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  • mosaic/software/parallel-computing/openfpm/openfpm_io
  • argupta/openfpm_io
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with 55 additions and 1220 deletions
install_VCDEVEL.sh deleted 100755 → 0
View file @ a2cb5096
#! /bin/bash
# check if the directory $1/VCDEVEL exist
if [ -d "$1/VCDEVEL" -a -f "$1/VCDEVEL/include/Vc/Vc" ]; then
echo "VCDEVEL already installed"
exit 0
fi
wget http://ppmcore.mpi-cbg.de/upload/Vc-1.4.1.tar.gz
#rm -rf Vc
tar -xf Vc-1.4.1.tar.gz
cd Vc-1.4.1
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX:PATH=$1/VCDEVEL -DCMAKE_C_COMPILER=$3 -DCMAKE_CXX_COMPILER=$4 ..
make
make install
run.sh deleted 100755 → 0
View file @ a2cb5096
#! /bin/bash
hostname=$(hostname)
branch=$3
# Make a directory in /tmp/openfpm_data
cd "openfpm_io"
echo "CHECKING MACHINE"
if [ x"$hostname" == x"cifarm-centos-node.mpi-cbg.de" ]; then
echo "CENTOS"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/HDF5/lib"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/BOOST/lib"
fi
if [ x"$hostname" == x"cifarm-ubuntu-node" ]; then
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/HDF5/lib"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/BOOST/lib"
fi
if [ x"$hostname" == x"cifarm-mac-node.mpi-cbg.de" ]; then
echo "MACOS X"
export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/HDF5/lib"
export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/BOOST/lib"
fi
pwd
./build/src/io
script/discover_os deleted 100755 → 0
View file @ a2cb5096
#! /bin/bash
function discover_os() {
platform=unknown
if [[ "$OSTYPE" == "linux-gnu" ]]; then
echo -e "We are on\033[1;34m LINUX \033[0m"
platform=linux
elif [[ "$OSTYPE" == "linux" ]]; then
echo -e "We are on\033[1;34m LINUX \033[0m"
platform=linux
elif [[ "$OSTYPE" == "darwin"* ]]; then
echo -e "We are on\033[1;34m MAC OSX \033[0m"
platform=osx
elif [[ "$OSTYPE" == "cygwin" ]]; then
echo -e "We are on\033[1;34m CYGWIN \033[0m"
platform=cygwin
elif [[ "$OSTYPE" == "msys" ]]; then
echo -e "We are on\033[1;34m Microsoft Window \033[0m"
echo "This platform is not supported"
exit 1
elif [[ "$OSTYPE" == "win32" ]]; then
echo -e "We are on\033[1;34m Microsoft Window \033[0m"
echo "This platform is not supported"
exit 1
elif [[ "$OSTYPE" == "freebsd"* ]]; then
echo -e "We are on\033[1;34m FREEBSD \033[0m"
echo "This platform is not supported"
exit 1
else
echo -e "We are on an\033[1;34m unknown OS \033[0m"
echo "This platform is not supported"
exit 1
fi
}
script/download_MPI.sh deleted 100755 → 0
View file @ a2cb5096
#!/bin/bash
# check if the directory $1/MPI exist
rm -rf openmpi-4.1.1
rm openmpi-4.1.1.tar.gz
wget http://ppmcore.mpi-cbg.de/upload/openmpi-4.1.1.tar.gz
tar -xvf openmpi-4.1.1.tar.gz
src/CMakeLists.txt
View file @ 26f879bd
...@@ -7,50 +7,45 @@ if(NOT CUDA_ON_BACKEND STREQUAL "None") ...@@ -7,50 +7,45 @@ if(NOT CUDA_ON_BACKEND STREQUAL "None")
endif() endif()
if ( CUDA_ON_BACKEND STREQUAL "HIP" AND HIP_FOUND ) if ( CUDA_ON_BACKEND STREQUAL "HIP" AND HIP_FOUND )
list(APPEND HIP_HIPCC_FLAGS ${CMAKE_CXX_FLAGS_DEBUG})
list(APPEND HIP_HIPCC_FLAGS ${CMAKE_CXX_FLAGS_DEBUG}) if (CMAKE_BUILD_TYPE STREQUAL "Debug")
list(APPEND HIP_HIPCC_FLAGS -O0)
if (CMAKE_BUILD_TYPE STREQUAL "Debug") endif()
list(APPEND HIP_HIPCC_FLAGS -O0)
endif()
# set(CMAKE_CXX_COMPILER ${HIP_HIPCC_EXECUTABLE}) #set(CMAKE_CXX_COMPILER ${HIP_HIPCC_EXECUTABLE})
list(APPEND HIP_HIPCC_FLAGS -D__NVCC__ -D__HIP__ -DCUDART_VERSION=11000 -D__CUDACC__ -D__CUDACC_VER_MAJOR__=11 -D__CUDACC_VER_MINOR__=0 -D__CUDACC_VER_BUILD__=0) list(APPEND HIP_HIPCC_FLAGS -D__NVCC__ -D__HIP__ -DCUDART_VERSION=11000 -D__CUDACC__ -D__CUDACC_VER_MAJOR__=11 -D__CUDACC_VER_MINOR__=0 -D__CUDACC_VER_BUILD__=0)
set_source_files_properties(${CUDA_SOURCES} PROPERTIES LANGUAGE CXX) set_source_files_properties(${CUDA_SOURCES} PROPERTIES LANGUAGE CXX)
hip_add_executable(io main.cpp
MetaParser/MetaParser_unit_test.cpp
${CUDA_SOURCES}
ObjReader/ObjReader_unit_test.cpp
CSVReader/tests/CSVReader_unit_test.cpp)
hip_add_executable(io main.cpp
MetaParser/MetaParser_unit_test.cpp
${CUDA_SOURCES}
ObjReader/ObjReader_unit_test.cpp
CSVReader/tests/CSVReader_unit_test.cpp)
else() else()
add_executable(io main.cpp add_executable(io main.cpp
MetaParser/MetaParser_unit_test.cpp MetaParser/MetaParser_unit_test.cpp
${CUDA_SOURCES} ${CUDA_SOURCES}
ObjReader/ObjReader_unit_test.cpp ObjReader/ObjReader_unit_test.cpp
CSVReader/tests/CSVReader_unit_test.cpp) CSVReader/tests/CSVReader_unit_test.cpp)
set_property(TARGET io PROPERTY CUDA_ARCHITECTURES OFF) set_property(TARGET io PROPERTY CUDA_ARCHITECTURES OFF)
endif() endif()
add_dependencies(io ofpmmemory) add_dependencies(io ofpmmemory)
add_dependencies(io vcluster) add_dependencies(io vcluster)
if ( CMAKE_COMPILER_IS_GNUCC ) if ( CMAKE_COMPILER_IS_GNUCC )
target_compile_options(io PRIVATE "-Wno-deprecated-declarations") target_compile_options(io PRIVATE "-Wno-deprecated-declarations")
if (TEST_COVERAGE) if (TEST_COVERAGE)
target_compile_options(io PRIVATE $<$<COMPILE_LANGUAGE:CXX>: -fprofile-arcs -ftest-coverage>) target_compile_options(io PRIVATE $<$<COMPILE_LANGUAGE:CXX>: -fprofile-arcs -ftest-coverage>)
endif() endif()
endif() endif()
if (CMAKE_CUDA_COMPILER_ID STREQUAL "Clang") if (CMAKE_CUDA_COMPILER_ID STREQUAL "Clang")
add_definitions(-D__STRICT_ANSI__) add_definitions(-D__STRICT_ANSI__)
endif() endif()
########################### ###########################
...@@ -58,12 +53,12 @@ endif() ...@@ -58,12 +53,12 @@ endif()
if (CUDA_FOUND) if (CUDA_FOUND)
target_include_directories (io PUBLIC ${MPI_C_INCLUDE_DIRS}) target_include_directories (io PUBLIC ${MPI_C_INCLUDE_DIRS})
if( CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0 ) if( CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0 )
add_compile_options( "-fabi-version=6" ) add_compile_options( "-fabi-version=6" )
