Merge pull request #1035 from pnorbert/fix_attributes (bae9c993) · Commits · Podhorszki, Norbert / ADIOS2

source/adios2/engine/insitumpi/InSituMPIReader.cpp

+0 −1

Original line number	Diff line number	Diff line
		@@ -182,7 +182,6 @@ StepStatus InSituMPIReader::BeginStep(const StepMode mode,

		// Parse metadata into Variables and Attributes maps
		m_IO.RemoveAllVariables();
		m_IO.RemoveAllAttributes();
		m_BP3Deserializer.ParseMetadata(m_BP3Deserializer.m_Metadata, m_IO);

		if (m_Verbosity == 5)

source/adios2/toolkit/format/bp3/BP3Base.h

+6 −2

Original line number	Diff line number	Diff line
		@@ -17,6 +17,7 @@
		#include <set>
		#include <string>
		#include <unordered_map>
		#include <unordered_set>
		#include <vector>
		/// \endcond

		@@ -87,8 +88,6 @@ public:
		/** @brief key: attribute name, value: bp metadata attribute index */
		std::unordered_map<std::string, SerialElementIndex> AttributesIndices;

		bool AreAttributesWritten = false;

		/** Fixed size for mini footer, adding 28 bytes for ADIOS version */
		const unsigned int MiniFooterSize = 28 + 28;

		@@ -176,6 +175,11 @@ public:
		/** tracks the overall size of deferred variables */
		size_t m_DeferredVariablesDataSize = 0;

		/** attributes are serialized only once, this set contains the names of ones
		* already serialized.
		*/
		std::unordered_set<std::string> m_SerializedAttributes;

		/**
		* Unique constructor
		* @param mpiComm for m_BP1Aggregator

source/adios2/toolkit/format/bp3/BP3Serializer.cpp

+23 −6

Original line number	Diff line number	Diff line
		@@ -482,6 +482,14 @@ void BP3Serializer::PutAttributes(core::IO &io)
		const std::string name(attributePair.first);
		const std::string type(attributePair.second.first);

		// each attribute is only written to output once
		// so filter out the ones already written
		auto it = m_SerializedAttributes.find(name);
		if (it != m_SerializedAttributes.end())
		{
		continue;
		}

		if (type == "unknown")
		{
		}
		@@ -635,20 +643,21 @@ void BP3Serializer::SerializeDataBuffer(core::IO &io) noexcept
		helper::CopyToBuffer(buffer, m_MetadataSet.DataPGVarsCountPosition,
		&varsLength);

		// attributes are only written once

		if (!m_MetadataSet.AreAttributesWritten)
		// each attribute is only written to output once
		size_t attributesSizeInData = GetAttributesSizeInData(io);
		if (attributesSizeInData)
		{
		const size_t attributesSizeInData = GetAttributesSizeInData(io);
		attributesSizeInData += 12; // count + length
		m_Data.Resize(position + attributesSizeInData,
		"when writing Attributes in rank=0\n");

		PutAttributes(io);
		m_MetadataSet.AreAttributesWritten = true;
		}
		else
		{
		m_Data.Resize(position + 12, "for empty Attributes\n");
		// Attribute index header for zero attributes: 0, 0LL
		// Resize() already takes care of this
		position += 12;
		absolutePosition += 12;
		}
		@@ -1614,7 +1623,7 @@ uint32_t BP3Serializer::GetFileIndex() const noexcept

		size_t BP3Serializer::GetAttributesSizeInData(core::IO &io) const noexcept
		{
		size_t attributesSizeInData = 12; // count + length
		size_t attributesSizeInData = 0;

		auto &attributes = io.GetAttributesDataMap();

		@@ -1622,6 +1631,14 @@ size_t BP3Serializer::GetAttributesSizeInData(core::IO &io) const noexcept
		{
		const std::string type = attribute.second.first;

		// each attribute is only written to output once
		// so filter out the ones already written
		auto it = m_SerializedAttributes.find(attribute.first);
		if (it != m_SerializedAttributes.end())
		{
		continue;
		}

		if (type == "compound")
		{
		}

source/adios2/toolkit/format/bp3/BP3Serializer.tcc

+2 −1

Original line number	Diff line number	Diff line
		@@ -334,8 +334,9 @@ void BP3Serializer::PutAttributeInIndex(const core::Attribute<T> &attribute,
		helper::CopyToBuffer(buffer, backPosition,
		&characteristicsLength); // length

		// Finish characteristic count length
		// Remember this attribute and its serialized piece
		m_MetadataSet.AttributesIndices.emplace(attribute.m_Name, index);
		m_SerializedAttributes.emplace(attribute.m_Name);
		}

		template <>

testing/adios2/engine/common/CMakeLists.txt

+8 −8

Original line number	Diff line number	Diff line
		@@ -19,9 +19,9 @@ endif()
		# 2nd arg: 1 for serialized execution, 0 for concurrent execution of Writer/Reader
		# 3rd arg: engine parameters

		#gtest_add_tests(TARGET TestEngineCommon ${extra_test_args}
		# EXTRA_ARGS "BPFile" "1"
		# TEST_SUFFIX _BPFile)
		gtest_add_tests(TARGET TestEngineCommon ${extra_test_args}
		EXTRA_ARGS "BPFile" "1"
		TEST_SUFFIX _BPFile)

		if(ADIOS2_HAVE_HDF5)
		gtest_add_tests(TARGET TestEngineCommon ${extra_test_args}
		@@ -38,11 +38,11 @@ gtest_add_tests(TARGET TestEngineCommon ${extra_test_args}
		TEST_SUFFIX _SST_BP)
		endif()

		#if(ADIOS2_HAVE_MPI)
		#gtest_add_tests(TARGET TestEngineCommon ${extra_test_args}
		# EXTRA_ARGS "InSituMPI" "0"
		# TEST_SUFFIX _InSituMPI)
		#endif()
		if(ADIOS2_HAVE_MPI)
		gtest_add_tests(TARGET TestEngineCommon ${extra_test_args}
		EXTRA_ARGS "InSituMPI" "0"
		TEST_SUFFIX _InSituMPI)
		endif()

		#if(ADIOS2_HAVE_DataMan)
		#gtest_add_tests(TARGET TestEngineCommon ${extra_test_args}

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