Merge pull request #1024 from pnorbert/hdf5-blockinfo (debceb36) · Commits · Podhorszki, Norbert / ADIOS2

source/adios2/engine/hdf5/HDF5ReaderP.cpp

+13 −0

Original line number	Diff line number	Diff line
		@@ -331,9 +331,22 @@ void HDF5ReaderP::PerformGets()
		{ \
		GetSyncCommon(variable, data); \
		} \
		\
		void HDF5ReaderP::DoGetDeferred(Variable<T> &variable, T *data) \
		{ \
		GetDeferredCommon(variable, data); \
		} \
		\
		std::map<size_t, std::vector<typename Variable<T>::Info>> \
		HDF5ReaderP::DoAllStepsBlocksInfo(const Variable<T> &variable) const \
		{ \
		return GetAllStepsBlocksInfo(variable); \
		} \
		\
		std::vector<typename Variable<T>::Info> HDF5ReaderP::DoBlocksInfo( \
		const Variable<T> &variable, const size_t step) const \
		{ \
		return GetBlocksInfo(variable, step); \
		}

		ADIOS2_FOREACH_TYPE_1ARG(declare_type)

source/adios2/engine/hdf5/HDF5ReaderP.h

+21 −1

Original line number	Diff line number	Diff line
		@@ -15,6 +15,9 @@
		#include "adios2/core/IO.h"
		#include "adios2/toolkit/interop/hdf5/HDF5Common.h"

		#include <map>
		#include <vector>

		namespace adios2
		{
		namespace core
		@@ -56,7 +59,12 @@ private:
		unsigned int m_StreamAt = 0; // stream step counter
		#define declare_type(T) \
		void DoGetSync(Variable<T> &, T *) final; \
		void DoGetDeferred(Variable<T> &, T *) final;
		void DoGetDeferred(Variable<T> &, T *) final; \
		std::map<size_t, std::vector<typename Variable<T>::Info>> \
		DoAllStepsBlocksInfo(const Variable<T> &variable) const final; \
		\
		std::vector<typename Variable<T>::Info> DoBlocksInfo( \
		const Variable<T> &variable, const size_t step) const final;
		ADIOS2_FOREACH_TYPE_1ARG(declare_type)
		#undef declare_type

		@@ -72,6 +80,18 @@ private:
		template <class T>
		void GetDeferredCommon(Variable<T> &variable, T *data);

		template <class T>
		std::map<size_t, std::vector<typename Variable<T>::Info>>
		GetAllStepsBlocksInfo(const Variable<T> &variable) const;

		template <class T>
		std::vector<typename Variable<T>::Info>
		GetBlocksInfo(const Variable<T> &variable, const size_t step) const;

		template <class T>
		std::vector<typename core::Variable<T>::Info>
		BlocksInfoCommon(const core::Variable<T> &variable) const;

		template <class T>
		void UseHDFRead(Variable<T> &variable, T *values, hid_t h5Type);

source/adios2/engine/hdf5/HDF5ReaderP.tcc

+46 −0

Original line number	Diff line number	Diff line
		@@ -59,6 +59,52 @@ void HDF5ReaderP::GetDeferredCommon(Variable<T> &variable, T *data)
		#endif
		}

		template <class T>
		std::vector<typename core::Variable<T>::Info>
		HDF5ReaderP::BlocksInfoCommon(const core::Variable<T> &variable) const
		{
		std::vector<typename core::Variable<T>::Info> blocksInfo;

		typename core::Variable<T>::Info blockInfo;
		blockInfo.Start = variable.m_Start;
		blockInfo.Count = variable.m_Shape;
		if (variable.m_ShapeID == ShapeID::GlobalValue \|\|
		variable.m_ShapeID == ShapeID::LocalValue)
		{
		blockInfo.IsValue = true;
		}
		else
		{
		blockInfo.IsValue = false;
		}
		blocksInfo.push_back(blockInfo);

		return blocksInfo;
		}

		template <class T>
		std::map<size_t, std::vector<typename Variable<T>::Info>>
		HDF5ReaderP::GetAllStepsBlocksInfo(const Variable<T> &variable) const
		{
		std::map<size_t, std::vector<typename core::Variable<T>::Info>>
		allStepsBlocksInfo;

		for (size_t step = variable.m_AvailableStepsStart;
		step < variable.m_AvailableStepsCount; ++step)
		{
		allStepsBlocksInfo[step - variable.m_AvailableStepsStart] =
		BlocksInfoCommon(variable);
		}
		return allStepsBlocksInfo;
		}

		template <class T>
		std::vector<typename Variable<T>::Info>
		HDF5ReaderP::GetBlocksInfo(const Variable<T> &variable, const size_t step) const
		{
		BlocksInfoCommon(variable);
		}

		} // end namespace engine
		} // end namespace core
		} // end namespace adios2

testing/utils/iotest/CMakeLists.txt

+71 −1

Original line number	Diff line number	Diff line
		@@ -16,7 +16,7 @@ set(mpicmd ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG})
		#------------------------------------------

