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Merge branch 'master' of bitbucket.org:glavaux/cosmotool

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This commit is contained in:
Guilhem Lavaux 2015-04-08 21:02:28 +02:00
commit 5e7437b7d4
4 changed files with 82 additions and 51 deletions
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36
CMakeLists.txt
View File

@ -13,14 +13,20 @@ set(NumPy_FIND_REQUIRED TRUE)
include(${CMAKE_SOURCE_DIR}/FindPyLibs.cmake) include(${CMAKE_SOURCE_DIR}/FindPyLibs.cmake)
include(${CMAKE_SOURCE_DIR}/FindNumPy.cmake) include(${CMAKE_SOURCE_DIR}/FindNumPy.cmake)
get_git_head_revision(HEAD GIT_VER)
option(BUILD_SHARED_LIBS "Build shared libraries." OFF) option(BUILD_SHARED_LIBS "Build shared libraries." OFF)
option(BUILD_STATIC_LIBS "Build static libraries." ON) option(BUILD_STATIC_LIBS "Build static libraries." ON)
option(ENABLE_SHARP "Enable SHARP support." ON) option(ENABLE_SHARP "Enable SHARP support." ON)
option(INTERNAL_HDF5 "Build internal version of HDF5" OFF) option(INTERNAL_HDF5 "Build internal version of HDF5" OFF)
option(INTERNAL_NETCDF "Build internal version of NETCDF" OFF) option(INTERNAL_NETCDF "Build internal version of NETCDF" OFF)
option(INTERNAL_BOOST "Build internal version of BOOST" OFF) option(INTERNAL_BOOST "Build internal version of BOOST" OFF)
option(USE_GIT_VERSION "Use GIT version to pad version number" OFF)
option(YORICK_SUPPORT "Add for pleasant yorick support" ON)
option(BUILD_PYTHON "Build the python modules" ON)
IF(USE_GIT_VERSION)
get_git_head_revision(HEAD GIT_VER)
SET(EXTRA_VERSION "-${GIT_VER}")
ENDIF(USE_GIT_VERSION)
#IF(NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS) #IF(NOT BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
# SET(CosmoTool_local CosmoTool_static) # SET(CosmoTool_local CosmoTool_static)
@ -32,13 +38,15 @@ MESSAGE(STATUS "Using the target ${CosmoTool_local} to build python module")
include(${CMAKE_SOURCE_DIR}/external/external_build.cmake) include(${CMAKE_SOURCE_DIR}/external/external_build.cmake)
IF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4") IF(YORICK_SUPPORT)
SET(FOUND_NETCDF4 1) IF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#define NETCDFCPP4 1") SET(FOUND_NETCDF4 1)
ELSE(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4") FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#define NETCDFCPP4 1")
SET(FOUND_NETCDF3 1) ELSE(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#undef NETCDFCPP4") SET(FOUND_NETCDF3 1)
ENDIF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4") FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#undef NETCDFCPP4")
ENDIF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
ENDIF(YORICK_SUPPORT)
find_program(CYTHON cython) find_program(CYTHON cython)
@ -48,7 +56,7 @@ endif(HDF5_ROOTDIR)
find_package(HDF5 COMPONENTS CXX HL) find_package(HDF5 COMPONENTS CXX HL)
set(NETCDF_FIND_REQUIRED TRUE) set(NETCDF_FIND_REQUIRED ${YORICK_SUPPORT})
set(GSL_FIND_REQUIRED TRUE) set(GSL_FIND_REQUIRED TRUE)
FIND_PACKAGE_HANDLE_STANDARD_ARGS(NetCDF DEFAULT_MSG NETCDF_LIBRARY NETCDFCPP_LIBRARY NETCDF_INCLUDE_PATH) FIND_PACKAGE_HANDLE_STANDARD_ARGS(NetCDF DEFAULT_MSG NETCDF_LIBRARY NETCDFCPP_LIBRARY NETCDF_INCLUDE_PATH)
FIND_PACKAGE_HANDLE_STANDARD_ARGS(GSL DEFAULT_MSG GSL_LIBRARY GSLCBLAS_LIBRARY GSL_INCLUDE_PATH) FIND_PACKAGE_HANDLE_STANDARD_ARGS(GSL DEFAULT_MSG GSL_LIBRARY GSLCBLAS_LIBRARY GSL_INCLUDE_PATH)
@ -60,14 +68,16 @@ SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2") SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2")
SET(CPACK_PACKAGE_VERSION_MAJOR "1") SET(CPACK_PACKAGE_VERSION_MAJOR "1")
SET(CPACK_PACKAGE_VERSION_MINOR "0") SET(CPACK_PACKAGE_VERSION_MINOR "0")
SET(CPACK_PACKAGE_VERSION_PATCH "0-${GIT_VER}") SET(CPACK_PACKAGE_VERSION_PATCH "0${EXTRA_VERSION}")
SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${GalaxExplorer_VERSION_MAJOR}.${GalaxExplorer_VERSION_MINOR}") SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}")
SET(CPACK_STRIP_FILES "lib/libCosmoTool.so") SET(CPACK_STRIP_FILES "lib/libCosmoTool.so")
SET(CPACK_SOURCE_IGNORE_FILES SET(CPACK_SOURCE_IGNORE_FILES
"/CVS/;/\\\\.git/;/\\\\.svn/;\\\\.swp$;\\\\.#;/#;.*~;cscope.*;/CMakeFiles/;.*\\\\.cmake;Makefile") "/CVS/;/\\\\.git/;/\\\\.svn/;\\\\.swp$;\\\\.#;/#;.*~;cscope.*;/CMakeFiles/;.*\\\\.cmake;Makefile")
add_subdirectory(src) add_subdirectory(src)
add_subdirectory(sample) add_subdirectory(sample)
add_subdirectory(python) if(BUILD_PYTHON)
add_subdirectory(python)
endif(BUILD_PYTHON)
include(CPack) include(CPack)

