diff --git a/examples/heatTransfer/write/CMakeLists.txt b/examples/heatTransfer/write/CMakeLists.txt
index 7144a8e7720987406c27e6bbf61c2e31f7a0b4a7..5034755f77f8c54ea8e46f98c650624b17b0b01b 100644
--- a/examples/heatTransfer/write/CMakeLists.txt
+++ b/examples/heatTransfer/write/CMakeLists.txt
@@ -53,6 +53,26 @@ if(ADIOS_USE_MPI)
)
endif()
+
+ if(ADIOS_USE_HDF5)
+ find_package(HDF5 REQUIRED)
+ find_package(MPI COMPONENTS C REQUIRED)
+
+ add_executable(heatTransfer_write_ph5
+ main.cpp
+ HeatTransfer.cpp
+ Settings.cpp
+ IO_ph5.cpp
+ )
+ target_include_directories(heatTransfer_write_ph5
+ PRIVATE ${MPI_C_INCLUDE_PATH} ${HDF5_C_INCLUDE_DIRS}
+ )
+ target_link_libraries(heatTransfer_write_ph5
+ ${MPI_C_LIBRARIES} ${HDF5_C_LIBRARIES}
+ )
+ endif()
+
+
if(ADIOS_USE_HDF5)
find_package(MPI COMPONENTS C REQUIRED)
diff --git a/examples/heatTransfer/write/IO_ph5.cpp b/examples/heatTransfer/write/IO_ph5.cpp
index bc0faa3d6977ee3f227d39ed995a5a37634f6c24..4d892157771ae2a4adecf99654c393c7f19355c6 100644
--- a/examples/heatTransfer/write/IO_ph5.cpp
+++ b/examples/heatTransfer/write/IO_ph5.cpp
@@ -21,179 +21,175 @@ class HDF5NativeWriter
{
public:
- HDF5NativeWriter(const std::string& fileName);
- ~HDF5NativeWriter();
+ HDF5NativeWriter(const std::string &fileName);
+ ~HDF5NativeWriter();
- bool Advance();
- void Close();
- void CheckWriteGroup();
+ bool Advance();
+ void Close();
+ void CheckWriteGroup();
- void WriteScalar(const std::string& varName, const void *data, hid_t h5Type);
- void WriteSimple(const std::string& varName, int dimSize, const void *data, hid_t h5Type, const hsize_t* shape, const hsize_t* offset, const hsize_t* count);
+ void WriteScalar(const std::string &varName, const void *data,
+ hid_t h5Type);
+ void WriteSimple(const std::string &varName, int dimSize, const void *data,
+ hid_t h5Type, const hsize_t *shape, const hsize_t *offset,
+ const hsize_t *count);
- int m_CurrentTimeStep;
- unsigned int m_TotalTimeSteps;
+ int m_CurrentTimeStep;
+ unsigned int m_TotalTimeSteps;
private:
- hid_t m_FilePropertyListId;
- hid_t m_FileId;
- hid_t m_GroupId;
+ hid_t m_FilePropertyListId;
+ hid_t m_FileId;
+ hid_t m_GroupId;
};
-HDF5NativeWriter::HDF5NativeWriter(const std::string& fileName)
- : m_CurrentTimeStep(0), m_TotalTimeSteps(0)
+HDF5NativeWriter::HDF5NativeWriter(const std::string &fileName)
+: m_CurrentTimeStep(0), m_TotalTimeSteps(0)
{
- m_FilePropertyListId = H5Pcreate(H5P_FILE_ACCESS);
+ m_FilePropertyListId = H5Pcreate(H5P_FILE_ACCESS);
#ifdef ADIOS2_HAVE_MPI
- // read a file collectively
- H5Pset_fapl_mpio(m_FilePropertyListId, MPI_COMM_WORLD, MPI_INFO_NULL);
+ // read a file collectively
+ H5Pset_fapl_mpio(m_FilePropertyListId, MPI_COMM_WORLD, MPI_INFO_NULL);
#endif
- m_FileId = H5Fcreate(fileName.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT,
- m_FilePropertyListId);
+ m_FileId = H5Fcreate(fileName.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT,
+ m_FilePropertyListId);
- if (m_FileId < 0)
+ if (m_FileId < 0)
{
- throw std::runtime_error("Unable to open " + fileName + " for reading");
+ throw std::runtime_error("Unable to open " + fileName + " for reading");
}
- std::string ts0 = "/TimeStep0";
+ std::string ts0 = "/TimeStep0";
- m_GroupId = H5Gcreate2(m_FileId, ts0.c_str(), H5P_DEFAULT,
- H5P_DEFAULT, H5P_DEFAULT);
- if (m_GroupId < 0)
+ m_GroupId = H5Gcreate2(m_FileId, ts0.c_str(), H5P_DEFAULT, H5P_DEFAULT,
+ H5P_DEFAULT);
+ if (m_GroupId < 0)
{
