added metadata info (98d987d2) · Commits · Podhorszki, Norbert / ADIOS2

source/adios2/toolkit/interop/hdf5/HDF5Common.cpp

+54 −21

Original line number	Diff line number	Diff line
		@@ -27,6 +27,21 @@ namespace interop

		const std::string HDF5Common::ATTRNAME_NUM_STEPS = "NumSteps";
		const std::string HDF5Common::ATTRNAME_GIVEN_ADIOSNAME = "ADIOSName";
		const std::string HDF5Common::PREFIX_BLOCKINFO = "ADIOS_BLOCKINFO_";
		const std::string HDF5Common::PREFIX_STAT = "ADIOS_STAT_";

		/*
		//need to know ndim before defining this.
		//inconvenient
		class HDF5BlockStat
		{
		public:
		size_t m_offset[ndim];
		size_t m_Count[ndim];
		double m_Min;
		double m_Max;
		};
		*/

		HDF5Common::HDF5Common(const bool debugMode) : m_DebugMode(debugMode)
		{
		@@ -41,6 +56,11 @@ HDF5Common::HDF5Common(const bool debugMode) : m_DebugMode(debugMode)
		H5Tinsert(m_DefH5TypeComplexDouble, "dreal", 0, H5T_NATIVE_DOUBLE);
		H5Tinsert(m_DefH5TypeComplexDouble, "dimg", H5Tget_size(H5T_NATIVE_DOUBLE),
		H5T_NATIVE_DOUBLE);

		m_PropertyTxfID = H5Pcreate(H5P_DATASET_XFER);
		#ifdef ADIOS2_HAVE_MPI
		H5Pset_dxpl_mpio(m_PropertyTxfID, H5FD_MPIO_COLLECTIVE);
		#endif
		}

		void HDF5Common::Init(const std::string &name, MPI_Comm comm, bool toWrite)
		@@ -50,6 +70,8 @@ void HDF5Common::Init(const std::string &name, MPI_Comm comm, bool toWrite)

		#ifdef ADIOS2_HAVE_MPI
		H5Pset_fapl_mpio(m_PropertyListId, comm, MPI_INFO_NULL);
		MPI_Comm_rank(comm, &m_CommRank);
		MPI_Comm_size(comm, &m_CommSize);
		#endif

		// std::string ts0 = "/AdiosStep0";
		@@ -211,13 +233,16 @@ void HDF5Common::FindVarsFromH5(core::IO &io, hid_t top_id, const char *gname,
		int currType = H5Gget_objtype_by_idx(gid, k);
		if ((currType == H5G_DATASET) \|\| (currType == H5G_TYPE))
		{
		// std::cout<<" ... handling native: "<<name<<" from
		// :"<<heritage<<"/"<<gname<<std::endl;
		std::string nameStr = name;
		if (!(0 == nameStr.find(PREFIX_BLOCKINFO)) &&
		!(0 == nameStr.find(PREFIX_STAT)))
		{
		hid_t datasetId = H5Dopen(gid, name, H5P_DEFAULT);
		HDF5TypeGuard d(datasetId, E_H5_DATASET);

		char longName[std::strlen(heritage) + std::strlen(gname) +
		std::strlen(name) + 10];
		char longName[std::strlen(heritage) +
		std::strlen(gname) + std::strlen(name) +
		10];

		if (strcmp(gname, "/") == 0)
		{
		@@ -225,12 +250,14 @@ void HDF5Common::FindVarsFromH5(core::IO &io, hid_t top_id, const char *gname,
		}
		else
		{
		sprintf(longName, "%s/%s/%s", heritage, gname, name);
		sprintf(longName, "%s/%s/%s", heritage, gname,
		name);
		}
		// CreateVar(io, datasetId, name);
		ReadNativeAttrToIO(io, datasetId, longName);
		CreateVar(io, datasetId, longName, ts);
		}
		}
		else if (currType == H5G_GROUP)
		{
		std::string heritageNext = heritage;
		@@ -306,6 +333,10 @@ void HDF5Common::ReadVariables(unsigned int ts, core::IO &io)
		FindVarsFromH5(io, gid, name, "", ts);
		}
		else if ((currType == H5G_DATASET) \|\| (currType == H5G_TYPE))
		{
		std::string nameStr = name;
		if (!(0 == nameStr.find(PREFIX_BLOCKINFO)) &&
		!(0 == nameStr.find(PREFIX_STAT)))
		{
		hid_t datasetId = H5Dopen(gid, name, H5P_DEFAULT);

