Merge pull request #3591 from eisenhauer/BP5MemSel (702cc8fe) · Commits · ecpcitest / ADIOS2

source/adios2/helper/adiosType.h

+11 −0

Original line number	Diff line number	Diff line
		@@ -134,6 +134,17 @@ public:
		typedef size_t *iterator;
		iterator begin() { return &DimensSpan[0]; }
		iterator end() { return &DimensSpan[DimCount]; }
		friend std::ostream &operator<<(std::ostream &os, const CoreDims &m)
		{
		os << "{";
		for (size_t i = 0; i < m.size(); i++)
		{
		os << m[i];
		if (i < m.size() - 1)
		os << ", ";
		}
		return os << "}";
		}
		};

		class DimsArray : public CoreDims

source/adios2/toolkit/format/bp/bp4/BP4Deserializer.tcc

+49 −5

Original line number	Diff line number	Diff line
		@@ -598,12 +598,56 @@ void BP4Deserializer::PostDataRead(
		? Dims(blockInfo.Count.size(), 0)
		: blockInfo.Start;

		if (!blockInfo.MemoryStart.empty())
		{
		if (endianReverse)
		{
		helper::Throw<std::invalid_argument>(
		"Toolkit", "format::bp::BP4Deserializer", "PostDataRead",
		"endianReverse "
		"not supported with MemorySelection");
		}

		if (m_ReverseDimensions)
		{
		helper::Throw<std::invalid_argument>(
		"Toolkit", "format::bp::BP4Deserializer", "PostDataRead",
		"ReverseDimensions not supported with "
		"MemorySelection");
		}

		helper::DimsArray intersectStart(
		subStreamBoxInfo.IntersectionBox.first);
		helper::DimsArray intersectCount(
		subStreamBoxInfo.IntersectionBox.second);
		helper::DimsArray blockStart(subStreamBoxInfo.BlockBox.first);
		helper::DimsArray blockCount(subStreamBoxInfo.BlockBox.second);
		helper::DimsArray memoryStart(blockInfoStart);
		for (size_t d = 0; d < intersectStart.size(); d++)
		{
		// change {intersect,block}Count from [start, end] to {start, count}
		intersectCount[d] -= (intersectStart[d] - 1);
		blockCount[d] -= (blockStart[d] - 1);
		// shift everything by MemoryStart
		intersectStart[d] += blockInfo.MemoryStart[d];
		blockStart[d] += blockInfo.MemoryStart[d];
		}
		helper::NdCopy(m_ThreadBuffers[threadID][0].data(), intersectStart,
		intersectCount, true, true,
		reinterpret_cast<char *>(blockInfo.Data), intersectStart,
		intersectCount, true, true, sizeof(T), intersectStart,
		blockCount, memoryStart,
		helper::DimsArray(blockInfo.MemoryCount), false);
		}
		else
		{
		helper::ClipContiguousMemory(
		blockInfo.Data, blockInfoStart, blockInfo.Count,
		m_ThreadBuffers[threadID][0].data(), subStreamBoxInfo.BlockBox,
		subStreamBoxInfo.IntersectionBox, m_IsRowMajor, m_ReverseDimensions,
		endianReverse, blockInfo.MemSpace);
		}
		}

		void BP4Deserializer::BackCompatDecompress(
		const helper::SubStreamBoxInfo &subStreamBoxInfo, const size_t threadID)

source/adios2/toolkit/format/bp5/BP5Deserializer.cpp

+63 −4

Original line number	Diff line number	Diff line
		@@ -1473,8 +1473,10 @@ static bool IntersectionStartCount(const size_t dimensionsSize,
		outstart[d] = intersectionStart;
		outcount[d] = intersectionEnd - intersectionStart + 1;
		if (outcount[d] == 0)
		{
		return false;
		}
		}
		return true;
		}

		@@ -1822,22 +1824,79 @@ void BP5Deserializer::FinalizeGet(const ReadRequest &Read, const bool freeAddr)
		}
		}

		VariableBase VB = static_cast<VariableBase >(Req.VarRec->Variable);
		DimsArray inStart(DimCount, RankOffset);
		DimsArray inCount(DimCount, RankSize);
		DimsArray outStart(DimCount, SelOffset);
		DimsArray outCount(DimCount, SelSize);
		DimsArray outMemStart(VB->m_MemoryStart);
		DimsArray outMemCount(VB->m_MemoryCount);
		if (!m_ReaderIsRowMajor)
		{
		std::reverse(inStart.begin(), inStart.end());
		std::reverse(inCount.begin(), inCount.end());
		std::reverse(outStart.begin(), outStart.end());
		std::reverse(outCount.begin(), outCount.end());
		std::reverse(outMemStart.begin(), outMemStart.end());
		std::reverse(outMemCount.begin(), outMemCount.end());
		}

		if (VB->m_MemoryStart.size() > 0)
		{
		#ifdef NOTDEF // haven't done endinness for BP5
		if (endianReverse)
		{
		helper::Throw<std::invalid_argument>(
		"Toolkit", "format::bp::BP5Deserializer", "PostDataRead",
		"endianReverse "
		"not supported with MemorySelection");
		}
		if (m_ReaderIsRowMajor)
		{
		helper::Throw<std::invalid_argument>(
		"Toolkit", "format::bp::BP5Deserializer", "PostDataRead",
		"ReverseDimensions not supported with "
		"MemorySelection");
		}
		#endif

