engine/bp/BPFileWriter.cpp
- packages/format/bp1/BP1Base.cpp
- packages/format/bp1/BP1Aggregator.cpp
- packages/format/bp1/BP1Writer.cpp
+ utilities/format/bp1/BP1Base.cpp
+ utilities/format/bp1/BP1Aggregator.cpp
+ utilities/format/bp1/BP1Writer.cpp
- packages/profiling/iochrono/Timer.cpp
+ utilities/profiling/iochrono/Timer.cpp
functions/adiosFunctions.cpp
diff --git a/source/core/Capsule.cpp b/source/core/Capsule.cpp
index 0b268a37065238800c19cdad2336774a2c553774..b30603ab42bc0137b0803d802a01e67b937eb7c0 100644
--- a/source/core/Capsule.cpp
+++ b/source/core/Capsule.cpp
@@ -15,8 +15,8 @@
namespace adios
{
-Capsule::Capsule(std::string type, std::string accessMode, int rankMPI,
- bool debugMode)
+Capsule::Capsule(const std::string type, const std::string accessMode,
+ int rankMPI, bool debugMode)
: m_Type{std::move(type)}, m_AccessMode{std::move(accessMode)},
m_RankMPI{rankMPI}, m_DebugMode{debugMode}
{
diff --git a/source/core/Engine.cpp b/source/core/Engine.cpp
index df35828eb6598bf1a692c52ed8988efdc9a1a0a6..a27a1c2863c71a063e966e8a44951b8d5a4316f5 100644
--- a/source/core/Engine.cpp
+++ b/source/core/Engine.cpp
@@ -8,6 +8,8 @@
* Author: wfg
*/
+#include <ios> //std::ios_base::failure
+
#include "core/Engine.h"
#include "core/Support.h"
#include "functions/adiosFunctions.h"
@@ -17,7 +19,8 @@ namespace adios
Engine::Engine(ADIOS &adios, const std::string engineType,
const std::string name, const std::string accessMode,
- MPI_Comm mpiComm, const Method &method, std::string endMessage)
+ MPI_Comm mpiComm, const Method &method,
+ const std::string endMessage)
: m_MPIComm{mpiComm}, m_EngineType{std::move(engineType)},
m_Name{std::move(name)}, m_AccessMode{std::move(accessMode)},
m_Method{method}, m_ADIOS(adios), m_EndMessage(std::move(endMessage)),
diff --git a/source/core/Method.cpp b/source/core/Method.cpp
index ee22d5bdc1471a6bda652a36416d98ec218bd13c..41397d5e5802352b05cf3c9b919fa2d58f98f2ed 100644
--- a/source/core/Method.cpp
+++ b/source/core/Method.cpp
@@ -8,6 +8,8 @@
* Author: wfg
*/
+#include <utility>
+
#include "core/Method.h"
#include "functions/adiosFunctions.h"
@@ -17,15 +19,11 @@ namespace adios
Method::Method(const std::string name, const bool debugMode)
: m_Name{name}, m_DebugMode{debugMode}
{
- // m_Type can stay empty (forcing the choice of the default engine)
- m_nThreads = 1;
}
-Method::~Method() {}
-
-bool Method::isUserDefined()
+bool Method::IsUserDefined()
{
- return false; // TODO: 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; }
@@ -33,9 +31,13 @@ void Method::SetEngine(const std::string type) { m_Type = type; }
void Method::AllowThreads(const unsigned int nThreads)
{
if (nThreads > 1)
+ {
m_nThreads = nThreads;
+ }
else
+ {
m_nThreads = 1;
+ }
}
// PRIVATE Functions
@@ -45,8 +47,10 @@ void Method::AddTransportParameters(const std::string type,
if (m_DebugMode == true)
{
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 =
@@ -54,13 +58,15 @@ void Method::AddTransportParameters(const std::string type,
if (m_DebugMode == true)
{
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);
}
-} // end namespace
+} // end namespace adios
diff --git a/source/core/Support.cpp b/source/core/Support.cpp
index 02be66d86108af579eeafd5805adad1e5a1537b4..65cac135af7ca6a6b428ba5fb5c3a15aedbf7324 100644
--- a/source/core/Support.cpp
+++ b/source/core/Support.cpp
@@ -19,10 +19,9 @@ const std::string Support::Version{"2.00"};
const std::set<std::string> Support::HostLanguages{{"C++", "C", "Fortran"}};
const std::set<std::string> Support::Transports{
- {"NULL", "POSIX", "FStream",
