diff --git a/examples/hello/hdf5Writer/helloHDF5Writer.cpp b/examples/hello/hdf5Writer/helloHDF5Writer.cpp
index aaf85ec64265345c685d90234226fe473f7e6aff..07088fb2ee76ab6276b5214960cb3836ce153c80 100644
--- a/examples/hello/hdf5Writer/helloHDF5Writer.cpp
+++ b/examples/hello/hdf5Writer/helloHDF5Writer.cpp
@@ -8,7 +8,8 @@
#include <iostream>
#include <vector>
-#include "adios2.h"
+#include <adios2.h>
+
#include <mpi.h>
int main(int argc, char *argv[])
diff --git a/source/adios2/ADIOS.cpp b/source/adios2/ADIOS.cpp
index db91c88f32038039e4341e4a99b93453a0f967e7..8fd661a80b0c3f3a15446728afa25955965cd928 100644
--- a/source/adios2/ADIOS.cpp
+++ b/source/adios2/ADIOS.cpp
@@ -196,9 +196,7 @@ std::shared_ptr<Engine> ADIOS::Open(const std::string &name,
}
else if (type == "HDF5Reader") // -Junmin
{
-//#if defined(ADIOS_HAVE_PHDF5) && defined(ADIOS_HAVE_MPI)
-#ifdef ADIOS_HAVE_HDF5
- //#ifdef ADIOS_HAVE_MPI
+#ifdef ADIOS2_HAVE_HDF5
return std::make_shared<HDF5Reader>(*this, name, accessMode, mpiComm,
method);
#else
diff --git a/source/adios2/engine/hdf5/HDF5Common.cpp b/source/adios2/engine/hdf5/HDF5Common.cpp
index 2b2e605ffa83e982914a6b2e32319d2c9398c599..e2a9c521ee6b08d50094910ea43e85920d395350 100644
--- a/source/adios2/engine/hdf5/HDF5Common.cpp
+++ b/source/adios2/engine/hdf5/HDF5Common.cpp
@@ -10,6 +10,7 @@
#include "HDF5Common.h"
+#include <complex>
#include <iostream>
#include "adios2/ADIOSMPI.h"
@@ -20,38 +21,37 @@ namespace adios
#define H5_ERROR std::cout << "[ADIOS H5 ERROR] "
HDF5Common::HDF5Common()
-: m_WriteMode(false), m_Total_timestep(0), m_CurrentTimeStep(0)
+: m_WriteMode(false), m_CurrentTimeStep(0), m_NumTimeSteps(0)
{
- m_DefH5T_COMPLEX_FLOAT =
+ m_DefH5TypeComplexFloat =
H5Tcreate(H5T_COMPOUND, sizeof(std::complex<float>));
- H5Tinsert(m_DefH5T_COMPLEX_FLOAT, "freal", 0, H5T_NATIVE_FLOAT);
- H5Tinsert(m_DefH5T_COMPLEX_FLOAT, "fimg", H5Tget_size(H5T_NATIVE_FLOAT),
+ H5Tinsert(m_DefH5TypeComplexFloat, "freal", 0, H5T_NATIVE_FLOAT);
+ H5Tinsert(m_DefH5TypeComplexFloat, "fimg", H5Tget_size(H5T_NATIVE_FLOAT),
H5T_NATIVE_FLOAT);
- m_DefH5T_COMPLEX_DOUBLE =
+ m_DefH5TypeComplexDouble =
H5Tcreate(H5T_COMPOUND, sizeof(std::complex<double>));
- H5Tinsert(m_DefH5T_COMPLEX_DOUBLE, "dreal", 0, H5T_NATIVE_DOUBLE);
- H5Tinsert(m_DefH5T_COMPLEX_DOUBLE, "dimg", H5Tget_size(H5T_NATIVE_DOUBLE),
+ H5Tinsert(m_DefH5TypeComplexDouble, "dreal", 0, H5T_NATIVE_DOUBLE);
+ H5Tinsert(m_DefH5TypeComplexDouble, "dimg", H5Tget_size(H5T_NATIVE_DOUBLE),
H5T_NATIVE_DOUBLE);
- m_DefH5T_COMPLEX_LongDOUBLE =
+ m_DefH5TypeComplexLongDouble =
H5Tcreate(H5T_COMPOUND, sizeof(std::complex<long double>));
- H5Tinsert(m_DefH5T_COMPLEX_LongDOUBLE, "ldouble real", 0,
+ H5Tinsert(m_DefH5TypeComplexLongDouble, "ldouble real", 0,
H5T_NATIVE_LDOUBLE);
