Commit 5cbb4a1b authored by Vít Hanousek's avatar Vít Hanousek
Browse files

Merge branch 'develop' into MIC-devel 

Nově zavedená stará implementace, lze přeložit s MIC i s CUDA, snad... Stále využívá Specializaci Array pro MIC.

Conflicts:
	build
	src/TNL/Assert.h
	src/TNL/Containers/Algorithms/ArrayOperations.h
	src/TNL/Containers/Algorithms/VectorOperations.h
	src/TNL/Containers/Array.h
	src/TNL/Containers/SharedArray.h
	src/TNL/Containers/SharedVector.h
	src/TNL/Containers/StaticArray.h
	src/TNL/File.h
	src/TNL/File_impl.h
	src/TNL/Matrices/CSR_impl.h
	src/TNL/Matrices/MatrixSetter.h
	src/TNL/Meshes/GridDetails/GridEntity_impl.h
	src/TNL/Meshes/GridDetails/NeighbourGridEntityGetter1D_impl.h
	src/TNL/Meshes/GridDetails/NeighbourGridEntityGetter2D_impl.h
	src/TNL/Meshes/GridDetails/NeighbourGridEntityGetter3D_impl.h
	src/TNL/Meshes/GridEntity.h
	src/TNL/Solvers/ODE/Euler_impl.h
	src/core/arrays/tnlArray_impl.h
	src/core/arrays/tnlSharedArray_impl.cpp
	src/core/arrays/tnlSharedArray_impl.h
	src/core/arrays/tnlStaticArray1D_impl.h
	src/core/arrays/tnlStaticArray2D_impl.h
	src/core/arrays/tnlStaticArray3D_impl.h
	src/core/arrays/tnlStaticArray_impl.h
	src/core/mfuncs.h
	src/core/tnlCuda.h
	src/core/tnlDevice.h
	src/core/tnlObject.h
	src/core/vectors/tnlSharedVector_impl.h
	src/core/vectors/tnlStaticVector.h
	src/core/vectors/tnlStaticVector1D_impl.h
	src/core/vectors/tnlStaticVector2D_impl.h
	src/core/vectors/tnlStaticVector3D_impl.h
	src/core/vectors/tnlStaticVector_impl.h
	src/core/vectors/tnlVectorOperationsHost_impl.h
	src/functions/tnlFunctionEvaluator_impl.h
	src/functions/tnlMeshFunction.h
	src/functions/tnlMeshFunctionEvaluator_impl.h
	src/functions/tnlMeshFunction_impl.h
	src/matrices/tnlMatrixSetter_impl.h
	src/mesh/grids/CMakeLists.txt
	src/mesh/grids/tnlGridTraverser.h
	src/mesh/grids/tnlGridTraverserCUDA_impl.h
	src/solvers/pde/tnlBoundaryConditionsSetter.h
	src/solvers/pde/tnlBoundaryConditionsSetter_impl.h
	src/solvers/pde/tnlExplicitUpdater.h
	src/solvers/pde/tnlExplicitUpdater_impl.h
	src/solvers/pde/tnlLinearSystemAssembler_impl.h
	src/solvers/tnlBuildConfigTags.h
	src/solvers/tnlSolverConfig_impl.h
	src/solvers/tnlSolverInitiator_impl.h
	tests/benchmarks/heat-equation-benchmark/tnlTestNeighbourGridEntitiesStorage.h
	tests/unit-tests/core/arrays/CMakeLists.txt
	tests/unit-tests/core/vectors/CMakeLists.txt
parents 29de7ac5 740d7d10

CMakeLists.txt

+79 −91
Original line number Diff line number Diff line
@@ -27,22 +27,22 @@ include( UseCodeCoverage ) 
# Settings for debug/release version

#

if( CMAKE_BUILD_TYPE STREQUAL "Debug")

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

    set( PROJECT_TESTS_PATH ${PROJECT_SOURCE_DIR}/Debug/tests )

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

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

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

    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 )

    set( PROJECT_TESTS_PATH ${PROJECT_SOURCE_DIR}/Release/tests )

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

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

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

    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" )

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

set( CMAKE_CXX_FLAGS_DEBUG "-g" )

set( CMAKE_CXX_FLAGS_RELEASE "-O3 -march=native -DNDEBUG" )

#set( CMAKE_CXX_FLAGS_RELEASE "-O3 -march=native -DNDEBUG -ftree-vectorizer-verbose=1 -ftree-vectorize -fopt-info-vec-missed -funroll-loops" )
@@ -68,6 +68,10 @@ if( WITH_CUDA STREQUAL "yes" ) 
        set(BUILD_SHARED_LIBS ON)

        set(CUDA_SEPARABLE_COMPILATION ON)        

