From 3614a287f4fecd0ff7a4731adaed5ba398278ca1 Mon Sep 17 00:00:00 2001
From: guj <jgu@lbl.gov>
Date: Fri, 5 May 2017 13:31:02 -0700
Subject: [PATCH] revised for coding standard
---
examples/hello/hdf5Writer/helloHDF5Writer.cpp | 36 ------
source/adios2/ADIOS.cpp | 2 +-
source/adios2/engine/hdf5/HDF5Common.cpp | 114 +++---------------
source/adios2/engine/hdf5/HDF5Common.h | 23 ++--
source/adios2/engine/hdf5/HDF5ReaderP.cpp | 81 ++++++-------
source/adios2/engine/hdf5/HDF5ReaderP.h | 9 +-
source/adios2/engine/hdf5/HDF5WriterP.cpp | 62 +++++-----
source/adios2/engine/hdf5/HDF5WriterP.h | 16 +--
8 files changed, 102 insertions(+), 241 deletions(-)
diff --git a/examples/hello/hdf5Writer/helloHDF5Writer.cpp b/examples/hello/hdf5Writer/helloHDF5Writer.cpp
index 39e9c0759..1426b07b7 100644
--- a/examples/hello/hdf5Writer/helloHDF5Writer.cpp
+++ b/examples/hello/hdf5Writer/helloHDF5Writer.cpp
@@ -13,7 +13,6 @@
#define ADIOS_HAVE_PHDF5 // so hdf5 related items are loaded in ADIOS_CPP.h
//#include "ADIOS_CPP.h"
#include "adios2.h"
-#include "adios2/engine/hdf5/HDF5ReaderP.h"
int main(int argc, char *argv[])
{
@@ -137,41 +136,6 @@ int main(int argc, char *argv[])
HDF5Writer->Advance();
}
HDF5Writer->Close();
-
-// now read out:
-/*
-HDF5Settings.SetEngine("HDF5Reader");
-std::cout<<"... Testing a copy of test.h5, [test1.h5] , b/c engine does not
-decrease name count !! "<<std::endl;
-auto HDF5Reader = adios.Open("test1.h5", "r", HDF5Settings);
-
-//int findts = HDF5Reader->getNumTimeSteps();
-//HDF5Reader->InquireVariableDouble("wrongMyDoubles", true);
-HDF5Reader->InquireVariableDouble(ioMyDoubles.m_Name, true);
-*/
-
-#ifndef NEVER
- adios::HDF5Common myReader;
- myReader.H5_Init("test.h5", MPI_COMM_WORLD, false);
- double values[15];
- ts = 0;
-
- while (ts < totalts)
- {
- // myReader.ReadMe(ioMyDoubles, values, H5T_NATIVE_DOUBLE);
- myReader.H5_Advance(totalts);
- ts++;
- }
-
-#else
-/*
-adios::HDF5Reader myReader(adios, "test.h5", "r", MPI_COMM_WORLD, HDF5Settings);
-double values[15];
-
-myReader.ReadMe(ioMyDoubles, values, H5T_NATIVE_DOUBLE);
-myReader.Close();
-*/
-#endif
}
catch (std::invalid_argument &e)
{
diff --git a/source/adios2/ADIOS.cpp b/source/adios2/ADIOS.cpp
index 9ba7d2fe8..db91c88f3 100644
--- a/source/adios2/ADIOS.cpp
+++ b/source/adios2/ADIOS.cpp
@@ -197,7 +197,7 @@ 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_PHDF5
+#ifdef ADIOS_HAVE_HDF5
//#ifdef ADIOS_HAVE_MPI
return std::make_shared<HDF5Reader>(*this, name, accessMode, mpiComm,
method);
diff --git a/source/adios2/engine/hdf5/HDF5Common.cpp b/source/adios2/engine/hdf5/HDF5Common.cpp
index f4eeeb952..2b2e605ff 100644
--- a/source/adios2/engine/hdf5/HDF5Common.cpp
+++ b/source/adios2/engine/hdf5/HDF5Common.cpp
@@ -10,9 +10,9 @@
#include "HDF5Common.h"
-#include <iostream> //needs to go away, this is just for demo purposes
+#include <iostream>
-//#include "adios2/ADIOSMPI.h"
+#include "adios2/ADIOSMPI.h"
namespace adios
