Commit cf0ef449 authored by Tomáš Oberhuber's avatar Tomáš Oberhuber
Browse files

Merge branch 'develop' into hamilton-jacobi 

Conflicts:
	CMakeLists.txt
	TODO
	build
	examples/CMakeLists.txt
	examples/hamilton-jacobi-parallel-map/no-Makefile
	examples/hamilton-jacobi-parallel/no-Makefile
	examples/hamilton-jacobi/HamiltonJacobiProblem.h
	examples/hamilton-jacobi/HamiltonJacobiProblemSetter.h
	examples/hamilton-jacobi/Makefile
	examples/hamilton-jacobi/main.cpp
	examples/heat-equation/tnl-heat-equation.h
	examples/inviscid-flow/2d/run-euler
	examples/mean-curvature-flow/Makefile
	examples/navier-stokes/navierStokesBoundaryConditions_impl.h
	examples/navier-stokes/navierStokesSolverMonitor_impl.h
	examples/simple-solver/Makefile
	examples/simple-solver/simpleProblemSetter.h
	src/core/CMakeLists.txt
	src/core/arrays/tnlArray_impl.h
	src/core/arrays/tnlConstSharedArray_impl.h
	src/core/arrays/tnlMultiArray1D_impl.h
	src/core/arrays/tnlMultiArray2D_impl.h
	src/core/arrays/tnlMultiArray3D_impl.h
	src/core/arrays/tnlMultiArray4D_impl.h
	src/core/arrays/tnlSharedArray_impl.h
	src/core/images/tnlPGMImage_impl.h
	src/core/terminal-colors.h
	src/core/tnlCudaDeviceInfo.cpp
	src/core/tnlCudaDeviceInfo.cu
	src/core/tnlCudaDeviceInfo.h
	src/core/tnlFile.h
	src/core/tnlHost.cpp
	src/core/tnlLogger.cpp
	src/core/tnlObject.cpp
	src/core/tnlStaticMultiIndex.h
	src/core/tnlTimerCPU.cpp
	src/core/tnlTimerRT.cpp
	src/core/vectors/tnlMultiVector1D_impl.h
	src/core/vectors/tnlMultiVector2D_impl.h
	src/core/vectors/tnlMultiVector3D_impl.h
	src/core/vectors/tnlMultiVector4D_impl.h
	src/core/vectors/tnlVectorOperationsHost_impl.h
	src/core/vectors/tnlVector_impl.h
	src/functions/CMakeLists.txt
	src/functions/tnlDomain.h
	src/functions/tnlMeshFunction.h
	src/functions/tnlMeshFunctionVTKWriter.h
	src/functions/tnlMeshFunctionVTKWriter_impl.h
	src/functions/tnlMeshFunction_impl.h
	src/functions/tnlTestFunction.h
	src/functions/tnlTestFunction_impl.h
	src/implementation/core/tnlHost.cpp
	src/legacy/benchmarks/tnlSpmvBenchmarkBase_impl.h
	src/legacy/benchmarks/tnlSpmvBenchmarkHybridMatrix.h
	src/legacy/matrices/tnlAdaptiveRgCSRMatrix.h
	src/legacy/matrices/tnlCSRMatrix.h
	src/legacy/matrices/tnlEllpackMatrix.h
	src/legacy/matrices/tnlFastCSRMatrix.h
	src/legacy/matrices/tnlFastRgCSRMatrix.h
	src/legacy/matrices/tnlFastRgCSRMatrixCUDA.h
	src/legacy/matrices/tnlRgCSRMatrix.h
	src/legacy/solvers/tnlMatrixSolver.h
	src/matrices/tnlCSRMatrix_impl.h
	src/matrices/tnlDenseMatrix.h
	src/matrices/tnlDenseMatrix_impl.h
	src/matrices/tnlEllpackMatrix_impl.h
	src/matrices/tnlMultidiagonalMatrix_impl.h
	src/matrices/tnlSlicedEllpackMatrix_impl.h
	src/matrices/tnlTridiagonalMatrix_impl.h
	src/mesh/grids/tnlGrid1D_impl.h
	src/mesh/grids/tnlGrid2D_impl.h
	src/mesh/grids/tnlGrid3D_impl.h
	src/mesh/grids/tnlGridTraverser.h
	src/mesh/grids/tnlGridTraverser_impl.h
