Merge pull request #980 from guj/1101 (7a33e0ca) · Commits · Podhorszki, Norbert / ADIOS2

examples/hello/hdf5Writer/helloHDF5Writer.cpp

+4 −0

Original line number	Diff line number	Diff line
		@@ -27,6 +27,7 @@ int main(int argc, char *argv[])
		/** Application variable */
		std::vector<float> myFloats = {0, 1, 2, 3, 4, 5, 6, 7, 8, 9};
		std::vector<int> myInts = {0, -1, -2, -3, -4, -5, -6, -7, -8, -9};
		double myScalar = 1.234;
		const std::size_t Nx = myFloats.size();

		try
		@@ -47,6 +48,8 @@ int main(int argc, char *argv[])
		adios2::Variable<int> h5Ints = hdf5IO.DefineVariable<int>(
		"h5Ints", {size * Nx}, {rank * Nx}, {Nx}, adios2::ConstantDims);

		adios2::Variable<double> h5ScalarDouble =
		hdf5IO.DefineVariable<double>("h5ScalarDouble");
		/** Engine derived class, spawned to start IO operations */
		adios2::Engine hdf5Writer =
		hdf5IO.Open("myVector.h5", adios2::Mode::Write);
		@@ -54,6 +57,7 @@ int main(int argc, char *argv[])
		/** Write variable for buffering */
		hdf5Writer.Put<float>(h5Floats, myFloats.data());
		hdf5Writer.Put(h5Ints, myInts.data());
		hdf5Writer.Put(h5ScalarDouble, &myScalar);

		std::vector<int64_t> m_globalDims = {10, 20, 30, 40};
		hdf5IO.DefineAttribute<std::string>(

source/adios2/engine/hdf5/HDF5ReaderP.cpp

+5 −3

Original line number	Diff line number	Diff line
		@@ -68,10 +68,12 @@ void HDF5ReaderP::Init()
		m_H5File.ReadAttrToIO(m_IO);
		if (!m_InStreamMode)
		{
		// m_H5File.ReadVariables(0, m_IO);
		m_H5File.ReadAllVariables(m_IO);
		}
		else
		{
		// m_H5File.ReadVariables(0, m_IO);
		m_H5File.ReadAllVariables(m_IO);
		}
		}
		@@ -260,12 +262,12 @@ StepStatus HDF5ReaderP::BeginStep(StepMode mode, const float timeoutSeconds)

		if (m_StreamAt >= ts)
		{
		m_IO.m_ReadStreaming = false;
		return StepStatus::EndOfStream;
		}

		m_IO.RemoveAllVariables();
		m_IO.RemoveAllAttributes();
		m_H5File.ReadVariables(m_StreamAt, m_IO);
		m_IO.m_ReadStreaming = true;
		m_IO.m_EngineStep = m_StreamAt;

		return StepStatus::OK;
		}

source/adios2/engine/hdf5/HDF5WriterP.cpp

+2 −0

Original line number	Diff line number	Diff line
		@@ -24,6 +24,7 @@ HDF5WriterP::HDF5WriterP(IO &io, const std::string &name, const Mode mode,
		MPI_Comm mpiComm)
		: Engine("HDF5Writer", io, name, mode, mpiComm), m_H5File(io.m_DebugMode)
		{
		m_IO.m_ReadStreaming = false;
		m_EndMessage = ", in call to IO HDF5Writer Open " + m_Name + "\n";
		Init();
		}
		@@ -32,6 +33,7 @@ HDF5WriterP::~HDF5WriterP() { DoClose(); }

		StepStatus HDF5WriterP::BeginStep(StepMode mode, const float timeoutSeconds)
		{
		m_IO.m_ReadStreaming = false;
		return StepStatus::OK;
		}

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

+110 −53

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";
		@@ -174,7 +196,7 @@ void HDF5Common::ReadAllVariables(core::IO &io)
		{
		if (!m_IsGeneratedByAdios)
		{
		FindVarsFromH5(io, m_FileId, "/", "");
		FindVarsFromH5(io, m_FileId, "/", "", 0);
		return;
		}