- throw std::runtime_error("HDF5: Unable to create group " + ts0);
+ throw std::runtime_error("HDF5: Unable to create group " + ts0);
}
}
-HDF5NativeWriter::~HDF5NativeWriter()
-{
- Close();
-}
+HDF5NativeWriter::~HDF5NativeWriter() { Close(); }
void HDF5NativeWriter::Close()
{
- if (m_FileId < 0)
- return;
+ if (m_FileId < 0)
+ return;
- hid_t s = H5Screate(H5S_SCALAR);
- hid_t attr = H5Acreate(m_FileId, "NumTimeSteps", H5T_NATIVE_UINT, s,
- H5P_DEFAULT, H5P_DEFAULT);
- uint totalTimeSteps = m_CurrentTimeStep + 1;
+ hid_t s = H5Screate(H5S_SCALAR);
+ hid_t attr = H5Acreate(m_FileId, "NumTimeSteps", H5T_NATIVE_UINT, s,
+ H5P_DEFAULT, H5P_DEFAULT);
+ uint totalTimeSteps = m_CurrentTimeStep + 1;
- if (m_GroupId < 0)
+ if (m_GroupId < 0)
{
- totalTimeSteps = m_CurrentTimeStep;
- }
- H5Awrite(attr, H5T_NATIVE_UINT, &totalTimeSteps);
- H5Sclose(s);
- H5Aclose(attr);
-
+ totalTimeSteps = m_CurrentTimeStep;
+ }
+ H5Awrite(attr, H5T_NATIVE_UINT, &totalTimeSteps);
+ H5Sclose(s);
+ H5Aclose(attr);
- if (m_GroupId >= 0)
+ if (m_GroupId >= 0)
{
- H5Gclose(m_GroupId);
- m_GroupId = -1;
- }
+ H5Gclose(m_GroupId);
+ m_GroupId = -1;
+ }
- H5Fclose(m_FileId);
- m_FileId = -1;
- H5Pclose(m_FilePropertyListId);
+ H5Fclose(m_FileId);
+ m_FileId = -1;
+ H5Pclose(m_FilePropertyListId);
}
bool HDF5NativeWriter::Advance()
{
- if (m_GroupId >= 0)
+ if (m_GroupId >= 0)
{
- H5Gclose(m_GroupId);
- m_GroupId = -1;
+ H5Gclose(m_GroupId);
+ m_GroupId = -1;
}
- ++m_CurrentTimeStep;
+ ++m_CurrentTimeStep;
- return true;
+ return true;
}
-
void HDF5NativeWriter::CheckWriteGroup()
{
- if (m_GroupId >= 0)
+ if (m_GroupId >= 0)
{
- return;
+ return;
}
- std::string timeStepName = "/TimeStep" + std::to_string(m_CurrentTimeStep);
- m_GroupId = H5Gcreate2(m_FileId, timeStepName.c_str(), H5P_DEFAULT,
- H5P_DEFAULT, H5P_DEFAULT);
- if (m_GroupId < 0)
+ std::string timeStepName = "/TimeStep" + std::to_string(m_CurrentTimeStep);
+ m_GroupId = H5Gcreate2(m_FileId, timeStepName.c_str(), H5P_DEFAULT,
+ H5P_DEFAULT, H5P_DEFAULT);
+ if (m_GroupId < 0)
{
- throw std::runtime_error("HDF5: Unable to create group " +
- timeStepName);
+ throw std::runtime_error("HDF5: Unable to create group " +
+ timeStepName);
}
}
+void HDF5NativeWriter::WriteScalar(const std::string &varName, const void *data,
+ hid_t h5Type)
+{
+ CheckWriteGroup();
+ // scalar
+ hid_t filespaceID = H5Screate(H5S_SCALAR);
+ hid_t dsetID = H5Dcreate(m_GroupId, varName.c_str(), h5Type, filespaceID,
+ H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ herr_t status =
+ H5Dwrite(dsetID, h5Type, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
+
+ H5Sclose(filespaceID);
+ H5Dclose(dsetID);
+}
-void HDF5NativeWriter::WriteScalar(const std::string& varName, const void *data, hid_t h5Type)
+void HDF5NativeWriter::WriteSimple(const std::string &varName, int dimSize,
+ const void *data, hid_t h5Type,
+ const hsize_t *shape, const hsize_t *offset,
+ const hsize_t *count)
{
- CheckWriteGroup();
- // scalar
- hid_t filespaceID = H5Screate(H5S_SCALAR);
- hid_t dsetID =
- H5Dcreate(m_GroupId, varName.c_str(), h5Type,
- filespaceID, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
- herr_t status =
- H5Dwrite(dsetID, h5Type, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
-
- H5Sclose(filespaceID);
- H5Dclose(dsetID);
+ CheckWriteGroup();
+ hid_t fileSpace = H5Screate_simple(dimSize, shape, NULL);
-}
+ hid_t dsetID = H5Dcreate(m_GroupId, varName.c_str(), h5Type, fileSpace,
