Merge branch 'develop' into periodic-bc (96901122) · Commits · TNL / tnl-dev

.gitlab-ci.yml

+11 −4

Original line number	Diff line number	Diff line
		@@ -30,10 +30,14 @@ stages:
		# - export NUM_CORES=$(grep "core id" /proc/cpuinfo \| wc -l)
		# # all pyhsical cores
		- export NUM_CORES=$(grep "core id" /proc/cpuinfo \| sort -u \| wc -l)
		- export MAKEFLAGS="-l$(echo 1.5*$NUM_CORES \| bc) -j$NUM_CORES"
		# ninja does not have -l
		# - export MAKEFLAGS="-l$(echo 1.5*$NUM_CORES \| bc) -j$NUM_CORES"
		- export NINJAFLAGS="-j$NUM_CORES"
		- export CTEST_OUTPUT_ON_FAILURE=1
		- mkdir -p "./builddir/$CI_JOB_NAME"
		- pushd "./builddir/$CI_JOB_NAME"
		- cmake ../..
		-G Ninja
		-DCMAKE_BUILD_TYPE=${BUILD_TYPE}
		-DCMAKE_INSTALL_PREFIX=$(pwd)/${BUILD_TYPE}_install_prefix
		-DWITH_OPENMP=${WITH_OPENMP}
		@@ -43,9 +47,12 @@ stages:
		-DWITH_TESTS=${WITH_TESTS}
		-DWITH_COVERAGE=${WITH_COVERAGE}
		-DWITH_EXAMPLES=${WITH_EXAMPLES}
		- make
		- make test CTEST_OUTPUT_ON_FAILURE=1
		- make install
		# - make
		# - make test
		# - make install
		- ninja ${NINJAFLAGS}
		- ninja test
		- ninja install
		- popd
		variables:
		<<: *default_cmake_flags

CMakeLists.txt

+11 −8

Original line number	Diff line number	Diff line
		@@ -97,8 +97,8 @@ if( CXX_COMPILER_NAME MATCHES "icpc" )
		endif()

		# force colorized output in continuous integration
		if( DEFINED ENV{CI_JOB_NAME} )
		message(STATUS "Continuous integration detected -- forcing compilers to produce colorized output.")
		if( DEFINED ENV{CI_JOB_NAME} OR ${CMAKE_GENERATOR} STREQUAL "Ninja" )
		message(STATUS "Continuous integration or Ninja detected -- forcing compilers to produce colorized output.")
		if( CXX_COMPILER_NAME MATCHES "clang" )
		set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fcolor-diagnostics" )
		else()
		@@ -405,15 +405,18 @@ INCLUDE_DIRECTORIES( src )
		INCLUDE_DIRECTORIES( ${PROJECT_BUILD_PATH} )
		LINK_DIRECTORIES( ${LIBRARY_OUTPUT_PATH} )

		#Pokracujeme dalsimi podadresari
		add_subdirectory( src )
		add_subdirectory( share )
		if( WITH_TESTS STREQUAL "yes" )
		add_subdirectory( tests )
		endif( WITH_TESTS STREQUAL "yes" )
		# Add all subdirectories
		# Note that it is important to start building examples as soon as possible,
		# because they take the longest time and other stuff can be pipelined before
		# they are finished (at least with Ninja).
		if( WITH_EXAMPLES STREQUAL "yes" )
		add_subdirectory( examples )
		endif( WITH_EXAMPLES STREQUAL "yes" )
		if( WITH_TESTS STREQUAL "yes" )
		add_subdirectory( tests )
		endif( WITH_TESTS STREQUAL "yes" )
		add_subdirectory( src )
		add_subdirectory( share )

		set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Template Numerical Library")
		set(CPACK_PACKAGE_VENDOR "MMG")

build

+87 −63

Original line number	Diff line number	Diff line
		#!/bin/bash

		set -e

		TARGET=TNL
		PREFIX=${HOME}/.local
		INSTALL="no"
		@@ -78,8 +80,7 @@ do
		esac
		done