- "MdtmMan"} // "MPI", "MPI_LUSTRE", "MPI_AGGREGATE", "DATASPACES", "DIMES",
- // "FLEXPATH", "PHDF5", "NC4", "ICEE" }
-};
+ {"NULL", "POSIX", "FStream", "MdtmMan"}};
+// TODO(chuckatkins): Add transports MPI, MPI_LUSTRE, MPI_AGGREGATE,
+// DATASPACES, DIMES, FLEXPATH, PHDF5, NC4, ICEE
const std::set<std::string> Support::Transforms{
{"none", "identity", "bzip2", "isobar", "szip", "zlib"}};
@@ -90,4 +89,4 @@ const std::map<std::string, std::set<std::string>> Support::DatatypesAliases{
const std::set<std::string> Support::FileTransports{
{"POSIX", "File", "FStream", "MPIFile"}};
-} // end namespace
+} // end namespace adios
diff --git a/source/core/Transform.cpp b/source/core/Transform.cpp
index 0b719ccc86bcdf858a93c1417f662982817e45c3..7549342b26640480331644a5bdcc0adaded88a55 100644
--- a/source/core/Transform.cpp
+++ b/source/core/Transform.cpp
@@ -7,24 +7,23 @@
* Created on: Dec 5, 2016
* Author: wfg
*/
+#include <utility>
#include "core/Transform.h"
namespace adios
{
-Transform::Transform(const std::string method) : m_Method(method) {}
+Transform::Transform(std::string method) : m_Method(std::move(method)) {}
-Transform::~Transform() {}
-
-void Transform::Compress(const std::vector<char> &bufferIn,
- std::vector<char> &bufferOut)
+void Transform::Compress(const std::vector<char> & /*bufferIn*/,
+ std::vector<char> & /*bufferOut*/)
{
}
-void Transform::Decompress(const std::vector<char> &bufferIn,
- std::vector<char> &bufferOut)
+void Transform::Decompress(const std::vector<char> & /*bufferIn*/,
+ std::vector<char> & /*bufferOut*/)
{
}
-} // end namespace
+} // end namespace adios
diff --git a/source/core/Transport.cpp b/source/core/Transport.cpp
index 42fcb79ee4331ae0e468aca768284eca63e066ba..a1f12ac44a993c13e449b3acac971a47e79bf20c 100644
--- a/source/core/Transport.cpp
+++ b/source/core/Transport.cpp
@@ -8,22 +8,21 @@
* Author: wfg
*/
+#include <utility>
+
#include "core/Transport.h"
namespace adios
{
-Transport::Transport(const std::string type, MPI_Comm mpiComm,
- const bool debugMode)
+Transport::Transport(std::string type, MPI_Comm mpiComm, bool debugMode)
: m_Type{type}, m_MPIComm{mpiComm}, m_DebugMode{debugMode}
{
MPI_Comm_rank(m_MPIComm, &m_RankMPI);
MPI_Comm_size(m_MPIComm, &m_SizeMPI);
}
-Transport::~Transport() {}
-
-void Transport::SetBuffer(char *buffer, size_t size) {}
+void Transport::SetBuffer(char * /*buffer*/, size_t /*size*/) {}
void Transport::Flush() {}
@@ -49,4 +48,4 @@ void Transport::InitProfiler(const std::string accessMode,
m_Profiler.IsActive = true;
}
-} // end namespace
+} // end namespace adios
diff --git a/source/engine/adios1/ADIOS1Reader.cpp b/source/engine/adios1/ADIOS1Reader.cpp
index 406c752d39d2e8357c1a0a008c2d2a975cf80425..0d666ec9cf6142011f726f8941bae08053be9eb5 100644
--- a/source/engine/adios1/ADIOS1Reader.cpp
+++ b/source/engine/adios1/ADIOS1Reader.cpp
@@ -8,26 +8,21 @@
* Author: wfg
*/
-#include "engine/bp/BPFileReader.h"
-
#include "core/Support.h"
-#include "functions/adiosFunctions.h" //CSVToVector
+#include "engine/bp/BPFileReader.h"
+#include "functions/adiosFunctions.h" // CSVToVector
+#include "transport/file/FStream.h" // uses C++ fstream
#include "transport/file/FileDescriptor.h" // uses POSIX
#include "transport/file/FilePointer.h" // uses C FILE*
-// supported transports
-#include "transport/file/FStream.h" // uses C++ fstream
-
namespace adios
{
BPFileReader::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,
- const unsigned int nthreads)
-: Engine(adios, "BPFileReader", name, accessMode, mpiComm, method, debugMode,
- nthreads, " BPFileReader constructor (or call to ADIOS Open).\n"),