- H5Tinsert(m_DefH5T_COMPLEX_LongDOUBLE, "ldouble img",
+ H5Tinsert(m_DefH5TypeComplexLongDouble, "ldouble img",
H5Tget_size(H5T_NATIVE_LDOUBLE), H5T_NATIVE_LDOUBLE);
}
-void HDF5Common::H5_Init(const std::string name, MPI_Comm m_MPIComm,
- bool toWrite)
+void HDF5Common::Init(const std::string name, MPI_Comm comm, bool toWrite)
{
m_WriteMode = toWrite;
//
- m_Plist_id = H5Pcreate(H5P_FILE_ACCESS);
+ m_PropertyListId = H5Pcreate(H5P_FILE_ACCESS);
#ifdef ADIOS2_HAVE_MPI
- H5Pset_fapl_mpio(m_Plist_id, m_MPIComm, MPI_INFO_NULL);
+ H5Pset_fapl_mpio(m_PropertyListId, comm, MPI_INFO_NULL);
#endif
std::string ts0 = "/TimeStep0";
@@ -61,32 +61,35 @@ void HDF5Common::H5_Init(const std::string name, MPI_Comm m_MPIComm,
/*
* Create a new file collectively and release property list identifier.
*/
- m_File_id =
- H5Fcreate(name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, m_Plist_id);
- if (m_File_id >= 0)
+ m_FileId = H5Fcreate(name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT,
+ m_PropertyListId);
+ if (m_FileId >= 0)
{
- m_Group_id = H5Gcreate2(m_File_id, ts0.c_str(), H5P_DEFAULT,
- H5P_DEFAULT, H5P_DEFAULT);
+ m_GroupId = H5Gcreate2(m_FileId, ts0.c_str(), H5P_DEFAULT,
+ H5P_DEFAULT, H5P_DEFAULT);
+ if (m_GroupId < 0)
+ {
+ std::clog << "H5Common::Init: ERROR" << std::endl;
+ throw std::runtime_error("HDF5: Unable to create group " + ts0);
+ }
}
}
else
{
// read a file collectively
- m_File_id = H5Fopen(name.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
- if (m_File_id >= 0)
+ m_FileId = H5Fopen(name.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+ if (m_FileId >= 0)
{
- m_Group_id = H5Gopen(m_File_id, ts0.c_str(), H5P_DEFAULT);
+ m_GroupId = H5Gopen(m_FileId, ts0.c_str(), H5P_DEFAULT);
}
}
- H5Pclose(m_Plist_id);
+ H5Pclose(m_PropertyListId);
}
-// HDF5Common::~HDF5Common() {}
-
void HDF5Common::WriteTimeSteps()
{
- if (m_File_id < 0)
+ if (m_FileId < 0)
{
// std::cerr<<"[ADIOS HDF5Error]: Invalid file to record timestep
// to."<<std::endl;
@@ -101,29 +104,29 @@ void HDF5Common::WriteTimeSteps()
hid_t s = H5Screate(H5S_SCALAR);
- hid_t attr = H5Acreate(m_File_id, "NumTimeSteps", H5T_NATIVE_UINT, s,
+ hid_t attr = H5Acreate(m_FileId, "NumTimeSteps", H5T_NATIVE_UINT, s,
H5P_DEFAULT, H5P_DEFAULT);
- uint totalts = m_CurrentTimeStep + 1;
+ uint totalTimeSteps = m_CurrentTimeStep + 1;
- if (m_Group_id < 0)
+ if (m_GroupId < 0)
{
- totalts = m_CurrentTimeStep;
+ totalTimeSteps = m_CurrentTimeStep;
}
- H5Awrite(attr, H5T_NATIVE_UINT, &totalts);
+ H5Awrite(attr, H5T_NATIVE_UINT, &totalTimeSteps);
H5Sclose(s);
H5Aclose(attr);
}
-int HDF5Common::GetNumTimeSteps()
+unsigned int HDF5Common::GetNumTimeSteps()
{
if (m_WriteMode)
{
return -1;
}
- if (m_File_id < 0)
+ if (m_FileId < 0)
{
std::cerr
<< "[ADIOS HDF5Error]: Invalid file to read timestep attribute."