		const Box<Dims> selectionBox =
		helper::StartEndBox(Dims(outStart.begin(), outStart.end()),
		Dims(outCount.begin(), outCount.end()));
		const Box<Dims> BlockBox =
		helper::StartEndBox(Dims(inStart.begin(), inStart.end()),
		Dims(inCount.begin(), inCount.end()));
		const Box<Dims> IntersectionBox =
		helper::IntersectionBox(selectionBox, BlockBox);
		VirtualIncomingData =
		Read.DestinationAddr; // Don't do the fake offset thing
		helper::DimsArray intersectStart(IntersectionBox.first);
		helper::DimsArray intersectCount(IntersectionBox.second);
		helper::DimsArray blockStart(BlockBox.first);
		helper::DimsArray blockCount(BlockBox.second);
		helper::DimsArray memoryStart(DimCount, SelOffset);
		helper::DimsArray memoryCount(VB->m_MemoryCount);
		for (size_t d = 0; d < intersectStart.size(); d++)
		{
		// change {intersect,block}Count from [start, end] to {start, count}
		intersectCount[d] -= (intersectStart[d] - 1);
		blockCount[d] -= (blockStart[d] - 1);
		// shift everything by MemoryStart
		intersectStart[d] += VB->m_MemoryStart[d];
		blockStart[d] += VB->m_MemoryStart[d];
		}
		helper::NdCopy(VirtualIncomingData, intersectStart, intersectCount,
		true, true, (char *)Req.Data, intersectStart,
		intersectCount, true, true, ElementSize, intersectStart,
		blockCount, memoryStart, memoryCount, false);
		}
		else
		{
		helper::NdCopy(VirtualIncomingData, inStart, inCount, true, true,
		(char *)Req.Data, outStart, outCount, true, true,
		ElementSize, CoreDims(), CoreDims(), CoreDims(), CoreDims(),
		false, Req.MemSpace);
		ElementSize, CoreDims(), CoreDims(), CoreDims(),
		CoreDims(), false, Req.MemSpace);
		}
		if (freeAddr)
		{
		free((char *)Read.DestinationAddr);

source/adios2/toolkit/format/bp5/BP5Serializer.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -894,7 +894,7 @@ void BP5Serializer::Marshal(void Variable, const char Name,
		lf_QueueSpanMinMax(*Span, ElemCount, (DataType)Rec->Type,
		MemSpace, Rec->MetaOffset,
		Rec->MinMaxOffset,
		MetaEntry->BlockCount /BlockNum/);
		MetaEntry->BlockCount - 1 /BlockNum/);
		}
		}

testing/adios2/interface/CMakeLists.txt

+19 −2

Original line number	Diff line number	Diff line
		@@ -6,9 +6,26 @@
		# These tests should be very fast
		set(CTEST_TEST_TIMEOUT 10)

		gtest_add_tests_helper(Interface MPI_ALLOW ADIOS Interface. "")
		set(BP3_DIR ${CMAKE_CURRENT_BINARY_DIR}/bp3)
		set(BP4_DIR ${CMAKE_CURRENT_BINARY_DIR}/bp4)
		set(BP5_DIR ${CMAKE_CURRENT_BINARY_DIR}/bp5)
		set(BPfile_DIR ${CMAKE_CURRENT_BINARY_DIR}/bpfile)
		set(FS_DIR ${CMAKE_CURRENT_BINARY_DIR}/filestream)
		file(MAKE_DIRECTORY ${BP3_DIR})
		file(MAKE_DIRECTORY ${BP4_DIR})
		file(MAKE_DIRECTORY ${BP5_DIR})
		file(MAKE_DIRECTORY ${BPfile_DIR})
		file(MAKE_DIRECTORY ${FS_DIR})

		gtest_add_tests_helper(Interface MPI_ALLOW ADIOS Interface. .BP3
		WORKING_DIRECTORY ${BP3_DIR} EXTRA_ARGS "BP3")
		gtest_add_tests_helper(Interface MPI_ALLOW ADIOS Interface. .BPfile
		WORKING_DIRECTORY ${BPfile_DIR} EXTRA_ARGS "BPfile")
		gtest_add_tests_helper(Write MPI_ALLOW ADIOSInterface Interface. "")
		gtest_add_tests_helper(DefineVariable MPI_ALLOW ADIOS Interface. "")
		gtest_add_tests_helper(DefineAttribute MPI_ALLOW ADIOS Interface. "")
		gtest_add_tests_helper(Selection MPI_NONE ADIOS Interface. "")
		gtest_add_tests_helper(Selection MPI_NONE ADIOS Interface. .BP3
		WORKING_DIRECTORY ${BP3_DIR} EXTRA_ARGS "BP3")
		gtest_add_tests_helper(Selection MPI_NONE ADIOS Interface. .BPfile
		WORKING_DIRECTORY ${BPfile_DIR} EXTRA_ARGS "BPfile")
		gtest_add_tests_helper(NoMpi MPI_NONE ADIOS Interface. "")

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