+ const Method &method)
+: Engine(adios, "BPFileReader", name, accessMode, mpiComm, method,
+ " BPFileReader constructor (or call to ADIOS Open).\n"),
m_Buffer(accessMode, m_RankMPI, m_DebugMode)
{
Init();
diff --git a/source/engine/bp/BPFileReader.cpp b/source/engine/bp/BPFileReader.cpp
index 4a542c4a9546bbec4219d7d9c6f0579afd838c9f..5adce59e69caa432227c35c08f46e23a2478f9bd 100644
--- a/source/engine/bp/BPFileReader.cpp
+++ b/source/engine/bp/BPFileReader.cpp
@@ -11,13 +11,11 @@
#include "engine/bp/BPFileReader.h"
#include "core/Support.h"
-#include "functions/adiosFunctions.h" //CSVToVector
+#include "functions/adiosFunctions.h" // CSVToVector
+#include "transport/file/FStream.h" // uses C++ fstream
#include "transport/file/FileDescriptor.h" // uses POSIX
#include "transport/file/FilePointer.h" // uses C FILE*
-// supported transports
-#include "transport/file/FStream.h" // uses C++ fstream
-
namespace adios
{
@@ -31,12 +29,10 @@ BPFileReader::BPFileReader(ADIOS &adios, const std::string name,
Init();
}
-BPFileReader::~BPFileReader() {}
-
-Variable<void> *
-BPFileReader::InquireVariable(const std::string name,
- const bool readIn) // not yet implemented
+Variable<void> *BPFileReader::InquireVariable(const std::string /*name*/,
+ const bool /*readIn*/)
{
+ // not yet implemented
return nullptr;
}
@@ -136,13 +132,14 @@ BPFileReader::InquireVariableCLDouble(const std::string name, const bool readIn)
return InquireVariableCommon<std::complex<long double>>(name, readIn);
}
-VariableCompound *BPFileReader::InquireVariableCompound(const std::string name,
- const bool readIn)
+VariableCompound *
+BPFileReader::InquireVariableCompound(const std::string /*name*/,
+ const bool /*readIn*/)
{
return nullptr;
}
-void BPFileReader::Close(const int transportIndex) {}
+void BPFileReader::Close(const int /*transportIndex*/) {}
// PRIVATE
void BPFileReader::Init()
@@ -150,9 +147,11 @@ 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");
+ }
}
InitCapsules();
@@ -212,19 +211,23 @@ void BPFileReader::InitTransports() // maybe move this?
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
+} // end namespace adios
diff --git a/source/engine/bp/BPFileWriter.cpp b/source/engine/bp/BPFileWriter.cpp
index 09d6a90c87dc577dae38150a29fbf4cb3c9227c5..414deec61b3092c06b83d6f6567b28abe80e676b 100644
--- a/source/engine/bp/BPFileWriter.cpp
+++ b/source/engine/bp/BPFileWriter.cpp
@@ -32,7 +32,7 @@ BPFileWriter::BPFileWriter(ADIOS &adios, const std::string name,
Init();
}
-BPFileWriter::~BPFileWriter() {}
+BPFileWriter::~BPFileWriter() = default;
void BPFileWriter::Init()
{
@@ -131,7 +131,10 @@ void BPFileWriter::Write(Variable<std::complex<long double>> &variable,
WriteVariableCommon(variable, values);
}
-void BPFileWriter::Write(VariableCompound &variable, const void *values) {}
+void BPFileWriter::Write(VariableCompound & /*variable*/,
+ const void * /*values*/)
+{
+}
// String version
void BPFileWriter::Write(const std::string variableName, const char *values)
@@ -230,12 +233,12 @@ void BPFileWriter::Write(const std::string variableName,
m_ADIOS.GetVariable<std::complex<long double>>(variableName), values);
}
-void BPFileWriter::Write(const std::string variableName,
- const void *values) // Compound type
+void BPFileWriter::Write(const std::string /*variableName*/,
+ const void * /*values*/) // Compound type
{
}
-void BPFileWriter::Advance(float timeout_sec)
+void BPFileWriter::Advance(float /*timeout_sec*/)
{
m_BP1Writer.Advance(m_MetadataSet, m_Buffer);
}
@@ -245,10 +248,11 @@ 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?
