Merge branch 'py_hdf5' into fix_hdf5 (70e54994) · Commits · Podhorszki, Norbert / ADIOS2

source/adios2/core/Stream.cpp

+3 −1

Original line number	Diff line number	Diff line
		@@ -21,7 +21,7 @@ namespace core
		Stream::Stream(const std::string &name, const Mode mode, MPI_Comm comm,
		const std::string engineType, const std::string hostLanguage)
		: m_Name(name), m_ADIOS(std::make_shared<ADIOS>(comm, DebugON, hostLanguage)),
		m_IO(&m_ADIOS->DeclareIO(name)), m_Mode(mode)
		m_IO(&m_ADIOS->DeclareIO(name)), m_Mode(mode), m_EngineType(engineType)
		{
		if (mode == adios2::Mode::Read)
		{
		@@ -105,10 +105,12 @@ void Stream::CheckOpen()
		{
		if (m_Engine == nullptr)
		{
		m_IO->SetEngine(m_EngineType);
		m_Engine = &m_IO->Open(m_Name, m_Mode);
		if (m_Mode == adios2::Mode::Write)
		{
		m_Engine->BeginStep();
		m_StepStatus = true;
		}
		}
		}

source/adios2/core/Stream.h

+5 −0

Original line number	Diff line number	Diff line
		@@ -108,9 +108,14 @@ private:
		/** mode to open engine at first read/write */
		Mode m_Mode;

		/** Sets engine type to be opened at first read/write */
		std::string m_EngineType = "BPFile";

		/** internal flag to check if getstep was called */
		bool m_FirstStep = true;

		bool m_StepStatus = false;

		template <class T>
		std::vector<T> GetCommon(Variable<T> &variable);

source/adios2/core/Stream.tcc

+6 −1

Original line number	Diff line number	Diff line
		@@ -44,13 +44,18 @@ void Stream::Write(const std::string &name, const T *data, const Dims &shape,
		}

		CheckOpen();
		if (!m_StepStatus)
		{
		m_Engine->BeginStep();
		m_StepStatus = true;
		}

		m_Engine->Put(*variable, data, adios2::Mode::Sync);

		if (endStep)
		{
		m_Engine->EndStep();
		m_Engine->BeginStep();
		m_StepStatus = false;
		}
		}

testing/adios2/bindings/python/CMakeLists.txt

+2 −0

Original line number	Diff line number	Diff line
		@@ -15,6 +15,8 @@ if(ADIOS2_HAVE_MPI)
		SCRIPT TestBPWriteReadTypes.py)
		python_add_test(NAME PythonBPWriteReadHighLevelAPI ${test_parameters}
		SCRIPT TestBPWriteTypesHighLevelAPI.py)
		python_add_test(NAME PythonBPWriteReadHighLevelAPI_HDF5 ${test_parameters}
		SCRIPT TestBPWriteTypesHighLevelAPI_HDF5.py)
		python_add_test(NAME PythonBPReadMultisteps ${test_parameters}
		SCRIPT TestBPReadMultisteps.py)
		endif()

testing/adios2/bindings/python/TestBPWriteTypesHighLevelAPI.py

+33 −27

Original line number	Diff line number	Diff line
		@@ -10,6 +10,7 @@
		# Author: William F Godoy godoywf@ornl.gov


		import sys
		from adios2NPTypes import SmallTestData
		from mpi4py import MPI
		import numpy as np
		@@ -30,7 +31,11 @@ count = [nx]
		# Writer
		with adios2.open("types_np.bp", "w", comm) as fw:

		if(rank == 0):
		for i in range(0, 5):

		data.update(rank, i, size)

		if(rank == 0 and i == 0):
		fw.write("tag", "Testing ADIOS2 high-level API")
		fw.write("gvarI8", np.array(data.I8[0]))
		fw.write("gvarI16", np.array(data.I16[0]))
		@@ -43,11 +48,8 @@ with adios2.open("types_np.bp", "w", comm) as fw:
		fw.write("gvarR32", np.array(data.R32[0]))
		fw.write("gvarR64", np.array(data.R64[0]))

		for i in range(0, 5):

		print("i: " + str(i))
		print("Write Step: " + str(i) + " rank: " + str(rank))
		fw.write("steps", "Step:" + str(i))

		fw.write("varI8", data.I8, shape, start, count)
		fw.write("varI16", data.I16, shape, start, count)
		fw.write("varI32", data.I32, shape, start, count)
		@@ -59,13 +61,20 @@ with adios2.open("types_np.bp", "w", comm) as fw:
		fw.write("varR32", data.R32, shape, start, count)
		fw.write("varR64", data.R64, shape, start, count, endl=True)

		comm.Barrier()
		sys.stdout.flush()

		# Reader
		data = SmallTestData()

		with adios2.open("types_np.bp", "r", comm) as fr:

		for fr_step in fr:

		step = fr_step.currentstep()
		print("Step: " + str(step))
		data.update(rank, step, size)

		print("Reader Step: " + str(step))

		step_vars = fr_step.availablevariables()

		@@ -101,24 +110,21 @@ with adios2.open("types_np.bp", "r", comm) as fr:
		if(inI32[0] != data.I32[0]):
		raise ValueError('gvarI32 read failed')

		if(inU16[0] != data.U16[0]):
		raise ValueError('gvarU16 read failed')

		if(inI64[0] != data.I64[0]):
		raise ValueError('gvarI64 read failed')

		if(inU64[0] != data.U64[0]):
		raise ValueError('gvarU64 read failed')

		if(inI8[0] != data.I8[0]):
		raise ValueError('gvarI8 read failed')

		if(inU8[0] != data.U8[0]):
		raise ValueError('gvarU8 read failed')

		if(inU16[0] != data.U16[0]):
		raise ValueError('gvarU16 read failed')

		if(inU32[0] != data.U32[0]):
		raise ValueError('gvarU32 read failed')

		if(inU64[0] != data.U64[0]):
		raise ValueError('gvarU64 read failed')

		if(inR32[0] != data.R32[0]):
		raise ValueError('gvarR32 read failed')