From 8f7389e982552abdaed233454a865976e788e53c Mon Sep 17 00:00:00 2001
From: guj <jgu@lbl.gov>
Date: Fri, 14 Apr 2017 12:24:44 -0700
Subject: [PATCH] hdf5 basic support
---
CMakeLists.txt | 2 +
cmake/FindPHDF5.cmake | 59 -------
examples/hello/CMakeLists.txt | 4 +
examples/hello/hdf5Writer/CMakeLists.txt | 30 ++++
examples/hello/hdf5Writer/helloHDF5Writer.cpp | 137 +++++++++++++++
.../hdf5Writer/helloHDF5Writer_nompi.cpp | 134 ++++++++++++++
include/engine/hdf5/HDF5ReaderP.h | 11 ++
include/engine/hdf5/HDF5WriterP.h | 33 ++--
source/ADIOS.cpp | 15 ++
source/CMakeLists.txt | 33 +++-
source/engine/hdf5/HDF5ReaderP.cpp | 11 +-
source/engine/hdf5/HDF5WriterP.cpp | 166 ++++++------------
12 files changed, 439 insertions(+), 196 deletions(-)
delete mode 100644 cmake/FindPHDF5.cmake
create mode 100644 examples/hello/hdf5Writer/CMakeLists.txt
create mode 100644 examples/hello/hdf5Writer/helloHDF5Writer.cpp
create mode 100644 examples/hello/hdf5Writer/helloHDF5Writer_nompi.cpp
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 9e267cc5b..0d70affa2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -73,6 +73,7 @@ endif()
option(ADIOS_USE_BZip2 "Enable support for BZip2 transforms" OFF)
option(ADIOS_USE_ADIOS1 "Enable support for the ADIOS 1 engine" OFF)
option(ADIOS_USE_DataMan "Enable support for the DataMan engine" OFF)
+option(ADIOS_USE_PHDF5 "Enable support for hdf5" OFF)
#------------------------------------------------------------------------------#
# Third party libraries
@@ -134,4 +135,5 @@ message(" MPI: ${ADIOS_USE_MPI}")
message(" BZip2: ${ADIOS_USE_BZip2}")
message(" ADIOS1: ${ADIOS_USE_ADIOS1}")
message(" DataMan: ${ADIOS_USE_DataMan}")
+message(" HDF5: ${ADIOS_USE_PHDF5}")
message("")
diff --git a/cmake/FindPHDF5.cmake b/cmake/FindPHDF5.cmake
deleted file mode 100644
index e357e7279..000000000
--- a/cmake/FindPHDF5.cmake
+++ /dev/null
@@ -1,59 +0,0 @@
-#------------------------------------------------------------------------------#
-# Distributed under the OSI-approved Apache License, Version 2.0. See
-# accompanying file Copyright.txt for details.
-#------------------------------------------------------------------------------#
-#
-# FindPHDF5
-# ---------
-#
-
-
-if(NOT PHDF5_FOUND)
- if((NOT HDF5_DIR) AND (NOT (ENV{HDF5_DIR} STREQUAL "")))
- set(HDF5_DIR "$ENV{HDF5_DIR}")
- endif()
-
- # Search for the core libraries
- if(HDF5_DIR)
- # If a root directory is specified, then don't look anywhere else
- find_path(PHDF5_INCLUDE_DIR hdf5.h
- HINTS ${HDF5_DIR}/include
- NO_DEFAULT_PATHS
- )
- set(_PHDF5_LIBRARY_HINT HINTS ${HDF5_DIR}/lib NO_DEFAULT_PATHS)
- else()
- # Otherwise use the include dir as a basis to search for the lib
- find_path(PHDF5_INCLUDE_DIR hdf5.h)
- if(PHDF5_INCLUDE_DIR)
- get_filename_component(_PHDF5_PREFIX "${PHDF5_INCLUDE_DIR}" PATH)
- set(_PHDF5_LIBRARY_HINT HINTS ${_PHDF5_PREFIX}/lib)
- unset(_PHDF5_PREFIX)
- endif()
- endif()
- find_library(PHDF5_LIBRARY hdf5 ${_PHDF5_LIBRARY_HINT})
- unset(_PHDF5_LIBRARY_HINT)
-
-
- include(FindPackageHandleStandardArgs)
- find_package_handle_standard_args(PHDF5 DEFAULT_MSG PHDF5_LIBRARY PHDF5_INCLUDE_DIR)
-
- find_package_handle_standard_args(PHDF5
- FOUND_VAR PHDF5_FOUND
- REQUIRED_VARS
- PHDF5_INCLUDE_DIR
- PHDF5_LIBRARY
- )
-
- MESSAGE(STATUS "PHDF5_FOUND: " ${PHDF5_FOUND} "HDF5_DIR: " ${HDF5_DIR} "TARGET=" ${TARGET} )
- if(PHDF5_FOUND)
- set(PHDF5_INCLUDE_DIRS ${PHDF5_INCLUDE_DIR})
- set(PHDF5_LIBRARIES ${PHDF5_LIBRARY})
- if(PHDF5_FOUND AND NOT TARGET PHDF5::PHDF5)
- add_library(PHDF5::PHDF5 UNKNOWN IMPORTED)
- set_target_properties(PHDF5::PHDF5 PROPERTIES
- IMPORTED_LOCATION "${PHDF5_LIBRARY}"
- INTERFACE_INCLUDE_DIRECTORIES "${PHDF5_INCLUDE_DIR}"
- )
- endif()
- endif()
-endif()
diff --git a/examples/hello/CMakeLists.txt b/examples/hello/CMakeLists.txt
index 0cf0a5df5..73fa0f560 100644
--- a/examples/hello/CMakeLists.txt
+++ b/examples/hello/CMakeLists.txt
@@ -14,3 +14,7 @@ if(ADIOS_USE_DataMan)
add_subdirectory(datamanReader)
add_subdirectory(datamanWriter)
endif()
+
+if(ADIOS_USE_PHDF5)
+ add_subdirectory(hdf5Writer)
+endif()
diff --git a/examples/hello/hdf5Writer/CMakeLists.txt b/examples/hello/hdf5Writer/CMakeLists.txt
new file mode 100644
index 000000000..742560057
--- /dev/null
+++ b/examples/hello/hdf5Writer/CMakeLists.txt
@@ -0,0 +1,30 @@
+#------------------------------------------------------------------------------#
+# Distributed under the OSI-approved Apache License, Version 2.0. See
+# accompanying file Copyright.txt for details.