26
sample/CMakeLists.txt
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@ -1,7 +1,9 @@
SET(tolink ${GSL_LIBRARIES} ${CosmoTool_local} ${CosmoTool_LIBS}) SET(tolink ${GSL_LIBRARIES} ${CosmoTool_local} ${CosmoTool_LIBS})
include_directories(${CMAKE_SOURCE_DIR}/src) include_directories(${CMAKE_SOURCE_DIR}/src)
include_directories(${FFTW3_INCLUDE_DIRS} include_directories(${FFTW3_INCLUDE_DIRS} ${EIGEN3_INCLUDE_DIRS} ${GSL_INCLUDE_PATH})
${EIGEN3_INCLUDE_DIRS} ${NETCDF_INCLUDE_PATH} ${GSL_INCLUDE_PATH}) if(YORICK_SUPPORT)
include_directories(${NETCDF_INCLUDE_PATH})
endif(YORICK_SUPPORT)
include_directories(${CMAKE_SOURCE_DIR}/sample) include_directories(${CMAKE_SOURCE_DIR}/sample)
IF(SHARP_INCLUDE_PATH) IF(SHARP_INCLUDE_PATH)
@ -63,8 +65,10 @@ if (FFTW3_FOUND AND FFTW3F_FOUND AND EIGEN3_FOUND)
IF (FFTW3_LIBRARY_FULL) IF (FFTW3_LIBRARY_FULL)
SET(FFTW3_LIB ${FFTW3_LIB} ${FFTW3_LIBRARY_FULL}) SET(FFTW3_LIB ${FFTW3_LIB} ${FFTW3_LIBRARY_FULL})
ENDIF (FFTW3_LIBRARY_FULL) ENDIF (FFTW3_LIBRARY_FULL)
add_executable(test_fft_calls test_fft_calls.cpp) IF(YORICK_SUPPORT)
target_link_libraries(test_fft_calls ${tolink} ${FFTW3_LIB}) add_executable(test_fft_calls test_fft_calls.cpp)
target_link_libraries(test_fft_calls ${tolink} ${FFTW3_LIB})
ENDIF(YORICK_SUPPORT)
endif (FFTW3_FOUND AND FFTW3F_FOUND AND EIGEN3_FOUND) endif (FFTW3_FOUND AND FFTW3F_FOUND AND EIGEN3_FOUND)
if (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND) if (ENABLE_SHARP AND SHARP_LIBRARY AND SHARP_INCLUDE_PATH AND EIGEN3_FOUND)
@ -81,15 +85,17 @@ target_link_libraries(test_cosmopower ${tolink})
if (Boost_FOUND) if (Boost_FOUND)
include_directories(${Boost_INCLUDE_DIRS}) include_directories(${Boost_INCLUDE_DIRS})
add_executable(testSmooth testSmooth.cpp) IF (YORICK_SUPPORT)
target_link_libraries(testSmooth ${tolink}) add_executable(testSmooth testSmooth.cpp)
target_link_libraries(testSmooth ${tolink})
add_executable(simple3DFilter simple3DFilter.cpp) add_executable(simple3DFilter simple3DFilter.cpp)
target_link_libraries(simple3DFilter ${tolink}) target_link_libraries(simple3DFilter ${tolink})
ENDIF (YORICK_SUPPORT)
endif (Boost_FOUND) endif (Boost_FOUND)
IF (ENABLE_OPENMP) IF (ENABLE_OPENMP AND YORICK_SUPPORT)
add_executable(gadgetToDensity gadgetToDensity.cpp) add_executable(gadgetToDensity gadgetToDensity.cpp)
target_link_libraries(gadgetToDensity ${tolink}) target_link_libraries(gadgetToDensity ${tolink})
ENDIF (ENABLE_OPENMP) ENDIF (ENABLE_OPENMP AND YORICK_SUPPORT)