	src/mesh/grids/tnlTraverser_Grid1D.h
	src/mesh/initializer/tnlMeshSuperentityStorageInitializer.h
	src/mesh/traits/tnlDimensionsTraits.h
	src/operators/CMakeLists.txt
	src/operators/diffusion/nonlinear-diffusion-operators/tnlFiniteVolumeNonlinearOperator.h
	src/operators/diffusion/nonlinear-diffusion-operators/tnlFiniteVolumeNonlinearOperator_impl.h
	src/operators/diffusion/tnlExactMeanCurvature.h
	src/operators/diffusion/tnlExactNonlinearDiffusion.h
	src/operators/diffusion/tnlLinearDiffusion.h
	src/operators/diffusion/tnlLinearDiffusion_impl.h
	src/operators/diffusion/tnlNonlinearDiffusion_impl.h
	src/operators/diffusion/tnlOneSidedMeanCurvature.h
	src/operators/diffusion/tnlOneSidedNonlinearDiffusion.h
	src/operators/euler/fvm/tnlLaxFridrichs_impl.h
	src/operators/geometric/tnlExactGradientNorm.h
	src/operators/hamilton-jacobi/upwind/CMakeLists.txt~
	src/operators/tnlDirichletBoundaryConditions.h
	src/operators/tnlNeumannBoundaryConditions.h
	src/operators/tnlNeumannBoundaryConditions_impl.h
	src/problems/tnlHeatEquationProblem.h
	src/problems/tnlHeatEquationProblem_impl.h
	src/problems/tnlPDEProblem.h
	src/problems/tnlPDEProblem_impl.h
	src/problems/tnlProblem.h
	src/solvers/linear/CMakeLists.txt
	src/solvers/linear/krylov/tnlBICGStabSolver_impl.h
	src/solvers/linear/krylov/tnlCGSolver_impl.h
	src/solvers/linear/krylov/tnlGMRESSolver_impl.h
	src/solvers/linear/krylov/tnlTFQMRSolver.h
	src/solvers/linear/krylov/tnlTFQMRSolver_impl.h
	src/solvers/linear/stationary/tnlSORSolver_impl.h
	src/solvers/ode/tnlEulerSolver_impl.h
	src/solvers/ode/tnlMersonSolver_impl.h
	src/solvers/ode/tnlODESolverMonitor_impl.h
	src/solvers/pde/tnlExplicitTimeStepper.h
	src/solvers/pde/tnlExplicitTimeStepper_impl.h
	src/solvers/pde/tnlExplicitUpdater.h
	src/solvers/pde/tnlExplicitUpdater_impl.h
	src/solvers/pde/tnlLinearSystemAssembler.h
	src/solvers/pde/tnlPDESolver.h
	src/solvers/pde/tnlPDESolver_impl.h
	src/solvers/pde/tnlSemiImplicitTimeStepper.h
	src/solvers/pde/tnlSemiImplicitTimeStepper_impl.h
	src/solvers/tnlBuildConfigTags.h
	src/solvers/tnlIterativeSolver.h
	src/solvers/tnlIterativeSolverMonitor_impl.h
	src/solvers/tnlIterativeSolver_impl.h
	src/solvers/tnlSolverConfig_impl.h
	src/solvers/tnlSolverStarter_impl.h
	src/solvers/tnlSolver_impl.h
	tests/benchmarks/CMakeLists.txt
	tests/benchmarks/tnl-benchmark-simple-heat-equation.h
	tests/benchmarks/tnl-benchmark-spmv.h
	tests/benchmarks/tnl-cuda-benchmarks.h
	tests/long-time-unit-tests/CMakeLists.txt
	tests/unit-tests/core/arrays/CMakeLists.txt
	tests/unit-tests/matrices/CMakeLists.txt
	tests/unit-tests/matrices/tnlRgCSRMatrixTester.h
	tests/unit-tests/operators/diffusion/CMakeLists.txt
	tests/unit-tests/operators/diffusion/tnlOneSidedMeanCurvatureTest.h
	tools/src/functions-benchmark.h
	tools/src/tnl-view.h
	tools/tnl-compile.in
	tools/tnl-quickstart/tnl-quickstart.py
parents 8a70122d 638ed6c7