		if test ${HELP} = "yes";
		then
		if [[ ${HELP} == "yes" ]]; then
		echo "TNL build options:"
		echo ""
		echo " --build=Debug/Release Build type."
		@@ -96,8 +97,8 @@ then
		echo " --with-tests=yes/no Enables unit tests. 'yes' by default."
		echo " --with-coverage=yes/no Enables code coverage reports for unit tests. 'no' by default (lcov is required)."
		echo " --with-examples=yes/no Compile the 'examples' directory. 'yes' by default."
		echo " --with-tools=yes/no Compile the 'tools' directory. 'yes' by default."
		echo " --with-python=yes/no Compile with the python bindings. 'yes' by default."
		echo " --with-tools=yes/no Compile the 'src/Tools' directory. 'yes' by default."
		echo " --with-python=yes/no Compile the Python bindings. 'yes' by default."
		echo " --with-templates-instantiation=yes/no Precompiles some TNL templates during the build. 'no' by default."
		echo " --cmake=CMAKE Path to cmake. 'cmake' by default."
		echo " --verbose It enables verbose build."
		@@ -107,63 +108,91 @@ then
		exit 1
		fi

		if test ${WITH_CLANG} = "yes";
		then
		if [[ ${WITH_CLANG} == "yes" ]]; then
		export CXX=clang++
		export CC=clang
		fi

		if test ${WITH_MPI} = "yes";
		then
		if ! [ -x "$(command -v mpic++)" ]; then
		if [[ ${WITH_MPI} == "yes" ]]; then
		if [[ ! -x "$(command -v mpic++)" ]]; then
		echo "Warning:mpic++ is not installed on this system. MPI support is turned off."
		else
		# instruct OpenMPI to use the original compiler
		# reference: https://www.open-mpi.org/faq/?category=mpi-apps#override-wrappers-after-v1.0
		# FIXME: this does not work with CUDA_HOST_COMPILER=mpic++
		# if [ -n "$CXX" ]; then
		# export OMPI_CXX="$CXX"
		# fi
		export CXX=mpic++
		export CUDA_HOST_COMPILER=mpic++
		fi
		if ! [ -x "$(command -v mpicc)" ]; then
		if [[ ! -x "$(command -v mpicc)" ]]; then
		echo "Warning: mpicc is not installed on this system."
		else
		# instruct OpenMPI to use the original compiler
		# reference: https://www.open-mpi.org/faq/?category=mpi-apps#override-wrappers-after-v1.0
		# if [ -n "$CC" ]; then
		# export OMPI_CC="$CC"
		# fi
		export CC=mpicc
		fi
		fi

		if hash ninja 2>/dev/null; then
		generator=Ninja
		make=ninja
		check_file="build.ninja"
		else
		generator="Unix Makefiles"
		make=make
		check_file="Makefile"
		fi

		echo "Configuring ${BUILD} $TARGET ..."

		${CMAKE} ${ROOT_DIR} \
		-DCMAKE_BUILD_TYPE=${BUILD} \
		-DCMAKE_INSTALL_PREFIX=${PREFIX} \
		-DOFFLINE_BUILD=${OFFLINE_BUILD} \
		-DWITH_MIC=${WITH_MIC} \
		-DWITH_CUDA=${WITH_CUDA} \
		-DWITH_CUDA_ARCH=${WITH_CUDA_ARCH} \
		-DWITH_OPENMP=${WITH_OPENMP} \
		-DWITH_GMP=${WITH_GMP} \
		-DWITH_TESTS=${WITH_TESTS} \
		-DWITH_COVERAGE=${WITH_COVERAGE} \
		-DWITH_EXAMPLES=${WITH_EXAMPLES} \
		-DWITH_TOOLS=${WITH_TOOLS} \
		-DWITH_PYTHON=${WITH_PYTHON} \
		-DDCMTK_DIR=${DCMTK_DIR} \
		-DWITH_TEMPLATE_INSTANTIATION=${WITH_TEMPLATE_INSTANTIATION} \
		-DINSTANTIATE_FLOAT=${INSTANTIATE_FLOAT} \
		-DINSTANTIATE_DOUBLE=${INSTANTIATE_DOUBLE} \
		-DINSTANTIATE_LONG_DOUBLE=${INSTANTIATE_LONG_DOUBLE} \
		-DINSTANTIATE_INT=${INSTANTIATE_INT} \
		-DINSTANTIATE_LONG_INT=${INSTANTIATE_LONG_INT} \
		cmake_command=(
		${CMAKE} ${ROOT_DIR}
		-G "${generator}"
		-DCMAKE_BUILD_TYPE=${BUILD}
		-DCMAKE_INSTALL_PREFIX=${PREFIX}
		-DOFFLINE_BUILD=${OFFLINE_BUILD}
		-DWITH_MIC=${WITH_MIC}
		-DWITH_CUDA=${WITH_CUDA}
		-DWITH_CUDA_ARCH=${WITH_CUDA_ARCH}
		-DWITH_OPENMP=${WITH_OPENMP}
		-DWITH_GMP=${WITH_GMP}
		-DWITH_TESTS=${WITH_TESTS}
		-DWITH_COVERAGE=${WITH_COVERAGE}
		-DWITH_EXAMPLES=${WITH_EXAMPLES}
		-DWITH_TOOLS=${WITH_TOOLS}
		-DWITH_PYTHON=${WITH_PYTHON}
		-DDCMTK_DIR=${DCMTK_DIR}
		-DWITH_TEMPLATE_INSTANTIATION=${WITH_TEMPLATE_INSTANTIATION}
		-DINSTANTIATE_FLOAT=${INSTANTIATE_FLOAT}
		-DINSTANTIATE_DOUBLE=${INSTANTIATE_DOUBLE}
		-DINSTANTIATE_LONG_DOUBLE=${INSTANTIATE_LONG_DOUBLE}
		-DINSTANTIATE_INT=${INSTANTIATE_INT}
		-DINSTANTIATE_LONG_INT=${INSTANTIATE_LONG_INT}
		-DOPTIMIZED_VECTOR_HOST_OPERATIONS=${OPTIMIZED_VECTOR_HOST_OPERATIONS}
		)