+#------------------------------------------------------------------------------#
+
+add_executable(hello_hdf5Writer_nompi helloHDF5Writer_nompi.cpp)
+message(" HDF5: ${HDF5_INCLUDE_DIRS}")
+include_directories(${HDF5_INCLUDE_DIRS})
+target_link_libraries(hello_hdf5Writer_nompi adios2_nompi)
+
+if(ADIOS_BUILD_TESTING)
+ add_test(
+ NAME Example::hello::hdf5Writer_nompi
+ COMMAND hello_hdf5Writer_nompi
+ )
+endif()
+
+if(ADIOS_USE_MPI)
+ find_package(MPI COMPONENTS C REQUIRED)
+
+ add_executable(hello_hdf5Writer helloHDF5Writer.cpp)
+ target_link_libraries(hello_hdf5Writer adios2)
+ target_include_directories(hello_hdf5Writer PRIVATE ${MPI_C_INCLUDE_PATH})
+ target_link_libraries(hello_hdf5Writer adios2 ${MPI_C_LIBRARIES})
+
+ if(ADIOS_BUILD_TESTING)
+ add_test(NAME Example::hello::hdf5Writer COMMAND hello_hdf5Writer)
+ endif()
+endif()
+
diff --git a/examples/hello/hdf5Writer/helloHDF5Writer.cpp b/examples/hello/hdf5Writer/helloHDF5Writer.cpp
new file mode 100644
index 000000000..8dd6260bf
--- /dev/null
+++ b/examples/hello/hdf5Writer/helloHDF5Writer.cpp
@@ -0,0 +1,137 @@
+/*
+ * HDF5Writer.cpp
+ *
+ * Created on: March 20, 2017
+ * Author: Junmin
+ */
+
+
+
+#include <vector>
+#include <iostream>
+
+
+#include <mpi.h>
+
+
+#include "ADIOS_CPP.h"
+
+
+int main( int argc, char* argv [] )
+{
+ MPI_Init( &argc, &argv );
+ int rank, size;
+ MPI_Comm_rank( MPI_COMM_WORLD, &rank );
+ MPI_Comm_size( MPI_COMM_WORLD, &size );
+
+ const bool adiosDebug = true;
+ adios::ADIOS adios(MPI_COMM_WORLD, adios::Verbose::INFO, adiosDebug);
+
+
+ //Application variable
+ const std::size_t intDim1 = 4;
+ const std::size_t intDim2 = 3;
+ std::vector<int> myInts = {10,11,12,13,14,15,16,17,18,19,20,21};
+
+ std::vector<double> myDoubles = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 };
+ const std::size_t Nx = myDoubles.size();
+
+ std::vector<std::complex<float>> myCFloats;
+ const std::size_t ComplexDataSize = 3;
+ myCFloats.reserve( ComplexDataSize );
+ myCFloats.emplace_back( 1, 3 );
+ myCFloats.emplace_back( 2, 2 );
+ myCFloats.emplace_back( 3, 1 );
+
+
+ std::vector<std::complex<double>> myCDoubles;
+ myCDoubles.reserve( ComplexDataSize );
+ myCDoubles.emplace_back( 1.1, -3.3 );
+ myCDoubles.emplace_back( 2.1, -2.2 );
+ myCDoubles.emplace_back( 3.1, -1.1 );
+
+ std::vector<std::complex<long double>> myCLongDoubles;
+ myCLongDoubles.reserve( ComplexDataSize );
+ myCLongDoubles.emplace_back( 1.11, -3.33 );
+ myCLongDoubles.emplace_back( 2.11, -2.22 );
+ myCLongDoubles.emplace_back( 3.11, -1.11 );
+
+
+ std::size_t doubleVCount = Nx/size;
+ std::size_t complexCount = ComplexDataSize/size;
+ std::size_t intCountDim1 = intDim1/size;
+
+ std::size_t doubleVOffset = rank * doubleVCount;
+ std::size_t complexOffset = rank * complexCount;
+ std::size_t intOffsetDim1 = rank * intCountDim1;
+ std::size_t intOffsetDim2 = 0;
+
+ if ((size > 1) && (rank == size-1))
+ {
+ doubleVCount = Nx - rank*(Nx/size);
+ complexCount = ComplexDataSize - rank * (ComplexDataSize/size);
+ intCountDim1 = intDim1 - rank * (intDim1/size);
+ }
+
+ try
+ {
+ //Define variable and local size
+ auto& ioMyInts = adios.DefineVariable<int>( "myInts", {intCountDim1, intDim2}, {4,3}, {intOffsetDim1, intOffsetDim2} );
+ auto& ioMyDoubles = adios.DefineVariable<double>( "myDoubles", {doubleVCount}, {Nx}, {doubleVOffset} );
+ auto& ioMyCFloats = adios.DefineVariable<std::complex<float>>( "myCFloats", {complexCount}, {3}, {complexOffset} );
+ auto& ioMyCDoubles = adios.DefineVariable<std::complex<double>>( "myCDoubles", {complexCount}, {3}, {complexOffset} );
+ auto& ioMyCLongDoubles = adios.DefineVariable<std::complex<long double>>( "myCLongDoubles", {complexCount}, {3}, {complexOffset} );