        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( ALL_CUDA_ARCHS -gencode arch=compute_20,code=sm_20

                            -gencode arch=compute_30,code=sm_30
@@ -84,10 +88,10 @@ if( WITH_CUDA STREQUAL "yes" ) 
                # Select GPU architecture

                #

                set( CUDA_ARCH_EXECUTABLE ${EXECUTABLE_OUTPUT_PATH}/tnl-cuda-arch)

                set( CUDA_ARCH_SOURCE ${PROJECT_SOURCE_DIR}/tools/src/tnl-cuda-arch.cu)

                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 ${CUDA_ARCH_SOURCE} -o ${CUDA_ARCH_EXECUTABLE}

                execute_process( COMMAND nvcc --compiler-bindir ${CUDA_HOST_COMPILER} ${CUDA_ARCH_SOURCE} -o ${CUDA_ARCH_EXECUTABLE}

                                 RESULT_VARIABLE CUDA_ARCH_RESULT

                                 OUTPUT_VARIABLE CUDA_ARCH_OUTPUT

                                 ERROR_VARIABLE CUDA_ARCH_OUTPUT )
@@ -108,7 +112,7 @@ if( WITH_CUDA STREQUAL "yes" ) 
                set( CUDA_ARCH -gencode arch=compute_${WITH_CUDA_ARCH},code=sm_${WITH_CUDA_ARCH} )

            endif()

        endif()

        set( CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS} ; ${CUDA_ARCH} )

        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)
@@ -118,11 +122,19 @@ if( WITH_CUDA STREQUAL "yes" ) 
        ####

        # Check for cuBLAS

        #

        if( WITH_CUBLAS STREQUAL "yes" ) 

            message( "Enabling CUBLAS." )

            set( HAVE_CUBLAS TRUE)

        if( NOT WITH_CUBLAS STREQUAL "no" )

            find_path( CUBLAS_INCLUDE_DIR cublas_v2.h

                       /usr/local/cuda/include

                       ${CUDA_INCLUDE_DIR}

                       DOC "CUBLAS headers." )

            if( ${CUBLAS_INCLUDE_DIR} STREQUAL "CUBLAS_INCLUDE_DIR-NOTFOUND" )

                message( "CUBLAS not found." )

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

            else()

                message( "CUBLAS found. -- ${CUBLAS_INCLUDE_DIR}" )

                set( HAVE_CUBLAS "#define HAVE_CUBLAS 1" )

        endif( WITH_CUBLAS STREQUAL "yes" )       

            endif()

        endif( NOT WITH_CUBLAS STREQUAL "no" )



        ####

        # Check for CUSP
@@ -142,7 +154,6 @@ if( WITH_CUDA STREQUAL "yes" ) 
        # Check for CUSPARSE

        #

        if( NOT WITH_CUSPARSE STREQUAL "no" )

        

           find_path( CUSPARSE_INCLUDE_DIR cusparse.h

                      /usr/local/cuda/include                   

                      ${CUDA_INCLUDE_DIR}
@@ -168,6 +179,7 @@ if( OPENMP_FOUND ) 
   message( "Compiler supports OpenMP." )

   set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DHAVE_OPENMP -fopenmp" )

endif()

#set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DHAVE_OPENMP -fopenmp=libgomp" )



####

# Check for MPI
@@ -237,59 +249,27 @@ else() 
    set( HAVE_SYS_RESOURCE_H "#define HAVE_SYS_RESOURCE_H 1" )

endif()



####

# Check for cppunit

#

if( WITH_TESTS STREQUAL "yes" )

    FIND_PATH(CPPUNIT_INCLUDE_DIR cppunit/TestCase.h

      /usr/local/include

find_path( SYS_IOCTL_INCLUDE_DIR sys/ioctl.h

           /usr/include/x86_64-linux-gnu

           /usr/include  

      DOC "CppUnit headers."

