From 2f9ad950f4e6b36e19dec265754b5b19dcc64c50 Mon Sep 17 00:00:00 2001
From: guj <jgu@lbl.gov>
Date: Tue, 2 May 2017 10:21:12 -0700
Subject: [PATCH] added to handle common hdf5 operations for both read/write
---
source/adios2/engine/hdf5/HDF5Common.cpp | 154 +++++++++++++++++++++++
source/adios2/engine/hdf5/HDF5Common.h | 58 +++++++++
2 files changed, 212 insertions(+)
create mode 100644 source/adios2/engine/hdf5/HDF5Common.cpp
create mode 100644 source/adios2/engine/hdf5/HDF5Common.h
diff --git a/source/adios2/engine/hdf5/HDF5Common.cpp b/source/adios2/engine/hdf5/HDF5Common.cpp
new file mode 100644
index 000000000..2ce291398
--- /dev/null
+++ b/source/adios2/engine/hdf5/HDF5Common.cpp
@@ -0,0 +1,154 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
+ * HDF5Common.cpp
+ *
+ * Created on: April 20, 2017
+ * Author: Junmin
+ */
+
+#include <iostream> //needs to go away, this is just for demo purposes
+
+#include "engine/hdf5/HDF5Common.h"
+
+namespace adios
+{
+
+#define H5_ERROR std::cout<<"[ADIOS H5 ERROR] "
+
+HDF5Common::HDF5Common()
+ :_writeMode(false),
+ _total_timestep(0),
+ _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),
+ H5T_NATIVE_FLOAT);
+
+ 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),
+ H5T_NATIVE_DOUBLE);
+
+ 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",
+ H5Tget_size(H5T_NATIVE_LDOUBLE), H5T_NATIVE_LDOUBLE);
+}
+
+
+void HDF5Common::H5_Init(const std::string name, MPI_Comm m_MPIComm, bool toWrite)
+{
+ _writeMode = toWrite;
+
+ //
+ _plist_id = H5Pcreate(H5P_FILE_ACCESS);
+
+#ifdef ADIOS2_HAVE_MPI
+ H5Pset_fapl_mpio(_plist_id, m_MPIComm, MPI_INFO_NULL);
+#endif
+
+ std::string ts0 = "/TimeStep0";
+
+ if (toWrite) {
+ /*
+ * Create a new file collectively and release property list identifier.
+ */
+ _file_id = H5Fcreate(name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, _plist_id);
+ if (_file_id >= 0)
+ {
+ _group_id =
+ H5Gcreate2(_file_id, ts0.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ }
+ } else {
+ // read a file collectively
+ _file_id = H5Fopen(name.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+ if (_file_id >= 0)
+ {
+ _group_id = H5Gopen(_file_id, ts0.c_str(), H5P_DEFAULT);
+ }
+ }
+
+ H5Pclose(_plist_id);
+}
+
+HDF5Common::~HDF5Common() {}
+
+void HDF5Common::WriteTimeSteps()
+{
+ if (_file_id < 0)
+ {
+ //std::cerr<<"[ADIOS HDF5Error]: Invalid file to record timestep to."<<std::endl;
+ H5_ERROR<<"Invalid file to record timestep to."<<std::endl;
+ return;
+ }
+
+ hid_t s = H5Screate(H5S_SCALAR);
+
+ hid_t attr = H5Acreate(_file_id, "NumTimeSteps", H5T_NATIVE_UINT, s, H5P_DEFAULT, H5P_DEFAULT);
+ uint totalts = _currentTimeStep+1;
+ H5Awrite(attr,H5T_NATIVE_UINT,&totalts);
+
+ H5Sclose(s);
+ H5Aclose(attr);
+}
+
+
+int HDF5Common::GetNumTimeSteps()
+{
+ if (_file_id < 0)
+ {
+ std::cerr<<"[ADIOS HDF5Error]: Invalid file to read timestep attribute."<<std::endl;
+ return -1;
+ }
+
+ if (_total_timestep <= 0) {
+ hid_t attr = H5Aopen(_file_id, "NumTimeSteps", H5P_DEFAULT);
+
+ H5Aread(attr,H5T_NATIVE_UINT, &_total_timestep);
+ H5Aclose(attr);
+ }
+
+ return _total_timestep;
+}
+
+
+
+void HDF5Common::H5_Close() {
+ WriteTimeSteps();
+
+ H5Gclose(_group_id);
+ H5Fclose(_file_id);
+}
+
+void HDF5Common::H5_Advance(int totalts)
+{
+ _currentTimeStep++;
+ if (_currentTimeStep > 0) {
+ H5Gclose(_group_id);
+ }
+
+ std::string tsname="/TimeStep";
+ tsname.append(std::to_string(_currentTimeStep));
+
+ if (_writeMode) {
+ _group_id =
+ H5Gcreate2(_file_id, tsname.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ } else {
+ if ((totalts > 0) && (totalts <= _currentTimeStep))
+ {
+ return;
+ }
+ //std::cout<<" ... current group "<<tsname.c_str()<<std::endl;
+ _group_id =
+ H5Gopen(_file_id, tsname.c_str(), H5P_DEFAULT);
+ }
+}
+
+
+
+}
diff --git a/source/adios2/engine/hdf5/HDF5Common.h b/source/adios2/engine/hdf5/HDF5Common.h
new file mode 100644
index 000000000..d5978b534
--- /dev/null
+++ b/source/adios2/engine/hdf5/HDF5Common.h
@@ -0,0 +1,58 @@
+
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
+ * HDF5CommonP.h
+ *
+ * Created on: March 20, 2017
+ * Author: Junmin
+ */
+
+#ifndef HDF5_COMMON_P_H_
+#define HDF5_COMMON_P_H_
+
+#include "core/Engine.h"
+#include "ADIOS_MPI.h"
+
+#include <hdf5.h>
+
+namespace adios
+{
+
+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);
+
+ int GetNumTimeSteps();
+ void WriteTimeSteps();
+
+ hid_t _plist_id, _file_id;
+ hid_t _group_id;
+
+ hid_t DefH5T_COMPLEX_DOUBLE;
+ hid_t DefH5T_COMPLEX_FLOAT;
+ hid_t DefH5T_COMPLEX_LongDOUBLE;
+
+ int _currentTimeStep;
+ private:
+ void H5_AdvanceWrite();
+ bool _writeMode;
+ int _total_timestep;
+};
+
+} // end namespace adios
+
+#endif /* HDF5_COMMON_P_H_ */
--
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