		#
		# Pipe2 InsituMPI version
		# Pipe2 BP version
		#
		set(WORKDIR ${CMAKE_CURRENT_BINARY_DIR}/Pipe2.BP)
		file(MAKE_DIRECTORY ${WORKDIR})
		@@ -83,6 +83,76 @@ set_property(TEST Utils.IOTest.Pipe2.BP.ValidateRead
		)


		if (ADIOS2_HAVE_HDF5)
		#
		# Pipe2 HDF5 version
		#
		set(WORKDIR ${CMAKE_CURRENT_BINARY_DIR}/Pipe2.HDF5)
		file(MAKE_DIRECTORY ${WORKDIR})

		# HDF5 file version Write part
		add_test(NAME Utils.IOTest.Pipe2.HDF5.Write
		COMMAND ${mpicmd} 2 ${PROJECT_BINARY_DIR}/bin/adios_iotest -a 1 -c ${CMAKE_CURRENT_SOURCE_DIR}/pipe2-HDF5.txt -x ${CMAKE_CURRENT_SOURCE_DIR}/pipe2-HDF5.xml -d 2 1 --strong-scaling
		WORKING_DIRECTORY ${WORKDIR}
		)

		add_test(NAME Utils.IOTest.Pipe2.HDF5.DumpWrite
		COMMAND ${CMAKE_COMMAND}
		-DARGS=-laD
		-DINPUT_FILE=pipe2_write.h5
		-DOUTPUT_FILE=IOTest.Pipe2.HDF5.Write.bpls.txt
		-P "${PROJECT_BINARY_DIR}/$<CONFIG>/bpls.cmake"
		WORKING_DIRECTORY ${WORKDIR}
		)

		set_property(TEST Utils.IOTest.Pipe2.HDF5.DumpWrite
		PROPERTY DEPENDS Utils.IOTest.Pipe2.HDF5.Write
		)

		add_test(NAME Utils.IOTest.Pipe2.HDF5.ValidateWrite
		COMMAND ${CMAKE_COMMAND}
		-E compare_files
		${CMAKE_CURRENT_SOURCE_DIR}/IOTest.Pipe2.HDF5.Write.bpls.txt
		${WORKDIR}/IOTest.Pipe2.HDF5.Write.bpls.txt
		WORKING_DIRECTORY ${WORKDIR}
		)
		set_property(TEST Utils.IOTest.Pipe2.HDF5.ValidateWrite
		PROPERTY DEPENDS Utils.IOTest.Pipe2.HDF5.DumpWrite
		)

		# HDF5 file version Read part

		add_test(NAME Utils.IOTest.Pipe2.HDF5.Read
		COMMAND ${mpicmd} 2 ${PROJECT_BINARY_DIR}/bin/adios_iotest -a 2 -c ${CMAKE_CURRENT_SOURCE_DIR}/pipe2-HDF5.txt -x ${CMAKE_CURRENT_SOURCE_DIR}/pipe2-HDF5.xml -d 2 1 --strong-scaling
		WORKING_DIRECTORY ${WORKDIR}
		)

		add_test(NAME Utils.IOTest.Pipe2.HDF5.DumpRead
		COMMAND ${CMAKE_COMMAND}
		-DARGS=-laD
		-DINPUT_FILE=pipe2_read.h5
		-DOUTPUT_FILE=IOTest.Pipe2.HDF5.Read.bpls.txt
		-P "${PROJECT_BINARY_DIR}/$<CONFIG>/bpls.cmake"
		WORKING_DIRECTORY ${WORKDIR}
		)

		set_property(TEST Utils.IOTest.Pipe2.HDF5.DumpRead
		PROPERTY DEPENDS Utils.IOTest.Pipe2.HDF5.Read
		)

		add_test(NAME Utils.IOTest.Pipe2.HDF5.ValidateRead
		COMMAND ${CMAKE_COMMAND}
		-E compare_files
		${CMAKE_CURRENT_SOURCE_DIR}/IOTest.Pipe2.HDF5.Read.bpls.txt
		${WORKDIR}/IOTest.Pipe2.HDF5.Read.bpls.txt
		WORKING_DIRECTORY ${WORKDIR}
		)
		set_property(TEST Utils.IOTest.Pipe2.HDF5.ValidateRead
		PROPERTY DEPENDS Utils.IOTest.Pipe2.HDF5.DumpRead
		)

		endif (ADIOS2_HAVE_HDF5)

		#
		math(EXPR HAVE_2_PROCS "${MPIEXEC_MAX_NUMPROCS} - 1")
		if (${HAVE_2_PROCS})

testing/utils/iotest/IOTest.Pipe2.HDF5.Read.bpls.txt

0 → 100644

+14 −0

Original line number	Diff line number	Diff line
		double a 3*{100, 200} = 0 / 0
		step 0:
		block 0: [ 0:99, 0:199] = 0 / 0
		step 1:
		block 0: [ 0:99, 0:199] = 0 / 0
		step 2:
		block 0: [ 0:99, 0:199] = 0 / 0
		float b 3*{100} = 0 / 0
		step 0:
		block 0: [ 0:99] = 0 / 0
		step 1:
		block 0: [ 0:99] = 0 / 0
		step 2:
		block 0: [ 0:99] = 0 / 0

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