+
+
+ //Define method for engine creation, it is basically straight-forward parameters
+ adios::Method& HDF5Settings = adios.DeclareMethod("w" );
+ HDF5Settings.SetEngine("HDF5Writer");
+ HDF5Settings.SetParameters( "chunck=yes", "collectiveIO=yes");
+ //HDF5Settings.AddTransport( "Mdtm", "localIP=128.0.0.0.1", "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
+
+ //Create engine smart pointer to HDF5 Engine due to polymorphism,
+ //Open returns a smart pointer to Engine containing the Derived class HDF5
+ auto HDF5Writer = adios.Open( "test.bp", "w", HDF5Settings );
+
+ if( HDF5Writer == nullptr )
+ throw std::ios_base::failure( "ERROR: failed to create HDF5 I/O engine at Open\n" );
+
+ HDF5Writer->Write( ioMyDoubles, myDoubles.data()+doubleVOffset ); // Base class Engine own the Write<T> that will call overloaded Write from Derived
+ HDF5Writer->Write( ioMyInts, myInts.data()+(intOffsetDim1*intDim2*rank) );
+
+ HDF5Writer->Write( ioMyCFloats, myCFloats.data()+complexOffset );
+ HDF5Writer->Write( ioMyCDoubles, myCDoubles.data()+complexOffset );
+ HDF5Writer->Write( ioMyCLongDoubles, myCLongDoubles.data()+complexOffset );
+ HDF5Writer->Close( );
+
+ }
+ catch( std::invalid_argument& e )
+ {
+ if( rank == 0 )
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+ catch( std::ios_base::failure& e )
+ {
+ if( rank == 0 )
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+ catch( std::exception& e )
+ {
+ if( rank == 0 )
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+
+ MPI_Finalize( );
+
+ return 0;
+
+}
diff --git a/examples/hello/hdf5Writer/helloHDF5Writer_nompi.cpp b/examples/hello/hdf5Writer/helloHDF5Writer_nompi.cpp
new file mode 100644
index 000000000..e49794eae
--- /dev/null
+++ b/examples/hello/hdf5Writer/helloHDF5Writer_nompi.cpp
@@ -0,0 +1,134 @@
+/*
+ * HDF5Writer.cpp
+ *
+ * Created on: March 20, 2017
+ * Author: Junmin
+ */
+
+
+
+#include <vector>
+#include <iostream>
+
+
+//#include <mpi.h>
+#include "ADIOS_MPI.h"
+
+#ifndef HAVE_MPI
+// mpidummy has namespace adios
+using namespace adios;
+#endif
+#include "ADIOS_CPP.h"
+
+
+int main( int argc, char* argv [] )
+{
+ MPI_Init( &argc, &argv );
+ int rank, size;
+ MPI_Comm_rank( MPI_COMM_WORLD, &rank );
+ MPI_Comm_size( MPI_COMM_WORLD, &size );
+
+ const bool adiosDebug = true;
+ adios::ADIOS adios(MPI_COMM_WORLD, adios::Verbose::INFO, adiosDebug);
+
+
+ //Application variable
+ const std::size_t intDim1 = 4;
+ const std::size_t intDim2 = 3;
+ std::vector<int> myInts = {10,11,12,13,14,15,16,17,18,19,20,21};
+
+ std::vector<double> myDoubles = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9 };
+ const std::size_t Nx = myDoubles.size();
+
+ std::vector<std::complex<float>> myCFloats;
+ const std::size_t CFloatSize = 3;
+ myCFloats.reserve( CFloatSize );
+ myCFloats.emplace_back( 1, 3 );
+ myCFloats.emplace_back( 2, 2 );
+ myCFloats.emplace_back( 3, 1 );
+
+
+ std::vector<std::complex<double>> myCDoubles;
+ const std::size_t CDoubleSize = 3;
+ myCDoubles.reserve( CDoubleSize );
+ myCDoubles.emplace_back( 1, 3 );
+ myCDoubles.emplace_back( 2, 2 );
+ myCDoubles.emplace_back( 3, 1 );
+
+
+ std::size_t doubleVCount = Nx/size;
+ std::size_t floatCount = CFloatSize/size;
+ std::size_t intCountDim1 = intDim1/size;
+
+ std::size_t doubleVOffset = rank * doubleVCount;
+ std::size_t floatOffset = rank * floatCount;
+ std::size_t intOffsetDim1 = rank * intCountDim1;
+ std::size_t intOffsetDim2 = 0;
+
+ if ((size > 1) && (rank == size-1)) {
+ doubleVCount = Nx - rank*(Nx/size);
+ floatCount = CFloatSize - rank * (CFloatSize/size);
+ intCountDim1 = intDim1 - rank * (intDim1/size);