{
@@ -22,21 +22,23 @@ namespace adios
HDF5Common::HDF5Common()
: m_WriteMode(false), m_Total_timestep(0), m_CurrentTimeStep(0)
{
- DefH5T_COMPLEX_FLOAT = H5Tcreate(H5T_COMPOUND, sizeof(std::complex<float>));
- H5Tinsert(DefH5T_COMPLEX_FLOAT, "freal", 0, H5T_NATIVE_FLOAT);
- H5Tinsert(DefH5T_COMPLEX_FLOAT, "fimg", H5Tget_size(H5T_NATIVE_FLOAT),
+ m_DefH5T_COMPLEX_FLOAT =
+ 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),
H5T_NATIVE_FLOAT);
- DefH5T_COMPLEX_DOUBLE =
+ m_DefH5T_COMPLEX_DOUBLE =
H5Tcreate(H5T_COMPOUND, sizeof(std::complex<double>));
- H5Tinsert(DefH5T_COMPLEX_DOUBLE, "dreal", 0, H5T_NATIVE_DOUBLE);
- H5Tinsert(DefH5T_COMPLEX_DOUBLE, "dimg", H5Tget_size(H5T_NATIVE_DOUBLE),
+ H5Tinsert(m_DefH5T_COMPLEX_DOUBLE, "dreal", 0, H5T_NATIVE_DOUBLE);
+ H5Tinsert(m_DefH5T_COMPLEX_DOUBLE, "dimg", H5Tget_size(H5T_NATIVE_DOUBLE),
H5T_NATIVE_DOUBLE);
- DefH5T_COMPLEX_LongDOUBLE =
+ m_DefH5T_COMPLEX_LongDOUBLE =
H5Tcreate(H5T_COMPOUND, sizeof(std::complex<long double>));
- H5Tinsert(DefH5T_COMPLEX_LongDOUBLE, "ldouble real", 0, H5T_NATIVE_LDOUBLE);
- H5Tinsert(DefH5T_COMPLEX_LongDOUBLE, "ldouble img",
+ H5Tinsert(m_DefH5T_COMPLEX_LongDOUBLE, "ldouble real", 0,
+ H5T_NATIVE_LDOUBLE);
+ H5Tinsert(m_DefH5T_COMPLEX_LongDOUBLE, "ldouble img",
H5Tget_size(H5T_NATIVE_LDOUBLE), H5T_NATIVE_LDOUBLE);
}
@@ -142,6 +144,11 @@ int HDF5Common::GetNumTimeSteps()
void HDF5Common::H5_Close()
{
+ if (m_File_id < 0)
+ {
+ return;
+ }
+
WriteTimeSteps();
if (m_Group_id >= 0)
@@ -150,6 +157,8 @@ void HDF5Common::H5_Close()
}
H5Fclose(m_File_id);
+ m_File_id = -1;
+ m_Group_id = -1;
}
void HDF5Common::H5_Advance(int totalts)
@@ -197,87 +206,4 @@ void HDF5Common::CheckWriteGroup()
m_Group_id = H5Gcreate2(m_File_id, tsname.c_str(), H5P_DEFAULT, H5P_DEFAULT,
H5P_DEFAULT);
}
-
-#ifdef NEVER
-template <class T>
-void HDF5Common::ReadMe(Variable<T> &variable, T *data_array, hid_t h5type)
-{
- hid_t datasetID = H5Dopen(m_Group_id, variable.m_Name.c_str(), H5P_DEFAULT);
-
- if (datasetID < 0)
- {
- return;
- }
-
- hid_t filespace = H5Dget_space(datasetID);
-
- if (filespace < 0)
- {
- return;
- }
-
- const int ndims = H5Sget_simple_extent_ndims(filespace);
- hsize_t dims[ndims];
- H5Sget_simple_extent_dims(filespace, dims, NULL);
-
- // int dims_in = variable.m_GlobalDimensions.size();
- variable.m_GlobalDimensions.clear();
- for (int i = 0; i < ndims; i++)
- {
- variable.m_GlobalDimensions.push_back(dims[i]);
- }
-
- std::vector<hsize_t> count, offset, stride;
-
- int elementsRead = 1;
- for (int i = 0; i < ndims; i++)
- {
- if (variable.m_LocalDimensions.size() == ndims)
- {
- count.push_back(variable.m_LocalDimensions[i]);
- elementsRead *= variable.m_LocalDimensions[i];
- }
- else
- {
- count.push_back(variable.m_GlobalDimensions[i]);
- elementsRead *= variable.m_GlobalDimensions[i];
- }
-
- if (variable.m_Offsets.size() == ndims)
- {
- offset.push_back(variable.m_Offsets[i]);
- }
- else
- {
- offset.push_back(0);
- }