		@@ -188,7 +210,7 @@ void HDF5Common::ReadAllVariables(core::IO &io)
		}

		void HDF5Common::FindVarsFromH5(core::IO &io, hid_t top_id, const char *gname,
		const char *heritage)
		const char *heritage, unsigned int ts)
		{
		// int i = 0;
		// std::string stepStr;
		@@ -211,13 +233,20 @@ 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)))
		// cave in to cadacity requirement to pass pull request.
		// This is odd
		if (std::string::npos == nameStr.find(PREFIX_BLOCKINFO) &&
		std::string::npos == 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)
		{
		@@ -225,11 +254,13 @@ 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);
		CreateVar(io, datasetId, longName, ts);
		}
		}
		else if (currType == H5G_GROUP)
		{
		@@ -239,7 +270,7 @@ void HDF5Common::FindVarsFromH5(core::IO &io, hid_t top_id, const char *gname,
		heritageNext += "/";
		heritageNext += gname;
		}
		FindVarsFromH5(io, gid, name, heritageNext.c_str());
		FindVarsFromH5(io, gid, name, heritageNext.c_str(), ts);
		}
		}
		}
		@@ -303,15 +334,24 @@ void HDF5Common::ReadVariables(unsigned int ts, core::IO &io)
		int currType = H5Gget_objtype_by_idx(gid, k);
		if (currType == H5G_GROUP)
		{
		FindVarsFromH5(io, gid, name, "");
		FindVarsFromH5(io, gid, name, "", ts);
		}
		else if ((currType == H5G_DATASET) \|\| (currType == H5G_TYPE))
		{
		hid_t datasetId = H5Dopen(gid, name, H5P_DEFAULT);
		std::string nameStr = name;
		// if (!(0 == nameStr.find(PREFIX_BLOCKINFO)) &&
		// !(0 == nameStr.find(PREFIX_STAT)))
		// cave in to cadacity requirement to pass pull request.
		// This is odd
		if (std::string::npos == nameStr.find(PREFIX_BLOCKINFO) &&
		std::string::npos == nameStr.find(PREFIX_STAT))

		{
		hid_t datasetId = H5Dopen(gid, name, H5P_DEFAULT);
		HDF5TypeGuard d(datasetId, E_H5_DATASET);
		ReadNativeAttrToIO(io, datasetId, name);
		CreateVar(io, datasetId, name);
		CreateVar(io, datasetId, name, ts);
		}
		}
		}
		}
		@@ -321,7 +361,8 @@ void HDF5Common::ReadVariables(unsigned int ts, core::IO &io)
		}

		template <class T>
		void HDF5Common::AddVar(core::IO &io, std::string const &name, hid_t datasetId)
		void HDF5Common::AddVar(core::IO &io, std::string const &name, hid_t datasetId,
		unsigned int ts)
		{
		core::Variable<T> *v = io.InquireVariable<T>(name);
		if (NULL == v)
		@@ -355,9 +396,13 @@ void HDF5Common::AddVar(core::IO &io, std::string const &name, hid_t datasetId)
		try
		{
		auto &foo = io.DefineVariable<T>(name, shape, zeros, shape);

		// 0 is a dummy holder. Just to make sure the ts entry is in there
		foo.m_AvailableStepBlockIndexOffsets[ts + 1] =
		std::vector<size_t>({0});
		foo.m_AvailableStepsStart = ts;
		// default was set to 0 while m_AvailabelStepsStart is 1.
		// correcting

		if (0 == foo.m_AvailableStepsCount)
		{
		foo.m_AvailableStepsCount++;
		@@ -378,11 +423,12 @@ void HDF5Common::AddVar(core::IO &io, std::string const &name, hid_t datasetId)
		}
		*/
		v->m_AvailableStepsCount++;
		v->m_AvailableStepBlockIndexOffsets[ts + 1] = std::vector<size_t>({0});
		}
		}

		void HDF5Common::CreateVar(core::IO &io, hid_t datasetId,
		std::string const &nameSuggested)
		std::string const &nameSuggested, unsigned int ts)
		{
		std::string name;
		ReadADIOSName(datasetId, name);
		@@ -402,83 +448,83 @@ void HDF5Common::CreateVar(core::IO &io, hid_t datasetId,
		if (H5Tget_class(h5Type) == H5T_STRING)
		// if (H5Tequal(H5T_STRING, h5Type))
		{
		AddVar<std::string>(io, name, datasetId);
		AddVar<std::string>(io, name, datasetId, ts);
		return;
		}