.cproject

deleted100644 → 0
+0 −53
Original line number Diff line number Diff line 
<?xml version="1.0" encoding="UTF-8" standalone="no"?>

<?fileVersion 4.0.0?><cproject storage_type_id="org.eclipse.cdt.core.XmlProjectDescriptionStorage">

	<storageModule moduleId="org.eclipse.cdt.core.settings">

		<cconfiguration id="cdt.managedbuild.toolchain.gnu.base.2134791445">

			<storageModule buildSystemId="org.eclipse.cdt.managedbuilder.core.configurationDataProvider" id="cdt.managedbuild.toolchain.gnu.base.2134791445" moduleId="org.eclipse.cdt.core.settings" name="Default">

				<externalSettings/>

				<extensions>

					<extension id="org.eclipse.cdt.core.GmakeErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>

					<extension id="org.eclipse.cdt.core.CWDLocator" point="org.eclipse.cdt.core.ErrorParser"/>

					<extension id="org.eclipse.cdt.core.GCCErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>

					<extension id="org.eclipse.cdt.core.GASErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>

					<extension id="org.eclipse.cdt.core.GLDErrorParser" point="org.eclipse.cdt.core.ErrorParser"/>

					<extension id="org.eclipse.cdt.core.ELF" point="org.eclipse.cdt.core.BinaryParser"/>

				</extensions>

			</storageModule>

			<storageModule moduleId="cdtBuildSystem" version="4.0.0">

				<configuration buildProperties="" description="" id="cdt.managedbuild.toolchain.gnu.base.2134791445" name="Default" parent="org.eclipse.cdt.build.core.emptycfg">

					<folderInfo id="cdt.managedbuild.toolchain.gnu.base.2134791445.1799170915" name="/" resourcePath="">

						<toolChain id="cdt.managedbuild.toolchain.gnu.base.1762402759" name="cdt.managedbuild.toolchain.gnu.base" superClass="cdt.managedbuild.toolchain.gnu.base">

							<targetPlatform archList="all" binaryParser="org.eclipse.cdt.core.ELF" id="cdt.managedbuild.target.gnu.platform.base.840154721" name="Debug Platform" osList="linux,hpux,aix,qnx" superClass="cdt.managedbuild.target.gnu.platform.base"/>

							<builder id="cdt.managedbuild.target.gnu.builder.base.573876641" keepEnvironmentInBuildfile="false" managedBuildOn="false" name="Gnu Make Builder" superClass="cdt.managedbuild.target.gnu.builder.base"/>

							<tool id="cdt.managedbuild.tool.gnu.archiver.base.958650307" name="GCC Archiver" superClass="cdt.managedbuild.tool.gnu.archiver.base"/>

							<tool id="cdt.managedbuild.tool.gnu.cpp.compiler.base.1237330740" name="GCC C++ Compiler" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.base">

								<inputType id="cdt.managedbuild.tool.gnu.cpp.compiler.input.1856262209" superClass="cdt.managedbuild.tool.gnu.cpp.compiler.input"/>

							</tool>

							<tool id="cdt.managedbuild.tool.gnu.c.compiler.base.315517693" name="GCC C Compiler" superClass="cdt.managedbuild.tool.gnu.c.compiler.base">

								<inputType id="cdt.managedbuild.tool.gnu.c.compiler.input.950045328" superClass="cdt.managedbuild.tool.gnu.c.compiler.input"/>

							</tool>

							<tool id="cdt.managedbuild.tool.gnu.c.linker.base.1786292703" name="GCC C Linker" superClass="cdt.managedbuild.tool.gnu.c.linker.base"/>