+ }
+
+ try
+ {
+ //Define variable and local size
+ //auto& ioMyDoubles = adios.DefineVariable<double>( "myDoubles", {Nx}, {Nx} );
+ //auto& ioMyCFloats = adios.DefineVariable<std::complex<float>>( "myCFloats", {3}, {3} );
+ //auto& ioMyInts = adios.DefineVariable<int>( "myInts", {4,3}, {4,3} );
+
+ auto& ioMyDoubles = adios.DefineVariable<double>( "myDoubles", {doubleVCount}, {Nx}, {doubleVOffset} );
+ auto& ioMyCFloats = adios.DefineVariable<std::complex<float>>( "myCFloats", {floatCount}, {3}, {floatOffset} );
+ auto& ioMyCDoubles = adios.DefineVariable<std::complex<double>>( "myCDoubles", {floatCount}, {3}, {floatOffset} );
+ auto& ioMyInts = adios.DefineVariable<int>( "myInts", {intCountDim1, intDim2}, {4,3}, {intOffsetDim1, intOffsetDim2} );
+
+ //Define method for engine creation, it is basically straight-forward parameters
+ adios::Method& HDF5Settings = adios.DeclareMethod("HDF5Writer" ); //default method type is Writer
+ HDF5Settings.SetParameters( "chunck=yes", "collectiveIO=yes");
+ //HDF5Settings.AddTransport( "Mdtm", "localIP=128.0.0.0.1", "remoteIP=128.0.0.0.2", "tolerances=1,2,3" );
+
+ //Create engine smart pointer to HDF5 Engine due to polymorphism,
+ //Open returns a smart pointer to Engine containing the Derived class HDF5
+ auto HDF5Writer = adios.Open( "test.bp", "w", HDF5Settings );
+
+ if( HDF5Writer == nullptr )
+ throw std::ios_base::failure( "ERROR: failed to create HDF5 I/O engine at Open\n" );
+
+ HDF5Writer->Write( ioMyDoubles, myDoubles.data()+doubleVOffset ); // Base class Engine own the Write<T> that will call overloaded Write from Derived
+ HDF5Writer->Write( ioMyInts, myInts.data()+(intOffsetDim1*intDim2*rank) );
+ HDF5Writer->Write( ioMyCFloats, myCFloats.data() );
+ HDF5Writer->Write( ioMyCDoubles, myCDoubles.data() );
+ HDF5Writer->Close( );
+
+ }
+ catch( std::invalid_argument& e )
+ {
+ if( rank == 0 )
+ {
+ std::cout << "Invalid argument exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+ catch( std::ios_base::failure& e )
+ {
+ if( rank == 0 )
+ {
+ std::cout << "System exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+ catch( std::exception& e )
+ {
+ if( rank == 0 )
+ {
+ std::cout << "Exception, STOPPING PROGRAM\n";
+ std::cout << e.what() << "\n";
+ }
+ }
+
+ MPI_Finalize( );
+
+ return 0;
+
+}
diff --git a/include/engine/hdf5/HDF5ReaderP.h b/include/engine/hdf5/HDF5ReaderP.h
index 28d688208..959b08e91 100644
--- a/include/engine/hdf5/HDF5ReaderP.h
+++ b/include/engine/hdf5/HDF5ReaderP.h
@@ -1,3 +1,14 @@
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
+ * HDF5ReaderP.h
+ *
+ * Created on: March 20, 2017
+ * Author: Junmin
+ */
+
+
#ifndef HDF5_READER_P_H
#define HDF5_READER_P_H
diff --git a/include/engine/hdf5/HDF5WriterP.h b/include/engine/hdf5/HDF5WriterP.h
index 27d5e8d10..098a56c45 100644
--- a/include/engine/hdf5/HDF5WriterP.h
+++ b/include/engine/hdf5/HDF5WriterP.h
@@ -1,4 +1,8 @@
+
/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
* HDF5WriterP.h
*
* Created on: March 20, 2017
@@ -8,24 +12,23 @@
#ifndef HDF5_WRITER_P_H_
#define HDF5_WRITER_P_H_
-#include <iostream> //std::cout must be removed, only used for hello example
#include <unistd.h> //sleep must be removed
#include "core/Engine.h"
-#include "format/BP1Writer.h"
+
// supported capsules
#include "capsule/heap/STLVector.h"
#include "ADIOS_MPI.h"
-#include "hdf5.h"
+#include <hdf5.h>
namespace adios {
-
+ /*
typedef struct {
- double _re; /*real part*/
- double _im; /*imaginary part*/
+ double _re; //real part
+ double _im; //imaginary part
} ADIOS2_Complex_Double;
typedef struct {
@@ -36,10 +39,10 @@ typedef struct {
