Merge branch 'master' of bitbucket.org:glavaux/cosmotool
This commit is contained in:
Guilhem Lavaux
commit
1b971e96c0
@ -5,20 +5,22 @@ project(CosmoToolbox)
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include(GetGitRevisionDescription)
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include(ExternalProject)
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include(FindOpenMP)
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include(FindPkgConfig)
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include(FindPackageHandleStandardArgs)
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include(FindPythonInterp)
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set(NumPy_FIND_REQUIRED TRUE)
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include(${CMAKE_SOURCE_DIR}/FindPyLibs.cmake)
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include(${CMAKE_SOURCE_DIR}/FindNumPy.cmake)
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get_git_head_revision(HEAD GIT_VER)
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option(BUILD_SHARED_LIBS "Build shared libraries." OFF)
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option(BUILD_STATIC_LIBS "Build static libraries." ON)
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option(ENABLE_OPENMP "Enable OpenMP support." OFF)
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option(ENABLE_SHARP "Enable SPHT support." ON)
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option(ENABLE_SHARP "Enable SHARP support." ON)
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option(INTERNAL_HDF5 "Build internal version of HDF5" OFF)
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option(INTERNAL_NETCDF "Build internal version of NETCDF" OFF)
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option(INTERNAL_BOOST "Build internal version of BOOST" OFF)
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IF(BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
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SET(CosmoTool_local CosmoTool_static)
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@ -26,10 +28,7 @@ ELSE(BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
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SET(CosmoTool_local CosmoTool)
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ENDIF(BUILD_SHARED_LIBS AND BUILD_STATIC_LIBS)
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find_path(NETCDF_INCLUDE_PATH NAMES netcdf.h)
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find_path(NETCDFCPP_INCLUDE_PATH NAMES netcdfcpp.h netcdf)
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find_path(GSL_INCLUDE_PATH NAMES gsl/gsl_blas.h)
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find_library(NETCDFCPP_LIBRARY NAMES netcdf_c++ netcdf_c++4)
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include(${CMAKE_SOURCE_DIR}/external/external_build.cmake)
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IF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
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SET(FOUND_NETCDF4 1)
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@ -39,52 +38,20 @@ ELSE(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "n
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FILE(WRITE ${CMAKE_BINARY_DIR}/src/ctool_netcdf_ver.hpp "#undef NETCDFCPP4")
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ENDIF(EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4")
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find_library(NETCDF_LIBRARY netcdf)
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find_library(GSL_LIBRARY gsl)
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find_library(GSLCBLAS_LIBRARY gslcblas)
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find_program(CYTHON cython)
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find_package(Boost 1.53)
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include(${CMAKE_SOURCE_DIR}/external/external_build.cmake)
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set(HDF5_FIND_COMPONENTS HL CXX)
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if(HDF5_ROOTDIR)
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SET(ENV{HDF5_ROOT} ${HDF5_ROOTDIR})
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endif(HDF5_ROOTDIR)
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include(FindHDF5)
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include(FindPkgConfig)
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pkg_check_modules(FFTW3 fftw3>=3.3)
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pkg_check_modules(FFTW3F fftw3f>=3.3)
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pkg_check_modules(EIGEN3 eigen3)
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find_library(FFTW3F_LIBRARY_FULL fftw3f PATHS ${FFTW3F_LIBDIR} NO_DEFAULT_PATH)
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find_library(FFTW3_LIBRARY_FULL fftw3 PATHS ${FFTW3_LIBDIR} NO_DEFAULT_PATH)
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include(FindPackageHandleStandardArgs)
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set(NETCDF_FIND_REQUIRED TRUE)
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set(GSL_FIND_REQUIRED TRUE)
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FIND_PACKAGE_HANDLE_STANDARD_ARGS(NetCDF DEFAULT_MSG NETCDF_LIBRARY NETCDFCPP_LIBRARY NETCDF_INCLUDE_PATH)
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FIND_PACKAGE_HANDLE_STANDARD_ARGS(GSL DEFAULT_MSG GSL_LIBRARY GSLCBLAS_LIBRARY GSL_INCLUDE_PATH)
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IF(ENABLE_OPENMP)
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IF (NOT OPENMP_FOUND)
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MESSAGE(ERROR "No known compiler option for enabling OpenMP")
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ENDIF(NOT OPENMP_FOUND)
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SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
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SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
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SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_C_FLAGS}")
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ENDIF(ENABLE_OPENMP)
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set(GSL_LIBRARIES ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY})
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# CPACK Configuration
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SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "A toolbox for impatient cosmologists")
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223
external/external_build.cmake
vendored
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external/external_build.cmake
vendored