		if (H5Tequal(H5T_NATIVE_SCHAR, h5Type))
		{
		AddVar<signed char>(io, name, datasetId);
		AddVar<signed char>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_NATIVE_CHAR, h5Type))
		{
		AddVar<char>(io, name, datasetId);
		AddVar<char>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_NATIVE_UCHAR, h5Type))
		{
		AddVar<unsigned char>(io, name, datasetId);
		AddVar<unsigned char>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_NATIVE_SHORT, h5Type))
		{
		AddVar<short>(io, name, datasetId);
		AddVar<short>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_NATIVE_USHORT, h5Type))
		{
		AddVar<unsigned short>(io, name, datasetId);
		AddVar<unsigned short>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_NATIVE_INT, h5Type))
		{
		AddVar<int>(io, name, datasetId);
		AddVar<int>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_NATIVE_UINT, h5Type))
		{
		AddVar<unsigned int>(io, name, datasetId);
		AddVar<unsigned int>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_STD_I64LE, h5Type))
		{
		/*
		*/
		AddVar<int64_t>(io, name, datasetId);
		AddVar<int64_t>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_STD_U64LE, h5Type))
		{
		AddVar<uint64_t>(io, name, datasetId);
		AddVar<uint64_t>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_NATIVE_LONG, h5Type))
		{
		AddVar<long>(io, name, datasetId);
		AddVar<long>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_NATIVE_ULONG, h5Type))
		{
		AddVar<unsigned long>(io, name, datasetId);
		AddVar<unsigned long>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_NATIVE_LLONG, h5Type))
		{
		AddVar<long long>(io, name, datasetId);
		AddVar<long long>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_NATIVE_ULLONG, h5Type))
		{
		AddVar<unsigned long long>(io, name, datasetId);
		AddVar<unsigned long long>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_NATIVE_FLOAT, h5Type))
		{
		AddVar<float>(io, name, datasetId);
		AddVar<float>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_NATIVE_DOUBLE, h5Type))
		{
		AddVar<double>(io, name, datasetId);
		AddVar<double>(io, name, datasetId, ts);
		}
		else if (H5Tequal(H5T_NATIVE_LDOUBLE, h5Type))
		{
		AddVar<long double>(io, name, datasetId);
		AddVar<long double>(io, name, datasetId, ts);
		}
		else if (H5Tequal(m_DefH5TypeComplexFloat, h5Type))
		{
		AddVar<std::complex<float>>(io, name, datasetId);
		AddVar<std::complex<float>>(io, name, datasetId, ts);
		}
		else if (H5Tequal(m_DefH5TypeComplexDouble, h5Type))
		{
		AddVar<std::complex<double>>(io, name, datasetId);
		AddVar<std::complex<double>>(io, name, datasetId, ts);
		}

		// H5Tclose(h5Type);
		@@ -498,6 +544,7 @@ void HDF5Common::Close()
		H5Gclose(m_GroupId);
		}

		H5Pclose(m_PropertyTxfID);
		H5Fclose(m_FileId);
		m_FileId = -1;
		m_GroupId = -1;
		@@ -673,8 +720,10 @@ void HDF5Common::CreateDataset(const std::string &varName, hid_t h5Type,
		hid_t dsetID = H5Dcreate(topId, list.back().c_str(), h5Type, filespaceID,
		H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);

		StoreADIOSName(varName, dsetID);

		if (list.back().compare(varName) != 0)
		{
		StoreADIOSName(varName, dsetID); // only stores when not the same
		}
		datasetChain.push_back(dsetID);
		// return dsetID;
		}
		@@ -1233,9 +1282,16 @@ void HDF5Common::ReadNativeAttrToIO(core::IO &io, hid_t datasetId,
		// herr_t ret = H5Gget_num_objs(m_FileId, &numObj);
		H5O_info_t oinfo;
		herr_t ret = H5Oget_info(datasetId, &oinfo);

		if (ret >= 0)
		{
		numAttrs = oinfo.num_attrs;

		if (numAttrs <= 0)
		{
		return; // warning: reading attrs at every var can be very time
		// consuimg
		}
		int k = 0;
		char name[50];
		int MAX_ATTR_NAME_SIZE = 100;
		@@ -1252,16 +1308,17 @@ void HDF5Common::ReadNativeAttrToIO(core::IO &io, hid_t datasetId,
		{
		continue;
		}
		if (ATTRNAME_GIVEN_ADIOSNAME.compare(attrName) == 0)
		{
		continue;
		}

		hid_t sid = H5Aget_space(attrId);
		H5S_class_t stype = H5Sget_simple_extent_type(sid);

		hid_t attrType = H5Aget_type(attrId);
		bool isString = (H5Tget_class(attrType) == H5T_STRING);

		if (ATTRNAME_GIVEN_ADIOSNAME.compare(attrName) == 0)
		{
		continue;
		}
		std::string attrNameInAdios = pathFromRoot + "/" + attrName;
		if (isString)
		{

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

+18 −4

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);

		@@ -145,15 +147,17 @@ public:

		void ReadVariables(unsigned int ts, core::IO &io);
		void FindVarsFromH5(core::IO &io, hid_t gid, const char *name,
		const char *heritage);
		const char *heritage, unsigned int ts);
		void ReadAllVariables(core::IO &io);

		void ReadStringScalarDataset(hid_t dataSetId, std::string &result);
		hid_t GetTypeStringScalar(const std::string &input);
		void CreateVar(core::IO &io, hid_t h5Type, std::string const &name);
		void CreateVar(core::IO &io, hid_t h5Type, std::string const &name,
		unsigned int ts);

		template <class T>
		void AddVar(core::IO &io, std::string const &name, hid_t datasetId);
		void AddVar(core::IO &io, std::string const &name, hid_t datasetId,
		unsigned int ts);

		template <class T>
		void AddNonStringAttribute(core::IO &io, std::string const &attrName,
		@@ -162,11 +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;

		@@ -195,13 +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