-
- stride.push_back(1);
- }
-
- hid_t ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset.data(),
- stride.data(), count.data(), NULL);
- if (ret < 0)
- {
- return;
- }
-
- hid_t mem_dataspace = H5Screate_simple(ndims, count.data(), NULL);
-
- // T data_array[elementsRead];
- ret = H5Dread(datasetID, h5type, mem_dataspace, filespace, H5P_DEFAULT,
- data_array);
-
- /* for (int i = 0; i < elementsRead; i++)
- {
- std::cout << "... ts " << m_CurrentTimeStep << ", "
- << data_array[i] << std::endl;
- }
- */
- H5Sclose(mem_dataspace);
-
- H5Sclose(filespace);
- H5Dclose(datasetID);
-}
-#endif
}
diff --git a/source/adios2/engine/hdf5/HDF5Common.h b/source/adios2/engine/hdf5/HDF5Common.h
index aa2cd36d9..367bad64f 100644
--- a/source/adios2/engine/hdf5/HDF5Common.h
+++ b/source/adios2/engine/hdf5/HDF5Common.h
@@ -8,11 +8,11 @@
* Author: Junmin
*/
-#ifndef HDF5_COMMON_P_H_
-#define HDF5_COMMON_P_H_
+#ifndef ADIOS2_ENGINE_HDF5_HDF5COMMON_P_H_
+#define ADIOS2_ENGINE_HDF5_HDF5COMMON_P_H_
-//#include "adios2/ADIOSMPICommOnly.h"
-#include "adios2/core/Engine.h"
+#include "adios2.h"
+#include "adios2/ADIOSMPICommOnly.h"
#include <hdf5.h>
@@ -25,12 +25,9 @@ class HDF5Common
public:
/**
* Constructor for HDF5 file
- * @param file name
*/
HDF5Common();
- // virtual ~HDF5Common();
-
void H5_Init(const std::string name, MPI_Comm m_MPIComm, bool toWrite);
void H5_Close();
void H5_Advance(int totalts);
@@ -38,24 +35,18 @@ public:
int GetNumTimeSteps();
void WriteTimeSteps();
- // template <class T>
- // void ReadMe(Variable<T> &variable, T *data_array, hid_t h5type);
-
- // void ReadFromHDF5(const char* name, void* data_array);
-
hid_t m_Plist_id, m_File_id;
hid_t m_Group_id;
- hid_t DefH5T_COMPLEX_DOUBLE;
- hid_t DefH5T_COMPLEX_FLOAT;
- hid_t DefH5T_COMPLEX_LongDOUBLE;
+ hid_t m_DefH5T_COMPLEX_DOUBLE;
+ hid_t m_DefH5T_COMPLEX_FLOAT;
+ hid_t m_DefH5T_COMPLEX_LongDOUBLE;
int m_CurrentTimeStep;
void CheckWriteGroup();
private:
- // void H5_AdvanceWrite();
bool m_WriteMode;
int m_Total_timestep;
};
diff --git a/source/adios2/engine/hdf5/HDF5ReaderP.cpp b/source/adios2/engine/hdf5/HDF5ReaderP.cpp
index 1d7102f23..8f3cb8f4d 100644
--- a/source/adios2/engine/hdf5/HDF5ReaderP.cpp
+++ b/source/adios2/engine/hdf5/HDF5ReaderP.cpp
@@ -20,13 +20,12 @@ HDF5Reader::HDF5Reader(ADIOS &adios, const std::string name,
const Method &method)
: Engine(adios, "HDF5Reader", name, accessMode, mpiComm, method,
" HDF5Reader constructor (or call to ADIOS Open).\n")
+
{
Init();
- MPI_Comm_rank(mpiComm, &_mpi_rank);
- MPI_Comm_size(mpiComm, &_mpi_size);
}
-HDF5Reader::~HDF5Reader() {}
+HDF5Reader::~HDF5Reader() { Close(); }
bool HDF5Reader::isValid()
{
@@ -34,7 +33,7 @@ bool HDF5Reader::isValid()
{
return false;
}
- if (_H5File.m_File_id >= 0)
+ if (m_H5File.m_File_id >= 0)
{
return true;
}
@@ -48,142 +47,142 @@ void HDF5Reader::Init()
", in call to ADIOS Open or HDF5Reader constructor\n");
}
- _H5File.H5_Init(m_Name, m_MPIComm, false);