@@ -131,62 +134,70 @@ int HDF5Common::GetNumTimeSteps()
return -1;
}
- if (m_Total_timestep <= 0)
+ if (m_NumTimeSteps <= 0)
{
- hid_t attr = H5Aopen(m_File_id, "NumTimeSteps", H5P_DEFAULT);
+ hid_t attr = H5Aopen(m_FileId, "NumTimeSteps", H5P_DEFAULT);
- H5Aread(attr, H5T_NATIVE_UINT, &m_Total_timestep);
+ H5Aread(attr, H5T_NATIVE_UINT, &m_NumTimeSteps);
H5Aclose(attr);
}
- return m_Total_timestep;
+ return m_NumTimeSteps;
}
-void HDF5Common::H5_Close()
+void HDF5Common::Close()
{
- if (m_File_id < 0)
+ if (m_FileId < 0)
{
return;
}
WriteTimeSteps();
- if (m_Group_id >= 0)
+ if (m_GroupId >= 0)
{
- H5Gclose(m_Group_id);
+ H5Gclose(m_GroupId);
}
- H5Fclose(m_File_id);
- m_File_id = -1;
- m_Group_id = -1;
+ H5Fclose(m_FileId);
+ m_FileId = -1;
+ m_GroupId = -1;
}
-void HDF5Common::H5_Advance(int totalts)
+void HDF5Common::Advance()
{
- m_CurrentTimeStep++;
- if (m_CurrentTimeStep > 0)
+ if (m_GroupId >= 0)
{
- H5Gclose(m_Group_id);
- m_Group_id = -1;
+ H5Gclose(m_GroupId);
+ m_GroupId = -1;
}
- std::string tsname = "/TimeStep";
- tsname.append(std::to_string(m_CurrentTimeStep));
-
if (m_WriteMode)
{
- // m_Group_id = H5Gcreate2(m_File_id, tsname.c_str(), H5P_DEFAULT,
+ // m_GroupId = H5Gcreate2(m_FileId, tsname.c_str(), H5P_DEFAULT,
// H5P_DEFAULT, H5P_DEFAULT);
}
else
{
- if ((totalts > 0) && (totalts <= m_CurrentTimeStep))
+ if (m_NumTimeSteps == 0)
+ {
+ GetNumTimeSteps();
+ }
+ if (m_CurrentTimeStep + 1 >= m_NumTimeSteps)
{
return;
}
- // std::cout<<" ... current group "<<tsname.c_str()<<std::endl;
- m_Group_id = H5Gopen(m_File_id, tsname.c_str(), H5P_DEFAULT);
+
+ std::string timeStepName =
+ "/TimeStep" + std::to_string(m_CurrentTimeStep + 1);
+ m_GroupId = H5Gopen(m_FileId, timeStepName.c_str(), H5P_DEFAULT);
+ if (m_GroupId < 0)
+ {
+ throw std::runtime_error("HDF5: Unable to open group " +
+ timeStepName);
+ }
}
+ ++m_CurrentTimeStep;
}
void HDF5Common::CheckWriteGroup()
@@ -195,15 +206,18 @@ void HDF5Common::CheckWriteGroup()
{
return;
}
-
- if (m_Group_id >= 0)
+ if (m_GroupId >= 0)
{
return;
}
- std::string tsname = "/TimeStep";
- tsname.append(std::to_string(m_CurrentTimeStep));
- m_Group_id = H5Gcreate2(m_File_id, tsname.c_str(), H5P_DEFAULT, H5P_DEFAULT,
- H5P_DEFAULT);
+ 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);
+ }
}
}
diff --git a/source/adios2/engine/hdf5/HDF5Common.h b/source/adios2/engine/hdf5/HDF5Common.h
index 367bad64ffa0c6b18ecc3eede7618b75eb3749a8..d5a6a77190b1ed2465bf62b82073835b061afe27 100644
--- a/source/adios2/engine/hdf5/HDF5Common.h
+++ b/source/adios2/engine/hdf5/HDF5Common.h
@@ -11,7 +11,8 @@
#ifndef ADIOS2_ENGINE_HDF5_HDF5COMMON_P_H_