endif() endif()
if (TEST_COVERAGE) if (TEST_COVERAGE)
target_compile_options(io PRIVATE $<$<COMPILE_LANGUAGE:CUDA>: -Xcompiler "-fprofile-arcs -ftest-coverage" >) target_compile_options(io PRIVATE $<$<COMPILE_LANGUAGE:CUDA>: -Xcompiler "-fprofile-arcs -ftest-coverage" >)
endif() endif()
endif() endif()
...@@ -73,11 +68,10 @@ target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_ ...@@ -73,11 +68,10 @@ target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_
target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_vcluster/src/) target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_vcluster/src/)
target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_data/src/) target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../openfpm_data/src/)
target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../src/) target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../../src/)
target_include_directories (io PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/config) target_include_directories (io PUBLIC ${CMAKE_BINARY_DIR}/config)
target_include_directories (io PUBLIC ${HDF5_ROOT}/include) target_include_directories (io PUBLIC ${HDF5_ROOT}/include)
target_include_directories (io PUBLIC ${TINYOBJLOADER_INCLUDE_DIRS} ) target_include_directories (io PUBLIC ${TINYOBJLOADER_INCLUDE_DIRS} )
target_include_directories (io PUBLIC ${Boost_INCLUDE_DIRS}) target_include_directories (io PUBLIC ${Boost_INCLUDE_DIRS})
target_include_directories (io PUBLIC ${OPENFPM_PDATA_DIR}/src)
target_include_directories (io PUBLIC ${ALPAKA_ROOT}/include) target_include_directories (io PUBLIC ${ALPAKA_ROOT}/include)
if (PETSC_FOUND) if (PETSC_FOUND)
...@@ -89,12 +83,13 @@ target_link_libraries(io ${HDF5_LIBRARIES}) ...@@ -89,12 +83,13 @@ target_link_libraries(io ${HDF5_LIBRARIES})
target_link_libraries(io ${TINYOBJLOADER_LIBRARIES} ) target_link_libraries(io ${TINYOBJLOADER_LIBRARIES} )
target_link_libraries(io vcluster) target_link_libraries(io vcluster)
target_link_libraries(io ofpmmemory) target_link_libraries(io ofpmmemory)
if (OPENMP_FOUND) if (OPENMP_FOUND)
target_link_libraries(io OpenMP::OpenMP_CXX) target_link_libraries(io OpenMP::OpenMP_CXX)
endif() endif()
if (PETSC_FOUND) if (PETSC_FOUND)
target_link_libraries(io ${PETSC_LIBRARIES}) target_link_libraries(io ${PETSC_LIBRARIES})
endif() endif()
# Request that particles be built with -std=c++11 # Request that particles be built with -std=c++11
...@@ -103,25 +98,26 @@ endif() ...@@ -103,25 +98,26 @@ endif()
target_compile_features(io PUBLIC cxx_std_11) target_compile_features(io PUBLIC cxx_std_11)
target_link_libraries(io ${MPI_C_LIBRARIES}) target_link_libraries(io ${MPI_C_LIBRARIES})
target_link_libraries(io ${MPI_CXX_LIBRARIES}) target_link_libraries(io ${MPI_CXX_LIBRARIES})
if (TEST_COVERAGE) if (TEST_COVERAGE)
target_link_libraries(io -lgcov) target_link_libraries(io -lgcov)
endif() endif()
install(FILES RawReader/RawReader.hpp install(FILES RawReader/RawReader.hpp
RawReader/RawReader_unit_tests.hpp RawReader/RawReader_unit_tests.hpp
DESTINATION openfpm_io/include/RawReader DESTINATION openfpm_io/include/RawReader
COMPONENT OpenFPM) COMPONENT OpenFPM)
install(FILES CSVWriter/csv_multiarray.hpp install(FILES CSVWriter/csv_multiarray.hpp
CSVWriter/CSVWriter.hpp CSVWriter/CSVWriter.hpp
CSVWriter/is_csv_writable.hpp CSVWriter/is_csv_writable.hpp
DESTINATION openfpm_io/include/CSVWriter/ DESTINATION openfpm_io/include/CSVWriter/
COMPONENT OpenFPM) COMPONENT OpenFPM)
install(FILES CSVReader/CSVReader.hpp install(FILES CSVReader/CSVReader.hpp
DESTINATION openfpm_io/include/CSVReader/ DESTINATION openfpm_io/include/CSVReader/
COMPONENT OpenFPM) COMPONENT OpenFPM)
install(FILES GraphMLWriter/GraphMLWriter.hpp install(FILES GraphMLWriter/GraphMLWriter.hpp
DESTINATION openfpm_io/include/GraphMLWriter DESTINATION openfpm_io/include/GraphMLWriter
COMPONENT OpenFPM) COMPONENT OpenFPM)
...@@ -131,15 +127,15 @@ install(FILES util/util.hpp util/GBoxes.hpp ...@@ -131,15 +127,15 @@ install(FILES util/util.hpp util/GBoxes.hpp
COMPONENT OpenFPM) COMPONENT OpenFPM)
install(FILES VTKWriter/VTKWriter.hpp install(FILES VTKWriter/VTKWriter.hpp
VTKWriter/byteswap_portable.hpp VTKWriter/byteswap_portable.hpp
VTKWriter/VTKWriter_dist_graph.hpp VTKWriter/VTKWriter_dist_graph.hpp
VTKWriter/VTKWriter_graph.hpp VTKWriter/VTKWriter_graph.hpp
VTKWriter/VTKWriter_point_set.hpp VTKWriter/VTKWriter_point_set.hpp
VTKWriter/VTKWriter_grids.hpp VTKWriter/VTKWriter_grids.hpp
VTKWriter/VTKWriter_grids_st.hpp VTKWriter/VTKWriter_grids_st.hpp
VTKWriter/VTKWriter_grids_util.hpp VTKWriter/VTKWriter_grids_util.hpp
VTKWriter/VTKWriter_vector_box.hpp VTKWriter/VTKWriter_vector_box.hpp
VTKWriter/is_vtk_writable.hpp VTKWriter/is_vtk_writable.hpp
DESTINATION openfpm_io/include/VTKWriter/ DESTINATION openfpm_io/include/VTKWriter/
COMPONENT OpenFPM) COMPONENT OpenFPM)
...@@ -148,11 +144,11 @@ install(FILES MetaParser/MetaParser.hpp ...@@ -148,11 +144,11 @@ install(FILES MetaParser/MetaParser.hpp
COMPONENT OpenFPM) COMPONENT OpenFPM)
install(FILES HDF5_wr/HDF5_wr.hpp install(FILES HDF5_wr/HDF5_wr.hpp
HDF5_wr/HDF5_writer.hpp HDF5_wr/HDF5_writer.hpp
HDF5_wr/HDF5_writer_vd.hpp HDF5_wr/HDF5_writer_vd.hpp
HDF5_wr/HDF5_writer_gd.hpp HDF5_wr/HDF5_writer_gd.hpp
HDF5_wr/HDF5_reader_gd.hpp HDF5_wr/HDF5_reader_gd.hpp
HDF5_wr/HDF5_reader.hpp HDF5_wr/HDF5_reader.hpp
HDF5_wr/HDF5_reader_vd.hpp HDF5_wr/HDF5_reader_vd.hpp
DESTINATION openfpm_io/include/HDF5_wr DESTINATION openfpm_io/include/HDF5_wr
COMPONENT OpenFPM) COMPONENT OpenFPM)
...@@ -169,21 +165,3 @@ install(FILES Plot/GoogleChart.hpp Plot/util.hpp ...@@ -169,21 +165,3 @@ install(FILES Plot/GoogleChart.hpp Plot/util.hpp
DESTINATION openfpm_io/include/Plot DESTINATION openfpm_io/include/Plot
COMPONENT OpenFPM) COMPONENT OpenFPM)
#if(BUILD_TESTING)
