HDF5Common.cpp moved to a new location and this one is no longer used

source/adios2/engine/hdf5/HDF5Common.cpp

-/*
- * 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 "HDF5Common.h"
-
-#include <complex>
-#include <iostream>
-
-#include "adios2/ADIOSMPI.h"
-
-namespace adios
-{
-
-#define H5_ERROR std::cout << "[ADIOS H5 ERROR] "
-
-HDF5Common::HDF5Common()
-: m_WriteMode(false), m_CurrentTimeStep(0), m_NumTimeSteps(0)
-{
-    m_DefH5TypeComplexFloat =
-        H5Tcreate(H5T_COMPOUND, sizeof(std::complex<float>));
-    H5Tinsert(m_DefH5TypeComplexFloat, "freal", 0, H5T_NATIVE_FLOAT);
-    H5Tinsert(m_DefH5TypeComplexFloat, "fimg", H5Tget_size(H5T_NATIVE_FLOAT),
-              H5T_NATIVE_FLOAT);
-
-    m_DefH5TypeComplexDouble =
-        H5Tcreate(H5T_COMPOUND, sizeof(std::complex<double>));
-    H5Tinsert(m_DefH5TypeComplexDouble, "dreal", 0, H5T_NATIVE_DOUBLE);
-    H5Tinsert(m_DefH5TypeComplexDouble, "dimg", H5Tget_size(H5T_NATIVE_DOUBLE),
-              H5T_NATIVE_DOUBLE);
-
-    m_DefH5TypeComplexLongDouble =
-        H5Tcreate(H5T_COMPOUND, sizeof(std::complex<long double>));
-    H5Tinsert(m_DefH5TypeComplexLongDouble, "ldouble real", 0,
-              H5T_NATIVE_LDOUBLE);
-    H5Tinsert(m_DefH5TypeComplexLongDouble, "ldouble img",
-              H5Tget_size(H5T_NATIVE_LDOUBLE), H5T_NATIVE_LDOUBLE);
-}
-
-void HDF5Common::Init(const std::string name, MPI_Comm comm, bool toWrite)
-{
-    m_WriteMode = toWrite;
-
-    //
-    m_PropertyListId = H5Pcreate(H5P_FILE_ACCESS);
-
-#ifdef ADIOS2_HAVE_MPI
-    H5Pset_fapl_mpio(m_PropertyListId, comm, MPI_INFO_NULL);
-#endif
-
-    std::string ts0 = "/TimeStep0";
-
-    if (toWrite)
-    {
-        /*
-         * Create a new file collectively and release property list identifier.
-         */
-        m_FileId = H5Fcreate(name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT,
-                             m_PropertyListId);
-        if (m_FileId >= 0)
-        {
-            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_FileId = H5Fopen(name.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
-        if (m_FileId >= 0)
-        {
-            m_GroupId = H5Gopen(m_FileId, ts0.c_str(), H5P_DEFAULT);
-        }
-    }
-
-    H5Pclose(m_PropertyListId);
-}
-
-void HDF5Common::WriteTimeSteps()
-{
-    if (m_FileId < 0)
-    {
-        // std::cerr<<"[ADIOS HDF5Error]: Invalid file to record timestep
-        // to."<<std::endl;
-        H5_ERROR << "Invalid file to record timestep to." << std::endl;
-        return;
-    }
-
-    if (!m_WriteMode)
-    {
-        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;
-
-    if (m_GroupId < 0)
-    {
-        totalTimeSteps = m_CurrentTimeStep;
-    }
-
-    H5Awrite(attr, H5T_NATIVE_UINT, &totalTimeSteps);
-
-    H5Sclose(s);
-    H5Aclose(attr);
-}
-
-unsigned int HDF5Common::GetNumTimeSteps()
-{
-    if (m_WriteMode)
-    {
-        return -1;
-    }
-
-    if (m_FileId < 0)
-    {
-        std::cerr
-            << "[ADIOS HDF5Error]: Invalid file to read timestep attribute."
-            << std::endl;
-        return -1;
-    }
-
-    if (m_NumTimeSteps <= 0)
-    {
-        hid_t attr = H5Aopen(m_FileId, "NumTimeSteps", H5P_DEFAULT);
-
-        H5Aread(attr, H5T_NATIVE_UINT, &m_NumTimeSteps);
-        H5Aclose(attr);
-    }
-
-    return m_NumTimeSteps;
-}
-
-void HDF5Common::Close()
-{
-    if (m_FileId < 0)
-    {
-        return;
-    }
-
-    WriteTimeSteps();
-
-    if (m_GroupId >= 0)
-    {
-        H5Gclose(m_GroupId);
-    }
-
-    H5Fclose(m_FileId);
-    m_FileId = -1;
-    m_GroupId = -1;
-
-    H5Tclose(m_DefH5TypeComplexFloat);
-    H5Tclose(m_DefH5TypeComplexDouble);
-    H5Tclose(m_DefH5TypeComplexLongDouble);
-}
-
-void HDF5Common::Advance()
-{
-    if (m_GroupId >= 0)
-    {
-        H5Gclose(m_GroupId);
-        m_GroupId = -1;
-    }
-
-    if (m_WriteMode)
-    {
-        // m_GroupId = H5Gcreate2(m_FileId, tsname.c_str(), H5P_DEFAULT,
-        //                       H5P_DEFAULT, H5P_DEFAULT);
-    }
-    else
-    {
-        if (m_NumTimeSteps == 0)
-        {
-            GetNumTimeSteps();
-        }
-        if (m_CurrentTimeStep + 1 >= m_NumTimeSteps)
-        {
-            return;
-        }
-
-        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()
-{
-    if (!m_WriteMode)
-    {
-        return;
-    }
-    if (m_GroupId >= 0)
-    {
-        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)
-    {
-        throw std::runtime_error("HDF5: Unable to create group " +
-                                 timeStepName);
-    }
-}
-}