#define ADIOS2_ENGINE_HDF5_HDF5COMMON_P_H_
-#include "adios2.h"
+#include <string>
+
#include "adios2/ADIOSMPICommOnly.h"
#include <hdf5.h>
@@ -28,29 +29,29 @@ public:
*/
HDF5Common();
- void H5_Init(const std::string name, MPI_Comm m_MPIComm, bool toWrite);
- void H5_Close();
- void H5_Advance(int totalts);
+ void Init(const std::string name, MPI_Comm comm, bool toWrite);
+ void Close();
+ void Advance();
- int GetNumTimeSteps();
+ unsigned int GetNumTimeSteps();
void WriteTimeSteps();
- hid_t m_Plist_id, m_File_id;
- hid_t m_Group_id;
+ hid_t m_PropertyListId, m_FileId;
+ hid_t m_GroupId;
- hid_t m_DefH5T_COMPLEX_DOUBLE;
- hid_t m_DefH5T_COMPLEX_FLOAT;
- hid_t m_DefH5T_COMPLEX_LongDOUBLE;
+ hid_t m_DefH5TypeComplexDouble;
+ hid_t m_DefH5TypeComplexFloat;
+ hid_t m_DefH5TypeComplexLongDouble;
- int m_CurrentTimeStep;
+ unsigned int m_CurrentTimeStep;
void CheckWriteGroup();
private:
bool m_WriteMode;
- int m_Total_timestep;
+ unsigned int m_NumTimeSteps;
};
} // end namespace adios
-#endif /* HDF5_COMMON_P_H_ */
+#endif /* ADIOS2_ENGINE_HDF5_HDF5COMMON_P_H_ */
diff --git a/source/adios2/engine/hdf5/HDF5ReaderP.cpp b/source/adios2/engine/hdf5/HDF5ReaderP.cpp
index 8f3cb8f4ddbfbb2716e77ffd54290f6027e4830a..7f3ead729cae47aaa634e6a0d2365a2294584a06 100644
--- a/source/adios2/engine/hdf5/HDF5ReaderP.cpp
+++ b/source/adios2/engine/hdf5/HDF5ReaderP.cpp
@@ -33,7 +33,7 @@ bool HDF5Reader::isValid()
{
return false;
}
- if (m_H5File.m_File_id >= 0)
+ if (m_H5File.m_FileId >= 0)
{
return true;
}
@@ -47,7 +47,7 @@ void HDF5Reader::Init()
", in call to ADIOS Open or HDF5Reader constructor\n");
}
- m_H5File.H5_Init(m_Name, m_MPIComm, false);
+ m_H5File.Init(m_Name, m_MPIComm, false);
m_H5File.GetNumTimeSteps();
}
@@ -180,26 +180,26 @@ template <class T>
void HDF5Reader::UseHDFRead(const std::string &variableName, T *values,
hid_t h5Type)
{
- hid_t datasetID =
- H5Dopen(m_H5File.m_Group_id, variableName.c_str(), H5P_DEFAULT);
+ hid_t dataSetId =
+ H5Dopen(m_H5File.m_GroupId, variableName.c_str(), H5P_DEFAULT);
if (m_RankMPI == 0)
{
std::cout << " opened to read: " << variableName << std::endl;
}
- if (datasetID < 0)
+ if (dataSetId < 0)
{
return;
}
- hid_t filespace = H5Dget_space(datasetID);
+ hid_t fileSpace = H5Dget_space(dataSetId);
- if (filespace < 0)
+ if (fileSpace < 0)
{
return;
}
- int ndims = H5Sget_simple_extent_ndims(filespace);
+ int ndims = H5Sget_simple_extent_ndims(fileSpace);
hsize_t dims[ndims];
- herr_t status_n = H5Sget_simple_extent_dims(filespace, dims, NULL);
+ herr_t status_n = H5Sget_simple_extent_dims(fileSpace, dims, NULL);
hsize_t start[ndims] = {0}, count[ndims] = {0}, stride[ndims] = {1};