							<tool id="cdt.managedbuild.tool.gnu.cpp.linker.base.1133414639" name="GCC C++ Linker" superClass="cdt.managedbuild.tool.gnu.cpp.linker.base">

								<inputType id="cdt.managedbuild.tool.gnu.cpp.linker.input.692614544" superClass="cdt.managedbuild.tool.gnu.cpp.linker.input">

									<additionalInput kind="additionalinputdependency" paths="$(USER_OBJS)"/>

									<additionalInput kind="additionalinput" paths="$(LIBS)"/>

								</inputType>

							</tool>

							<tool id="cdt.managedbuild.tool.gnu.assembler.base.336757143" name="GCC Assembler" superClass="cdt.managedbuild.tool.gnu.assembler.base">

								<inputType id="cdt.managedbuild.tool.gnu.assembler.input.1329383797" superClass="cdt.managedbuild.tool.gnu.assembler.input"/>

							</tool>

						</toolChain>

					</folderInfo>

				</configuration>

			</storageModule>

			<storageModule moduleId="org.eclipse.cdt.core.externalSettings"/>

		</cconfiguration>

	</storageModule>

	<storageModule moduleId="cdtBuildSystem" version="4.0.0">

		<project id="tnl.null.219466708" name="tnl"/>

	</storageModule>

	<storageModule moduleId="scannerConfiguration">

		<autodiscovery enabled="true" problemReportingEnabled="true" selectedProfileId=""/>

	</storageModule>

	<storageModule moduleId="org.eclipse.cdt.core.LanguageSettingsProviders"/>

</cproject>

.gitignore

+4 −40
Original line number Diff line number Diff line 


# /

/build

/missing

/Makefile.in

/ltmain.sh

/install-sh

/depcomp

/configure

/config.*

/aclocal.m4

/m4

/autom4te.cache

.settings

/nbproject

/Debug

/Release

.settings



.settings



# /src/

/src/Makefile.in



# /src/core/

/src/core/Makefile.in



# /src/debug/

/src/debug/Makefile.in



# /src/diff/

/src/diff/Makefile.in



# /src/matrix/

/src/matrix/*.in



# /tools/

/tools/Makefile.in



# /tools/share/

/tools/share/Makefile.in



# /tools/src/

/tools/src/Makefile.in

/Testing

/CMakeLists.txt.user

/doc/_build

/Build

CMakeLists.txt

+62 −42
Original line number Diff line number Diff line
@@ -12,7 +12,7 @@ 
# Vladimir Klement

# Jakub Klinkovsky



cmake_minimum_required( VERSION 2.8.10 )

cmake_minimum_required( VERSION 3.4 )



project( tnl )
@@ -33,22 +33,28 @@ if( CMAKE_BUILD_TYPE STREQUAL "Debug") 
    set( LIBRARY_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/Debug/lib )

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

    set( debugExt -dbg )

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

    #AddCompilerFlag( "-g" )

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( LIBRARY_OUTPUT_PATH ${PROJECT_SOURCE_DIR}/Release/lib)

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

    #OptimizeForArchitecture()

    AddCompilerFlag( "-O3 -march=native -DNDEBUG -g" )

endif()



# set Debug/Release options

set( CMAKE_CXX_FLAGS "-std=c++11" )

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" )

# 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 "" )



get_filename_component( CXX_COMPILER_NAME ${CMAKE_CXX_COMPILER} NAME )

if( CXX_COMPILER_NAME MATCHES "icpc" )

   message( "Intel compiler detected..."    )

   AddCompilerFlag( "-DHAVE_ICPC" )

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

endif()



#####
@@ -102,18 +108,29 @@ if( WITH_CUDA STREQUAL "yes" ) 
                set( CUDA_ARCH -gencode arch=compute_${WITH_CUDA_ARCH},code=sm_${WITH_CUDA_ARCH} )

            endif()

        endif()

        set( CUDA_ADD_EXECUTABLE_OPTIONS ${CUDA_ARCH} )

        set( CUDA_ADD_LIBRARY_OPTIONS ${CUDA_ARCH} -shared )

        set( CUDA_LINKER_OPTIONS "-arch sm_20 -shared" )