+ 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
{
@@ -290,9 +294,11 @@ void BPFileWriter::InitParameters()
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");
+ }
}
m_BP1Writer.m_GrowthFactor = growthFactor;
@@ -305,9 +311,11 @@ void BPFileWriter::InitParameters()
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_MaxBufferSize = std::stoul(itMaxBufferSize->second) *
@@ -321,9 +329,11 @@ void BPFileWriter::InitParameters()
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;
}
@@ -335,24 +345,22 @@ void BPFileWriter::InitParameters()
if (itProfile->second == "mus" || itProfile->second == "microseconds")
profiler.Timers.emplace_back("buffering", Support::Resolutions::mus);
-
else if (itProfile->second == "ms" || itProfile->second == "milliseconds")
profiler.Timers.emplace_back("buffering", Support::Resolutions::ms);
-
else if (itProfile->second == "s" || itProfile->second == "seconds")
profiler.Timers.emplace_back("buffering", Support::Resolutions::s);
-
else if (itProfile->second == "min" || itProfile->second == "minutes")
profiler.Timers.emplace_back("buffering", Support::Resolutions::m);
-
else if (itProfile->second == "h" || itProfile->second == "hours")
profiler.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.IsActive = true;
@@ -381,26 +389,33 @@ void BPFileWriter::InitTransports()
if (itProfile != parameters.end())
{
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;
}
@@ -416,7 +431,9 @@ void BPFileWriter::InitTransports()
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));
@@ -426,7 +443,9 @@ void BPFileWriter::InitTransports()
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));
@@ -438,7 +457,9 @@ void BPFileWriter::InitTransports()
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));
@@ -449,23 +470,28 @@ void BPFileWriter::InitTransports()
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);
+ }
}
}
}
void BPFileWriter::InitProcessGroup()
{
+
if (m_MetadataSet.Log.IsActive == true)
m_MetadataSet.Log.Timers[0].SetInitialTime();
diff --git a/source/functions/adiosFunctions.cpp b/source/functions/adiosFunctions.cpp
index 0886e029ad14a4e6fc4dd8b04b296071175d3678..78393c641f2c502c35728c46e590252ff8580749 100644
--- a/source/functions/adiosFunctions.cpp
+++ b/source/functions/adiosFunctions.cpp
@@ -37,10 +37,12 @@ void DumpFileToString(const std::string fileName, std::string &fileContent)
{
std::ifstream fileStream(fileName);
- if (fileStream.good() == false) // check file
+ 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();
@@ -48,7 +50,9 @@ void DumpFileToString(const std::string fileName, std::string &fileContent)
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,
@@ -101,25 +105,35 @@ void GetSubString(const std::string initialTag, const std::string finalTag,
(singleQuotePosition == content.npos && end < doubleQuotePosition) ||
(doubleQuotePosition == content.npos && end < singleQuotePosition) ||
(end < singleQuotePosition && end < doubleQuotePosition))
+ {
break;
+ }
// find the closing corresponding quote
std::string::size_type closingQuotePosition;
- if (singleQuotePosition == content.npos) // no ' anywhere
+ if (singleQuotePosition == content.npos)
+ { // no ' anywhere
lf_SetPositions('\"', doubleQuotePosition, content, currentPosition,
closingQuotePosition);
- else if (doubleQuotePosition == content.npos) // no " anywhere
+ }
+ 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 "
+ }
+ else
+ { // find the closing "
lf_SetPositions('\"', doubleQuotePosition, content, currentPosition,
closingQuotePosition);
+ }
}
if (closingQuotePosition ==
@@ -132,7 +146,9 @@ void GetSubString(const std::string initialTag, const std::string finalTag,
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
@@ -151,8 +167,10 @@ void GetQuotedValue(const char quote,
auto nextQuotePosition = currentTag.find(quote);
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);
@@ -201,8 +219,10 @@ void GetPairsFromTag(
">"); // check for closing tagName
if (fileContent.find(closingTagName) == fileContent.npos)
+ {
throw std::invalid_argument("ERROR: closing tag " + closingTagName +
" missing, check XML file\n");
+ }
GetPairs(tag, pairs);
}
@@ -411,7 +431,9 @@ std::size_t GetTotalSize(const std::vector<std::size_t> &dimensions)
std::size_t product = 1;
for (const auto dimension : dimensions)
+ {
product *= dimension;
+ }
return product;
}
@@ -420,13 +442,17 @@ 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("/");
- if (fullPath[0] == '/' || fullPath[0] == '.') // find the second '/'
+ if (fullPath[0] == '/' || fullPath[0] == '.')
