Merge branch 'periodic-bc' of geraldine.fjfi.cvut.cz:/local/projects/tnl/tnl into periodic-bc (33235efe) · Commits · TNL / tnl-dev

.gitlab-ci.yml

+4 −1

Original line number	Diff line number	Diff line
		@@ -26,7 +26,10 @@ stages:
		.build_template_def: &build_template
		stage: build
		script:
		- export NUM_CORES=$(grep "core id" /proc/cpuinfo \| wc -l)
		# all cores including hyperthreading
		# - export NUM_CORES=$(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"
		- mkdir -p "./builddir/$CI_JOB_NAME"
		- pushd "./builddir/$CI_JOB_NAME"

CMakeLists.txt

+109 −42

Original line number	Diff line number	Diff line
		@@ -18,6 +18,20 @@ project( tnl )

		set( tnlVersion "0.1" )

		# declare all custom build options
		option(OFFLINE_BUILD "Offline build (i.e. without downloading libraries such as pybind11)" OFF)
		option(WITH_MIC "Build with MIC support" OFF)
		option(WITH_CUDA "Build with CUDA support" ON)
		set(WITH_CUDA_ARCH "auto" CACHE STRING "Build for these CUDA architectures")
		option(WITH_OPENMP "Build with OpenMP support" ON)
		option(WITH_GMP "Build with GMP support" OFF)
		option(WITH_TESTS "Build tests" ON)
		option(WITH_COVERAGE "Enable code coverage reports from unit tests" OFF)
		option(WITH_EXAMPLES "Compile the 'examples' directory" ON)
		option(WITH_TOOLS "Compile the 'src/Tools' directory" ON)
		option(WITH_PYTHON "Compile the Python bindings" ON)
		option(WITH_TEMPLATES_INSTANTIATION "Enable explicit template instantiation" OFF)

		# install paths relative to the cmake's prefix
		set( TNL_TARGET_INCLUDE_DIRECTORY "include/TNL" )
		set( TNL_TARGET_DATA_DIRECTORY "share/TNL" )
		@@ -50,13 +64,19 @@ endif()

		# set Debug/Release options
		set( CMAKE_CXX_FLAGS "-std=c++11 -pthread -Wall -Wno-unused-local-typedefs -Wno-unused-variable" )
		set( CMAKE_CXX_FLAGS_DEBUG "-g -rdynamic -ftemplate-backtrace-limit=0" )
		set( CMAKE_CXX_FLAGS_DEBUG "-g" )
		set( CMAKE_CXX_FLAGS_RELEASE "-O3 -march=native -mtune=native -DNDEBUG" )
		#set( CMAKE_CXX_FLAGS_RELEASE "-O3 -march=native -mtune=native -DNDEBUG -ftree-vectorizer-verbose=1 -ftree-vectorize -fopt-info-vec-missed -funroll-loops" )
		# pass -rdynamic only in Debug mode
		set( CMAKE_SHARED_LIBRARY_LINK_C_FLAGS "" )
		set( CMAKE_SHARED_LIBRARY_LINK_C_FLAGS_DEBUG "-rdynamic" )
		set( CMAKE_SHARED_LIBRARY_LINK_C_FLAGS_RELEASE "" )
		set( CMAKE_EXE_LINKER_FLAGS "" )
		set( CMAKE_EXE_LINKER_FLAGS_DEBUG "-rdynamic" )
		set( CMAKE_EXE_LINKER_FLAGS_RELEASE "" )
		set( CMAKE_SHARED_LINKER_FLAGS "" )
		set( CMAKE_SHARED_LINKER_FLAGS_DEBUG "-rdynamic" )
		set( CMAKE_SHARED_LINKER_FLAGS_RELEASE "" )