# add_executable(particle_test test.cu)
# set_target_properties(particle_test PROPERTIES CUDA_SEPARABLE_COMPILATION ON)
# target_link_libraries(particle_test PRIVATE particles)
# add_test(NAME particles_10k COMMAND particle_test 10000 )
# add_test(NAME particles_256k COMMAND particle_test 256000 )
# if(APPLE)
# We need to add the default path to the driver (libcuda.dylib) as an rpath,
# so that the static cuda runtime can find it at runtime.
# set_property(TARGET particle_test PROPERTY BUILD_RPATH ${CMAKE_CUDA_IMPLICIT_LINK_DIRECTORIES})
# endif()
#endif()
src/CSVReader/tests/CSVReader_unit_test.cpp
View file @ 26f879bd
...@@ -8,11 +8,7 @@ ...@@ -8,11 +8,7 @@
BOOST_AUTO_TEST_SUITE(CSVReaderTestSuite) BOOST_AUTO_TEST_SUITE(CSVReaderTestSuite)
BOOST_AUTO_TEST_CASE(csv_reader_int_test) BOOST_AUTO_TEST_CASE(csv_reader_int_test)
{ {
#ifdef OPENFPM_PDATA
std::string csv_file = std::string("openfpm_io/test_data/integer.csv");
#else
std::string csv_file = std::string("test_data/integer.csv"); std::string csv_file = std::string("test_data/integer.csv");
#endif
// Read csv file into vector while linearizing // Read csv file into vector while linearizing
openfpm::vector<int> v_lin; // Vector to which csv file will be read to openfpm::vector<int> v_lin; // Vector to which csv file will be read to
size_t m, n; // Number of rows m and columns n size_t m, n; // Number of rows m and columns n
...@@ -34,11 +30,7 @@ BOOST_AUTO_TEST_CASE(csv_reader_int_test) ...@@ -34,11 +30,7 @@ BOOST_AUTO_TEST_CASE(csv_reader_int_test)
BOOST_AUTO_TEST_CASE(csv_reader_char_test) BOOST_AUTO_TEST_CASE(csv_reader_char_test)
{ {
#ifdef OPENFPM_PDATA
std::string csv_file = std::string("openfpm_io/test_data/char.csv");
#else
std::string csv_file = std::string("test_data/char.csv"); std::string csv_file = std::string("test_data/char.csv");
#endif
// Read csv file into vector while linearizing // Read csv file into vector while linearizing
openfpm::vector<std::string> v_lin; // Vector to which csv file will be read to openfpm::vector<std::string> v_lin; // Vector to which csv file will be read to
size_t m, n; // Number of rows m and columns n size_t m, n; // Number of rows m and columns n
......
src/CSVWriter/CSVWriter_unit_tests.hpp
View file @ 26f879bd
...@@ -14,20 +14,9 @@ BOOST_AUTO_TEST_CASE( csv_writer_particles ) ...@@ -14,20 +14,9 @@ BOOST_AUTO_TEST_CASE( csv_writer_particles )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
if (v_cl.rank() != 0) {return;}
std::string c2 = std::string("openfpm_io/test_data/csv_out_test.csv");
std::string c3 = std::string("openfpm_io/test_data/csv_out_unk_test.csv");
#else
std::string c2 = std::string("test_data/csv_out_test.csv"); std::string c2 = std::string("test_data/csv_out_test.csv");
std::string c3 = std::string("test_data/csv_out_unk_test.csv"); std::string c3 = std::string("test_data/csv_out_unk_test.csv");
#endif
{ {
// Allocate a property vector // Allocate a property vector
auto v_prp = allocate_openfpm_prp(16); auto v_prp = allocate_openfpm_prp(16);
......
src/GraphMLWriter/GraphMLWriter_unit_tests.hpp
View file @ 26f879bd
...@@ -87,19 +87,9 @@ BOOST_AUTO_TEST_CASE( graphml_writer_use) ...@@ -87,19 +87,9 @@ BOOST_AUTO_TEST_CASE( graphml_writer_use)
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
if (v_cl.rank() != 0) {return;}
std::string c2 = std::string("openfpm_io/test_data/test_graph2_test.graphml");
std::string c3 = std::string("openfpm_io/test_data/test_graph_test.graphml");
#else
std::string c2 = std::string("test_data/test_graph2_test.graphml"); std::string c2 = std::string("test_data/test_graph2_test.graphml");
std::string c3 = std::string("test_data/test_graph_test.graphml"); std::string c3 = std::string("test_data/test_graph_test.graphml");
#endif
Graph_CSR<ne_cp,ne_cp> g_csr2; Graph_CSR<ne_cp,ne_cp> g_csr2;
// Add 4 vertex and connect // Add 4 vertex and connect
......
src/HDF5_wr/HDF5_writer_unit_tests.hpp
View file @ 26f879bd
...@@ -76,16 +76,8 @@ BOOST_AUTO_TEST_CASE( vector_dist_hdf5_load_test ) ...@@ -76,16 +76,8 @@ BOOST_AUTO_TEST_CASE( vector_dist_hdf5_load_test )
{ {
Vcluster<> & v_cl = create_vcluster(); Vcluster<> & v_cl = create_vcluster();
#ifdef OPENFPM_PDATA
std::string c2 = std::string("openfpm_io/test_data/vector_dist_24.h5");
#else
std::string c2 = std::string("test_data/vector_dist_24.h5"); std::string c2 = std::string("test_data/vector_dist_24.h5");
#endif
openfpm::vector<Point<3,float>> vpos; openfpm::vector<Point<3,float>> vpos;
openfpm::vector<aggregate<float[dim]>> vprp; openfpm::vector<aggregate<float[dim]>> vprp;
......
src/Plot/Plot_unit_tests.hpp
View file @ 26f879bd
...@@ -21,16 +21,8 @@ BOOST_AUTO_TEST_CASE( google_chart_bar_string ) ...@@ -21,16 +21,8 @@ BOOST_AUTO_TEST_CASE( google_chart_bar_string )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
std::string c2 = std::string("openfpm_io/test_data/gc_out_sc_test.html");
#else
std::string c2 = std::string("test_data/gc_out_sc_test.html"); std::string c2 = std::string("test_data/gc_out_sc_test.html");
#endif
//! [Producing an Histogram graph] //! [Producing an Histogram graph]
openfpm::vector<std::string> x; openfpm::vector<std::string> x;
...@@ -89,16 +81,8 @@ BOOST_AUTO_TEST_CASE( google_chart ) ...@@ -89,16 +81,8 @@ BOOST_AUTO_TEST_CASE( google_chart )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
std::string c2 = std::string("openfpm_io/test_data/gc_out_test.html");
#else
std::string c2 = std::string("test_data/gc_out_test.html"); std::string c2 = std::string("test_data/gc_out_test.html");
#endif
//! [Producing an Histogram graph] //! [Producing an Histogram graph]
openfpm::vector<std::string> x; openfpm::vector<std::string> x;
...@@ -155,16 +139,8 @@ BOOST_AUTO_TEST_CASE( google_chart2 ) ...@@ -155,16 +139,8 @@ BOOST_AUTO_TEST_CASE( google_chart2 )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
std::string c2 = std::string("openfpm_io/test_data/gc_out2_test.html");
#else
std::string c2 = std::string("test_data/gc_out2_test.html"); std::string c2 = std::string("test_data/gc_out2_test.html");
