Commit fe9646ce authored by Vít Hanousek's avatar Vít Hanousek
Browse files

Merge remote-tracking branch 'origin/develop' into mpi 

Conflicts:
	src/TNL/Meshes/GridDetails/Traverser_Grid1D_impl.h
	src/TNL/Meshes/GridDetails/Traverser_Grid2D_impl.h
	src/TNL/String.cpp
	tests/CMakeLists.txt
parents aa843d1d 0708c30d

CMakeLists.txt

100755 → 100644
+44 −27
Original line number Diff line number Diff line
@@ -12,7 +12,7 @@ 
# Vladimir Klement

# Jakub Klinkovsky



cmake_minimum_required( VERSION 3.4 )

cmake_minimum_required( VERSION 3.5.1 )



project( tnl )
@@ -21,28 +21,25 @@ set( tnlVersion "0.1" ) 
set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake")



include( OptimizeForArchitecture )

include( UseCodeCoverage )



####

# Settings for debug/release version

#

if( CMAKE_BUILD_TYPE STREQUAL "Debug")

    set( PROJECT_BUILD_PATH ${PROJECT_SOURCE_DIR}/Debug/src/TNL )

    set( PROJECT_TESTS_PATH ${PROJECT_SOURCE_DIR}/Debug/src/Tests )

    set( PROJECT_BUILD_PATH ${PROJECT_SOURCE_DIR}/Debug/src )

    set( PROJECT_TOOLS_PATH ${PROJECT_SOURCE_DIR}/Debug/bin )

    set( LIBRARY_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/Debug/lib )

    set( EXECUTABLE_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/Debug/bin )

    set( debugExt -dbg )

else()

    set( PROJECT_BUILD_PATH ${PROJECT_SOURCE_DIR}/Release/src/TNL )

    set( PROJECT_TESTS_PATH ${PROJECT_SOURCE_DIR}/Release/src/Tests )

    set( PROJECT_BUILD_PATH ${PROJECT_SOURCE_DIR}/Release/src )

    set( PROJECT_TOOLS_PATH ${PROJECT_SOURCE_DIR}/Release/bin )

    set( LIBRARY_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/Release/lib )

    set( EXECUTABLE_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/Release/bin )

endif()



# set Debug/Release options

set( CMAKE_CXX_FLAGS "-std=c++11 -Wall -Wno-unused-local-typedefs -Wno-unused-variable" )

set( CMAKE_CXX_FLAGS "-std=c++11 -pthread -Wall -Wno-unused-local-typedefs -Wno-unused-variable" )

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" )
@@ -54,7 +51,19 @@ set( CMAKE_SHARED_LIBRARY_LINK_C_FLAGS_RELEASE "" ) 
get_filename_component( CXX_COMPILER_NAME ${CMAKE_CXX_COMPILER} NAME )

if( CXX_COMPILER_NAME MATCHES "icpc" )

   message( "Intel compiler detected..."    )

   set( CMAKE_CXX_FLAGS "${CXXFLAGS} -DHAVE_ICPC ")

   set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DHAVE_ICPC -wd2568 -wd2571 -wd2570")

   #####

   #  Ckeck for MIC 

   #

   if( WITH_MIC STREQUAL "yes" )

       message( "Compile 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")

   else()

       set( MIC_CXX_FLAGS "")

   endif( )	

endif()



#####
@@ -67,12 +76,19 @@ if( WITH_CUDA STREQUAL "yes" ) 
        set(CUDA_ATTACH_VS_BUILD_RULE_TO_CUDA_FILE OFF)

        set(BUILD_SHARED_LIBS ON)

        set(CUDA_SEPARABLE_COMPILATION ON)        

        # Use the CUDA_HOST_COMPILER environment variable if the user specified it.

        if( NOT $ENV{CUDA_HOST_COMPILER} STREQUAL "" )

            message( "-- Setting CUDA_HOST_COMPILER to '$ENV{CUDA_HOST_COMPILER}'" )

            set( CUDA_HOST_COMPILER $ENV{CUDA_HOST_COMPILER} )

        else()

            message( "-- Setting CUDA_HOST_COMPILER to '${CMAKE_CXX_COMPILER}'" )

            set( CUDA_HOST_COMPILER ${CMAKE_CXX_COMPILER} )

