Commit 894963e2 authored by Tomáš Oberhuber's avatar Tomáš Oberhuber
Browse files

Merge branch 'develop' into arithmetics 

Conflicts:
	CMakeLists.txt
parents c5b09e1e 36b81712

CMakeLists.txt

100755 → 100644
+43 −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
@@ -257,7 +270,7 @@ 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()
@@ -269,7 +282,7 @@ 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()
@@ -281,16 +294,20 @@ 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 )
@@ -351,9 +368,6 @@ 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}/\" )
@@ -366,7 +380,6 @@ 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} )
@@ -374,7 +387,10 @@ 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")

Copyright

+1 −1
Original line number Diff line number Diff line 
MIT License



Copyright (c) 2004-2016 Tomáš Oberhuber et al.

Copyright (c) 2004-2017 Tomáš Oberhuber et al.



Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

README

+1 −1
Original line number Diff line number Diff line
@@ -9,7 +9,7 @@ Installation 
    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 optionaly install:

    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/)

TODO

+12 −12
Original line number Diff line number Diff line 
- pridet execution policy https://github.com/harrism/hemi/blob/master/hemi/execution_policy.h

- prejmenova Assert na TNL_ASSERT a rozsirit asserce podobne jako v GTest

- odstranit paramee lazy ze smart pointeru

TODO:

- pri zpracovani dat z MRI jde vetsinou o prilis male snimky na optimalni vyuziti GPU (ve 2D). Kdyby se ale pomoci CUDA streamu provadelo vice 

  vypoctu soucasne, mohlo by se dosahnout mnohem lepsiho urychleni



TODO:

- objekt NeighborEnities by mohl vracet i lokalni index dane neighbor entity, coz je potreba pro spravne vkladani maticovych elementu,

  ted se tyto indexy doplnuji rucne podle znalosti indexovani v gridu. Jelikoz neighbor entities mohou znat typ okoli/vzor numerickeho schematu,

  dokazaly by se prizpusobit i ruznym patternum. To by pak vyresilo i skladani operatoru s ruznymi patterny.



TODO:

- pridat execution policy https://github.com/harrism/hemi/blob/master/hemi/execution_policy.h

- odstranit parametr lazy ze smart pointeru



TODO:

 - implementovat tnlMixedGridBoundaryConditions, kde by se pro kazdou stranu gridu definoval jiny zvlastni typ
@@ -15,14 +24,6 @@ TODO: 
 - data by se na hostu preskupila do souvisleho bloku dat a ten se prenesl najednou





TODO:

 - zrejme bude potreba udrzovat ke kazdemu objektu jeho obraz na GPU/MIC

 - to by zarizovala metoda syncToDevice() napr. kazdy objekt by mel promennou modified, ktera by rikala, jestli se zmenil a zda je nutne ho

   prekopirovavat



TODO:

 - zavest namespaces



TODO: CUDA unified memory

 - pretizit operator new s cudaMallocManaged, pak by bylo mozne vytvaret CUDA objekty pristupne pro host a device

 - v TNL solveru by pak vlastne jen stacilo vytvaret objekty pomoci new
@@ -43,7 +44,6 @@ TODO: implementace maticovych resicu 
      * Gaussova eliminace

      * SOR metoda

      * Jacobiho metoda

      * TFQMR metoda

      * IDR metody 



TODO: Nahradit sablonovy parametr dimenze sitove entity za typ entity. Pak by se mohlo zkusit, napriklad u gridu

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