- _H5File.GetNumTimeSteps();
+ m_H5File.H5_Init(m_Name, m_MPIComm, false);
+ m_H5File.GetNumTimeSteps();
}
Variable<void> *HDF5Reader::InquireVariable(const std::string &variableName,
const bool readIn)
{
std::cout << "Not implemented: HDF5Reader::InquireVariable()" << std::endl;
- return NULL;
+ return nullptr;
}
Variable<char> *HDF5Reader::InquireVariableChar(const std::string &variableName,
const bool readIn)
{
- return NULL;
+ return nullptr;
}
Variable<unsigned char> *
HDF5Reader::InquireVariableUChar(const std::string &variableName,
const bool readIn)
{
- return NULL;
+ return nullptr;
}
Variable<short> *
HDF5Reader::InquireVariableShort(const std::string &variableName,
const bool readIn)
{
- return NULL;
+ return nullptr;
}
Variable<unsigned short> *
HDF5Reader::InquireVariableUShort(const std::string &variableName,
const bool readIn)
{
- return NULL;
+ return nullptr;
}
Variable<int> *HDF5Reader::InquireVariableInt(const std::string &variableName,
const bool)
{
- return NULL;
+ return nullptr;
}
Variable<unsigned int> *
HDF5Reader::InquireVariableUInt(const std::string &variableName, const bool)
{
- return NULL;
+ return nullptr;
}
Variable<long int> *
HDF5Reader::InquireVariableLInt(const std::string &variableName, const bool)
{
- return NULL;
+ return nullptr;
}
Variable<unsigned long int> *
HDF5Reader::InquireVariableULInt(const std::string &variableName, const bool)
{
- return NULL;
+ return nullptr;
}
Variable<long long int> *
HDF5Reader::InquireVariableLLInt(const std::string &variableName, const bool)
{
- return NULL;
+ return nullptr;
}
Variable<unsigned long long int> *
HDF5Reader::InquireVariableULLInt(const std::string &variableName, const bool)
{
- return NULL;
+ return nullptr;
}
Variable<float> *
HDF5Reader::InquireVariableFloat(const std::string &variableName, const bool)
{
- return NULL;
+ return nullptr;
}
Variable<double> *
HDF5Reader::InquireVariableDouble(const std::string &variableName, const bool)
{
- if (_mpi_rank == 0)
+ if (m_RankMPI == 0)
{
std::cout << " ... reading var: " << variableName << std::endl;
}
- int totalts = _H5File.GetNumTimeSteps();
+ int totalts = m_H5File.GetNumTimeSteps();
- if (_mpi_rank == 0)
+ if (m_RankMPI == 0)
{
std::cout << " ... I saw total timesteps: " << totalts << std::endl;
}
- return NULL;
+ return nullptr;
}
Variable<long double> *
HDF5Reader::InquireVariableLDouble(const std::string &variableName, const bool)
{
- return NULL;
+ return nullptr;
}
Variable<std::complex<float>> *
HDF5Reader::InquireVariableCFloat(const std::string &variableName, const bool)
{
- return NULL;
+ return nullptr;
}
Variable<std::complex<double>> *
HDF5Reader::InquireVariableCDouble(const std::string &variableName, const bool)
{
- return NULL;
+ return nullptr;
}
Variable<std::complex<long double>> *
HDF5Reader::InquireVariableCLDouble(const std::string &variableName, const bool)
{
- return NULL;
+ return nullptr;
}
VariableCompound *