20
src/CMakeLists.txt
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@ -15,13 +15,15 @@ SET(CosmoTool_SRCS
IF (ENABLE_OPENMP) IF (ENABLE_OPENMP)
ENDIF (ENABLE_OPENMP) ENDIF (ENABLE_OPENMP)
IF(FOUND_NETCDF3) IF (YORICK_SUPPORT)
IF(FOUND_NETCDF3)
SET(CosmoTool_SRCS ${CosmoTool_SRCS} yorick_nc3.cpp) SET(CosmoTool_SRCS ${CosmoTool_SRCS} yorick_nc3.cpp)
ELSE(FOUND_NETCDF3) ELSE(FOUND_NETCDF3)
IF(FOUND_NETCDF4) IF(FOUND_NETCDF4)
SET(CosmoTool_SRCS ${CosmoTool_SRCS} yorick_nc4.cpp) SET(CosmoTool_SRCS ${CosmoTool_SRCS} yorick_nc4.cpp)
ENDIF(FOUND_NETCDF4) ENDIF(FOUND_NETCDF4)
ENDIF(FOUND_NETCDF3) ENDIF(FOUND_NETCDF3)
ENDIF(YORICK_SUPPORT)
if (HDF5_FOUND) if (HDF5_FOUND)
@ -59,9 +61,13 @@ SET(CosmoTool_SRCS ${CosmoTool_SRCS}
growthFactor.hpp growthFactor.hpp
) )
include_directories(${GSL_INCLUDE_PATH} ${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src) include_directories(${Boost_INCLUDE_DIRS} ${GSL_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src)
set(CosmoTool_LIBS ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES}) set(CosmoTool_LIBS ${GSL_LIBRARIES})
if(YORICK_SUPPORT)
set(CosmoTool_LIBS ${CosmoTool_LIBS} ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES})
include_directories(${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH})
endif(YORICK_SUPPORT)
if (HDF5_FOUND) if (HDF5_FOUND)
set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_LIBRARIES}) set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_LIBRARIES})
include_directories(${HDF5_INCLUDE_DIRS}) include_directories(${HDF5_INCLUDE_DIRS})

51
src/hdf5_array.hpp
View File

@ -90,10 +90,31 @@ namespace CosmoTool {
#undef HDF5_TYPE #undef HDF5_TYPE
// Extent generator
template<std::size_t r>
struct hdf5_extent_gen {
typedef typename boost::detail::multi_array::extent_gen<r> type;
static inline type build(hsize_t *d)
{
return (hdf5_extent_gen<r-1>::build(d))[d[r-1]];
}
};
template<>
struct hdf5_extent_gen<0> {
static inline boost::multi_array_types::extent_gen build(hsize_t *d)
{
return boost::extents;
}
};
//!_______________________________________________________________________________________ //!_______________________________________________________________________________________
//! //!
//! write_hdf5 multi_array //! write_hdf5 multi_array
//! //!
//! \author Guilhem Lavaux (2014-2015)
//! \author leo Goodstadt (04 March 2013) //! \author leo Goodstadt (04 March 2013)
//! //!
//!_______________________________________________________________________________________ //!_______________________________________________________________________________________
@ -216,24 +237,11 @@ namespace CosmoTool {
class InvalidDimensions: virtual std::exception { class InvalidDimensions: virtual std::exception {
}; };
template<std::size_t r>
struct hdf5_extent_gen {
typedef typename boost::detail::multi_array::extent_gen<r> type;
static inline type build(hsize_t *d)
{
return (hdf5_extent_gen<r-1>::build(d))[d[r-1]];
}
};
template<>
struct hdf5_extent_gen<0> {
static inline boost::multi_array_types::extent_gen build(hsize_t *d)
{
return boost::extents;
}
};
// ----------------------------------------------------------------------
// Conditional resize support
// If the Array type support resize then it is called. Otherwise
// the dimensions are checked and lead to a failure if they are different
template<typename Array> class array_has_resize { template<typename Array> class array_has_resize {
struct Fallback { int resize; }; struct Fallback { int resize; };
@ -283,10 +291,12 @@ namespace CosmoTool {
hdf5_check_array(data, dims); hdf5_check_array(data, dims);
} }
// ----------------------------------------------------------------------
template<typename ArrayType, typename hdf5_data_type> template<typename ArrayType, typename hdf5_data_type>
void hdf5_read_array_typed(H5::CommonFG& fg, const std::string& data_set_name, void hdf5_read_array_typed(H5::CommonFG& fg, const std::string& data_set_name,
ArrayType& data, ArrayType& data,
const hdf5_data_type& datatype, bool auto_resize = true) const hdf5_data_type& datatype, bool auto_resize = true)
{ {
H5::DataSet dataset = fg.openDataSet(data_set_name); H5::DataSet dataset = fg.openDataSet(data_set_name);
H5::DataSpace dataspace = dataset.getSpace(); H5::DataSpace dataspace = dataset.getSpace();
@ -311,8 +321,7 @@ namespace CosmoTool {
{ {
typedef typename ArrayType::element T; typedef typename ArrayType::element T;
get_hdf5_data_type<T> hdf_data_type; hdf5_read_array_typed(fg, data_set_name, data, get_hdf5_data_type<T>::type(), auto_resize);
hdf5_read_array_typed(fg, data_set_name, data, hdf_data_type.type(), auto_resize);
} }