From a50768c6b2510c4772e55ea2ab7f254d5f76db33 Mon Sep 17 00:00:00 2001
From: Chuck Atkins <chuck.atkins@kitware.com>
Date: Mon, 19 Jun 2017 15:08:33 -0400
Subject: [PATCH] HDF5Common.cpp moved to a new location and this one is no
longer used
---
source/adios2/engine/hdf5/HDF5Common.cpp | 227 -----------------------
1 file changed, 227 deletions(-)
delete mode 100644 source/adios2/engine/hdf5/HDF5Common.cpp
diff --git a/source/adios2/engine/hdf5/HDF5Common.cpp b/source/adios2/engine/hdf5/HDF5Common.cpp
deleted file mode 100644
index d628689c7..000000000
--- a/source/adios2/engine/hdf5/HDF5Common.cpp
+++ /dev/null
@@ -1,227 +0,0 @@
-/*
- * 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);
- }
-}
-}
--
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