+ { // find the second '/'
directoryPosition = fullPath.find("/", directoryPosition + 1);
+ }
struct stat st = {0};
if (directoryPosition == fullPath.npos) // no subdirectories
@@ -464,9 +490,11 @@ void SetTransformsHelper(const std::vector<std::string> &transformNames,
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);
@@ -528,14 +556,18 @@ BuildParametersMap(const std::vector<std::string> ¶meters,
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);
@@ -553,8 +585,10 @@ BuildParametersMap(const std::vector<std::string> ¶meters,
if (debugMode == true)
{
if (parametersOutput.count(field) == 1)
+ {
throw std::invalid_argument("ERROR: parameter " + field +
" already exists, must be unique\n");
+ }
}
parametersOutput[field] = value;
@@ -567,7 +601,9 @@ 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
{
@@ -600,7 +636,9 @@ bool CheckBufferAllocation(const std::size_t newSize, const float growthFactor,
bool doTransportsFlush = (requiredDataSize > maxBufferSize) ? true : false;
if (GrowBuffer(requiredDataSize, growthFactor, buffer) == -1)
+ {
doTransportsFlush = true;
+ }
return doTransportsFlush;
}
@@ -639,8 +677,8 @@ int GrowBuffer(const std::size_t incomingDataSize, const float growthFactor,
bool IsLittleEndian() noexcept
{
- std::uint16_t hexa = 0x1234;
- return *reinterpret_cast<std::uint8_t *>(&hexa) != 0x12;
+ uint16_t hexa = 0x1234;
+ return *reinterpret_cast<uint8_t *>(&hexa) != 0x12; // NOLINT
}
-} // end namespace
+} // namespace adios
diff --git a/source/mpidummy.cpp b/source/mpidummy.cpp
index a0675138b3bf50af3f0a9e1108da5734207f9289..f85e40a44a64c84718691452db59a420e1b8f369 100644
--- a/source/mpidummy.cpp
+++ b/source/mpidummy.cpp
@@ -20,9 +20,10 @@
#include <cstring>
//#define _LARGEFILE64_SOURCE
+#include <unistd.h>
+
#include <sys/time.h>
#include <sys/types.h>
-#include <unistd.h>
/// \endcond
#include "mpidummy.h"
@@ -95,8 +96,9 @@ int MPI_Comm_free(MPI_Comm *comm)
MPI_Comm MPI_Comm_f2c(MPI_Fint comm) { return comm; }
-int MPI_Gather(void *sendbuf, int sendcnt, MPI_Datatype sendtype, void *recvbuf,
- int recvcnt, MPI_Datatype recvtype, int root, MPI_Comm comm)
+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;
@@ -146,8 +148,8 @@ int MPI_Gather(void *sendbuf, int sendcnt, MPI_Datatype sendtype, void *recvbuf,
return ier;
}
-int MPI_Gatherv(void *sendbuf, int sendcnt, MPI_Datatype sendtype,
- void *recvbuf, int *recvcnts, int *displs,
+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;
@@ -165,7 +167,7 @@ int MPI_Gatherv(void *sendbuf, int sendcnt, MPI_Datatype sendtype,
return ier;
}
-int MPI_Allgather(void *sendbuf, int sendcount, MPI_Datatype sendtype,
+int MPI_Allgather(const void *sendbuf, int sendcount, MPI_Datatype sendtype,
void *recvbuf, int recvcount, MPI_Datatype recvtype,
MPI_Comm comm)
{
@@ -173,7 +175,7 @@ int MPI_Allgather(void *sendbuf, int sendcount, MPI_Datatype sendtype,
0, comm);
}
-int MPI_Scatter(void *sendbuf, int sendcnt, MPI_Datatype sendtype,
+int MPI_Scatter(const void *sendbuf, int sendcnt, MPI_Datatype sendtype,
void *recvbuf, int recvcnt, MPI_Datatype recvtype, int root,
MPI_Comm comm)
{
@@ -216,7 +218,7 @@ int MPI_Scatter(void *sendbuf, int sendcnt, MPI_Datatype sendtype,
if (ier == MPI_SUCCESS)
{
- memcpy(sendbuf, recvbuf, nsent);
+ memcpy(recvbuf, sendbuf, nsent);
}
else
{
@@ -226,7 +228,7 @@ int MPI_Scatter(void *sendbuf, int sendcnt, MPI_Datatype sendtype,
return ier;
}
-int MPI_Scatterv(void *sendbuf, int *sendcnts, int *displs,
+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)
{
@@ -260,13 +262,13 @@ int MPI_Irecv(void * /*recvbuffer*/, int /*count*/, MPI_Datatype /*type*/,
return 0;
}
-int MPI_Send(void * /*sendbuffer*/, int /*count*/, MPI_Datatype /*type*/,
+int MPI_Send(const void * /*sendbuffer*/, int /*count*/, MPI_Datatype /*type*/,
int /*destination*/, int /*tag*/, MPI_Comm /*comm*/)
{
return 0;
}
-int MPI_Isend(void * /*recvbuffer*/, int /*count*/, MPI_Datatype /*type*/,
+int MPI_Isend(const void * /*recvbuffer*/, int /*count*/, MPI_Datatype /*type*/,
int /*source*/, int /*tag*/, MPI_Comm /*comm*/,
MPI_Request * /*request*/)
{
@@ -275,7 +277,7 @@ int MPI_Isend(void * /*recvbuffer*/, int /*count*/, MPI_Datatype /*type*/,
int MPI_Wait(MPI_Request * /*request*/, MPI_Status * /*status*/) { return 0; }
-int MPI_File_open(MPI_Comm /*comm*/, char *filename, int amode,