		get_filename_component( CXX_COMPILER_NAME ${CMAKE_CXX_COMPILER} NAME )
		if( CXX_COMPILER_NAME MATCHES "icpc" )
		@@ -65,12 +85,12 @@ if( CXX_COMPILER_NAME MATCHES "icpc" )
		#####
		# Check for MIC
		#
		if( WITH_MIC STREQUAL "yes" )
		message( "Compile MIC support..." )
		if( ${WITH_MIC} )
		message( "Enabled MIC support." )
		set( MIC_CXX_FLAGS "-DHAVE_MIC")
		# build all tests with MIC support
		set( CXX_TESTS_FLAGS ${CXX_TESTS_FLAGS} -DHAVE_MIC )
		set( WITH_CUDA "no")
		set( WITH_CUDA OFF CACHE BOOL "Build with CUDA support" )
		else()
		set( MIC_CXX_FLAGS "")
		endif()
		@@ -93,7 +113,6 @@ if( ${CXX_COMPILER_NAME} STREQUAL "mpic++" )
		message( "MPI compiler detected." )
		set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DHAVE_MPI" )
		set( CUDA_HOST_COMPILER "mpic++" )

		endif()

		####
		@@ -110,7 +129,7 @@ endif()
		#####
		# Check for CUDA
		#
		if( WITH_CUDA STREQUAL "yes" )
		if( ${WITH_CUDA} )
		find_package( CUDA )
		if( CUDA_FOUND )
		set( BUILD_CUDA TRUE)
		@@ -130,6 +149,22 @@ if( WITH_CUDA STREQUAL "yes" )
		set( CUDA_HOST_COMPILER ${CMAKE_CXX_COMPILER} )
		endif()
		endif()
		# An extra CUDA_ARCH_HOST_COMPILER variable for compiling tnl-cuda-arch alone,
		# because it SHOULD NOT be compiled using mpic++, which would cause weird
		# RPATH_CHANGE error in cmake.
		# FIXME: find better solution to switch between MPI-enabled and MPI-disabled binaries in cmake
		if( NOT $ENV{CUDA_ARCH_HOST_COMPILER} STREQUAL "" )
		message( "-- Setting CUDA_ARCH_HOST_COMPILER to '$ENV{CUDA_ARCH_HOST_COMPILER}'" )
		set( CUDA_ARCH_HOST_COMPILER $ENV{CUDA_ARCH_HOST_COMPILER} )
		else()
		if( EXISTS "${CUDA_TOOLKIT_ROOT_DIR}/bin/g++" )
		message( "-- Setting CUDA_ARCH_HOST_COMPILER to '${CUDA_TOOLKIT_ROOT_DIR}/bin/g++'" )
		set( CUDA_ARCH_HOST_COMPILER "${CUDA_TOOLKIT_ROOT_DIR}/bin/g++" )
		else()
		message( "-- Setting CUDA_ARCH_HOST_COMPILER to '${CMAKE_CXX_COMPILER}'" )
		set( CUDA_ARCH_HOST_COMPILER ${CMAKE_CXX_COMPILER} )
		endif()
		endif()
		set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} ;-DHAVE_CUDA)
		# disable false compiler warnings
		# reference for the -Xcudafe flag: http://stackoverflow.com/questions/14831051/how-to-disable-compiler-warnings-with-nvcc/17095910#17095910
		@@ -153,7 +188,7 @@ if( WITH_CUDA STREQUAL "yes" )
		set( CUDA_ARCH_SOURCE ${PROJECT_SOURCE_DIR}/src/Tools/tnl-cuda-arch.cu)
		message( "Compiling tnl-cuda-arch ..." )
		file( MAKE_DIRECTORY ${EXECUTABLE_OUTPUT_PATH} )
		execute_process( COMMAND nvcc --compiler-bindir ${CUDA_HOST_COMPILER} --std=c++11 ${CUDA_ARCH_SOURCE} -o ${CUDA_ARCH_EXECUTABLE}
		execute_process( COMMAND nvcc --compiler-bindir ${CUDA_ARCH_HOST_COMPILER} --std=c++11 ${CUDA_ARCH_SOURCE} -o ${CUDA_ARCH_EXECUTABLE}
		RESULT_VARIABLE CUDA_ARCH_RESULT
		OUTPUT_VARIABLE CUDA_ARCH_OUTPUT
		ERROR_VARIABLE CUDA_ARCH_OUTPUT )
		@@ -178,37 +213,18 @@ if( WITH_CUDA STREQUAL "yes" )
		endif()
		endif()
		endif()
		set( CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} ; ${CUDA_ARCH} -D_FORCE_INLINES -lineinfo )
		set( CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} ; ${CUDA_ARCH} -D_FORCE_INLINES )
		# TODO: this is necessary only due to a bug in cmake
		set( CUDA_ADD_LIBRARY_OPTIONS -shared )