		if test $? != 0; then
		echo "Error: cmake exited with error code."
		exit 1
		# Skip running cmake if it was already run and the cmake command is the same.
		# The build system (e.g. make) will call it automatically if necessary (e.g.
		# when some CMakeLists.txt changes).
		if [[ -f ".cmake_command" ]]; then
		last_cmake_command=$(cat ".cmake_command" 2>/dev/null)
		else
		last_cmake_command=""
		fi
		if [[ ! -f "$check_file" ]] \|\| [[ "$last_cmake_command" != "${cmake_command[@]}" ]]; then
		echo "Configuring ${BUILD} $TARGET ..."
		"${cmake_command[@]}"
		echo -n "${cmake_command[@]}" > ".cmake_command"
		fi

		if test ${CMAKE_ONLY} = "yes";
		then
		if [[ ${CMAKE_ONLY} == "yes" ]]; then
		exit 0
		fi

		if [[ "$make" == "make" ]]; then
		if [[ -n ${BUILD_JOBS} ]]; then
		# override $MAKEFLAGS from parent environment
		export MAKEFLAGS=-j${BUILD_JOBS}
		@@ -172,6 +201,12 @@ elif [[ -z ${MAKEFLAGS} ]]; then
		BUILD_JOBS=$(grep "core id" /proc/cpuinfo \| sort -u \| wc -l)
		export MAKEFLAGS=-j${BUILD_JOBS}
		fi
		else
		if [[ -z ${BUILD_JOBS} ]]; then
		BUILD_JOBS=$(grep "core id" /proc/cpuinfo \| sort -u \| wc -l)
		fi
		make="$make -j$BUILD_JOBS"
		fi

		if [[ -n ${BUILD_JOBS} ]]; then
		echo "Building ${BUILD} $TARGET using $BUILD_JOBS processors ..."
		@@ -187,19 +222,8 @@ else
		make_target="all"
		fi

		make ${VERBOSE} $make_target
		if test $? != 0; then
		echo "Error: Build process failed."
		exit 1
		fi
		$make ${VERBOSE} $make_target


		if test ${WITH_TESTS} = "yes";
		then
		make test CTEST_OUTPUT_ON_FAILURE=1
		if test $? != 0; then
		echo "Error: Some test did not pass successfuly."
		fi
		if [[ ${WITH_TESTS} == "yes" ]]; then
		CTEST_OUTPUT_ON_FAILURE=1 $make test
		fi

		exit 0

src/CMakeLists.txt

+8 −8

Original line number	Diff line number	Diff line
		if( WITH_PYTHON STREQUAL "yes" )
		ADD_SUBDIRECTORY( Python )
		endif( WITH_PYTHON STREQUAL "yes" )