@ -1,3 +1,30 @@
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include(FindOpenMP)
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OPTION(ENABLE_OPENMP "Set to Yes if Healpix and/or you need openMP" OFF)
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SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE URL "URL to download FFTW from")
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SET(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.1.4.tar.gz" CACHE URL "URL to download Eigen from")
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SET(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACHE STRING "URL to download gengetopt from")
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SET(HDF5_URL "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.9/src/hdf5-1.8.9.tar.gz" CACHE STRING "URL to download HDF5 from")
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SET(NETCDF_URL "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.1.3.tar.gz" CACHE STRING "URL to download NetCDF from")
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SET(BOOST_URL "http://sourceforge.net/projects/boost/files/boost/1.49.0/boost_1_49_0.tar.gz/download" CACHE STRING "URL to download Boost from")
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SET(GSL_URL "ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz" CACHE STRING "URL to download GSL from ")
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mark_as_advanced(FFTW_URL EIGEN_URL HDF5_URL NETCDF_URL BOOST_URL GSL_URL)
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IF(ENABLE_OPENMP)
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IF (NOT OPENMP_FOUND)
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MESSAGE(ERROR "No known compiler option for enabling OpenMP")
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ENDIF(NOT OPENMP_FOUND)
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SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
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SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
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SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_C_FLAGS}")
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ENDIF(ENABLE_OPENMP)
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SET(BUILD_PREFIX ${CMAKE_BINARY_DIR}/external_build)
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SET(EXT_INSTALL ${CMAKE_BINARY_DIR}/ext_install)
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if (ENABLE_SHARP)
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SET(SHARP_SOURCE ${CMAKE_SOURCE_DIR}/external/sharp)
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@ -17,6 +44,202 @@ if (ENABLE_SHARP)
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endif (ENABLE_SHARP)
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###############
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# Build HDF5
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###############
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if (INTERNAL_HDF5)
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SET(HDF5_SOURCE_DIR ${BUILD_PREFIX}/hdf5-prefix/src/hdf5)
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SET(HDF5_BIN_DIR ${EXT_INSTALL})
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ExternalProject_Add(hdf5
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PREFIX ${BUILD_PREFIX}/hdf5-prefix
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URL ${HDF5_URL}
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CONFIGURE_COMMAND ${HDF5_SOURCE_DIR}/configure
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--disable-shared --enable-cxx --with-pic
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--prefix=${HDF5_BIN_DIR} --libdir=${HDF5_BIN_DIR}/lib
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CPPFLAGS=${CONFIGURE_CPP_FLAGS} CC=${CMAKE_C_COMPILER}
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CXX=${CMAKE_CXX_COMPILER}
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BUILD_IN_SOURCE 1
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INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
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)
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SET(cosmotool_DEPS ${cosmotool_DEPS} hdf5)
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SET(hdf5_built hdf5)
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set(HDF5_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5.a CACHE STRING "HDF5 lib" FORCE)
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set(HDF5_CPP_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_cpp.a CACHE STRING "HDF5 C++ lib" FORCE)
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set(HDF5HL_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl.a CACHE STRING "HDF5-HL lib" FORCE)
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set(HDF5HL_CPP_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl_cpp.a CACHE STRING "HDF5-HL C++ lib" FORCE)
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SET(HDF5_INCLUDE_PATH ${HDF5_BIN_DIR}/include CACHE STRING "HDF5 include path" FORCE)
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SET(ENV{HDF5_ROOT} ${HDF5_BIN_DIR})
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SET(HDF5_ROOTDIR ${HDF5_BIN_DIR})
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SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${HDF5_BIN_DIR}/lib")
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else(INTERNAL_HDF5)
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find_path(HDF5_INCLUDE_PATH hdf5.h)
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find_library(HDF5_LIBRARY hdf5)
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find_library(HDF5_CPP_LIBRARY hdf5_cpp)
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find_library(HDF5HL_CPP_LIBRARY hdf5_hl_cpp)
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find_library(HDF5HL_LIBRARY hdf5_hl)
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endif (INTERNAL_HDF5)
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SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${HDF5_INCLUDE_PATH}")
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mark_as_advanced(HDF5_INCLUDE_PATH HDF5_LIBRARY HDF5_CPP_LIBRARY HDF5HL_LIBRARY HDF5HL_CPP_LIBRARY)
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###############
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# Build NetCDF
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###############
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if (INTERNAL_NETCDF)
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SET(NETCDF_SOURCE_DIR ${BUILD_PREFIX}/netcdf-prefix/src/netcdf)
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SET(NETCDF_BIN_DIR ${EXT_INSTALL})