		####
		# Check for CUSPARSE
		#
		if( NOT WITH_CUSPARSE STREQUAL "no" )
		find_path( CUSPARSE_INCLUDE_DIR cusparse.h
		/usr/local/cuda/include
		${CUDA_INCLUDE_DIRS}
		DOC "CUSPARSE headers." )
		if( ${CUSPARSE_INCLUDE_DIR} STREQUAL "CUSPARSE_INCLUDE_DIR-NOTFOUND" )
		message( "CUSPARSE not found." )
		set( HAVE_CUSPARSE "//#define HAVE_CUSPARSE 1" )
		else()
		message( "CUSPARSE found. -- ${CUSPARSE_INCLUDE_DIR}" )
		set( HAVE_CUSPARSE "#define HAVE_CUSPARSE 1" )
		cuda_include_directories( ${CUSPARSE_INCLUDE_DIR} )
		set( CUSPARSE_LIBRARY "${CUDA_cusparse_LIBRARY}" )
		endif()
		endif( NOT WITH_CUSPARSE STREQUAL "no" )
		endif( CUDA_FOUND )
		endif( WITH_CUDA STREQUAL "yes" )
		endif()


		####
		# Check for OpenMP
		#
		if( OPENMP_FOUND AND WITH_OPENMP STREQUAL "yes" )
		message( "Compiler supports OpenMP." )
		if( OPENMP_FOUND AND ${WITH_OPENMP} )
		message( "Enabled OpenMP support." )
		set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DHAVE_OPENMP ${OpenMP_CXX_FLAGS}" )
		endif()

		@@ -243,6 +259,36 @@ else()
		set( JPEG_LIBRARIES "" )
		endif()

		####
		# Test for GMP
		#
		if( ${WITH_GMP} )
		if (GMP_INCLUDES AND GMP_LIBRARIES)
		set(GMP_FIND_QUIETLY TRUE)
		endif (GMP_INCLUDES AND GMP_LIBRARIES)

		find_path(GMP_INCLUDES
		NAMES
		gmp.h
		PATHS
		$ENV{GMPDIR}
		${INCLUDE_INSTALL_DIR}
		)

		find_library(GMP_LIBRARIES gmp PATHS $ENV{GMPDIR} ${LIB_INSTALL_DIR})

		include(FindPackageHandleStandardArgs)
		find_package_handle_standard_args(GMP DEFAULT_MSG
		GMP_INCLUDES GMP_LIBRARIES)
		if( ${GMP_INCLUDES} STREQUAL "GMP_INCLUDES-NOTFOUND" OR ${GMP_LIBRARIES} STREQUAL "GMP_LIBRARIES-NOTFOUND" )
		message( "GMP was not found. Some tests for higher precision arithmetics will not be passed." )
		else()
		set( HAVE_GMP )
		set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -I${GMP_INCLUDES} -DHAVE_GMP" )
		set( CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${GMP_LIBRARIES}" )
		mark_as_advanced(GMP_INCLUDES GMP_LIBRARIES)
		endif()
		endif()

		####
		# Check for some system header
		@@ -283,17 +329,17 @@ else()
		set( HAVE_SYS_IOCTL_H "#define HAVE_SYS_IOCTL_H 1" )
		endif()

		if( WITH_TESTS STREQUAL "yes" )
		if( ${WITH_TESTS} )
		enable_testing()

		# build gtest libs
		include( BuildGtest )

		if( WITH_COVERAGE STREQUAL "yes" AND CMAKE_BUILD_TYPE STREQUAL "Debug" )
		if( ${WITH_COVERAGE} AND CMAKE_BUILD_TYPE STREQUAL "Debug" )
		# enable code coverage reports
		include( UseCodeCoverage )
		endif()
		endif( WITH_TESTS STREQUAL "yes" )
		endif()