        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

        #   list of possible tokens: http://www.ssl.berkeley.edu/~jimm/grizzly_docs/SSL/opt/intel/cc/9.0/lib/locale/en_US/mcpcom.msg

        set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} ; -Wno-deprecated-gpu-targets --expt-relaxed-constexpr -Xcudafe "\"--diag_suppress=code_is_unreachable --diag_suppress=implicit_return_from_non_void_function\"")

        #AddCompilerFlag( "-DHAVE_NOT_CXX11" ) # -U_GLIBCXX_ATOMIC_BUILTINS -U_GLIBCXX_USE_INT128 " )

        set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} ; -Wno-deprecated-gpu-targets --expt-relaxed-constexpr --expt-extended-lambda -Xcudafe "\"--diag_suppress=code_is_unreachable --diag_suppress=implicit_return_from_non_void_function\"")

        set( ALL_CUDA_ARCHS -gencode arch=compute_20,code=sm_20

                            -gencode arch=compute_30,code=sm_30

                            -gencode arch=compute_32,code=sm_32
@@ -115,9 +131,6 @@ if( WITH_CUDA STREQUAL "yes" ) 
        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 )

        # TODO: workaround for a bug in cmake 3.5.0 (fixed in 3.5.1)

        set( CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} ; -ccbin "${CMAKE_CXX_COMPILER}" )

        set( CUDA_HOST_COMPILER "" )



        ####

        # Check for cuBLAS
@@ -234,7 +247,7 @@ if( ${SYS_TIME_INCLUDE_DIR} STREQUAL "SYS_TIME_INCLUDE_DIR-NOTFOUND" ) 
    message(  "Missing header file sys/time.h" )

    set( HAVE_SYS_TIME_H "//#define HAVE_SYS_TIME_H 1" )

else()

    include_directories( ${SYS_TIME_INCLUDE_DIR}/tnl-${tnlVersion} )

    #include_directories( ${SYS_TIME_INCLUDE_DIR} )

    set( HAVE_SYS_TIME_H "#define HAVE_SYS_TIME_H 1" )

endif()
@@ -246,7 +259,7 @@ if( ${SYS_RESOURCE_INCLUDE_DIR} STREQUAL "SYS_RESOURCE_INCLUDE_DIR-NOTFOUND" ) 
    message( "Missing header file sys/time.h" )

    set( HAVE_SYS_RESOURCE_H "//#define HAVE_SYS_RESOURCE_H 1" )

else()

    include_directories( ${SYS_RESOURCE_INCLUDE_DIR}/tnl-${tnlVersion} )

    #include_directories( ${SYS_RESOURCE_INCLUDE_DIR} )

    set( HAVE_SYS_RESOURCE_H "#define HAVE_SYS_RESOURCE_H 1" )

endif()
@@ -258,15 +271,20 @@ if( ${SYS_IOCTL_INCLUDE_DIR} STREQUAL "SYS_IOCTL_INCLUDE_DIR-NOTFOUND" ) 
    message( "Missing header file sys/time.h" )

    set( HAVE_SYS_IOCTL_H "//#define HAVE_SYS_IOCTL_H 1" )

else()

    include_directories( ${SYS_IOCTL_INCLUDE_DIR}/tnl-${tnlVersion} )

    #include_directories( ${SYS_IOCTL_INCLUDE_DIR} )

    set( HAVE_SYS_IOCTL_H "#define HAVE_SYS_IOCTL_H 1" )

endif()



if( WITH_TESTS STREQUAL "yes" )

   find_package( GTest )

   if( GTEST_FOUND )

      set( CXX_TESTS_FLAGS "-DHAVE_GTEST" )

   endif( GTEST_FOUND )

   enable_testing()



   # build gtest libs

   include( BuildGtest )



   if( WITH_COVERAGE STREQUAL "yes" AND CMAKE_BUILD_TYPE STREQUAL "Debug" )