		@@ -316,6 +347,7 @@ void HDF5Common::ReadVariables(unsigned int ts, core::IO &io)
		}
		}
		}
		}
		/// H5Gclose(gid);
		///}
		}
		@@ -505,6 +537,7 @@ void HDF5Common::Close()
		H5Gclose(m_GroupId);
		}

		H5Pclose(m_PropertyTxfID);
		H5Fclose(m_FileId);
		m_FileId = -1;
		m_GroupId = -1;

source/adios2/toolkit/interop/hdf5/HDF5Common.h

+13 −1

Original line number	Diff line number	Diff line
		@@ -112,6 +112,8 @@ public:

		static const std::string ATTRNAME_NUM_STEPS;
		static const std::string ATTRNAME_GIVEN_ADIOSNAME;
		static const std::string PREFIX_BLOCKINFO;
		static const std::string PREFIX_STAT;

		void Init(const std::string &name, MPI_Comm comm, bool toWrite);

		@@ -164,11 +166,13 @@ public:
		static void StaticGetAdiosStepString(std::string &adiosStepName, int ts);

		hid_t m_PropertyListId = -1;
		hid_t m_PropertyTxfID = -1;
		hid_t m_FileId = -1;
		hid_t m_GroupId = -1;

		hid_t m_DefH5TypeComplexDouble;
		hid_t m_DefH5TypeComplexFloat;
		hid_t m_DefH5TypeBlockStat;

		unsigned int m_CurrentAdiosStep = 0;

		@@ -197,13 +201,21 @@ private:
		const bool m_DebugMode;
		bool m_WriteMode = false;
		unsigned int m_NumAdiosSteps = 0;

		int m_CommRank = 0;
		int m_CommSize = 1;

		template <class T>
		void AddBlockInfo(const core::Variable<T> &varaible, hid_t parentId);
		template <class T>
		void AddStats(const core::Variable<T> &variable, hid_t parentId,
		std::vector<T> &stats);
		};

		// Explicit declaration of the public template methods
		#define declare_template_instantiation(T) \
		extern template void HDF5Common::Write(core::Variable<T> &variable, \
		const T *value);

		ADIOS2_FOREACH_TYPE_1ARG(declare_template_instantiation)
		#undef declare_template_instantiation

source/adios2/toolkit/interop/hdf5/HDF5Common.tcc

+106 −17

Original line number	Diff line number	Diff line
		@@ -15,6 +15,8 @@
		#include <iostream>
		#include <vector>

		#include "adios2/helper/adiosFunctions.h"

		namespace adios2
		{
		namespace interop
		@@ -46,23 +48,23 @@ void HDF5Common::Write(core::Variable<T> &variable, const T *values)
		H5Dcreate(m_GroupId, variable.m_Name.c_str(), h5Type, filespaceID,
		H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
		*/

		/*
		hid_t plistID = H5Pcreate(H5P_DATASET_XFER);
		#ifdef ADIOS2_HAVE_MPI
		H5Pset_dxpl_mpio(plistID, H5FD_MPIO_COLLECTIVE);
		#endif

		*/
		herr_t status;
		if (std::is_same<T, std::string>::value)
		{
		status = H5Dwrite(dsetID, h5Type, H5S_ALL, H5S_ALL, plistID,
		status = H5Dwrite(dsetID, h5Type, H5S_ALL, H5S_ALL, m_PropertyTxfID,
		((std::string *)values)->data());
		H5Tclose(h5Type);
		}
		else
		{
		status =
		H5Dwrite(dsetID, h5Type, H5S_ALL, H5S_ALL, plistID, values);
		status = H5Dwrite(dsetID, h5Type, H5S_ALL, H5S_ALL, m_PropertyTxfID,
		values);
		}
		H5Sclose(filespaceID);
		// CloseDataset(dsetID);
		@@ -121,16 +123,18 @@ void HDF5Common::Write(core::Variable<T> &variable, const T *values)
		H5Sselect_hyperslab(fileSpace, H5S_SELECT_SET, offset.data(), NULL,
		count.data(), NULL);

		/*
		// Create property list for collective dataset write.