#endif
openfpm::vector<std::string> x; openfpm::vector<std::string> x;
openfpm::vector<openfpm::vector<float>> y; openfpm::vector<openfpm::vector<float>> y;
openfpm::vector<std::string> yn; openfpm::vector<std::string> yn;
...@@ -214,16 +190,8 @@ BOOST_AUTO_TEST_CASE( google_chart3 ) ...@@ -214,16 +190,8 @@ BOOST_AUTO_TEST_CASE( google_chart3 )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
std::string c2 = std::string("openfpm_io/test_data/gc_out3_test.html");
#else
std::string c2 = std::string("test_data/gc_out3_test.html"); std::string c2 = std::string("test_data/gc_out3_test.html");
#endif
openfpm::vector<std::string> x; openfpm::vector<std::string> x;
openfpm::vector<openfpm::vector<float>> y; openfpm::vector<openfpm::vector<float>> y;
openfpm::vector<std::string> yn; openfpm::vector<std::string> yn;
...@@ -272,16 +240,8 @@ BOOST_AUTO_TEST_CASE( google_chart4 ) ...@@ -272,16 +240,8 @@ BOOST_AUTO_TEST_CASE( google_chart4 )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
std::string c2 = std::string("openfpm_io/test_data/gc_out4_test.html");
#else
std::string c2 = std::string("test_data/gc_out4_test.html"); std::string c2 = std::string("test_data/gc_out4_test.html");
#endif
openfpm::vector<std::string> x; openfpm::vector<std::string> x;
openfpm::vector<openfpm::vector<float>> y; openfpm::vector<openfpm::vector<float>> y;
openfpm::vector<std::string> yn; openfpm::vector<std::string> yn;
...@@ -323,16 +283,8 @@ BOOST_AUTO_TEST_CASE( google_chart5 ) ...@@ -323,16 +283,8 @@ BOOST_AUTO_TEST_CASE( google_chart5 )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
std::string c2 = std::string("openfpm_io/test_data/gc_out5_test.html");
#else
std::string c2 = std::string("test_data/gc_out5_test.html"); std::string c2 = std::string("test_data/gc_out5_test.html");
#endif
openfpm::vector<std::string> x; openfpm::vector<std::string> x;
openfpm::vector<openfpm::vector<float>> y; openfpm::vector<openfpm::vector<float>> y;
...@@ -366,16 +318,8 @@ BOOST_AUTO_TEST_CASE( google_chart6 ) ...@@ -366,16 +318,8 @@ BOOST_AUTO_TEST_CASE( google_chart6 )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
std::string c2 = std::string("openfpm_io/test_data/gc_out6_test.html");
#else
std::string c2 = std::string("test_data/gc_out6_test.html"); std::string c2 = std::string("test_data/gc_out6_test.html");
#endif
openfpm::vector<openfpm::vector<float>> y; openfpm::vector<openfpm::vector<float>> y;
// Each colums can have multiple data-set // Each colums can have multiple data-set
...@@ -401,16 +345,8 @@ BOOST_AUTO_TEST_CASE( google_chart_with_inject_HTML ) ...@@ -401,16 +345,8 @@ BOOST_AUTO_TEST_CASE( google_chart_with_inject_HTML )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
std::string c2 = std::string("openfpm_io/test_data/gc_out7_test.html");
#else
std::string c2 = std::string("test_data/gc_out7_test.html"); std::string c2 = std::string("test_data/gc_out7_test.html");
#endif
//! [Producing a set of histograms graphs] //! [Producing a set of histograms graphs]
openfpm::vector<std::string> x; openfpm::vector<std::string> x;
...@@ -474,16 +410,8 @@ BOOST_AUTO_TEST_CASE( google_chart_number ) ...@@ -474,16 +410,8 @@ BOOST_AUTO_TEST_CASE( google_chart_number )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
std::string c2 = std::string("openfpm_io/test_data/gc_num_plot_test.html");
#else
std::string c2 = std::string("test_data/gc_num_plot_test.html"); std::string c2 = std::string("test_data/gc_num_plot_test.html");
#endif
//! [Producing a set of histograms graphs] //! [Producing a set of histograms graphs]
openfpm::vector<float> x; openfpm::vector<float> x;
...@@ -538,16 +466,8 @@ BOOST_AUTO_TEST_CASE( google_chart_number_lines_different_x ) ...@@ -538,16 +466,8 @@ BOOST_AUTO_TEST_CASE( google_chart_number_lines_different_x )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
std::string c2 = std::string("openfpm_io/test_data/gc_num_ydif_plot_test.html");
#else
std::string c2 = std::string("test_data/gc_num_ydif_plot_test.html"); std::string c2 = std::string("test_data/gc_num_ydif_plot_test.html");
#endif
//! [Producing a set of histograms graphs] //! [Producing a set of histograms graphs]
openfpm::vector<float> x1; openfpm::vector<float> x1;
...@@ -614,16 +534,8 @@ BOOST_AUTO_TEST_CASE( google_chart_linear_plot ) ...@@ -614,16 +534,8 @@ BOOST_AUTO_TEST_CASE( google_chart_linear_plot )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
std::string c2 = std::string("openfpm_io/test_data/gc_plot_out_test.html");
#else
std::string c2 = std::string("test_data/gc_plot_out_test.html"); std::string c2 = std::string("test_data/gc_plot_out_test.html");
#endif
//! [Producing lines graph with style] //! [Producing lines graph with style]
openfpm::vector<std::string> x; openfpm::vector<std::string> x;
...@@ -691,16 +603,8 @@ BOOST_AUTO_TEST_CASE( google_chart_linear_plot2 ) ...@@ -691,16 +603,8 @@ BOOST_AUTO_TEST_CASE( google_chart_linear_plot2 )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
std::string c2 = std::string("openfpm_io/test_data/gc_plot2_out_test.html");
#else
std::string c2 = std::string("test_data/gc_plot2_out_test.html"); std::string c2 = std::string("test_data/gc_plot2_out_test.html");
#endif
//! [Producing lines] //! [Producing lines]
openfpm::vector<std::string> x; openfpm::vector<std::string> x;
......
src/RawReader/RawReader_unit_tests.hpp
View file @ 26f879bd
...@@ -20,17 +20,8 @@ BOOST_AUTO_TEST_CASE( raw_reader_read_test ) ...@@ -20,17 +20,8 @@ BOOST_AUTO_TEST_CASE( raw_reader_read_test )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
if (v_cl.rank() != 0) {return;}
std::string c2 = std::string("openfpm_io/test_data/raw_read_sv_test.bin");
#else
std::string c2 = std::string("test_data/raw_read_sv_test.bin"); std::string c2 = std::string("test_data/raw_read_sv_test.bin");
#endif
grid_cpu<3,aggregate<float,float[3]>> read_bin_test; grid_cpu<3,aggregate<float,float[3]>> read_bin_test;
GridRawReader<3,aggregate<float,float[3]>,int> rr; GridRawReader<3,aggregate<float,float[3]>,int> rr;
......