+int MPI_File_open(MPI_Comm /*comm*/, const char *filename, int amode,
MPI_Info /*info*/, MPI_File *fh)
{
*fh = open64(filename, amode);
@@ -327,7 +329,7 @@ int MPI_File_seek(MPI_File fh, MPI_Offset offset, int whence)
return MPI_SUCCESS;
}
-int MPI_Get_count(MPI_Status *status, MPI_Datatype, int *count)
+int MPI_Get_count(const MPI_Status *status, MPI_Datatype, int *count)
{
*count = static_cast<int>(*status);
return MPI_SUCCESS;
diff --git a/source/transform/BZip2.cpp b/source/transform/BZip2.cpp
index 646b8bc6c75ba201e575cf245c54380eff9e712f..c267af7540249968dd42d9e9bb210b2917661150 100644
--- a/source/transform/BZip2.cpp
+++ b/source/transform/BZip2.cpp
@@ -17,15 +17,15 @@ namespace transform
BZIP2::BZIP2() : Transform("bzip2") {}
-BZIP2::~BZIP2() {}
+BZIP2::~BZIP2() = default;
-void BZIP2::Compress(const std::vector<char> &bufferIn,
- std::vector<char> &bufferOut)
+void BZIP2::Compress(const std::vector<char> & /*bufferIn*/,
+ std::vector<char> & /*bufferOut*/)
{
}
-void BZIP2::Decompress(const std::vector<char> &bufferIn,
- std::vector<char> &bufferOut)
+void BZIP2::Decompress(const std::vector<char> & /*bufferIn*/,
+ std::vector<char> & /*bufferOut*/)
{
}
diff --git a/source/transport/file/FStream.cpp b/source/transport/file/FStream.cpp
index 15bf60b58072ae17c4fa5fe171ef65789ea1c395..2a404ae6a96a10471e5ccd97acd547617a73fdb0 100644
--- a/source/transport/file/FStream.cpp
+++ b/source/transport/file/FStream.cpp
@@ -9,6 +9,7 @@
*/
/// \cond EXCLUDED_FROM_DOXYGEN
+#include <ios> // std::ios_base::failure
#include <stdexcept>
/// \endcond
@@ -19,33 +20,37 @@ namespace adios
namespace transport
{
-FStream::FStream(MPI_Comm mpiComm, const bool debugMode)
+FStream::FStream(MPI_Comm mpiComm, bool debugMode)
: Transport("fstream", mpiComm, debugMode)
{
}
-FStream::~FStream() {}
-
void FStream::Open(const std::string name, const std::string 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 (m_DebugMode == true)
{
if (!m_FStream)
+ {
throw std::ios_base::failure(
"ERROR: couldn't open file " + name +
", in call to Open from FStream transport\n");
+ }
}
}
@@ -61,8 +66,10 @@ void FStream::Write(const char *buffer, std::size_t size)
if (m_DebugMode == true)
{
if (!m_FStream)
+ {
throw std::ios_base::failure("ERROR: couldn't write to file " + m_Name +
", in call to FStream write\n");
+ }
}
}
@@ -71,4 +78,4 @@ void FStream::Flush() { m_FStream.flush(); }
void FStream::Close() { m_FStream.close(); }
} // end namespace transport
-} // end namespace
+} // end namespace adios
diff --git a/source/transport/file/FileDescriptor.cpp b/source/transport/file/FileDescriptor.cpp
index e64446e49a771620be22b5d6faad919046e83ad7..d469f017286e8dde70925f6da8c6ebb6dc61308c 100644
--- a/source/transport/file/FileDescriptor.cpp
+++ b/source/transport/file/FileDescriptor.cpp
@@ -54,6 +54,7 @@ void FileDescriptor::Open(const std::string name, const std::string accessMode)
}
else if (accessMode == "a" || accessMode == "append")
{
+
if (m_Profiler.IsActive == true)
m_Profiler.Timers[0].SetInitialTime();
@@ -65,6 +66,7 @@ void FileDescriptor::Open(const std::string name, const std::string accessMode)
}
else if (accessMode == "r" || accessMode == "read")
{
+
if (m_Profiler.IsActive == true)
m_Profiler.Timers[0].SetInitialTime();
@@ -77,14 +79,17 @@ void FileDescriptor::Open(const std::string name, const std::string accessMode)
if (m_DebugMode == true)
{
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.IsActive == true)
m_Profiler.Timers[1].SetInitialTime();
@@ -96,14 +101,18 @@ void FileDescriptor::Write(const char *buffer, std::size_t size)
if (m_DebugMode == true)
{
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");
+ }
}
}
@@ -120,12 +129,14 @@ void FileDescriptor::Close()
if (m_DebugMode == true)
{
if (status == -1)
+ {
throw std::ios_base::failure("ERROR: couldn't close file " + m_Name +
", in call to POSIX write\n");
+ }
}
m_IsOpen = false;
}
} // end namespace transport
-} // end namespace
+} // namespace adios
diff --git a/source/transport/file/FilePointer.cpp b/source/transport/file/FilePointer.cpp
index 704b93f08d55ad410d25f9a04a501c73d60d49a7..1ba57204e6a6827c7454c688b37b8e2f1d62e2c9 100644
--- a/source/transport/file/FilePointer.cpp
+++ b/source/transport/file/FilePointer.cpp
@@ -26,8 +26,10 @@ FilePointer::FilePointer(MPI_Comm mpiComm, const bool debugMode)