		hid_t plistID = H5Pcreate(H5P_DATASET_XFER);
		#ifdef ADIOS2_HAVE_MPI
		H5Pset_dxpl_mpio(plistID, H5FD_MPIO_COLLECTIVE);
		#endif
		*/
		herr_t status;

		status = H5Dwrite(dsetID, h5Type, memSpace, fileSpace, plistID, values);

		status =
		H5Dwrite(dsetID, h5Type, memSpace, fileSpace, m_PropertyTxfID, values);
		if (status < 0)
		{
		if (m_DebugMode)
		@@ -140,12 +144,97 @@ void HDF5Common::Write(core::Variable<T> &variable, const T *values)
		}
		}

		size_t valuesSize = adios2::helper::GetTotalSize(variable.m_Count);
		T min, max;
		adios2::helper::GetMinMaxThreads(values, valuesSize, min, max, 1);

		int chainSize = chain.size();
		hid_t parentId = m_GroupId;
		if (chainSize > 1)
		{
		parentId = chain[chainSize - 2];
		}

		AddBlockInfo(variable, parentId);

		std::vector<T> stats = {min, max};
		AddStats(variable, parentId, stats);

		// CloseDataset(dsetID);
		H5Sclose(fileSpace);
		H5Sclose(memSpace);
		H5Pclose(plistID);
		// H5Pclose(plistID);
		}

		template <class T>
		void HDF5Common::AddStats(const core::Variable<T> &variable, hid_t parentId,
		std::vector<T> &stats)
		{

		hid_t h5Type = GetHDF5Type<T>();

		std::string statInfo_name = PREFIX_STAT + variable.m_Name;
		hsize_t numStat = stats.size(); // min, max etc
		hsize_t statDim[2] = {(hsize_t)m_CommSize, numStat};
		hid_t statSpace_id = H5Screate_simple(numStat, statDim, NULL);
		hid_t statId =
		H5Dcreate(parentId, statInfo_name.c_str(), h5Type, statSpace_id,
		H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
		hsize_t statLocalDim[1] = {numStat};
		hid_t statLocal_id = H5Screate_simple(1, statLocalDim, NULL);

		hsize_t statOffset[2] = {(hsize_t)m_CommRank, 0};
		hsize_t statCount[2] = {1, numStat};
		H5Sselect_hyperslab(statSpace_id, H5S_SELECT_SET, statOffset, NULL,
		statCount, NULL);

		H5Dwrite(statId, h5Type, statLocal_id, statSpace_id, m_PropertyTxfID,
		stats.data());

		H5Sclose(statLocal_id);
		H5Sclose(statSpace_id);
		H5Dclose(statId);
		// H5Pclose(plistID);
		}

		template <class T>
		void HDF5Common::AddBlockInfo(const core::Variable<T> &variable, hid_t parentId)
		{
		int dimSize = std::max(variable.m_Shape.size(), variable.m_Count.size());
		hsize_t metaDim[2];
		metaDim[1] = dimSize * 2;
		metaDim[0] = m_CommSize;
		hid_t metaSpace_id = H5Screate_simple(2, metaDim, NULL);
		std::string blockInfo_name = PREFIX_BLOCKINFO + variable.m_Name;
		hid_t metaId =
		H5Dcreate(parentId, blockInfo_name.c_str(), H5T_NATIVE_HSIZE,
		metaSpace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

		size_t blocks[dimSize * 2];
		for (int i = 0; i < dimSize; i++)
		{
		blocks[i + dimSize] = variable.m_Count[i];
		blocks[i] = variable.m_Start[i];
		}
		hsize_t blockDim[1] = {(hsize_t)(dimSize * 2)};
		hid_t metaLocal_id = H5Screate_simple(1, blockDim, NULL);

		hsize_t metaOffset[2] = {(hsize_t)m_CommRank, 0};
		hsize_t metaCount[2] = {1, (hsize_t)(dimSize * 2)};
		H5Sselect_hyperslab(metaSpace_id, H5S_SELECT_SET, metaOffset, NULL,
		metaCount, NULL);

		H5Dwrite(metaId, H5T_NATIVE_HSIZE, metaLocal_id, metaSpace_id,
		m_PropertyTxfID, blocks);

		H5Sclose(metaLocal_id);
		H5Sclose(metaSpace_id);
		H5Dclose(metaId);

		// H5Pclose(plistID);
		}
		//
		//
		template <>
		hid_t HDF5Common::GetHDF5Type<std::string>()
		{