src/VTKWriter/VTKWriter_unit_tests.hpp
View file @ 26f879bd
...@@ -223,17 +223,8 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph3D ) ...@@ -223,17 +223,8 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph3D )
// Write the VTK file // Write the VTK file
#ifdef OPENFPM_PDATA
if (v_cl.rank() != 0) {return;}
std::string c2 = std::string("openfpm_io/test_data/vtk_graph_v2_test.vtk");
#else
std::string c2 = std::string("test_data/vtk_graph_v2_test.vtk"); std::string c2 = std::string("test_data/vtk_graph_v2_test.vtk");
#endif
VTKWriter<Graph_CSR<vertex2,edge>,VTK_GRAPH> vtk(gr); VTKWriter<Graph_CSR<vertex2,edge>,VTK_GRAPH> vtk(gr);
vtk.write("vtk_graph_v2.vtk"); vtk.write("vtk_graph_v2.vtk");
...@@ -317,17 +308,8 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph3D_edge ) ...@@ -317,17 +308,8 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph3D_edge )
// Write the VTK file // Write the VTK file
#ifdef OPENFPM_PDATA
if (v_cl.rank() != 0) {return;}
std::string c2 = std::string("openfpm_io/test_data/vtk_graph_v4_test.vtk");
#else
std::string c2 = std::string("test_data/vtk_graph_v4_test.vtk"); std::string c2 = std::string("test_data/vtk_graph_v4_test.vtk");
#endif
VTKWriter<Graph_CSR<vertex2,vertex2>,VTK_GRAPH> vtk(gr); VTKWriter<Graph_CSR<vertex2,vertex2>,VTK_GRAPH> vtk(gr);
vtk.write("vtk_graph_v4.vtk"); vtk.write("vtk_graph_v4.vtk");
...@@ -420,17 +402,8 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph2D ) ...@@ -420,17 +402,8 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph2D )
// Write the VTK file // Write the VTK file
#ifdef OPENFPM_PDATA
if (v_cl.rank() != 0) {return;}
std::string c2 = std::string("openfpm_io/test_data/vtk_graph_v3_test.vtk");
#else
std::string c2 = std::string("test_data/vtk_graph_v3_test.vtk"); std::string c2 = std::string("test_data/vtk_graph_v3_test.vtk");
#endif
VTKWriter<Graph_CSR<vertex3,edge>,VTK_GRAPH> vtk(gr); VTKWriter<Graph_CSR<vertex3,edge>,VTK_GRAPH> vtk(gr);
vtk.write("vtk_graph_v3.vtk"); vtk.write("vtk_graph_v3.vtk");
...@@ -514,17 +487,8 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph) ...@@ -514,17 +487,8 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_graph)
gr.addEdge(7,3); gr.addEdge(7,3);
gr.addEdge(3,1); gr.addEdge(3,1);
#ifdef OPENFPM_PDATA
if (v_cl.rank() != 0) {return;}
std::string c2 = std::string("openfpm_io/test_data/vtk_graph_test.vtk");
#else
std::string c2 = std::string("test_data/vtk_graph_test.vtk"); std::string c2 = std::string("test_data/vtk_graph_test.vtk");
#endif
// Write the VTK file // Write the VTK file
VTKWriter<Graph_CSR<vertex,edge>,VTK_GRAPH> vtk(gr); VTKWriter<Graph_CSR<vertex,edge>,VTK_GRAPH> vtk(gr);
...@@ -543,21 +507,10 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_vector_box) ...@@ -543,21 +507,10 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_vector_box)
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
if (v_cl.rank() != 0) {return;}
std::string c2 = std::string("openfpm_io/test_data/vtk_box_test.vtk");
std::string c3 = std::string("openfpm_io/test_data/vtk_box_3D_test.vtk");
std::string c4 = std::string("openfpm_io/test_data/vtk_box_3D_2_test.vtk");
#else
std::string c2 = std::string("test_data/vtk_box_test.vtk"); std::string c2 = std::string("test_data/vtk_box_test.vtk");
std::string c3 = std::string("test_data/vtk_box_3D_test.vtk"); std::string c3 = std::string("test_data/vtk_box_3D_test.vtk");
std::string c4 = std::string("test_data/vtk_box_3D_2_test.vtk"); std::string c4 = std::string("test_data/vtk_box_3D_2_test.vtk");
#endif
// Create a vector of boxes // Create a vector of boxes
openfpm::vector<Box<2,float>> vb; openfpm::vector<Box<2,float>> vb;
...@@ -717,25 +670,12 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_grids) ...@@ -717,25 +670,12 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_grids)
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
{return;} {return;}
#ifdef OPENFPM_PDATA
if (v_cl.rank() != 0) {return;}
std::string c2 = std::string("openfpm_io/test_data/vtk_grids_test_1d.vtk");
std::string c3 = std::string("openfpm_io/test_data/vtk_grids_test.vtk");
std::string c4 = std::string("openfpm_io/test_data/vtk_grids_st_test.vtk");
std::string c5 = std::string("openfpm_io/test_data/vtk_grids_prp_test.vtk");
std::string c6 = std::string("openfpm_io/test_data/vtk_grids_test.vtk");
#else
std::string c2 = std::string("test_data/vtk_grids_test_1d.vtk"); std::string c2 = std::string("test_data/vtk_grids_test_1d.vtk");
std::string c3 = std::string("test_data/vtk_grids_test.vtk"); std::string c3 = std::string("test_data/vtk_grids_test.vtk");
std::string c4 = std::string("test_data/vtk_grids_st_test.vtk"); std::string c4 = std::string("test_data/vtk_grids_st_test.vtk");
std::string c5 = std::string("test_data/vtk_grids_prp_test.vtk"); std::string c5 = std::string("test_data/vtk_grids_prp_test.vtk");
std::string c6 = std::string("test_data/vtk_grids_test.vtk"); std::string c6 = std::string("test_data/vtk_grids_test.vtk");
#endif
{ {
// Create box grids // Create box grids
...@@ -1033,21 +973,10 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set ) ...@@ -1033,21 +973,10 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
if (v_cl.rank() != 0) {return;}
std::string c2 = std::string("openfpm_io/test_data/vtk_points_test.vtk");
std::string c3 = std::string("openfpm_io/test_data/vtk_points_pp_test.vtk");
std::string c4 = std::string("openfpm_io/test_data/vtk_points_pp_header_test.vtk");
#else
std::string c2 = std::string("test_data/vtk_points_test.vtk"); std::string c2 = std::string("test_data/vtk_points_test.vtk");
std::string c3 = std::string("test_data/vtk_points_pp_test.vtk"); std::string c3 = std::string("test_data/vtk_points_pp_test.vtk");
std::string c4 = std::string("test_data/vtk_points_pp_header_test.vtk"); std::string c4 = std::string("test_data/vtk_points_pp_header_test.vtk");
#endif
{ {
// Create 3 vectors with random particles // Create 3 vectors with random particles
openfpm::vector<Point<3,double>> v1ps; openfpm::vector<Point<3,double>> v1ps;
...@@ -1178,17 +1107,8 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_properties ) ...@@ -1178,17 +1107,8 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_properties )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
if (v_cl.rank() != 0) {return;}
std::string c2 = std::string("openfpm_io/test_data/vtk_points_with_prp_names_test.vtk");
#else
std::string c2 = std::string("test_data/vtk_points_with_prp_names_test.vtk"); std::string c2 = std::string("test_data/vtk_points_with_prp_names_test.vtk");
#endif
{ {
// Create 3 vectors with random particles // Create 3 vectors with random particles
openfpm::vector<Point<3,double>> v1ps; openfpm::vector<Point<3,double>> v1ps;
...@@ -1241,17 +1161,8 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_check_out_precision ) ...@@ -1241,17 +1161,8 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_check_out_precision )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
if (v_cl.rank() != 0) {return;}
std::string c2 = std::string("openfpm_io/test_data/vtk_points_with_prp_names_prec_check_test.vtk");
#else
std::string c2 = std::string("test_data/vtk_points_with_prp_names_prec_check_test.vtk"); std::string c2 = std::string("test_data/vtk_points_with_prp_names_prec_check_test.vtk");
#endif
{ {
// Create 3 vectors with random particles // Create 3 vectors with random particles
openfpm::vector<Point<3,double>> v1ps; openfpm::vector<Point<3,double>> v1ps;
...@@ -1300,23 +1211,11 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_binary ) ...@@ -1300,23 +1211,11 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set_binary )
if (v_cl.getProcessUnitID() != 0) if (v_cl.getProcessUnitID() != 0)
return; return;
#ifdef OPENFPM_PDATA
if (v_cl.rank() != 0) {return;}
std::string c2 = std::string("openfpm_io/test_data/vtk_points_bin_test.vtk");
std::string c3 = std::string("openfpm_io/test_data/vtk_points_pp_bin_test.vtk");
std::string c4 = std::string("openfpm_io/test_data/vtk_points_2d_bin_test.vtk");
std::string c5 = std::string("openfpm_io/test_data/vtk_points_2d_pp_bin_test.vtk");
#else
std::string c2 = std::string("test_data/vtk_points_bin_test.vtk"); std::string c2 = std::string("test_data/vtk_points_bin_test.vtk");
std::string c3 = std::string("test_data/vtk_points_pp_bin_test.vtk"); std::string c3 = std::string("test_data/vtk_points_pp_bin_test.vtk");
std::string c4 = std::string("test_data/vtk_points_2d_bin_test.vtk"); std::string c4 = std::string("test_data/vtk_points_2d_bin_test.vtk");
std::string c5 = std::string("test_data/vtk_points_2d_pp_bin_test.vtk"); std::string c5 = std::string("test_data/vtk_points_2d_pp_bin_test.vtk");
#endif
{ {
// Create 3 vectors with random particles // Create 3 vectors with random particles
openfpm::vector<Point<3,double>> v1ps; openfpm::vector<Point<3,double>> v1ps;
......