    )

           DOC "System ioctl headers." )

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} )

    set( HAVE_SYS_IOCTL_H "#define HAVE_SYS_IOCTL_H 1" )

endif()



    ####

    # With Win32, important to have both

    #

    if(WIN32)

      FIND_LIBRARY(CPPUNIT_LIBRARY cppunit

                   ${CPPUNIT_INCLUDE_DIR}/../lib

                   /usr/local/lib

                   /usr/lib)

      FIND_LIBRARY(CPPUNIT_DEBUG_LIBRARY cppunitd

                   ${CPPUNIT_INCLUDE_DIR}/../lib

                   /usr/local/lib

                   /usr/lib)

    else(WIN32)

      # On unix system, debug and release have the same name

      FIND_LIBRARY(CPPUNIT_LIBRARY cppunit

                   ${CPPUNIT_INCLUDE_DIR}/../lib

                   /usr/local/lib

                   /usr/lib)

      FIND_LIBRARY(CPPUNIT_DEBUG_LIBRARY cppunit

                   ${CPPUNIT_INCLUDE_DIR}/../lib

                   /usr/local/lib

                   /usr/lib)

    endif(WIN32)





    if( ${CPPUNIT_INCLUDE_DIR} STREQUAL "CPPUNIT_INCLUDE_DIR-NOTFOUND" )

          message( "CPPUNIT not found." )

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

    else( ${CPPUNIT_INCLUDE_DIR} STREQUAL "CPPUNIT_INCLUDE_DIR-NOTFOUND" )

      message( "CPPUNIT headers found -- ${CPPUNIT_INCLUDE_DIR}" )

      if(CPPUNIT_LIBRARY)

        message( "CPPUNIT library found -- ${CPPUNIT_LIBRARY}" )

        set(CPPUNIT_FOUND "YES")

        set(CPPUNIT_LIBRARIES ${CPPUNIT_LIBRARY} ${CMAKE_DL_LIBS})

        set(CPPUNIT_DEBUG_LIBRARIES ${CPPUNIT_DEBUG_LIBRARY}

                                    ${CMAKE_DL_LIBS})

       set( HAVE_CPPUNIT "#define HAVE_CPPUNIT 1" )

      endif(CPPUNIT_LIBRARY)

    endif( ${CPPUNIT_INCLUDE_DIR} STREQUAL "CPPUNIT_INCLUDE_DIR-NOTFOUND" )

    ENABLE_TESTING()

    INCLUDE( Dart )

if( WITH_TESTS STREQUAL "yes" )

   find_package( GTest )

   if( GTEST_FOUND )

      set( CXX_TESTS_FLAGS "-DHAVE_GTEST" )

   endif( GTEST_FOUND )

endif( WITH_TESTS STREQUAL "yes" )



find_package( PythonInterp 3 )



#if( BUILD_MPI )

#   FIND_PATH( PETSC_INCLUDE_DIR petsc.h

#     /usr/include/petsc
@@ -318,28 +298,32 @@ endif( WITH_TESTS STREQUAL "yes" ) 
####

# Explicit template instantiation

#

if( WITH_TEMPLATE_INSTANTIATION STREQUAL "yes" )

   AddCompilerFlag( "-DTEMPLATE_EXPLICIT_INSTANTIATION " )



   if( INSTANTIATE_INT STREQUAL "yes" )

      AddCompilerFlag( "-DINSTANTIATE_INT " )

   endif()



   if( INSTANTIATE_LONG_INT STREQUAL "yes" )

      AddCompilerFlag( "-DINSTANTIATE_LONG_INT " )

   endif()



   if( INSTANTIATE_FLOAT STREQUAL "yes" )

      AddCompilerFlag( "-DINSTANTIATE_FLOAT " )

   endif()



   if( INSTANTIATE_DOUBLE STREQUAL "yes" )

      AddCompilerFlag( "-DINSTANTIATE_DOUBLE " )

   endif()

#if( WITH_TEMPLATE_INSTANTIATION STREQUAL "yes" )

#   AddCompilerFlag( "-DTEMPLATE_EXPLICIT_INSTANTIATION " )

#

#   if( INSTANTIATE_INT STREQUAL "yes" )

#      AddCompilerFlag( "-DINSTANTIATE_INT " )

#   endif()

#

#   if( INSTANTIATE_LONG_INT STREQUAL "yes" )

#      AddCompilerFlag( "-DINSTANTIATE_LONG_INT " )

#   endif()

#

#   if( INSTANTIATE_FLOAT STREQUAL "yes" )

#      AddCompilerFlag( "-DINSTANTIATE_FLOAT " )

#   endif()

#

#   if( INSTANTIATE_DOUBLE STREQUAL "yes" )

#      AddCompilerFlag( "-DINSTANTIATE_DOUBLE " )

#   endif()

#

#   if( INSTANTIATE_LONG_DOUBLE STREQUAL "yes" )

#      AddCompilerFlag( "-DINSTANTIATE_LONG_DOUBLE " )

#   endif()

#endif()



   if( INSTANTIATE_LONG_DOUBLE STREQUAL "yes" )