HDF5Reader::InquireVariableCompound(const std::string &variableName,
const bool readIn)
{
- return NULL;
+ return nullptr;
}
template <class T>
void HDF5Reader::UseHDFRead(const std::string &variableName, T *values,
- hid_t h5type)
+ hid_t h5Type)
{
hid_t datasetID =
- H5Dopen(_H5File.m_Group_id, variableName.c_str(), H5P_DEFAULT);
- if (_mpi_rank == 0)
+ H5Dopen(m_H5File.m_Group_id, variableName.c_str(), H5P_DEFAULT);
+ if (m_RankMPI == 0)
{
std::cout << " opened to read: " << variableName << std::endl;
}
@@ -212,12 +211,12 @@ void HDF5Reader::UseHDFRead(const std::string &variableName, T *values,
totalElements *= dims[i];
}
- start[0] = _mpi_rank * dims[0] / _mpi_size;
- count[0] = dims[0] / _mpi_size;
- if (_mpi_rank == _mpi_size - 1)
+ start[0] = m_RankMPI * dims[0] / m_SizeMPI;
+ count[0] = dims[0] / m_SizeMPI;
+ if (m_RankMPI == m_SizeMPI - 1)
{
- count[0] = dims[0] - count[0] * (_mpi_size - 1);
- std::cout << " rank = " << _mpi_rank << ", count=" << count[0]
+ count[0] = dims[0] - count[0] * (m_SizeMPI - 1);
+ std::cout << " rank = " << m_RankMPI << ", count=" << count[0]
<< std::endl;
}
@@ -237,12 +236,12 @@ 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, mem_dataspace, filespace, H5P_DEFAULT,
data_array);
for (int i = 0; i < elementsRead; i++)
{
- std::cout << "... rank " << _mpi_rank << " , " << data_array[i]
+ std::cout << "... rank " << m_RankMPI << " , " << data_array[i]
<< std::endl;
}
@@ -252,12 +251,12 @@ void HDF5Reader::UseHDFRead(const std::string &variableName, T *values,
H5Dclose(datasetID);
}
-void HDF5Reader::Advance(float timeout_sec)
+void HDF5Reader::Advance(float timeoutSec)
{
- int totalts = _H5File.GetNumTimeSteps();
- _H5File.H5_Advance(totalts);
+ int totalts = m_H5File.GetNumTimeSteps();
+ m_H5File.H5_Advance(totalts);
}
-void HDF5Reader::Close(const int transportIndex) { _H5File.H5_Close(); }
+void HDF5Reader::Close(const int transportIndex) { m_H5File.H5_Close(); }
} // end namespace adios
diff --git a/source/adios2/engine/hdf5/HDF5ReaderP.h b/source/adios2/engine/hdf5/HDF5ReaderP.h
index 7b05ba221..70c71137b 100644
--- a/source/adios2/engine/hdf5/HDF5ReaderP.h
+++ b/source/adios2/engine/hdf5/HDF5ReaderP.h
@@ -106,23 +106,20 @@ public:
VariableCompound *InquireVariableCompound(const std::string &variableName,
const bool readIn = true);
- void Advance(float timeout_sec = 0.0);
+ void Advance(float timeoutSecc = 0.0);
void Close(const int transportIndex = -1);
template <typename T>
- void UseHDFRead(const std::string &variableName, T *values, hid_t h5type);
+ void UseHDFRead(const std::string &variableName, T *values, hid_t h5Type);
/*
template <class T>
void ReadMe(Variable<T> &variable, T *values, hid_t h5type);
*/
private:
- HDF5Common _H5File;
+ HDF5Common m_H5File;
void Init();
-
- int _mpi_rank;
- int _mpi_size;
};
};
#endif /* ADIOS2_ENGINE_HDF5_HDF5READERP_H_ */
diff --git a/source/adios2/engine/hdf5/HDF5WriterP.cpp b/source/adios2/engine/hdf5/HDF5WriterP.cpp