		#if( BUILD_MPI )
		# FIND_PATH( PETSC_INCLUDE_DIR petsc.h
		@@ -323,7 +369,7 @@ endif( WITH_TESTS STREQUAL "yes" )
		####
		# Explicit template instantiation
		#
		#if( WITH_TEMPLATE_INSTANTIATION STREQUAL "yes" )
		#if( ${WITH_TEMPLATE_INSTANTIATION} )
		# AddCompilerFlag( "-DTEMPLATE_EXPLICIT_INSTANTIATION " )
		#
		# if( INSTANTIATE_INT STREQUAL "yes" )
		@@ -397,6 +443,20 @@ set(CPACK_SOURCE_STRIP_FILES "Release")
		#set(CPACK_PACKAGE_EXECUTABLES "MyExecutable" "My Executable")
		INCLUDE( CPack )

		# Print custom build options
		message( "-- Build options:" )
		message( " OFFLINE_BUILD=${OFFLINE_BUILD}" )
		message( " WITH_MIC=${WITH_MIC}" )
		message( " WITH_CUDA=${WITH_CUDA}" )
		message( " WITH_CUDA_ARCH=${WITH_CUDA_ARCH}" )
		message( " WITH_OPENMP=${WITH_OPENMP}" )
		message( " WITH_GMP=${WITH_GMP}" )
		message( " WITH_TESTS=${WITH_TESTS}" )
		message( " WITH_COVERAGE=${WITH_COVERAGE}" )
		message( " WITH_EXAMPLES=${WITH_EXAMPLES}" )
		message( " WITH_TOOLS=${WITH_TOOLS}" )
		message( " WITH_PYTHON=${WITH_PYTHON}" )
		message( " WITH_TEMPLATES_INSTANTIATION=${WITH_TEMPLATES_INSTANTIATION}" )
		# Print compiler options
		message( "-- Compiler options:" )
		message( " CMAKE_CXX_FLAGS = ${CMAKE_CXX_FLAGS}" )
		@@ -405,4 +465,11 @@ message( " CMAKE_CXX_FLAGS_RELEASE = ${CMAKE_CXX_FLAGS_RELEASE}" )
		message( " CMAKE_SHARED_LIBRARY_LINK_C_FLAGS = ${CMAKE_SHARED_LIBRARY_LINK_C_FLAGS}" )
		message( " CMAKE_SHARED_LIBRARY_LINK_C_FLAGS_DEBUG = ${CMAKE_SHARED_LIBRARY_LINK_C_FLAGS_DEBUG}" )
		message( " CMAKE_SHARED_LIBRARY_LINK_C_FLAGS_RELEASE = ${CMAKE_SHARED_LIBRARY_LINK_C_FLAGS_RELEASE}" )
		message( " CMAKE_EXE_LINKER_FLAGS = ${CMAKE_EXE_LINKER_FLAGS}" )
		message( " CMAKE_EXE_LINKER_FLAGS_DEBUG = ${CMAKE_EXE_LINKER_FLAGS_DEBUG}" )
		message( " CMAKE_EXE_LINKER_FLAGS_RELEASE = ${CMAKE_EXE_LINKER_FLAGS_RELEASE}" )
		message( " CMAKE_SHARED_LINKER_FLAGS = ${CMAKE_SHARED_LINKER_FLAGS}" )
		message( " CMAKE_SHARED_LINKER_FLAGS_DEBUG = ${CMAKE_SHARED_LINKER_FLAGS_DEBUG}" )
		message( " CMAKE_SHARED_LINKER_FLAGS_RELEASE = ${CMAKE_SHARED_LINKER_FLAGS_RELEASE}" )
		message( " CUDA_NVCC_FLAGS = ${CUDA_NVCC_FLAGS}" )
		message( " GMP_LIBRARIES = ${GMP_LIBRARIES}" )

build

+9 −0

Original line number	Diff line number	Diff line
		@@ -11,15 +11,18 @@ CMAKE="cmake"
		CMAKE_ONLY="no"
		HELP="no"
		VERBOSE=""
		OFFLINE_BUILD="no"