+ H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+ hid_t memSpace = H5Screate_simple(dimSize, count, NULL);
+
+ // Select hyperslab
+ fileSpace = H5Dget_space(dsetID);
+ H5Sselect_hyperslab(fileSpace, H5S_SELECT_SET, offset, NULL, count, NULL);
+
+ // Create property list for collective dataset write.
-void HDF5NativeWriter::WriteSimple(const std::string& varName, int dimSize, const void *data, hid_t h5Type, const hsize_t* shape, const hsize_t* offset, const hsize_t* count)
-{
- CheckWriteGroup();
- hid_t fileSpace = H5Screate_simple(dimSize, shape, NULL);
-
- hid_t dsetID =
- H5Dcreate(m_GroupId, varName.c_str(), h5Type,
- fileSpace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
-
- hid_t memSpace = H5Screate_simple(dimSize, count, NULL);
-
- // Select hyperslab
- fileSpace = H5Dget_space(dsetID);
- H5Sselect_hyperslab(fileSpace, H5S_SELECT_SET, offset, NULL,
- count, NULL);
-
- // Create property list for collective dataset write.
-
- hid_t plistID = H5Pcreate(H5P_DATASET_XFER);
+ hid_t plistID = H5Pcreate(H5P_DATASET_XFER);
#ifdef ADIOS2_HAVE_MPI
- H5Pset_dxpl_mpio(plistID, H5FD_MPIO_COLLECTIVE);
+ H5Pset_dxpl_mpio(plistID, H5FD_MPIO_COLLECTIVE);
#endif
- herr_t status;
-
- status = H5Dwrite(dsetID, h5Type, memSpace, fileSpace, plistID, data);
-
- if (status < 0)
+ herr_t status;
+
+ status = H5Dwrite(dsetID, h5Type, memSpace, fileSpace, plistID, data);
+
+ if (status < 0)
{
- // error
- std::cerr << " Write failed. " << std::endl;
+ // error
+ std::cerr << " Write failed. " << std::endl;
}
-
- H5Dclose(dsetID);
- H5Sclose(fileSpace);
- H5Sclose(memSpace);
- H5Pclose(plistID);
+
+ H5Dclose(dsetID);
+ H5Sclose(fileSpace);
+ H5Sclose(memSpace);
+ H5Pclose(plistID);
}
//
//
std::shared_ptr<HDF5NativeWriter> h5writer;
-//HDF5NativeWriter* h5writer;
-
+// HDF5NativeWriter* h5writer;
IO::IO(const Settings &s, MPI_Comm comm)
{
@@ -208,17 +204,18 @@ IO::IO(const Settings &s, MPI_Comm comm)
IO::~IO()
{
h5writer->Close();
- //delete h5writer;
+ // delete h5writer;
}
void IO::write(int step, const HeatTransfer &ht, const Settings &s,
MPI_Comm comm)
{
- std::vector<hsize_t> dims = {s.gndx, s.gndy};
+ std::vector<hsize_t> dims = {s.gndx, s.gndy};
std::vector<hsize_t> offset = {s.offsx, s.offsy};
- std::vector<hsize_t> count = {s.ndx, s.ndy};
+ std::vector<hsize_t> count = {s.ndx, s.ndy};
- h5writer->WriteSimple("T", 2, ht.data_noghost().data(), H5T_NATIVE_DOUBLE, dims.data(), offset.data(), count.data());
+ h5writer->WriteSimple("T", 2, ht.data_noghost().data(), H5T_NATIVE_DOUBLE,
+ dims.data(), offset.data(), count.data());
h5writer->WriteScalar("gndy", &(s.gndy), H5T_NATIVE_UINT);
h5writer->Advance();
diff --git a/examples/heatTransfer/write/IO_ph5_adios2.cpp b/examples/heatTransfer/write/IO_ph5_adios2.cpp
index abed29d13712e1da144744f01879724122f4d8c5..e694d9f291698cbb51f4bc8b0e304e32d6d90e1f 100644
--- a/examples/heatTransfer/write/IO_ph5_adios2.cpp
+++ b/examples/heatTransfer/write/IO_ph5_adios2.cpp
@@ -106,8 +106,8 @@ void IO::write(int step, const HeatTransfer &ht, const Settings &s,
h5writer->Write<double>(*varT, ht.data_noghost().data());
// h5writer->Write(*varT, ht.data_noghost().data());
- h5writer->Write<unsigned int>(*varGndx, s.gndx);
- h5writer->Write<unsigned int>("gndy", s.gndy);
+ h5writer->Write<unsigned int>(*varGndx, &(s.gndx));
+ h5writer->Write("gndy", &(s.gndy));
h5writer->Advance();
diff --git a/source/adios2/engine/hdf5/HDF5WriterP.cpp b/source/adios2/engine/hdf5/HDF5WriterP.cpp