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

        # 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

        #

        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
@@ -133,7 +150,6 @@ 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                   

                      ${CUDA_INCLUDE_DIR}
@@ -148,15 +164,9 @@ if( WITH_CUDA STREQUAL "yes" ) 
               set( CUSPARSE_LIBRARY "${CUDA_cusparse_LIBRARY}" )

           endif()            

        endif( NOT WITH_CUSPARSE STREQUAL "no" )        

   

    #else( CUDA_FOUND )

    #  AddCompilerFlag( "-std=c++11" )         

    endif( CUDA_FOUND )

#else( WITH_CUDA STREQUAL "yes" )

   #AddCompilerFlag( "-std=gnu++0x -ftree-vectorizer-verbose=1" )       

   #AddCompilerFlag( "-std=c++11" )       

endif( WITH_CUDA STREQUAL "yes" )

AddCompilerFlag( "-std=c++11" )       





####

# Check for OpenMP
@@ -318,7 +328,6 @@ endif( WITH_TESTS STREQUAL "yes" ) 
#

if( WITH_TEMPLATE_INSTANTIATION STREQUAL "yes" )

   AddCompilerFlag( "-DTEMPLATE_EXPLICIT_INSTANTIATION " )

endif()   



   if( INSTANTIATE_INT STREQUAL "yes" )

      AddCompilerFlag( "-DINSTANTIATE_INT " )
@@ -339,6 +348,7 @@ endif() 
   if( INSTANTIATE_LONG_DOUBLE STREQUAL "yes" )

      AddCompilerFlag( "-DINSTANTIATE_LONG_DOUBLE " )

   endif()

endif()



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

set( LD_TEST_FLAGS "-lgcov -coverage" )
@@ -388,3 +398,13 @@ set(CPACK_SOURCE_STRIP_FILES "Release") 


#set(CPACK_PACKAGE_EXECUTABLES "MyExecutable" "My Executable")

INCLUDE( CPack )



# Print compiler options

message( "-- Compiler options:" )

message( "   CMAKE_CXX_FLAGS = ${CMAKE_CXX_FLAGS}" )

message( "   CMAKE_CXX_FLAGS_DEBUG = ${CMAKE_CXX_FLAGS_DEBUG}" )

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( "   CUDA_NVCC_FLAGS = ${CUDA_NVCC_FLAGS}" )

TODO

+2 −0
Original line number Diff line number Diff line
@@ -10,6 +10,8 @@ TODO: 
 - data by se na hostu preskupila do souvisleho bloku dat a ten se prenesl najednou





TODO:



TODO:

 - zavest namespaces

build

+0 −3
Original line number Diff line number Diff line
@@ -6,7 +6,6 @@ WITH_CUDA="yes" 
WITH_TESTS="yes"



WITH_CUDA_ARCH="auto"

WITH_CUBLAS="no"

WITH_TEMPLATE_INSTANTIATION="yes"

INSTANTIATE_LONG_INT="no"

INSTANTIATE_INT="yes"
@@ -28,7 +27,6 @@ do 
        --build=*                        ) BUILD="${option#*=}" ;;

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

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

        --with-cublas=*                  ) WITH_CUBLAS="${option#*=}" ;;

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

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

        --instantiate-long-int=*         ) INSTANTIATE_LONG_INT="${option#*=}" ;;
@@ -82,7 +80,6 @@ ${CMAKE} ${ROOT_DIR} \ 
         -DCMAKE_INSTALL_PREFIX=${PREFIX} \

         -DWITH_CUDA=${WITH_CUDA} \

         -DWITH_CUDA_ARCH=${WITH_CUDA_ARCH} \

         -DWITH_CUBLAS=${WITH_CUBLAS} \

         -DWITH_TESTS=${WITH_TESTS} \

         -DPETSC_DIR=${PETSC_DIR} \

         -DDCMTK_DIR=${DCMTK_DIR} \