      # enable code coverage reports

      include( UseCodeCoverage )

   endif()

endif( WITH_TESTS STREQUAL "yes" )



find_package( PythonInterp 3 )
@@ -327,9 +345,6 @@ if( OPTIMIZED_VECTOR_HOST_OPERATIONS STREQUAL "yes" ) 
   AddCompilerFlag( "-DOPTIMIZED_VECTOR_HOST_OPERATIONS " )

endif()



set( CXX_TEST_FLAGS "-fprofile-arcs -ftest-coverage" )

set( LD_TEST_FLAGS "-lgcov -coverage" )



set( configDirectory \"${CMAKE_INSTALL_PREFIX}/share/tnl-${tnlVersion}/\")

set( sourceDirectory \"${PROJECT_SOURCE_DIR}/\" )

set( testsDirectory \"${PROJECT_TESTS_PATH}/\" )
@@ -342,7 +357,6 @@ endif( PYTHONINTERP_FOUND ) 


#Nastavime cesty k hlavickovym souborum a knihovnam

INCLUDE_DIRECTORIES( src )

INCLUDE_DIRECTORIES( tests )

INCLUDE_DIRECTORIES( ${PROJECT_BUILD_PATH} )

LINK_DIRECTORIES( ${LIBRARY_OUTPUT_PATH} )
@@ -350,7 +364,10 @@ LINK_DIRECTORIES( ${LIBRARY_OUTPUT_PATH} ) 
add_subdirectory( src )

add_subdirectory( share )

add_subdirectory( tests )



if( WITH_EXAMPLES STREQUAL "yes" )

   add_subdirectory( examples )

endif()



set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Template Numerical Library")

set(CPACK_PACKAGE_VENDOR "MMG")

INSTALL

+0 −1
Original line number Diff line number Diff line 
/usr/local/share/automake-1.11/INSTALL
 
 No newline at end of file

README

+80 −0
Original line number Diff line number Diff line 
Installation

============



    Requirements:



    To install TNL, you need:



    cmake 3.4 or later (https://cmake.org/download/)

    GNU g++ 4.8 or later (https://gcc.gnu.org/)

    CUDA 8.0 or later (https://developer.nvidia.com/cuda-downloads)



    For image processing problems, you may optionally install:

    DCMTK (http://dicom.offis.de/dcmtk.php.en)

    libpng (http://www.libpng.org/pub/png/libpng.html)

    libjpeg (http://libjpeg.sourceforge.net/)



    The latest release of TNL can be downloaded as:



    wget tnl-project.org/data/src/tnl-0.1.tar.bz2



    Unpack it as:



    tar xvf tnl-0.1.tar.bz2

    cd tnl-0.1



    Executing command



    ./install



    will install TNL to a folder ${HOME}/.local . You may change it by



    ./install --prefix=<TNL prefix>



    During the installation, TNL fetches latest version of Gtest and install it only 

    locally to sub-folders Debug and Release. At the end of the installation, the

    script is checking if the prefix folder is visible to your bash and your linker.

    If not, it informs you how to change your ${HOME}/.bashrc file to fix it.



How to write a simple solver

============================



To implement your own solver:



    Create and go to your working directory



    mkdir MyProblem

    cd Myproblem



    Execute a command tnl-quickstart



    tnl-quickstart



    Answer the questions as, for example, follows



    TNL Quickstart -- solver generator

    ----------------------------------

    Problem name:My Problem

    Problem class base name (base name acceptable in C++ code):MyProblem

    Operator name:Laplace



    Write your numerical scheme by editing a file



    Laplace_impl.h



    on lines:

        34, 141 and 265 for 1D, 2D and 3D problem respectively with explicit time discretization

        101, 211 and 332 for 1D, 2D and 3D problem respectively with (semi-)implicit time discretization

    Compile the program by executing



    make



    for CPU version only or 

   

    make WITH_CUDA=yes



    for a solver running on both CPU and GPU. Run it on your favourite HW architecture by executing



    ./MyProblem



    and following the printed help.

build

+49 −28
Original line number Diff line number Diff line
@@ -2,35 +2,51 @@ 


TARGET=TNL

PREFIX=${HOME}/.local

INSTALL="no"

ROOT_DIR="."