index acd523feca71fa7e9c59e006178b7efdf73a05da..db9d6c4e6e0e1a7d31e54aa5055eb2a325b9deb3 100644
--- a/source/adios2/engine/hdf5/HDF5WriterP.cpp
+++ b/source/adios2/engine/hdf5/HDF5WriterP.cpp
@@ -134,105 +134,105 @@ void HDF5Writer::Write(Variable<std::complex<long double>> &variable,
}
// String version
-void HDF5Writer::Write(const std::string variableName, const char *values)
+void HDF5Writer::Write(const std::string &variableName, const char *values)
{
UseHDFWrite(m_ADIOS.GetVariable<char>(variableName), values,
H5T_NATIVE_CHAR);
}
-void HDF5Writer::Write(const std::string variableName,
+void HDF5Writer::Write(const std::string &variableName,
const unsigned char *values)
{
UseHDFWrite(m_ADIOS.GetVariable<unsigned char>(variableName), values,
H5T_NATIVE_UCHAR);
}
-void HDF5Writer::Write(const std::string variableName, const short *values)
+void HDF5Writer::Write(const std::string &variableName, const short *values)
{
UseHDFWrite(m_ADIOS.GetVariable<short>(variableName), values,
H5T_NATIVE_SHORT);
}
-void HDF5Writer::Write(const std::string variableName,
+void HDF5Writer::Write(const std::string &variableName,
const unsigned short *values)
{
UseHDFWrite(m_ADIOS.GetVariable<unsigned short>(variableName), values,
H5T_NATIVE_USHORT);
}
-void HDF5Writer::Write(const std::string variableName, const int *values)
+void HDF5Writer::Write(const std::string &variableName, const int *values)
{
UseHDFWrite(m_ADIOS.GetVariable<int>(variableName), values, H5T_NATIVE_INT);
}
-void HDF5Writer::Write(const std::string variableName,
+void HDF5Writer::Write(const std::string &variableName,
const unsigned int *values)
{
UseHDFWrite(m_ADIOS.GetVariable<unsigned int>(variableName), values,
H5T_NATIVE_UINT);
}
-void HDF5Writer::Write(const std::string variableName, const long int *values)
+void HDF5Writer::Write(const std::string &variableName, const long int *values)
{
UseHDFWrite(m_ADIOS.GetVariable<long int>(variableName), values,
H5T_NATIVE_LONG);
}
-void HDF5Writer::Write(const std::string variableName,
+void HDF5Writer::Write(const std::string &variableName,
const unsigned long int *values)
{
UseHDFWrite(m_ADIOS.GetVariable<unsigned long int>(variableName), values,
H5T_NATIVE_ULONG);
}
-void HDF5Writer::Write(const std::string variableName,
+void HDF5Writer::Write(const std::string &variableName,
const long long int *values)
{
UseHDFWrite(m_ADIOS.GetVariable<long long int>(variableName), values,
H5T_NATIVE_LLONG);
}
-void HDF5Writer::Write(const std::string variableName,
+void HDF5Writer::Write(const std::string &variableName,
const unsigned long long int *values)
{
UseHDFWrite(m_ADIOS.GetVariable<unsigned long long int>(variableName),
values, H5T_NATIVE_ULLONG);
}
-void HDF5Writer::Write(const std::string variableName, const float *values)
+void HDF5Writer::Write(const std::string &variableName, const float *values)
{
UseHDFWrite(m_ADIOS.GetVariable<float>(variableName), values,
H5T_NATIVE_FLOAT);
}
-void HDF5Writer::Write(const std::string variableName, const double *values)
+void HDF5Writer::Write(const std::string &variableName, const double *values)
{
UseHDFWrite(m_ADIOS.GetVariable<double>(variableName), values,
H5T_NATIVE_DOUBLE);
}
-void HDF5Writer::Write(const std::string variableName,
+void HDF5Writer::Write(const std::string &variableName,
const long double *values)
{
UseHDFWrite(m_ADIOS.GetVariable<long double>(variableName), values,
H5T_NATIVE_LDOUBLE);
}