// using ADIOS2_Complex_Float = std::complex<float>;
typedef struct {
- long double _re; /*real part*/
- long double _im; /*imaginary part*/
+ long double _re; //real part
+ long double _im; //imaginary part
} ADIOS2_Complex_LongDouble;
-
+*/
class HDF5Writer : public Engine {
public:
@@ -52,12 +55,10 @@ public:
* @param method
* @param debugMode
*/
-
HDF5Writer(ADIOS &adios, const std::string name, const std::string accessMode,
- MPI_Comm mpiComm, const Method &method,
- const bool debugMode = false, const unsigned int cores = 1);
+ MPI_Comm mpiComm, const Method &method);
- ~HDF5Writer();
+ virtual ~HDF5Writer();
void Write(Variable<char> &variable, const char *values);
void Write(Variable<unsigned char> &variable, const unsigned char *values);
@@ -126,9 +127,9 @@ private:
hid_t DefH5T_COMPLEX_FLOAT;
hid_t DefH5T_COMPLEX_LongDOUBLE;
- hid_t DefH5T_filetype_COMPLEX_DOUBLE;
- hid_t DefH5T_filetype_COMPLEX_FLOAT;
- hid_t DefH5T_filetype_COMPLEX_LongDOUBLE;
+ //hid_t DefH5T_filetype_COMPLEX_DOUBLE;
+ //hid_t DefH5T_filetype_COMPLEX_FLOAT;
+ //hid_t DefH5T_filetype_COMPLEX_LongDOUBLE;
template <class T>
void UseHDFWrite(Variable<T> &variable, const T *values, hid_t h5type);
diff --git a/source/ADIOS.cpp b/source/ADIOS.cpp
index 729e6c8ee..47e3c333f 100644
--- a/source/ADIOS.cpp
+++ b/source/ADIOS.cpp
@@ -35,6 +35,12 @@
#include "engine/adios1/ADIOS1Writer.h"
#endif
+#ifdef ADIOS_HAVE_PHDF5 // external dependencies
+#ifdef ADIOS_HAVE_MPI
+#include "engine/hdf5/HDF5WriterP.h"
+#include "engine/hdf5/HDF5ReaderP.h"
+#endif
+#endif
namespace adios
{
@@ -185,6 +191,15 @@ std::shared_ptr<Engine> ADIOS::Open(const std::string &name,
// method,
// iomode, timeout_sec, m_DebugMode, method.m_nThreads );
}
+ else if (type == "HDF5Writer") // -junmin
+ {
+ #if defined(ADIOS_HAVE_PHDF5) && defined(ADIOS_HAVE_MPI)
+ return std::make_shared<HDF5Writer>(*this, name, accessMode, mpiComm, method);
+ #else
+ throw std::invalid_argument( "ERROR: this version didn't compile with HDF5 library, can't use HDF5\n" );
+ #endif
+ }
+
else
{
if (m_DebugMode == true)
diff --git a/source/CMakeLists.txt b/source/CMakeLists.txt
index 2ccf94700..4c5afc475 100644
--- a/source/CMakeLists.txt
+++ b/source/CMakeLists.txt
@@ -25,18 +25,18 @@ foreach(adios2_target IN LISTS adios2_targets)
engine/bp/BPFileReader.cpp
engine/bp/BPFileWriter.cpp
+
+ utilities/format/bp1/BP1Base.cpp
+ utilities/format/bp1/BP1Aggregator.cpp
+ utilities/format/bp1/BP1Writer.cpp
+
+ utilities/profiling/iochrono/Timer.cpp
functions/adiosFunctions.cpp
transport/file/FStream.cpp
transport/file/FileDescriptor.cpp
transport/file/FilePointer.cpp
-
- utilities/format/bp1/BP1Base.cpp
- utilities/format/bp1/BP1Aggregator.cpp
- utilities/format/bp1/BP1Writer.cpp
-
- utilities/profiling/iochrono/Timer.cpp
)
target_include_directories(${adios2_target}
PUBLIC ${ADIOS_SOURCE_DIR}/include
@@ -52,6 +52,7 @@ foreach(adios2_target IN LISTS adios2_targets)
target_compile_definitions(${adios2_target} PRIVATE ADIOS_HAVE_DATAMAN)
target_link_libraries(${adios2_target} PRIVATE DataMan::DataMan)
endif()
+
if(ADIOS_USE_BZip2)
find_package(BZip2 REQUIRED)
@@ -81,4 +82,24 @@ if(ADIOS_USE_MPI)
target_compile_definitions(adios2 PRIVATE ADIOS_HAVE_ADIOS1)
target_link_libraries(adios2 PRIVATE adios1::adios)
endif()
+
+ if(ADIOS_USE_PHDF5)
+ find_package(HDF5 REQUIRED)
+ message(" HDF5 ROOT: ${HDF5_ROOT}")
+ message(" HDF5 include: ${HDF5_INCLUDE_DIRS} is paralle? ${HDF5_IS_PARALLEL}")
+
+ get_property(dirs DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} PROPERTY INCLUDE_DIRECTORIES)
+ foreach(dir ${dirs})
+ message(STATUS "dir='${dir}'")
+ endforeach()
+ include_directories(${HDF5_INCLUDE_DIRS})