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SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${NETCDF_BIN_DIR}/include")
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SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${NETCDF_BIN_DIR}/lib")
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SET(EXTRA_NC_FLAGS CPPFLAGS=${CONFIGURE_CPP_FLAGS} LDFLAGS=${CONFIGURE_LDFLAGS})
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ExternalProject_Add(netcdf
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DEPENDS ${hdf5_built}
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PREFIX ${BUILD_PREFIX}/netcdf-prefix
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URL ${NETCDF_URL}
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CONFIGURE_COMMAND ${NETCDF_SOURCE_DIR}/configure
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--prefix=${NETCDF_BIN_DIR} --libdir=${NETCDF_BIN_DIR}/lib
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--enable-netcdf-4 --with-pic --disable-shared --disable-dap
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--disable-cdmremote --disable-rpc
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--disable-examples ${EXTRA_NC_FLAGS} CC=${CMAKE_C_COMPILER}
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CXX=${CMAKE_CXX_COMPILER}
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BUILD_IN_SOURCE 1
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INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
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)
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SET(CONFIGURE_CPP_LDFLAGS "${CONFIGURE_LDFLAGS}")
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SET(EXTRA_NC_FLAGS CPPFLAGS=${CONFIGURE_CPP_FLAGS} LDFLAGS=${CONFIGURE_CPP_LDFLAGS})
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SET(cosmotool_DEPS ${cosmotool_DEPS} netcdf)
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SET(NETCDF_LIBRARY ${NETCDF_BIN_DIR}/lib/libnetcdf.a CACHE STRING "NetCDF lib" FORCE)
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SET(NETCDFCPP_LIBRARY ${NETCDF_BIN_DIR}/lib/libnetcdf_c++.a CACHE STRING "NetCDF-C++ lib" FORCE)
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SET(NETCDF_INCLUDE_PATH ${NETCDF_BIN_DIR}/include CACHE STRING "NetCDF include" FORCE)
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SET(NETCDFCPP_INCLUDE_PATH ${NETCDF_INCLUDE_PATH} CACHE STRING "NetCDF C++ include path" FORCE)
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ELSE(INTERNAL_NETCDF)
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find_path(NETCDF_INCLUDE_PATH NAMES netcdf.h)
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find_path(NETCDFCPP_INCLUDE_PATH NAMES netcdfcpp.h netcdf)
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find_library(NETCDF_LIBRARY netcdf)
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find_library(NETCDFCPP_LIBRARY NAMES netcdf_c++ netcdf_c++4)
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SET(CONFIGURE_CPP_FLAGS ${CONFIGURE_CPP_FLAGS}
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-I${NETCDF_INCLUDE_PATH} -I${NETCDFCPP_INCLUDE_PATH})
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endif (INTERNAL_NETCDF)
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mark_as_advanced(NETCDF_LIBRARY NETCDFCPP_LIBRARY NETCDF_INCLUDE_PATH NETCDFCPP_INCLUDE_PATH)
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##################
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# Build BOOST
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##################
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if (INTERNAL_BOOST)
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SET(BOOST_SOURCE_DIR ${BUILD_PREFIX}/boost-prefix/src/boost)
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ExternalProject_Add(boost
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URL ${BOOST_URL}
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PREFIX ${BUILD_PREFIX}/boost-prefix
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CONFIGURE_COMMAND
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${BOOST_SOURCE_DIR}/bootstrap.sh --prefix=${CMAKE_BINARY_DIR}/ext_build/boost
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BUILD_IN_SOURCE 1
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BUILD_COMMAND ${BOOST_SOURCE_DIR}/b2 --with-exception
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INSTALL_COMMAND echo "No install"
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)
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set(Boost_INCLUDE_DIRS ${BOOST_SOURCE_DIR} CACHE STRING "Boost path" FORCE)
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set(Boost_LIBRARIES ${BOOST_SOURCE_DIR}/stage/lib/libboost_python.a CACHE STRING "Boost libraries" FORCE)
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ELSE (INTERNAL_BOOST)
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find_package(Boost 1.53)
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endif (INTERNAL_BOOST)
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mark_as_advanced(Boost_INCLUDE_DIRS Boost_LIBRARIES)
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##################
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# Build GSL
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##################
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IF(INTERNAL_GSL)
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SET(GSL_SOURCE_DIR ${BUILD_PREFIX}/gsl-prefix/src/gsl)
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ExternalProject_Add(gsl
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URL ${GSL_URL}
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PREFIX ${BUILD_PREFIX}/gsl-prefix
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CONFIGURE_COMMAND ${GSL_SOURCE_DIR}/configure
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--prefix=${EXT_INSTALL} --disable-shared
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--with-pic
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CPPFLAGS=${CONFIGURE_CPP_FLAGS} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}
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BUILD_IN_SOURCE 1
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BUILD_COMMAND ${CMAKE_MAKE_PROGRAM}
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INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
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)
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SET(GSL_INTERNAL_LIBS ${EXT_INSTALL}/lib)
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SET(GSL_LIBRARY ${GSL_INTERNAL_LIBS}/libgsl.a CACHE STRING "GSL internal path" FORCE)
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SET(GSLCBLAS_LIBRARY ${GSL_INTERNAL_LIBS}/libgslcblas.a CACHE STRING "GSL internal path" FORCE)