		ADD_SUBDIRECTORY( TNL )

		if( WITH_TOOLS STREQUAL "yes" )
		if( ${WITH_TOOLS} )
		ADD_SUBDIRECTORY( Tools )
		endif( WITH_TOOLS STREQUAL "yes" )
		endif()

		if( WITH_TESTS STREQUAL "yes" )
		if( ${WITH_TESTS} )
		ADD_SUBDIRECTORY( UnitTests )
		endif( WITH_TESTS STREQUAL "yes" )
		endif()

		if( ${WITH_PYTHON} )
		ADD_SUBDIRECTORY( Python )
		endif()

src/TNL/Communicators/MpiCommunicator.h

+32 −12

Original line number	Diff line number	Diff line
		@@ -277,7 +277,7 @@ class MpiCommunicator
		TNL_ASSERT_TRUE(IsInitialized(), "Fatal Error - MPI communicator is not initialized");
		TNL_ASSERT_NE(group, NullGroup, "ISend cannot be called with NullGroup");
		Request req;
		MPI_Isend((void*) data, count, MPIDataType(data) , dest, 0, group, &req);
		MPI_Isend((const void*) data, count, MPIDataType(data) , dest, 0, group, &req);
		return req;
		#else
		throw Exceptions::MPISupportMissing();
		@@ -285,7 +285,7 @@ class MpiCommunicator
		}

		template <typename T>
		static Request IRecv( const T *data, int count, int src, CommunicationGroup group)
		static Request IRecv( T* data, int count, int src, CommunicationGroup group)
		{
		#ifdef HAVE_MPI
		TNL_ASSERT_TRUE(IsInitialized(), "Fatal Error - MPI communicator is not initialized");
		@@ -337,7 +337,7 @@ class MpiCommunicator


		template< typename T >
		static void Reduce( T* data,
		static void Reduce( const T* data,
		T* reduced_data,
		int count,
		MPI_Op &op,
		@@ -346,14 +346,14 @@ class MpiCommunicator
		{
		#ifdef HAVE_MPI
		TNL_ASSERT_NE(group, NullGroup, "Reduce cannot be called with NullGroup");
		MPI_Reduce( (void) data, (void) reduced_data,count,MPIDataType(data),op,root,group);
		MPI_Reduce( (const void) data, (void) reduced_data,count,MPIDataType(data),op,root,group);
		#else
		throw Exceptions::MPISupportMissing();
		#endif
		}

		template< typename T >
		static void SendReceive( T* sendData,
		static void SendReceive( const T* sendData,
		int sendCount,
		int destination,
		int sendTag,
		@@ -366,7 +366,7 @@ class MpiCommunicator
		#ifdef HAVE_MPI
		TNL_ASSERT_NE(group, NullGroup, "SendReceive cannot be called with NullGroup");
		MPI_Status status;
		MPI_Sendrecv( ( void* ) sendData,
		MPI_Sendrecv( ( const void* ) sendData,
		sendCount,
		MPIDataType( sendData ),
		destination,
		@@ -383,6 +383,27 @@ class MpiCommunicator
		#endif
		}

		template< typename T >
		static void Alltoall( const T* sendData,
		int sendCount,
		T* receiveData,
		int receiveCount,
		CommunicationGroup group )
		{
		#ifdef HAVE_MPI
		TNL_ASSERT_NE(group, NullGroup, "SendReceive cannot be called with NullGroup");
		MPI_Alltoall( ( const void* ) sendData,
		sendCount,
		MPIDataType( sendData ),
		( void* ) receiveData,
		receiveCount,
		MPIDataType( receiveData ),
		group );
		#else
		throw Exceptions::MPISupportMissing();
		#endif
		}


		static void writeProlog( Logger& logger )
		{
		@@ -428,10 +449,9 @@ class MpiCommunicator
		{
		#ifdef HAVE_MPI
		#ifdef HAVE_CUDA
		int count,rank, gpuCount, gpuNumber;
		MPI_Comm_size(MPI_COMM_WORLD,&count);
		MPI_Comm_rank(MPI_COMM_WORLD,&rank);

		const int count = GetSize(AllGroup);
		const int rank = GetRank(AllGroup);
		int gpuCount;
		cudaGetDeviceCount(&gpuCount);

		procName names[count];
		@@ -454,7 +474,7 @@ class MpiCommunicator
		nodeRank++;
		}

		gpuNumber=nodeRank % gpuCount;
		const int gpuNumber = nodeRank % gpuCount;

		cudaSetDevice(gpuNumber);
		TNL_CHECK_CUDA_DEVICE;