src/config/config_cmake.h.in deleted 100644 → 0
View file @ a2cb5096
/* Coverty scan */
${DEFINE_COVERTY_SCAN}
/* HIP GPU support */
${DEFINE_HIP_GPU}
/* HIP Cudify GPU support */
${DEFINE_CUDIFY_USE_HIP}
/* GPU support */
${DEFINE_CUDA_GPU}
/* Define CUDIFY backend */
${DEFINE_CUDIFY_BACKEND}
/* OpenMP support */
${DEFINE_HAVE_OPENMP}
/* HIP GPU support */
${DEFINE_HIP_GPU}
/* HIP Cudify GPU support */
${DEFINE_CUDIFY_USE_HIP}
/* Debug */
${DEFINE_DEBUG} /**/
/* Debug */
${DEFINE_DEBUG_MODE} /**/
/* Define to dummy `main' function (if any) required to link to the Fortran
libraries. */
${DEFINE_F77_DUMMY_MAIN}
/* Define if F77 and FC dummy `main' functions are identical. */
${DEFINE_FC_DUMMY_MAIN_EQ_F77}
/* Define if you have a BLAS library. */
${DEFINE_HAVE_BLAS}
/* define if the Boost library is available */
${DEFINE_HAVE_BOOST}
/* define if the Boost::IOStreams library is available */
${DEFINE_HAVE_BOOST_IOSTREAMS} /**/
/* define if the Boost::PROGRAM_OPTIONS library is available */
${DEFINE_HAVE_BOOST_PROGRAM_OPTIONS} /**/
/* define if the Boost::Unit_Test_Framework library is available */
${DEFINE_HAVE_BOOST_UNIT_TEST_FRAMEWORK} /**/
/* define if the Boost::Context library is available */
${DEFINE_HAVE_BOOST_CONTEXT} /**/
/* define if the Boost::Fiber library is available */
${DEFINE_HAVE_BOOST_FIBER} /**/
/* Have clock time */
${DEFINE_HAVE_CLOCK_GETTIME} /**/
/* Define to 1 if you have the <dlfcn.h> header file. */
${DEFINE_HAVE_DLFCN_H}
/* Define if you have EIGEN library. */
${DEFINE_HAVE_EIGEN}
/* Define to 1 if you have the <Eigen/Dense> header file. */
${DEFINE_HAVE_EIGEN_DENSE}
/* Define to 1 if you have the <Eigen/LU> header file. */
${DEFINE_HAVE_EIGEN_LU}
/* Defined if you have HDF5 support */
${DEFINE_HAVE_HDF5}
/* Define to 1 if you have the <inttypes.h> header file. */
${DEFINE_HAVE_INTTYPES_H}
/* Define if you have LAPACK library */
${DEFINE_HAVE_LAPACK}
/* Define if you have LIBHILBERT library */
${DEFINE_HAVE_LIBHILBERT}
/* Have quad math lib */
${DEFINE_HAVE_LIBQUADMATH}
/* Define to 1 if you have the <memory.h> header file. */
${DEFINE_HAVE_MEMORY_H}
/* Define if you have METIS library */
${DEFINE_HAVE_METIS}
/* MPI Enabled */
${DEFINE_HAVE_MPI}
/* We have OSX */
${DEFINE_HAVE_OSX}
/* Define if you have PARMETIS library */
${DEFINE_HAVE_PARMETIS}
/* Define if you have PETSC library */
${DEFINE_HAVE_PETSC}
/* Define to 1 if you have the <stdint.h> header file. */
${DEFINE_HAVE_STDINT_H}
/* Define to 1 if you have the <stdlib.h> header file. */
${DEFINE_HAVE_STDLIB_H}
/* Define to 1 if you have the <strings.h> header file. */
${DEFINE_HAVE_STRINGS_H}
/* Define to 1 if you have the <string.h> header file. */
${DEFINE_HAVE_STRING_H}
/* Define if you have SUITESPARSE library. */
${DEFINE_HAVE_SUITESPARSE}
/* Define to 1 if you have the <sys/stat.h> header file. */
${DEFINE_HAVE_SYS_STAT_H}
/* Define to 1 if you have the <sys/types.h> header file. */
${DEFINE_HAVE_SYS_TYPES_H}
/* Define to 1 if you have the <unistd.h> header file. */
${DEFINE_HAVE_UNISTD_H}
/* Test TinyObjLoader */
${DEFINE_HAVE_TINYOBJLOADER}
/* ACTION to take in case of error */
${DEFINE_ACTION_ON_ERROR}
/* Define to the sub-directory where libtool stores uninstalled libraries. */
#define LT_OBJDIR ".libs/"
/* NVCC compiling */
${DEFINE_NVCC} /**/
/* Define if we have Alpaka */
${DEFINE_HAVE_ALPAKA}
/* Additional alpaka definitions */
${ALPAKA_ACC_CPU_B_SEQ_T_SEQ_ENABLE_DEF}
${ALPAKA_ACC_CPU_B_SEQ_T_THREADS_ENABLE_DEF}
${ALPAKA_ACC_CPU_B_SEQ_T_FIBERS_ENABLE_DEF}
${ALPAKA_ACC_CPU_B_TBB_T_SEQ_ENABLE_DEF}
${ALPAKA_ACC_CPU_B_OMP2_T_SEQ_ENABLE_DEF}
${ALPAKA_ACC_CPU_B_SEQ_T_OMP2_ENABLE_DEF}
${ALPAKA_ACC_CPU_BT_OMP4_ENABLE_DEF}
/* Name of package */
#define PACKAGE "openfpm_pdata"
/* Define to the address where bug reports for this package should be sent. */
#define PACKAGE_BUGREPORT "BUG-REPORT-ADDRESS"
/* Define to the full name of this package. */
#define PACKAGE_NAME "OpenFPM_pdata"
/* Define to the full name and version of this package. */
#define PACKAGE_STRING "OpenFPM_pdata 1.0.0"
/* Define to the one symbol short name of this package. */
#define PACKAGE_TARNAME "openfpm_pdata"
/* Define to the home page for this package. */
#define PACKAGE_URL ""
/* Define to the version of this package. */
#define PACKAGE_VERSION "1.0.0"
/* Test performance mode */
${DEFINE_PERFORMANCE_TEST}
/* Security enhancement class 1 */
${DEFINE_SE_CLASS1}
/* Security enhancement class 2 */
${DEFINE_SE_CLASS2}
/* Security enhancement class 3 */
${DEFINE_SE_CLASS3}
/* Define to 1 if you have the ANSI C header files. */
${DEFINE_STDC_HEADERS}
/* If an error occur stop the program */
${DEFINE_STOP_ON_ERROR}
/* Garbage injector*/
${DEFINE_GARBAGE_INJECTOR}
/* Test coverage mode */
${DEFINE_TEST_COVERAGE_MODE}
/* when an error accur continue but avoid unsafe operation */
/* #undef THROW_ON_ERROR */
/* Version number of package */
#define VERSION "1.0.0"
#define OPENFPM_IO
src/garbage/HDF5_XdmfWriter.hpp deleted 100644 → 0
View file @ a2cb5096
/*
* H5PartWriter.hpp
*
* Created on: Feb 7, 2016
* Author: i-bird
*/
#ifndef OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_HPP_
#define OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_HPP_
#define H5PART_WRITER 0x20000
#define H5_POINTSET 1
template <unsigned int imp>
class HDF5_XdmfWriter
{
};
#include "HDF5_XdmfWriter_point_set.hpp"
#endif /* OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_HPP_ */
src/garbage/HDF5_XdmfWriter_point_set.hpp deleted 100644 → 0
View file @ a2cb5096
/*
* H5PartWriter_point_set.hpp
*
* Created on: Feb 7, 2016
* Author: i-bird
*/
#ifndef OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_POINT_SET_HPP_
#define OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_POINT_SET_HPP_
#include "HDF5_XdmfWriter_util.hpp"
#include "Vector/map_vector.hpp"
#include "VCluster/VCluster.hpp"
/*! \brief this class is a functor for "for_each" algorithm
*
* This class is a functor for "for_each" algorithm. For each
* element of the boost::vector the operator() is called.