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set(GSL_INCLUDE_PATH ${CMAKE_BINARY_DIR}/ext_build/gsl/include CACHE STRING "GSL internal path" FORCE)
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SET(cosmotool_DEPS ${cosmotool_DEPS} gsl)
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ELSE(INTERNAL_GSL)
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find_path(GSL_INCLUDE_PATH NAMES gsl/gsl_blas.h)
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find_library(GSL_LIBRARY gsl)
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find_library(GSLCBLAS_LIBRARY gslcblas)
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set(GSL_LIBRARIES ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY})
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ENDIF(INTERNAL_GSL)
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mark_as_advanced(GSL_LIBRARY GSLCBLAS_LIBRARY GSL_INCLUDE_PATH)
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#############
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# Build FFTW
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#############
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IF(INTERNAL_FFTW)
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SET(EXTRA_FFTW_CONF)
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IF(HAVE_SSE)
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SET(EXTRA_FFTW_CONF ${EXTRA_FFTW_CONF} --enable-sse)
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ENDIF(HAVE_SSE)
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IF(HAVE_SSE2)
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SET(EXTRA_FFTW_CONF ${EXTRA_FFTW_CONF} --enable-sse2)
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ENDIF(HAVE_SSE2)
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IF(HAVE_AVX)
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SET(EXTRA_FFTW_CONF ${EXTRA_FFTW_CONF} --enable-avx)
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ENDIF(HAVE_AVX)
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SET(cosmotool_DEPS ${cosmotool_DEPS} fftw)
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SET(FFTW_SOURCE ${BUILD_PREFIX}/fftw-prefix/src/fftw)
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ExternalProject_Add(fftw
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URL ${FFTW_URL}
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PREFIX ${BUILD_PREFIX}/fftw-prefix
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CONFIGURE_COMMAND
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${FFTW_SOURCE}/configure
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--prefix=${EXT_INSTALL}
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${EXTRA_FFTW_CONF} --disable-shared --enable-threads
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BUILD_COMMAND ${CMAKE_MAKE_PROGRAM}
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INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install
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)
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SET(FFTW3_LIBRARY_DIRS ${EXT_INSTALL}/lib)
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SET(FFTW3_INCLUDE_PATH ${EXT_INSTALL}/include)
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SET(FFTW3_THREADS ${EXT_INSTALL}/lib/libfftw3_threads.a)
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SET(FFTW3_LIBRARIES ${EXT_INSTALL}/lib/libfftw3.a)
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ELSE (INTERNAL_FFTW)
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pkg_check_modules(FFTW3 fftw3>=3.3)
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pkg_check_modules(FFTW3F fftw3f>=3.3)
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find_library(FFTW3F_LIBRARY_FULL fftw3f PATHS ${FFTW3F_LIBDIR} NO_DEFAULT_PATH)
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find_library(FFTW3_LIBRARY_FULL fftw3 PATHS ${FFTW3_LIBDIR} NO_DEFAULT_PATH)
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ENDIF(INTERNAL_FFTW)
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##############
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# Build Eigen
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##############
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IF (INTERNAL_EIGEN)
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ExternalProject_Add(eigen
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URL ${EIGEN_URL}
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PREFIX ${BUILD_PREFIX}/eigen-prefix
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CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL}
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)
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SET(EIGEN_INCLUDE_PATH ${EXT_INSTALL}/include/eigen3)
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ELSE (INTERNAL_EIGEN)
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pkg_check_modules(EIGEN3 eigen3)
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ENDIF(INTERNAL_EIGEN)
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SET(OMPTL_BUILD_DIR ${CMAKE_BINARY_DIR}/omptl-prefix/src/omptl)
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ExternalProject_Add(omptl
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@ -115,7 +115,7 @@ cdef class CosmologyPower:
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cdef double _compute(self, double k):
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k *= self.power.h
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return self.power.power(k)
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return self.power.power(k) * self.power.h**3
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def compute(self, k):
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"""compute(self, k)
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@ -4,10 +4,10 @@ import cosmolopy as cpy
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from cosmogrowth import *
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import borgadaptor as ba
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def gen_posgrid(N, L):
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def gen_posgrid(N, L, delta=1, dtype=np.float32):
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""" Generate an ordered lagrangian grid"""
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ix = (np.arange(N)*L/N).astype(np.float32)
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ix = (np.arange(N)*L/N*delta).astype(dtype)
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x = ix[:,None,None].repeat(N, axis=1).repeat(N, axis=2)
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y = ix[None,:,None].repeat(N, axis=0).repeat(N, axis=2)
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|
||||
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