DCMTK_DIR="/usr/include/dcmtk"

BUILD=""

BUILD_JOBS=""

CMAKE="cmake"

CMAKE_ONLY="no"

HELP="no"

VERBOSE=""



WITH_CLANG="no"

WITH_CUDA="yes"

WITH_CUDA_ARCH="auto"

WITH_TESTS="yes"

WITH_COVERAGE="no"

WITH_EXAMPLES="yes"



WITH_CUDA_ARCH="auto"

WITH_TEMPLATE_INSTANTIATION="yes"

WITH_TEMPLATE_INSTANTIATION="no"

INSTANTIATE_LONG_INT="no"

INSTANTIATE_INT="yes"

INSTANTIATE_LONG_DOUBLE="no"

INSTANTIATE_DOUBLE="yes"

INSTANTIATE_FLOAT="no"

OPTIMIZED_VECTOR_HOST_OPERATIONS="no"

CMAKE="cmake"

CMAKE_ONLY="no"

HELP="no"

VERBOSE=""

ROOT_DIR="."

DCMTK_DIR="/usr/include/dcmtk"

BUILD_JOBS=""



for option in "$@"

do

    case $option in

        --prefix=*                       ) PREFIX="${option#*=}" ;;

        --install=*                      ) INSTALL="${option#*=}" ;;

        --root-dir=*                     ) ROOT_DIR="${option#*=}" ;;

        --dcmtk-dir=*                    ) DCMTK_DIR="${option#*=}" ;;

        --build=*                        ) BUILD="${option#*=}" ;;

        --build-jobs=*                   ) BUILD_JOBS="${option#*=}" ;;

        --cmake=*                        ) CMAKE="${option#*=}" ;;

        --cmake-only=*                   ) CMAKE_ONLY="${option#*=}" ;;

        --verbose                        ) VERBOSE="VERBOSE=1" ;;

        --help                           ) HELP="yes" ;;

        --with-clang=*                   ) WITH_CLANG="${option#*=}" ;;

        --with-tests=*                   ) WITH_TESTS="${option#*=}" ;;

        --with-mic=*                     ) WITH_MIC="${option#*=}" ;;

        --with-cuda=*                    ) WITH_CUDA="${option#*=}" ;;

        --with-cuda-arch=*               ) WITH_CUDA_ARCH="${option#*=}";;

        --with-tests=*                   ) WITH_TESTS="${option#*=}" ;;

        --with-coverage=*                ) WITH_COVERAGE="${option#*=}" ;;

        --with-examples=*                ) WITH_EXAMPLES="${option#*=}" ;;

        --with-templates-instantiation=* ) WITH_TEMPLATE_INSTANTIATION="${option#*=}" ;;

        --instantiate-long-int=*         ) INSTANTIATE_LONG_INT="${option#*=}" ;;

        --instantiate-int=*              ) INSTANTIATE_INT="${option#*=}" ;;
@@ -44,13 +60,6 @@ do 
                                           INSTANTIATE_FLOAT="no"

                                           WITH_CUDA_ARCH="auto" ;;

        --optimize-vector-host-operations=* ) OPTIMIZED_VECTOR_HOST_OPERATIONS="yes" ;;

        --with-cmake=*                   ) CMAKE="${option#*=}" ;;

        --build-jobs=*                   ) BUILD_JOBS="${option#*=}" ;;

        --cmake-only=*                   ) CMAKE_ONLY="${option#*=}" ;;

        --verbose                        ) VERBOSE="VERBOSE=1" ;;

        --root-dir=*                     ) ROOT_DIR="${option#*=}" ;;

        --dcmtk-dir=*                    ) DCMTK_DIR="${option#*=}" ;;

        --help                           ) HELP="yes" ;;

        *                                ) 

           echo "Unknown option ${option}. Use --help for more information."

           exit 1 ;;
@@ -61,15 +70,18 @@ if test ${HELP} = "yes"; 
then

    echo "TNL build options:"

    echo ""

    echo "   --prefix=PATH                         Prefix for the installation directory. ${HOME}/local by default."

    echo "   --build=Debug/Release                 Build type."

    echo "   --with-tests=yes/no                   Enable unit tests. 'yes' by default (libcppunit-dev is required)."