+
+ target_sources(adios2 PRIVATE
+ engine/hdf5/HDF5ReaderP.cpp
+ engine/hdf5/HDF5WriterP.cpp
+ )
+ target_compile_definitions(adios2 PRIVATE ADIOS_HAVE_PHDF5)
+ target_link_libraries(adios2 PRIVATE hdf5)
+ endif()
+
endif()
diff --git a/source/engine/hdf5/HDF5ReaderP.cpp b/source/engine/hdf5/HDF5ReaderP.cpp
index 2412944f4..3716bfea5 100644
--- a/source/engine/hdf5/HDF5ReaderP.cpp
+++ b/source/engine/hdf5/HDF5ReaderP.cpp
@@ -1,10 +1,15 @@
/*
- * HDF5ReaderP.cpp
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
*
- * Created on: Mar 23, 2017
- * Author: junmin
+ * HDF5WriterP.cpp
+ *
+ * Created on: March 20, 2017
+ * Author: Junmin
*/
+
+
#include <iostream> //needs to go away, this is just for demo purposes
#include "engine/hdf5/HDF5ReaderP.h"
diff --git a/source/engine/hdf5/HDF5WriterP.cpp b/source/engine/hdf5/HDF5WriterP.cpp
index 5d07fd6e7..196744ac2 100644
--- a/source/engine/hdf5/HDF5WriterP.cpp
+++ b/source/engine/hdf5/HDF5WriterP.cpp
@@ -1,10 +1,14 @@
/*
+ * Distributed under the OSI-approved Apache License, Version 2.0. See
+ * accompanying file Copyright.txt for details.
+ *
* HDF5WriterP.cpp
*
- * Created on: Mar 23, 2017
- * Author: junmin
+ * Created on: March 20, 2017
+ * Author: Junmin
*/
+
#include <iostream> //needs to go away, this is just for demo purposes
#ifdef ADIOS_HAVE_MPI
@@ -13,59 +17,34 @@
#include "core/Support.h"
#include "functions/adiosFunctions.h" //CSVToVector
-// supported transports
-//#include "transport/file/FD.h" // uses POSIX
-//#include "transport/file/FP.h" // uses C FILE*
-//#include "transport/file/FStream.h" // uses C++ fstream
-
namespace adios {
HDF5Writer::HDF5Writer(ADIOS &adios, const std::string name,
const std::string accessMode, MPI_Comm mpiComm,
- const Method &method, const bool debugMode,
- const unsigned int cores)
- : Engine(adios, "HDF5Writer", name, accessMode, mpiComm, method, debugMode,
- cores, " HDF5Writer constructor (or call to ADIOS Open).\n"),
- m_Buffer(accessMode, m_RankMPI, m_DebugMode) {
- DefH5T_COMPLEX_DOUBLE =
- H5Tcreate(H5T_COMPOUND, sizeof(ADIOS2_Complex_Double));
- DefH5T_COMPLEX_FLOAT = H5Tcreate(H5T_COMPOUND, sizeof(ADIOS2_Complex_Float));
- DefH5T_COMPLEX_LongDOUBLE =
- H5Tcreate(H5T_COMPOUND, sizeof(ADIOS2_Complex_LongDouble));
-
- // compound data type for memory
- H5Tinsert(DefH5T_COMPLEX_DOUBLE, "double real",
- HOFFSET(ADIOS2_Complex_Double, _re), H5T_NATIVE_DOUBLE);
- H5Tinsert(DefH5T_COMPLEX_DOUBLE, "double img",
- HOFFSET(ADIOS2_Complex_Double, _im), H5T_NATIVE_DOUBLE);
- H5Tinsert(DefH5T_COMPLEX_FLOAT, "float real",
- HOFFSET(ADIOS2_Complex_Float, _re), H5T_NATIVE_FLOAT);
- H5Tinsert(DefH5T_COMPLEX_FLOAT, "float img",
- HOFFSET(ADIOS2_Complex_Float, _im), H5T_NATIVE_FLOAT);
- H5Tinsert(DefH5T_COMPLEX_LongDOUBLE, "ldouble real",
- HOFFSET(ADIOS2_Complex_LongDouble, _re), H5T_NATIVE_LDOUBLE);
- H5Tinsert(DefH5T_COMPLEX_LongDOUBLE, "ldouble img",
- HOFFSET(ADIOS2_Complex_LongDouble, _im), H5T_NATIVE_LDOUBLE);
-
- // data type for file
- int ldsize = H5Tget_size(H5T_NATIVE_DOUBLE);
- DefH5T_filetype_COMPLEX_DOUBLE = H5Tcreate(H5T_COMPOUND, ldsize + ldsize);
- H5Tinsert(DefH5T_filetype_COMPLEX_DOUBLE, "double real", 0, H5T_IEEE_F64BE);
- H5Tinsert(DefH5T_filetype_COMPLEX_DOUBLE, "double img", ldsize,
- H5T_IEEE_F64BE);
-
- ldsize = H5Tget_size(H5T_NATIVE_FLOAT);
- DefH5T_filetype_COMPLEX_FLOAT = H5Tcreate(H5T_COMPOUND, ldsize + ldsize);
- H5Tinsert(DefH5T_filetype_COMPLEX_FLOAT, "float real", 0, H5T_IEEE_F32BE);
- H5Tinsert(DefH5T_filetype_COMPLEX_FLOAT, "float img", ldsize, H5T_IEEE_F32BE);
-
- ldsize = H5Tget_size(
- H5T_NATIVE_LDOUBLE); // note that sizeof(H5T_NATIVE_LDOUBLE) returned 4!!