@@ -220,14 +220,14 @@ void HDF5Reader::UseHDFRead(const std::string &variableName, T *values,
<< std::endl;
}
- hid_t ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, start, stride,
+ hid_t ret = H5Sselect_hyperslab(fileSpace, H5S_SELECT_SET, start, stride,
count, NULL);
if (ret < 0)
{
return;
}
- hid_t mem_dataspace = H5Screate_simple(ndims, count, NULL);
+ hid_t memDataSpace = H5Screate_simple(ndims, count, NULL);
int elementsRead = 1;
for (int i = 0; i < ndims; i++)
@@ -236,7 +236,7 @@ void HDF5Reader::UseHDFRead(const std::string &variableName, T *values,
}
T data_array[elementsRead];
- ret = H5Dread(datasetID, h5Type, mem_dataspace, filespace, H5P_DEFAULT,
+ ret = H5Dread(dataSetId, h5Type, memDataSpace, fileSpace, H5P_DEFAULT,
data_array);
for (int i = 0; i < elementsRead; i++)
@@ -245,18 +245,14 @@ void HDF5Reader::UseHDFRead(const std::string &variableName, T *values,
<< std::endl;
}
- H5Sclose(mem_dataspace);
+ H5Sclose(memDataSpace);
- H5Sclose(filespace);
- H5Dclose(datasetID);
+ H5Sclose(fileSpace);
+ H5Dclose(dataSetId);
}
-void HDF5Reader::Advance(float timeoutSec)
-{
- int totalts = m_H5File.GetNumTimeSteps();
- m_H5File.H5_Advance(totalts);
-}
+void HDF5Reader::Advance(float timeoutSec) { m_H5File.Advance(); }
-void HDF5Reader::Close(const int transportIndex) { m_H5File.H5_Close(); }
+void HDF5Reader::Close(const int transportIndex) { m_H5File.Close(); }
} // end namespace adios
diff --git a/source/adios2/engine/hdf5/HDF5WriterP.cpp b/source/adios2/engine/hdf5/HDF5WriterP.cpp
index 89e0ec54d1c3a61641d64afb190798a8efbacdaf..784f1aea4267c84f47d071637f93a936bd6d6a51 100644
--- a/source/adios2/engine/hdf5/HDF5WriterP.cpp
+++ b/source/adios2/engine/hdf5/HDF5WriterP.cpp
@@ -40,7 +40,7 @@ void HDF5Writer::Init()
", in call to ADIOS Open or HDF5Writer constructor\n");
}
- m_H5File.H5_Init(m_Name, m_MPIComm, true);
+ m_H5File.Init(m_Name, m_MPIComm, true);
}
void HDF5Writer::Write(Variable<char> &variable, const char *values)
@@ -118,19 +118,19 @@ void HDF5Writer::Write(Variable<long double> &variable,
void HDF5Writer::Write(Variable<std::complex<float>> &variable,
const std::complex<float> *values)
{
- UseHDFWrite(variable, values, m_H5File.m_DefH5T_COMPLEX_FLOAT);
+ UseHDFWrite(variable, values, m_H5File.m_DefH5TypeComplexFloat);
}
void HDF5Writer::Write(Variable<std::complex<double>> &variable,
const std::complex<double> *values)
{
- UseHDFWrite(variable, values, m_H5File.m_DefH5T_COMPLEX_DOUBLE);
+ UseHDFWrite(variable, values, m_H5File.m_DefH5TypeComplexDouble);
}
void HDF5Writer::Write(Variable<std::complex<long double>> &variable,
const std::complex<long double> *values)
{