index a77f78a4a..ec1278e13 100644
--- a/source/adios2/engine/hdf5/HDF5WriterP.cpp
+++ b/source/adios2/engine/hdf5/HDF5WriterP.cpp
@@ -28,7 +28,7 @@ HDF5Writer::HDF5Writer(ADIOS &adios, const std::string name,
Init();
}
-HDF5Writer::~HDF5Writer() {}
+HDF5Writer::~HDF5Writer() { Close(); }
void HDF5Writer::Init()
{
@@ -40,7 +40,7 @@ void HDF5Writer::Init()
", in call to ADIOS Open or HDF5Writer constructor\n");
}
- _H5File.H5_Init(m_Name, m_MPIComm, true);
+ m_H5File.H5_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, _H5File.DefH5T_COMPLEX_FLOAT);
+ UseHDFWrite(variable, values, m_H5File.m_DefH5T_COMPLEX_FLOAT);
}
void HDF5Writer::Write(Variable<std::complex<double>> &variable,
const std::complex<double> *values)
{
- UseHDFWrite(variable, values, _H5File.DefH5T_COMPLEX_DOUBLE);
+ UseHDFWrite(variable, values, m_H5File.m_DefH5T_COMPLEX_DOUBLE);
}
void HDF5Writer::Write(Variable<std::complex<long double>> &variable,
const std::complex<long double> *values)
{
- UseHDFWrite(variable, values, _H5File.DefH5T_COMPLEX_LongDOUBLE);
+ UseHDFWrite(variable, values, m_H5File.m_DefH5T_COMPLEX_LongDOUBLE);
}
// String version
@@ -222,24 +222,24 @@ void HDF5Writer::Write(const std::string variableName,
const std::complex<float> *values)
{
UseHDFWrite(m_ADIOS.GetVariable<std::complex<float>>(variableName), values,
- _H5File.DefH5T_COMPLEX_FLOAT);
+ m_H5File.m_DefH5T_COMPLEX_FLOAT);
}
void HDF5Writer::Write(const std::string variableName,
const std::complex<double> *values)
{
UseHDFWrite(m_ADIOS.GetVariable<std::complex<double>>(variableName), values,
- _H5File.DefH5T_COMPLEX_DOUBLE);
+ m_H5File.m_DefH5T_COMPLEX_DOUBLE);
}
void HDF5Writer::Write(const std::string variableName,
const std::complex<long double> *values)
{
UseHDFWrite(m_ADIOS.GetVariable<std::complex<long double>>(variableName),
- values, _H5File.DefH5T_COMPLEX_LongDOUBLE);
+ values, m_H5File.m_DefH5T_COMPLEX_LongDOUBLE);
}
-void HDF5Writer::Advance(float timeout_sec) { _H5File.H5_Advance(0); }
+void HDF5Writer::Advance(float timeoutSec) { m_H5File.H5_Advance(0); }
void HDF5Writer::Close(const int transportIndex)
{
@@ -247,26 +247,26 @@ void HDF5Writer::Close(const int transportIndex)
//void* hi = H5Iobject_verify(H5S_SCALAR, H5I_DATASPACE);
hid_t s = H5Screate(H5S_SCALAR);
- //hid_t attr = H5Acreate(_H5File.m_Group_id, "NumTimeSteps",
+ //hid_t attr = H5Acreate(m_H5File.m_Group_id, "NumTimeSteps",
H5T_NATIVE_UINT,
s, H5P_DEFAULT, H5P_DEFAULT);
- hid_t attr = H5Acreate(_H5File.m_File_id, "NumTimeSteps", H5T_NATIVE_UINT,
+ hid_t attr = H5Acreate(m_H5File.m_File_id, "NumTimeSteps", H5T_NATIVE_UINT,
s,
H5P_DEFAULT, H5P_DEFAULT);
- uint totalts = _H5File.m_CurrentTimeStep+1;
+ uint totalts = m_H5File.m_CurrentTimeStep+1;
H5Awrite(attr,H5T_NATIVE_UINT,&totalts);
H5Sclose(s);
H5Aclose(attr);
*/
- _H5File.H5_Close();
+ m_H5File.H5_Close();
}
template <class T>
void HDF5Writer::UseHDFWrite(Variable<T> &variable, const T *values,
hid_t h5type)
{