-void HDF5Writer::Write(const std::string variableName,
+void HDF5Writer::Write(const std::string &variableName,
const std::complex<float> *values)
{
UseHDFWrite(m_ADIOS.GetVariable<std::complex<float>>(variableName), values,
m_H5File.m_DefH5TypeComplexFloat);
}
-void HDF5Writer::Write(const std::string variableName,
+void HDF5Writer::Write(const std::string &variableName,
const std::complex<double> *values)
{
UseHDFWrite(m_ADIOS.GetVariable<std::complex<double>>(variableName), values,
m_H5File.m_DefH5TypeComplexDouble);
}
-void HDF5Writer::Write(const std::string variableName,
+void HDF5Writer::Write(const std::string &variableName,
const std::complex<long double> *values)
{
UseHDFWrite(m_ADIOS.GetVariable<std::complex<long double>>(variableName),
diff --git a/source/adios2/engine/hdf5/HDF5WriterP.h b/source/adios2/engine/hdf5/HDF5WriterP.h
index 3ab1b970ec75231a04537a74d9ad97967af8dd75..22a1b8f57ef079c04f87680c57bb52fa340f74a0 100644
--- a/source/adios2/engine/hdf5/HDF5WriterP.h
+++ b/source/adios2/engine/hdf5/HDF5WriterP.h
@@ -64,25 +64,26 @@ public:
void Write(Variable<std::complex<long double>> &variable,
const std::complex<long double> *values);
- void Write(const std::string variableName, const char *values);
- void Write(const std::string variableName, const unsigned char *values);
- void Write(const std::string variableName, const short *values);
- void Write(const std::string variableName, const unsigned short *values);
- void Write(const std::string variableName, const int *values);
- void Write(const std::string variableName, const unsigned int *values);
- void Write(const std::string variableName, const long int *values);
- void Write(const std::string variableName, const unsigned long int *values);
- void Write(const std::string variableName, const long long int *values);
- void Write(const std::string variableName,
+ void Write(const std::string &variableName, const char *values);
+ void Write(const std::string &variableName, const unsigned char *values);
+ void Write(const std::string &variableName, const short *values);
+ void Write(const std::string &variableName, const unsigned short *values);
+ void Write(const std::string &variableName, const int *values);
+ void Write(const std::string &variableName, const unsigned int *values);
+ void Write(const std::string &variableName, const long int *values);
+ void Write(const std::string &variableName,
+ const unsigned long int *values);
+ void Write(const std::string &variableName, const long long int *values);
+ void Write(const std::string &variableName,
const unsigned long long int *values);
- void Write(const std::string variableName, const float *values);
- void Write(const std::string variableName, const double *values);
- void Write(const std::string variableName, const long double *values);
- void Write(const std::string variableName,
+ void Write(const std::string &variableName, const float *values);
+ void Write(const std::string &variableName, const double *values);
+ void Write(const std::string &variableName, const long double *values);
+ void Write(const std::string &variableName,
const std::complex<float> *values);
- void Write(const std::string variableName,
+ void Write(const std::string &variableName,
const std::complex<double> *values);
- void Write(const std::string variableName,
+ void Write(const std::string &variableName,
const std::complex<long double> *values);
void Advance(float timeoutSec = 0.0);