FilePointer::~FilePointer()
{
- if (m_File != NULL)
+ if (m_File != nullptr)
+ {
fclose(m_File);
+ }
}
void FilePointer::Open(const std::string name, const std::string accessMode)
@@ -36,20 +38,26 @@ void FilePointer::Open(const std::string name, const std::string accessMode)
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 == NULL)
+ if (m_File == nullptr)
+ {
throw std::ios_base::failure("ERROR: couldn't open file " + name +
", "
"in call to Open from File* transport\n");
+ }
}
}
@@ -60,8 +68,10 @@ void FilePointer::SetBuffer(char *buffer, std::size_t size)
if (m_DebugMode == true)
{
if (status == 1)
+ {
throw std::ios_base::failure("ERROR: could not set buffer in rank " +
std::to_string(m_RankMPI) + "\n");
+ }
}
}
@@ -72,8 +82,10 @@ void FilePointer::Write(const char *buffer, std::size_t size)
if (m_DebugMode == true)
{
if (ferror(m_File))
+ {
throw std::ios_base::failure("ERROR: couldn't write to file " + m_Name +
", in call to File* write\n");
+ }
}
}
@@ -87,4 +99,4 @@ void FilePointer::Close()
}
} // end namespace transport
-} // end namespace
+} // namespace adios
diff --git a/source/packages/format/bp1/BP1Aggregator.cpp b/source/utilities/format/bp1/BP1Aggregator.cpp
similarity index 98%
rename from source/packages/format/bp1/BP1Aggregator.cpp
rename to source/utilities/format/bp1/BP1Aggregator.cpp
index aa6a5d2f61dd63e49541d06bd63cd2b7320f13fb..2d2ff740a29c7b62e01bf78578495f7b875ddb71 100644
--- a/source/packages/format/bp1/BP1Aggregator.cpp
+++ b/source/utilities/format/bp1/BP1Aggregator.cpp
@@ -9,13 +9,13 @@
*/
/// \cond EXCLUDE_FROM_DOXYGEN
+#include "utilities/format/bp1/BP1Aggregator.h"
+
#include <fstream>
#include <stdexcept>
#include <vector>
/// \endcond
-#include "packages/format/bp1/BP1Aggregator.h"
-
namespace adios
{
namespace format
diff --git a/source/packages/format/bp1/BP1Base.cpp b/source/utilities/format/bp1/BP1Base.cpp
similarity index 91%
rename from source/packages/format/bp1/BP1Base.cpp
rename to source/utilities/format/bp1/BP1Base.cpp
index ddb0b042e356ce9137396ccf5379dab32b8ae9f2..b6eea6a7fbb8ff4b7727450dc9c287a1f0521391 100644
--- a/source/packages/format/bp1/BP1Base.cpp
+++ b/source/utilities/format/bp1/BP1Base.cpp
@@ -8,7 +8,7 @@
* Author: wfg
*/
-#include "packages/format/bp1/BP1Base.h"
+#include "utilities/format/bp1/BP1Base.h"
#include "functions/adiosFunctions.h"
namespace adios
@@ -39,8 +39,8 @@ void BP1Base::OpenRankFiles(const std::string name,
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
+ // name.bp/name.bp.rank reserve that
+ // location for writing
}
std::vector<std::uint8_t> BP1Base::GetMethodIDs(
diff --git a/source/packages/format/bp1/BP1Writer.cpp b/source/utilities/format/bp1/BP1Writer.cpp
similarity index 99%
rename from source/packages/format/bp1/BP1Writer.cpp
rename to source/utilities/format/bp1/BP1Writer.cpp
index 4f908f293203713785f7a433e6742c22361115ce..db59eb9eef83d1b8739635956444a762386b355e 100644
--- a/source/packages/format/bp1/BP1Writer.cpp
+++ b/source/utilities/format/bp1/BP1Writer.cpp
@@ -9,12 +9,12 @@
*/
/// \cond EXCLUDE_FROM_DOXYGEN
+#include "utilities/format/bp1/BP1Writer.h"
+
#include <string>
#include <vector>
/// \endcond
-#include "packages/format/bp1/BP1Writer.h"
-
namespace adios
{
namespace format
diff --git a/source/packages/profiling/iochrono/Timer.cpp b/source/utilities/profiling/iochrono/Timer.cpp
similarity index 98%
rename from source/packages/profiling/iochrono/Timer.cpp
rename to source/utilities/profiling/iochrono/Timer.cpp
index 9f6356f4a3412841e16848dfc1ae2999435534c6..7aab0c5a09b34fcb274fc3f337a04747cb943dc5 100644
--- a/source/packages/profiling/iochrono/Timer.cpp
+++ b/source/utilities/profiling/iochrono/Timer.cpp
@@ -8,7 +8,7 @@
* Author: wfg
*/
-#include "packages/profiling/iochrono/Timer.h"
+#include "utilities/profiling/iochrono/Timer.h"
namespace adios
{
diff --git a/thirdparty/CMakeLists.txt b/thirdparty/CMakeLists.txt
index 0825c4704eca3867613ee2f58fdd5636d2fdee5b..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
--- a/thirdparty/CMakeLists.txt
+++ b/thirdparty/CMakeLists.txt
@@ -1,41 +0,0 @@
-#------------------------------------------------------------------------------#
-# Distributed under the OSI-approved Apache License, Version 2.0. See
-# accompanying file Copyright.txt for details.