* Is mainly used to produce write each property in H5Part
*
* \tparam ele_v is the vector of properties
* \tparam seq, sequence of property to output
* \tparam has_name define if the structure define names for the properties
*
*/
template<typename ele_v, bool has_name>
struct H5_prop_out
{
//! HDF5 file
hid_t file_id;
//! vector that we are processing
ele_v & vv;
//! Up to which element to write
size_t stop;
/*! \brief constructor
*
* \param v_out string to fill with the vertex properties
*
*/
H5_prop_out(hid_t file_id, ele_v & vv, size_t stop)
:file_id(file_id),vv(vv),stop(stop)
{};
/*! \brief It produce an output for each property
*
* \param t property id
*
*/
template<typename T>
void operator()(T& t) const
{
typedef typename boost::mpl::at<typename ele_v::value_type::value_type::type,boost::mpl::int_<T::value>>::type ptype;
H5_write<ptype,T::value,ele_v>::write(file_id,std::string(ele_v::value_type::attributes::names[T::value]),vv,stop);
}
};
/*! \brief this class is a functor for "for_each" algorithm
*
* This class is a functor for "for_each" algorithm. For each
* element of the boost::vector the operator() is called.
* Is mainly used to produce an output for each property
*
* \tparam ele_v is the vector of properties
* \tparam seq, sequence of property to output
* \tparam has_name define if the structure define names
*
*/
template<typename ele_v>
struct H5_prop_out<ele_v,false>
{
//! HDF5 file
hid_t file_id;
//! vector that we are processing
ele_v & vv;
//! Up to which element to write
size_t stop;
/*! \brief constructor
*
* \param file_id handle of the file
* \param vv element to write
* \param stop up to which element to write
*
*/
H5_prop_out(hid_t file_id, ele_v & vv, size_t stop)
:file_id(file_id),vv(vv),stop(stop)
{};
/*! \brief It produce an output for each property
*
* \param t property id
*
*/
template<typename T>
void operator()(T& t) const
{
typedef typename boost::mpl::at<typename ele_v::value_type::type,boost::mpl::int_<T::value>>::type ptype;
H5_write<ptype,T::value,ele_v>::write(file_id,std::string("attr") + std::to_string(T::value),vv,stop);
}
};
/*! \brief HDF5 writer for a point set
*
*
*/
template <>
class HDF5_XdmfWriter<H5_POINTSET>
{
//! HDF5 file
hid_t file_id;
public:
/*!
*
* H5PartWriter constructor
*
*/
HDF5_XdmfWriter()
{}
/*!
*
* \brief Write a set of particle positions and properties into HDF5
*
* \tparam Pos Vector of positions type
* \taparam Prp Vector of properties type
* \tparam prp list of properties to output
*
* \param file output file
* \param v_pos Vector with the positions
* \param v_prp Vector with the properties
* \param stop size of the vector to output
*
*/
template<typename VPos, typename VPrp, int ... prp >
bool write(const std::string & file,
openfpm::vector<VPos> & v_pos,
openfpm::vector<VPrp> & v_prp,
size_t stop)
{
Vcluster & v_cl = create_vcluster();
// Open and HDF5 file in parallel
hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(plist_id, v_cl.getMPIComm(), MPI_INFO_NULL);
file_id = H5Fcreate(file.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
H5Pclose(plist_id);
// Single coordinate positional vector
openfpm::vector<typename VPos::coord_type> x_n;
x_n.resize(stop);
//for each component, fill x_n
for (size_t i = 0 ; i < VPos::dims ; i++)
{
//
for (size_t j = 0 ; j < stop ; j++)
x_n.get(j) = v_pos.template get<0>(j)[i];
std::stringstream str;
str << "x" << i;
HDF5CreateDataSet<typename VPos::coord_type>(file_id,str.str(),x_n.getPointer(),stop*sizeof(typename VPos::coord_type));
}
// Now we write the properties
typedef typename to_boost_vmpl<prp ... >::type v_prp_seq;
H5_prop_out<openfpm::vector<VPrp>,has_attributes<VPrp>::value> f(file_id,v_prp,stop);
boost::mpl::for_each_ref<v_prp_seq>(f);
H5Fclose(file_id);
return true;
}
};
#endif /* OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_POINT_SET_HPP_ */
src/garbage/HDF5_XdmfWriter_unit_tests.hpp deleted 100644 → 0
View file @ a2cb5096
/*
* H5PartWriter_unit_tests.hpp
*
* Created on: Feb 22, 2016
* Author: i-bird
*/
#ifndef OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UNIT_TESTS_HPP_
#define OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UNIT_TESTS_HPP_
#include "VCluster.hpp"
#include "util/SimpleRNG.hpp"
#include "HDF5_XdmfWriter.hpp"
BOOST_AUTO_TEST_SUITE( HDF5_writer_test )
BOOST_AUTO_TEST_CASE( HDF5_writer_use)
{
openfpm::vector<Point<3,double>> pv;
openfpm::vector<Point_test<double>> pvp;
SimpleRNG rng;
Vcluster & v_cl = *global_v_cluster;
if (v_cl.getProcessingUnits() != 3)
return;
double z_base = v_cl.getProcessUnitID();
// fill 1000 particles for each processors
for (size_t i = 0 ; i < 1000 ; i++)
{
Point<3,double> p;
p[0] = rng.GetUniform();
p[1] = rng.GetUniform();
p[2] = z_base+rng.GetUniform();
pv.add(p);
p[0] += 2.0;
Point_test<double> pt;
pt.fill();
pvp.add(pt);
}
HDF5_XdmfWriter<H5_POINTSET> h5p;
h5p.template write<Point<3,double>,Point_test<double>,0,1,4,5>("h5part.h5",pv,pvp,1000);
// check that match
bool test = compare("test_h5part.h5part","test_h5part_test.h5part");
BOOST_REQUIRE_EQUAL(true,test);
}
BOOST_AUTO_TEST_SUITE_END()
#endif /* OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UNIT_TESTS_HPP_ */
src/garbage/HDF5_XdmfWriter_util.hpp deleted 100644 → 0
View file @ a2cb5096
/*
* H5PartWriteData_meta.hpp
*
* Created on: Feb 22, 2016
* Author: i-bird
*/
#ifndef OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UTIL_HPP_
#define OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UTIL_HPP_
#include "hdf5.h"
#include "Vector/map_vector.hpp"
/*! \brief HDF5 Create the data-set in the file
*
* \tparam type Type to write
*
* \param file_id Id of the file
* \param filespace id where to write
* \param str dataset to write
* \param ptr pointer with the data to write
* \param sz size of the data to write
*
* \return true if the function succeed
*
*/
template<typename type> bool HDF5CreateDataSet(hid_t file_id, const std::string & str ,void * ptr, size_t sz)
{
hid_t plist_id = H5Pcreate(H5P_DATASET_XFER);
if (plist_id < 0)
return false;
/* Create the dataspace for the position dataset. */
hsize_t dimsf[1] = {sz};
hid_t filespace = H5Screate_simple(1, dimsf, NULL);
if (filespace < 0)
return false;
if (std::is_same<type,char>::value == true)
{
hid_t dset_id = H5Dcreate(file_id, str.c_str(), H5T_NATIVE_CHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (dset_id < 0)
return false;
herr_t status = H5Dwrite(dset_id, H5T_NATIVE_CHAR, H5S_ALL, H5S_ALL, plist_id, ptr);
if (status < 0)
return false;
H5Dclose(dset_id);
H5Dclose(filespace);
return true;
}
/* else if (std::is_same<type,signed char>::value == true)
{
dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_SCHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
H5Dclose(dset_id);
return status;
}
else if (std::is_same<type,unsigned char>::value == true)
{
dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_UCHAR, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
else if (std::is_same<type,short>::value == true)
{
dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_SHORT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
else if (std::is_same<type,unsigned short>::value == true)
{
dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_USHORT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