      AddCompilerFlag( "-DINSTANTIATE_LONG_DOUBLE " )

   endif()

if( OPTIMIZED_VECTOR_HOST_OPERATIONS STREQUAL "yes" )

   AddCompilerFlag( "-DOPTIMIZED_VECTOR_HOST_OPERATIONS " )

endif()



set( CXX_TEST_FLAGS "-fprofile-arcs -ftest-coverage" )
@@ -348,8 +332,12 @@ set( LD_TEST_FLAGS "-lgcov -coverage" ) 
set( configDirectory \"${CMAKE_INSTALL_PREFIX}/share/tnl-${tnlVersion}/\")

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

set( testsDirectory \"${PROJECT_TESTS_PATH}/\" )

CONFIGURE_FILE( "tnlConfig.h.in" "${PROJECT_BUILD_PATH}/tnlConfig.h" )

INSTALL( FILES ${PROJECT_BUILD_PATH}/tnlConfig.h DESTINATION include/tnl-${tnlVersion} )

CONFIGURE_FILE( "tnlConfig.h.in" "${PROJECT_BUILD_PATH}/TNL/tnlConfig.h" )

INSTALL( FILES ${PROJECT_BUILD_PATH}/TNL/tnlConfig.h DESTINATION include/tnl-${tnlVersion}/TNL )

if( PYTHONINTERP_FOUND )

    CONFIGURE_FILE( "Config.py.in" "${PROJECT_BUILD_PATH}/TNL/Config.py" )

    INSTALL( FILES ${PROJECT_BUILD_PATH}/TNL/Config.py DESTINATION lib/python${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}/site-packages/TNL )

endif( PYTHONINTERP_FOUND )



#Nastavime cesty k hlavickovym souborum a knihovnam

INCLUDE_DIRECTORIES( src )
@@ -359,8 +347,8 @@ LINK_DIRECTORIES( ${LIBRARY_OUTPUT_PATH} ) 


#Pokracujeme dalsimi podadresari

add_subdirectory( src )

add_subdirectory( share )

add_subdirectory( tests )

add_subdirectory( tools )

add_subdirectory( examples )



set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Template Numerical Library")

COPYING

deleted100644 → 0
+0 −1
Original line number Diff line number Diff line 
/usr/local/share/automake-1.11/COPYING
 
 No newline at end of file

Config.py.in

0 → 100644
+2 −0
Original line number Diff line number Diff line 
tnl_install_prefix = "@CMAKE_INSTALL_PREFIX@"

tnl_version = "@tnlVersion@"

Copyright

0 → 100644
+21 −0
Original line number Diff line number Diff line 
MIT License



Copyright (c) 2004-2016 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

in the Software without restriction, including without limitation the rights

to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

copies of the Software, and to permit persons to whom the Software is

furnished to do so, subject to the following conditions:



The above copyright notice and this permission notice shall be included in all

copies or substantial portions of the Software.



THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE

AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,

OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE

SOFTWARE.
 
 No newline at end of file

TODO

+11 −6
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:

 - implementovat tnlMixedGridBoundaryConditions, kde by se pro kazdou stranu gridu definoval jiny zvlastni typ

   okrajovych podminek

 - dalo by se tim resit i skladani zpetnych a doprednych diferenci u nelinearni difuze, kdy je potreba napr. dopredne diference

   vycislit i na leve a dolni hranici 2D gridu

   - tohle resit spis primym rozepsanim schematu



TODO:

 - implementovat tuple pro snazsi a snad efektoivnejsi prenos dat na GPU

 - implementovat tuple pro snazsi a snad efektivnejsi prenos dat na GPU

 - nebylo by nutne definovat pomocne datove structury pro traverser

 - 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
@@ -21,11 +31,6 @@ TODO: CUDA unified memory 
se s nimi pracovat postaru

 - bylo by dobre to obalit unique poinetry, aby se nemusela delat dealokace rucne



TODO: shared pointery

 - mohli bysme pomoci nich odstranit Shared objekty

 - asi by bylo lepsi datcounter z shared pointeru primo do array a tento counter by se alokoval az po porvnim sdileni dat

 - diky tomu by se array mohlo vytvaret i na gpu bez nutnosti dynamicke alokace, jen by nebylo mozne delat bind (nebo nejaky zjednoduseny)



TODO: Mesh

 * vsechny traits zkusit presunout do jednotneho MeshTraits, tj. temer MeshConfigTraits ale pojmenovat jako MeshTraits

 * omezit tnlDimesnionsTag - asi to ale nepujde