    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 "   --with-mic=yes/no                     Enable MIC (Intel Xeon Phi). 'no' by default (Intel Compiler required)."

    echo "   --with-cuda=yes/no                    Enable CUDA. 'yes' by default (CUDA Toolkit is required)."

    echo "   --with-cuda-arch=all/auto/30/35/...   Choose CUDA architecture."   

    echo "   --with-templates-instantiation=yes/no Some TNL templates are precompiled during the build. 'yes' by default."

    echo "   --full-build                          Instantiate all -- long int indexing, float and long double floating point arithmetics."

    echo "   --with-cmake=CMAKE                    Path to cmake. 'cmake' by default."

    echo "   --build-jobs=NUM                      Number of processes to be used for the build. It is set to a number of CPU cores by default."

    echo "   --with-cuda-arch=all/auto/30/35/...   Choose CUDA architecture. 'auto' by default."

    echo "   --with-tests=yes/no                   Enable unit tests. 'yes' by default."

    echo "   --with-coverage=yes/no                Enable 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-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."

    echo "   --root-dir=PATH                       Path to the TNL source code root dir."

    echo "   --dcmtk-dir=PATH                      Path to the DCMTK (Dicom Toolkit) root dir."
@@ -89,10 +101,12 @@ echo "Configuring ${BUILD} $TARGET ..." 
${CMAKE} ${ROOT_DIR} \

         -DCMAKE_BUILD_TYPE=${BUILD} \

         -DCMAKE_INSTALL_PREFIX=${PREFIX} \

         -DWITH_MIC=${WITH_MIC} \

         -DWITH_CUDA=${WITH_CUDA} \

         -DWITH_CUDA_ARCH=${WITH_CUDA_ARCH} \

         -DWITH_TESTS=${WITH_TESTS} \

         -DPETSC_DIR=${PETSC_DIR} \

         -DWITH_COVERAGE=${WITH_COVERAGE} \

         -DWITH_EXAMPLES=${WITH_EXAMPLES} \

         -DDCMTK_DIR=${DCMTK_DIR} \

         -DWITH_TEMPLATE_INSTANTIATION=${WITH_TEMPLATE_INSTANTIATION} \

         -DINSTANTIATE_FLOAT=${INSTANTIATE_FLOAT} \
@@ -109,7 +123,7 @@ fi 


if test ${CMAKE_ONLY} = "yes";

then

    exit 1

    exit 0

fi



if [[ -n ${BUILD_JOBS} ]]; then
@@ -128,14 +142,21 @@ else 
    echo "Building ${BUILD} $TARGET ..."

fi



make ${VERBOSE}

if [[ "$INSTALL" == "yes" ]]; then

   # install implies all

   make_target="install"

else

   make_target="all"

fi



make ${VERBOSE} $make_target

if test $? != 0; then

    echo "Error: Build process failed."

    exit 1

fi





if test WITH_TESTS = "yes";

if test ${WITH_TESTS} = "yes";

then

    make test

    if test $? != 0; then

cmake/BuildGtest.cmake

0 → 100644
+45 −0
Original line number Diff line number Diff line 
# Gtest developers recommend to build the gtest libraries directly from

# the projects' build systems, see

# https://github.com/google/googletest/tree/master/googletest#incorporating-into-an-existing-cmake-project



#find_package( GTest )

#if( GTEST_FOUND )

#   set( CXX_TESTS_FLAGS "${CXX_TESTS_FLAGS} -DHAVE_GTEST" )

#endif( GTEST_FOUND )





# compatibility with the GTest package

set( GTEST_BOTH_LIBRARIES gtest gtest_main )

set( CXX_TESTS_FLAGS ${CXX_TESTS_FLAGS} -DHAVE_GTEST )





# Download and unpack googletest at configure time

configure_file(cmake/Gtest.cmake.in googletest-download/CMakeLists.txt)

execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .

 RESULT_VARIABLE result

 WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/googletest-download )

if(result)

 message(FATAL_ERROR "CMake step for googletest failed: ${result}")

endif()

execute_process(COMMAND ${CMAKE_COMMAND} --build .

 RESULT_VARIABLE result

 WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/googletest-download )

if(result)

 message(FATAL_ERROR "Build step for googletest failed: ${result}")

endif()



# Prevent overriding the parent project's compiler/linker

# settings on Windows

set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)



# Add googletest directly to our build. This defines

# the gtest and gtest_main targets.

add_subdirectory(${CMAKE_BINARY_DIR}/googletest-src

                ${CMAKE_BINARY_DIR}/googletest-build)



# The gtest/gtest_main targets carry header search path

# dependencies automatically when using CMake 2.8.11 or

# later. Otherwise we have to add them here ourselves.

if (CMAKE_VERSION VERSION_LESS 2.8.11)

    include_directories("${gtest_SOURCE_DIR}/include")

endif()