else if (std::is_same<type,int>::value == true)
{
dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_INT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
else if (std::is_same<type,unsigned int>::value == true)
{
dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_UINT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
else if (std::is_same<type,long>::value == true)
{
dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_LONG, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
else if (std::is_same<type,unsigned long>::value == true)
{
dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_ULONG, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
else if (std::is_same<type,long long>::value == true)
{
dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_LLONG, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
else if (std::is_same<type,unsigned long long>::value == true)
{
dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_ULLONG, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}
else if (std::is_same<type,float>::value == true)
{
dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_FLOAT, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}*/
else if (std::is_same<type,double>::value == true)
{
hid_t dset_id = H5Dcreate(file_id, str.c_str(), H5T_NATIVE_DOUBLE, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (dset_id < 0)
return false;
herr_t status = H5Dwrite(dset_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, plist_id, ptr);
if (status < 0)
return false;
H5Dclose(dset_id);
H5Dclose(filespace);
return true;
}
/*else if (std::is_same<type,long double>::value == true)
{
dset_id = H5Dcreate(file_id, std.c_str(), H5T_NATIVE_LDOUBLE, filespace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
}*/
return true;
}
/*! \brief Write an HDF5 dataset in case of scalars and vectors
*
* \tparam T type to write
* \tparam pid Property id
* \tparam V Vector containing the information
*
*/
template<typename T,size_t pid, typename V>
struct H5_write
{
/*! \brief write
*
* \param file_id HDF5 file
* \param str dataset name
* \param v Vector containing the information
* \param stop size to store
*
*/
static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
{
// Create the buffer
openfpm::vector<T> buffer;
buffer.resize(stop);
for (size_t j = 0 ; j < stop ; j++)
buffer.get(j) = v.template get<pid>(j);
HDF5CreateDataSet<T>(file_id,str.c_str(),buffer.getPointer(),stop*sizeof(T));
}
};
//! Partial specialization for N=1 1D-Array
template<typename T,size_t pid, typename V,size_t N1>
struct H5_write<T[N1],pid,V>
{
/*! \brief write
*
* \param file_id HDF5 file
* \param str dataset name
* \param v Vector containing the information
* \param stop size to store
*
*/
static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
{
for (size_t i1 = 0 ; i1 < N1 ; i1++)
{
// Create the buffer
openfpm::vector<T> buffer;
buffer.resize(stop);
for (size_t j = 0 ; j < stop ; j++)
buffer.get(j) = v.template get<pid>(j)[i1];
std::stringstream sstr;
sstr << "_" << i1;
HDF5CreateDataSet<T>(file_id,std::string(str) + sstr.str(),v.getPointer(),stop*sizeof(T));
}
}
};
//! Partial specialization for N=2 2D-Array
template<typename T, size_t pid, typename V,size_t N1,size_t N2>
struct H5_write<T[N1][N2],pid,V>
{
/*! \brief write
*
* \param file_id HDF5 file
* \param str dataset name
* \param v Vector containing the information
* \param stop size to store
*
*/
static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
{
for (size_t i1 = 0 ; i1 < N1 ; i1++)
{
for (size_t i2 = 0 ; i2 < N2 ; i2++)
{
// Create the buffer
openfpm::vector<T> buffer;
buffer.resize(stop);
for (size_t j = 0 ; j < stop ; j++)
buffer.get(j) = v.template get<pid>(j)[i1][i2];
std::stringstream sstr;
sstr << "_" << i1 << "_" << i2;
HDF5CreateDataSet<T>(file_id,std::string(str) + sstr.str(),v.getPointer(),stop*sizeof(T));
}
}
}
};
//! Partial specialization for N=3
template<typename T, size_t pid, typename V,size_t N1,size_t N2,size_t N3>
struct H5_write<T[N1][N2][N3],pid,V>
{
/*! \brief write
*
* \param file_id HDF5 file
* \param str dataset name
* \param v Vector containing the information
* \param stop size to store
*
*/
static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
{
for (size_t i1 = 0 ; i1 < N1 ; i1++)
{
for (size_t i2 = 0 ; i2 < N2 ; i2++)
{
for (size_t i3 = 0 ; i3 < N3 ; i3++)
{
// Create the buffer
openfpm::vector<T> buffer;
buffer.resize(stop);
for (size_t j = 0 ; j < stop ; j++)
buffer.get(j) = v.template get<pid>(j)[i1][i2][i3];
std::stringstream sstr;
sstr << "_" << i1 << "_" << i2 << "_" << i3;
HDF5CreateDataSet<T>(file_id,std::string(str) + sstr.str(),v.getPointer(),stop*sizeof(T));
}
}
}
}
};
//! Partial specialization for N=4
template<typename T, size_t pid, typename V ,size_t N1,size_t N2,size_t N3,size_t N4>
struct H5_write<T[N1][N2][N3][N4],pid,V>
{
/*! \brief write
*
* \param file_id HDF5 file
* \param str dataset name
* \param v Vector containing the information
* \param stop size to store
*
*/
static inline void write(hid_t file_id, const std::string & str, V & v, size_t stop)
{
for (size_t i1 = 0 ; i1 < N1 ; i1++)
{
for (size_t i2 = 0 ; i2 < N2 ; i2++)
{
for (size_t i3 = 0 ; i3 < N3 ; i3++)
{
for (size_t i4 = 0 ; i4 < N4 ; i4++)
{
// Create the buffer
openfpm::vector<T> buffer;
buffer.resize(stop);
for (size_t j = 0 ; j < stop ; j++)
buffer.get(j) = v.template get<pid>(j)[i1][i2][i3][i4];
std::stringstream sstr;
sstr << "_" << i1 << "_" << i2 << "_" << i3 << "_" << i4;
HDF5CreateDataSet<T>(file_id,std::string(str) + sstr.str(),v.getPointer(),stop*sizeof(T));
}
}
}
}
}
};
#endif /* OPENFPM_IO_SRC_HDF5_XDMFWRITER_HDF5_XDMFWRITER_UTIL_HPP_ */
src/main.cpp
View file @ 26f879bd
...@@ -3,10 +3,6 @@ ...@@ -3,10 +3,6 @@
#include <iostream> #include <iostream>
#ifdef OPENFPM_PDATA
#include "VCluster/VCluster.hpp"
#endif
#define BOOST_DISABLE_ASSERTS #define BOOST_DISABLE_ASSERTS
#define BOOST_TEST_DYN_LINK #define BOOST_TEST_DYN_LINK
...@@ -32,11 +28,9 @@ int main(int argc, char* argv[]) ...@@ -32,11 +28,9 @@ int main(int argc, char* argv[])
#endif #endif
#include "VCluster/VCluster.hpp"
#include "CSVWriter/CSVWriter_unit_tests.hpp" #include "CSVWriter/CSVWriter_unit_tests.hpp"
#include "GraphMLWriter/GraphMLWriter_unit_tests.hpp" #include "GraphMLWriter/GraphMLWriter_unit_tests.hpp"
#include "VTKWriter/VTKWriter_unit_tests.hpp" #include "VTKWriter/VTKWriter_unit_tests.hpp"
//#include "HDF5_XdmfWriter/HDF5_XdmfWriter_unit_tests.hpp"
#include "Plot/Plot_unit_tests.hpp" #include "Plot/Plot_unit_tests.hpp"
#include "RawReader/RawReader_unit_tests.hpp" #include "RawReader/RawReader_unit_tests.hpp"
#include "HDF5_wr/HDF5_writer_unit_tests.hpp" #include "HDF5_wr/HDF5_writer_unit_tests.hpp"
success.sh deleted 100755 → 0
View file @ a2cb5096
#! /bin/bash
if [ $1 -eq 1 ]; then
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Info:\", \"color\": \"#00FF00\", \"text\":\"$2 completed succeffuly the $3 tests with $4\" }] }" https://hooks.slack.com/services/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
else
curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Info:\", \"color\": \"#00FF00\", \"text\":\"$2 completed succeffuly the $3 tests \" }] }" https://hooks.slack.com/services/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
fi