- DefH5T_filetype_COMPLEX_LongDOUBLE = H5Tcreate(H5T_COMPOUND, ldsize + ldsize);
- H5Tinsert(DefH5T_filetype_COMPLEX_LongDOUBLE, "ldouble real", 0,
- H5T_NATIVE_LDOUBLE);
- H5Tinsert(DefH5T_filetype_COMPLEX_LongDOUBLE, "ldouble img", ldsize,
- H5T_NATIVE_LDOUBLE);
+ const Method &method)
+ : Engine(adios, "HDF5Writer", name, accessMode, mpiComm, method, /*debugMode, cores,*/
+ " HDF5Writer constructor (or call to ADIOS Open).\n"),
+ m_Buffer(accessMode, m_RankMPI, m_DebugMode)
+{
+ //
+ // 16, 4 vs: 8
+ //std::cout<<sizeof(std::complex<double>)<<", "<<sizeof(H5T_NATIVE_DOUBLE)<<" vs: "<<H5Tget_size(H5T_NATIVE_DOUBLE)<<std::endl;
+ // 8, 4 vs: 4
+ //std::cout<<sizeof(std::complex<float>)<<", "<<sizeof(H5T_NATIVE_FLOAT)<<" vs: "<<H5Tget_size(H5T_NATIVE_FLOAT)<<std::endl;
+ // 32, 4 vs: 16
+ //std::cout<<sizeof(std::complex<long double>)<<", "<<sizeof(H5T_NATIVE_LDOUBLE)<<" vs: "<<H5Tget_size(H5T_NATIVE_LDOUBLE)<<std::endl;
+
+ 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);
Init();
}
@@ -74,20 +53,20 @@ HDF5Writer::~HDF5Writer() {}
void HDF5Writer::Init() {
if (m_AccessMode != "w" && m_AccessMode != "write" && m_AccessMode != "a" &&
- m_AccessMode != "append") {
- throw std::invalid_argument(
- "ERROR: HDF5Writer doesn't support access mode " + m_AccessMode +
- ", in call to ADIOS Open or HDF5Writer constructor\n");
+ m_AccessMode != "append")
+ {
+ throw std::invalid_argument("ERROR: HDF5Writer doesn't support access mode " + m_AccessMode +
+ ", in call to ADIOS Open or HDF5Writer constructor\n");
}
- std::cout << "method: # of inputs:" << m_Method.m_Parameters.size()
- << std::endl;
- std::cout << "::Init hdf5 parallel writer. File name:" << m_Name << std::endl;
+ //std::cout << "method: # of inputs:" << m_Method.m_Parameters.size() << std::endl;
+
+ //std::cout << "::Init hdf5 parallel writer. File name:" << m_Name << std::endl;
_plist_id = H5Pcreate(H5P_FILE_ACCESS);
-#ifdef HAVE_MPI
+
H5Pset_fapl_mpio(_plist_id, m_MPIComm, MPI_INFO_NULL);
-#endif
+
/*
* Create a new file collectively and release property list identifier.