- _H5File.CheckWriteGroup();
+ m_H5File.CheckWriteGroup();
// here comes your magic at Writing now variable.m_UserValues has the data
// passed by the user
// set variable
@@ -308,30 +308,29 @@ void HDF5Writer::UseHDFWrite(Variable<T> &variable, const T *values,
}
}
- hid_t _filespace = H5Screate_simple(dimSize, dimsf.data(), NULL);
+ hid_t fileSpace = H5Screate_simple(dimSize, dimsf.data(), NULL);
- hid_t _dset_id =
- H5Dcreate(_H5File.m_Group_id, variable.m_Name.c_str(), h5type,
- _filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
- // H5Sclose(_filespace);
+ hid_t dsetID =
+ H5Dcreate(m_H5File.m_Group_id, variable.m_Name.c_str(), h5type,
+ fileSpace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ // H5Sclose(fileSpace);
- hid_t _memspace = H5Screate_simple(dimSize, count.data(), NULL);
+ hid_t memSpace = H5Screate_simple(dimSize, count.data(), NULL);
// Select hyperslab
- _filespace = H5Dget_space(_dset_id);
- H5Sselect_hyperslab(_filespace, H5S_SELECT_SET, offset.data(), NULL,
+ fileSpace = H5Dget_space(dsetID);
+ H5Sselect_hyperslab(fileSpace, H5S_SELECT_SET, offset.data(), NULL,
count.data(), NULL);
// Create property list for collective dataset write.
- hid_t _plist_id = H5Pcreate(H5P_DATASET_XFER);
+ hid_t plistID = H5Pcreate(H5P_DATASET_XFER);
#ifdef ADIOS2_HAVE_MPI
- H5Pset_dxpl_mpio(_plist_id, H5FD_MPIO_COLLECTIVE);
+ H5Pset_dxpl_mpio(plistID, H5FD_MPIO_COLLECTIVE);
#endif
herr_t status;
- status =
- H5Dwrite(_dset_id, h5type, _memspace, _filespace, _plist_id, values);
+ status = H5Dwrite(dsetID, h5type, memSpace, fileSpace, plistID, values);
if (status < 0)
{
@@ -339,13 +338,10 @@ void HDF5Writer::UseHDFWrite(Variable<T> &variable, const T *values,
std::cerr << " Write failed. " << std::endl;
}
- // std::cout << " ==> User is responsible for freeing the data " <<
- // std::endl;
-
- H5Dclose(_dset_id);
- H5Sclose(_filespace);
- H5Sclose(_memspace);
- H5Pclose(_plist_id);
+ H5Dclose(dsetID);
+ H5Sclose(fileSpace);
+ H5Sclose(memSpace);
+ H5Pclose(plistID);
}
} // end namespace adios
diff --git a/source/adios2/engine/hdf5/HDF5WriterP.h b/source/adios2/engine/hdf5/HDF5WriterP.h
index 3141cca75..f915e9ccb 100644
--- a/source/adios2/engine/hdf5/HDF5WriterP.h
+++ b/source/adios2/engine/hdf5/HDF5WriterP.h
@@ -85,7 +85,7 @@ public:
void Write(const std::string variableName,
const std::complex<long double> *values);
- void Advance(float timeout_sec = 0.0);
+ void Advance(float timeoutSec = 0.0);
void Close(const int transportIndex = -1);
@@ -95,20 +95,8 @@ private:
void Init();
- HDF5Common _H5File;
+ HDF5Common m_H5File;
- /*
- hid_t _plist_id, _file_id, _dset_id;
- hid_t _memspace, _filespace;
-
- hid_t _group_id;
-
- hid_t DefH5T_COMPLEX_DOUBLE;
- hid_t DefH5T_COMPLEX_FLOAT;
- hid_t DefH5T_COMPLEX_LongDOUBLE;
-
- int _currentTimeStep;
- */
template <class T>
void UseHDFWrite(Variable<T> &variable, const T *values, hid_t h5type);
};
--
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