		WITH_CLANG="no"
		WITH_MPI="yes"
		WITH_CUDA="yes"
		WITH_CUDA_ARCH="auto"
		WITH_OPENMP="yes"
		WITH_GMP="no"
		WITH_TESTS="yes"
		WITH_COVERAGE="no"
		WITH_EXAMPLES="yes"
		WITH_PYTHON="yes"
		WITH_TOOLS="yes"

		WITH_TEMPLATE_INSTANTIATION="no"
		@@ -43,12 +46,14 @@ do
		--cmake-only=* ) CMAKE_ONLY="${option#*=}" ;;
		--verbose ) VERBOSE="VERBOSE=1" ;;
		--help ) HELP="yes" ;;
		--offline-build ) OFFLINE_BUILD="yes" ;;
		--with-clang=* ) WITH_CLANG="${option#*=}" ;;
		--with-mpi=* ) WITH_MPI="${option#*=}" ;;
		--with-mic=* ) WITH_MIC="${option#*=}" ;;
		--with-cuda=* ) WITH_CUDA="${option#*=}" ;;
		--with-cuda-arch=* ) WITH_CUDA_ARCH="${option#*=}";;
		--with-openmp=* ) WITH_OPENMP="${option#*=}" ;;
		--with-gmp=* ) WITH_GMP="${option#*=}" ;;
		--with-tests=* ) WITH_TESTS="${option#*=}" ;;
		--with-coverage=* ) WITH_COVERAGE="${option#*=}" ;;
		--with-examples=* ) WITH_EXAMPLES="${option#*=}" ;;
		@@ -81,11 +86,13 @@ then
		echo " --build-jobs=NUM Number of processes to be used for the build. It is set to the number of available CPU cores by default."
		echo " --prefix=PATH Prefix for the installation directory. ${HOME}/local by default."
		echo " --install=yes/no Enables the installation of TNL files."
		echo " --offline-build=yes/no Disables online updates during the build. 'no' by default."
		echo " --with-mpi=yes/no Enables MPI. 'no' by default (Intel Compiler required)."
		echo " --with-mic=yes/no Enables MIC (Intel Xeon Phi). 'no' by default (Intel Compiler required)."
		echo " --with-cuda=yes/no Enables CUDA. 'yes' by default (CUDA Toolkit is required)."
		echo " --with-cuda-arch=all/auto/30/35/... Chooses CUDA architecture. 'auto' by default."
		echo " --with-openmp=yes/no Enables OpenMP. 'yes' by default."
		echo " --with-gmp=yes/no Enables the wrapper for GNU Multiple Precision Arithmetic Library. 'no' by default."
		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."
		@@ -127,10 +134,12 @@ 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} \

cmake/Gtest.cmake.in

+3 −0

Original line number	Diff line number	Diff line
		@@ -19,4 +19,7 @@ ExternalProject_Add(googletest
		BUILD_COMMAND ""
		INSTALL_COMMAND ""
		TEST_COMMAND ""
		# Disable update of the external project in an offline build
		# reference: https://stackoverflow.com/a/40423683
		UPDATE_DISCONNECTED ${OFFLINE_BUILD}
		)

examples/CMakeLists.txt

+2 −2

Original line number	Diff line number	Diff line
		add_subdirectory( heat-equation )
		add_subdirectory( transport-equation )
		add_subdirectory( navier-stokes )
		add_subdirectory( inviscid-flow )

		#add_subdirectory( mean-curvature-flow )
		#add_subdirectory( hamilton-jacobi )
		@@ -9,7 +10,6 @@ add_subdirectory( navier-stokes )
		#add_subdirectory( hamilton-jacobi-parallel-map )
		#add_subdirectory( fast-sweeping-map )
		#add_subdirectory( narrow-band )

		add_subdirectory( inviscid-flow )
		#add_subdirectory( incompressible-navier-stokes )
		#add_subdirectory( mean-curvature-flow )