@@ -157,17 +136,17 @@ void HDF5Writer::Write(Variable<long double> &variable,
void HDF5Writer::Write(Variable<std::complex<float>> &variable,
const std::complex<float> *values) {
- UseHDFWrite(variable, values, DefH5T_filetype_COMPLEX_FLOAT);
+ UseHDFWrite(variable, values, DefH5T_COMPLEX_FLOAT);
}
void HDF5Writer::Write(Variable<std::complex<double>> &variable,
const std::complex<double> *values) {
- UseHDFWrite(variable, values, DefH5T_filetype_COMPLEX_DOUBLE);
+ UseHDFWrite(variable, values, DefH5T_COMPLEX_DOUBLE);
}
void HDF5Writer::Write(Variable<std::complex<long double>> &variable,
const std::complex<long double> *values) {
- UseHDFWrite(variable, values, DefH5T_filetype_COMPLEX_LongDOUBLE);
+ UseHDFWrite(variable, values, DefH5T_COMPLEX_LongDOUBLE);
}
// String version
@@ -260,7 +239,7 @@ void HDF5Writer::Write(const std::string variableName,
}
void HDF5Writer::Close(const int transportIndex) {
- std::cout << " ===> CLOSING HDF5 <===== " << std::endl;
+ //std::cout << " ===> CLOSING HDF5 <===== " << std::endl;
// H5Dclose(_dset_id);
// H5Sclose(_filespace);
// H5Sclose(_memspace);
@@ -277,21 +256,23 @@ void HDF5Writer::UseHDFWrite(Variable<T> &variable, const T *values,
variable.m_AppValues = values;
m_WrittenVariables.insert(variable.m_Name);
+ int dimSize = variable.m_GlobalDimensions.size();
+ /*
std::cout << "writting : " << variable.m_Name
<< " dim size:" << variable.m_GlobalDimensions.size() << std::endl;
- int dimSize = variable.m_GlobalDimensions.size();
for (int i = 0; i < dimSize; i++) {
std::cout << " dim: " << i << ", size:" << variable.m_GlobalDimensions[i]
- << " offset=" << variable.m_GlobalOffsets[i]
- << " count=" << variable.m_Dimensions[i] << std::endl;
+ << " offset=" << variable.m_Offsets[i]
+ << " count=" << variable.m_LocalDimensions[i] << std::endl;
}
+ */
std::vector<hsize_t> dimsf, count, offset;
for (int i = 0; i < dimSize; i++) {
dimsf.push_back(variable.m_GlobalDimensions[i]);
- count.push_back(variable.m_Dimensions[i]);
- offset.push_back(variable.m_GlobalOffsets[i]);
+ count.push_back(variable.m_LocalDimensions[i]);
+ offset.push_back(variable.m_Offsets[i]);
}
_filespace = H5Screate_simple(dimSize, dimsf.data(), NULL);
@@ -308,60 +289,21 @@ void HDF5Writer::UseHDFWrite(Variable<T> &variable, const T *values,
count.data(), NULL);
// Create property list for collective dataset write.
+
_plist_id = H5Pcreate(H5P_DATASET_XFER);
H5Pset_dxpl_mpio(_plist_id, H5FD_MPIO_COLLECTIVE);
herr_t status;
- if (h5type == DefH5T_filetype_COMPLEX_FLOAT) {
- /*
- ADIOS2_Complex_Float v[3];
- v[0]._re = 1.1, v[0]._im = 1.2;
- v[1]._re = 2.1, v[1]._im = 2.2;
- v[2]._re = 3.1, v[2]._im = 3.2;
- // status = H5Dwrite(_dset_id, DefH5T_COMPLEX_FLOAT, _memspace, _filespace,
- // _plist_id, values);
- status = H5Dwrite(_dset_id, DefH5T_COMPLEX_FLOAT, _memspace, _filespace,
- _plist_id, v);
- */
- } else if (h5type == DefH5T_filetype_COMPLEX_DOUBLE) {
- /*
- ADIOS2_Complex_Double v[3];
- v[0]._re = 1.1, v[0]._im = 1.2;
- v[1]._re = 2.1, v[1]._im = 2.2;
- v[2]._re = 3.1, v[2]._im = 3.2;
- status = H5Dwrite(_dset_id, DefH5T_COMPLEX_DOUBLE, _memspace, _filespace,
- _plist_id, v);
- */
- } else if (h5type == DefH5T_filetype_COMPLEX_LongDOUBLE) {
- /*
- ADIOS2_Complex_LongDouble v[3];
- v[0]._re = 1.1, v[0]._im = 1.2;
- v[1]._re = 2.1, v[1]._im = 2.2;
- v[2]._re = 3.1, v[2]._im = 3.2;
- status = H5Dwrite(_dset_id, DefH5T_COMPLEX_LongDOUBLE, _memspace,
- _filespace, _plist_id, v);
- */
- } else {
- status =
- H5Dwrite(_dset_id, h5type, _memspace, _filespace, _plist_id, values);
- }
+ status =
+ H5Dwrite(_dset_id, h5type, _memspace, _filespace, _plist_id, values);
if (status < 0) {
// error
std::cerr << " Write failed. " << std::endl;
}
- std::cout << " ==> User is responsible for freeing the data " << std::endl;
- // free(values);
-
- // Close/release resources.
-
- // H5Dclose(_dset_id);
- // H5Sclose(_filespace);
- // H5Sclose(_memspace);
- // H5Pclose(_plist_id);
- // H5Fclose(_file_id);
+ //std::cout << " ==> User is responsible for freeing the data " << std::endl;
H5Dclose(_dset_id);
H5Sclose(_filespace);
--
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