-#------------------------------------------------------------------------------#
-
-set(ADIOS_THIRDPARTY_DOWNLOAD_DIR ${CMAKE_CURRENT_BINARY_DIR}/downloads
- CACHE PATH "Download directory for third party dependencies")
-
-include(ExternalProject)
-
-# Boilerplate settings for a common external project infrastructure
-set(EP_ARGS
- DOWNLOAD_DIR ${ADIOS_THIRDPARTY_DOWNLOAD_DIR}
- PREFIX .
- SOURCE_DIR source
- BINARY_DIR build
- STAMP_DIR stamp
- INSTALL_DIR install)
-
-# Use Google Test for a unit testing framework
-cmake_dependent_option(ADIOS_USE_SYSTEM_GOOGLETEST
- "Use a system-supplied Google Test framework" ON
- "BUILD_TESTING" OFF)
-if(BUILD_TESTING)
- if(ADIOS_USE_SYSTEM_GOOGLETEST)
- find_package(GTest REQUIRED)
- if(NOT GTEST_FOUND)
- message(WARNING
- "Unable to find Google Test framework. "
- "Using an internal version")
- set(ADIOS_USE_SYSTEM_GOOGLETEST OFF
- CACHE BOOL "Use a system-supplied Google Test framework" FORCE)
- endif()
- endif()
- if(NOT ADIOS_USE_SYSTEM_GOOGLETEST)
- add_subdirectory(googletest)
- find_package(GTest REQUIRED)
- add_dependencies(GTest::GTest googletest)
- add_dependencies(GTest::Main googletest)
- endif()
-endif()
diff --git a/thirdparty/googletest/CMakeLists.txt b/thirdparty/googletest/CMakeLists.txt
deleted file mode 100644
index 5fc4fa9ee1dfe938e27473fbc1ae7ea0b9c90aea..0000000000000000000000000000000000000000
--- a/thirdparty/googletest/CMakeLists.txt
+++ /dev/null
@@ -1,40 +0,0 @@
-#------------------------------------------------------------------------------#
-# Distributed under the OSI-approved Apache License, Version 2.0. See
-# accompanying file Copyright.txt for details.
-#------------------------------------------------------------------------------#
-
-ExternalProject_Add(googletest
- URL https://github.com/google/googletest/archive/release-1.8.0.zip
- URL_MD5 adfafc8512ab65fd3cf7955ef0100ff5
- ${EP_ARGS}
- CMAKE_ARGS
- -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/install
- -DCMAKE_POLICY_DEFAULT_CMP0048=OLD
- -DCMAKE_POLICY_DEFAULT_CMP0063=NEW
- -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
- -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
- -DBUILD_GMOCK=OFF
- -DBUILD_GTEST=ON
- -Dgtest_build_samples=OFF
- -Dgtest_build_tests=OFF
- -Dgtest_hide_internal_symbols=ON
- -Dgtest_disable_pthreads=OFF
- -Dgtest_force_shared_crt=OFF)
-
-function(get_libfile var name)
- if(BUILD_SHARED_LIBS)
- set(${var} ${CMAKE_SHARED_LIBRARY_PREFIX}${name}${CMAKE_SHARED_LIBRARY_SUFFIX} PARENT_SCOPE)
- else()
- set(${var} ${CMAKE_STATIC_LIBRARY_PREFIX}${name}${CMAKE_STATIC_LIBRARY_SUFFIX} PARENT_SCOPE)
- endif()
-endfunction()
-
-get_libfile(GTEST_LIBRARY gtest)
-get_libfile(GTEST_MAIN_LIBRARY gtest_main)
-set(GTEST_ROOT ${CMAKE_CURRENT_BINARY_DIR}/install)
-set(GTEST_INCLUDE_DIR ${GTEST_ROOT}/include
- CACHE PATH "")
-set(GTEST_LIBRARY ${GTEST_ROOT}/lib/${GTEST_LIBRARY}
- CACHE FILEPATH "")
-set(GTEST_MAIN_LIBRARY ${GTEST_ROOT}/lib/${GTEST_MAIN_LIBRARY}
- CACHE FILEPATH "")