- UseHDFWrite(variable, values, m_H5File.m_DefH5T_COMPLEX_LongDOUBLE);
+ UseHDFWrite(variable, values, m_H5File.m_DefH5TypeComplexLongDouble);
}
// String version
@@ -222,30 +222,30 @@ void HDF5Writer::Write(const std::string variableName,
const std::complex<float> *values)
{
UseHDFWrite(m_ADIOS.GetVariable<std::complex<float>>(variableName), values,
- m_H5File.m_DefH5T_COMPLEX_FLOAT);
+ m_H5File.m_DefH5TypeComplexFloat);
}
void HDF5Writer::Write(const std::string variableName,
const std::complex<double> *values)
{
UseHDFWrite(m_ADIOS.GetVariable<std::complex<double>>(variableName), values,
- m_H5File.m_DefH5T_COMPLEX_DOUBLE);
+ m_H5File.m_DefH5TypeComplexDouble);
}
void HDF5Writer::Write(const std::string variableName,
const std::complex<long double> *values)
{
UseHDFWrite(m_ADIOS.GetVariable<std::complex<long double>>(variableName),
- values, m_H5File.m_DefH5T_COMPLEX_LongDOUBLE);
+ values, m_H5File.m_DefH5TypeComplexLongDouble);
}
-void HDF5Writer::Advance(float timeoutSec) { m_H5File.H5_Advance(0); }
+void HDF5Writer::Advance(float timeoutSec) { m_H5File.Advance(); }
-void HDF5Writer::Close(const int transportIndex) { m_H5File.H5_Close(); }
+void HDF5Writer::Close(const int transportIndex) { m_H5File.Close(); }
template <class T>
void HDF5Writer::UseHDFWrite(Variable<T> &variable, const T *values,
- hid_t h5type)
+ hid_t h5Type)
{
m_H5File.CheckWriteGroup();
// here comes your magic at Writing now variable.m_UserValues has the data
@@ -292,7 +292,7 @@ void HDF5Writer::UseHDFWrite(Variable<T> &variable, const T *values,
hid_t fileSpace = H5Screate_simple(dimSize, dimsf.data(), NULL);
hid_t dsetID =
- H5Dcreate(m_H5File.m_Group_id, variable.m_Name.c_str(), h5type,
+ H5Dcreate(m_H5File.m_GroupId, variable.m_Name.c_str(), h5Type,
fileSpace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
// H5Sclose(fileSpace);
@@ -311,7 +311,7 @@ void HDF5Writer::UseHDFWrite(Variable<T> &variable, const T *values,
#endif
herr_t status;
- status = H5Dwrite(dsetID, h5type, memSpace, fileSpace, plistID, values);
+ status = H5Dwrite(dsetID, h5Type, memSpace, fileSpace, plistID, values);
if (status < 0)
{
diff --git a/source/adios2/engine/hdf5/HDF5WriterP.h b/source/adios2/engine/hdf5/HDF5WriterP.h
index f915e9ccbe5978703a5b07e62b74086fabe3db4c..21151a18ab648cab1b8d389436a13dfb3518c3ef 100644
--- a/source/adios2/engine/hdf5/HDF5WriterP.h
+++ b/source/adios2/engine/hdf5/HDF5WriterP.h
@@ -98,7 +98,7 @@ private:
HDF5Common m_H5File;
template <class T>
- void UseHDFWrite(Variable<T> &variable, const T *values, hid_t h5type);
+ void UseHDFWrite(Variable<T> &variable, const T *values, hid_t h5Type);
};
} // end namespace adios