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Fixed HDF5 support in cmake. Fixed fortran.

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This commit is contained in:
Guilhem Lavaux 2017-05-05 09:09:51 +02:00
parent 537a68b668
commit d720854361
8 changed files with 63 additions and 106 deletions
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2
CMakeLists.txt
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@ -9,11 +9,13 @@ include(GetGitRevisionDescription)
include(ExternalProject)
include(FindPkgConfig)
include(FindPackageHandleStandardArgs)
include(color_msg)
option(BUILD_SHARED_LIBS "Build shared libraries." OFF)
option(BUILD_STATIC_LIBS "Build static libraries." ON)
option(ENABLE_SHARP "Enable SHARP support." ON)
option(INTERNAL_HDF5 "Build internal version of HDF5" OFF)
option(INTERNAL_EIGEN "Build internal version of Eigen" ON)
option(INTERNAL_NETCDF "Build internal version of NETCDF" OFF)
option(INTERNAL_BOOST "Build internal version of BOOST" OFF)
option(USE_GIT_VERSION "Use GIT version to pad version number" OFF)

86
FindHDF5.cmake
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@ -1,86 +0,0 @@
#
# To be used by projects that make use of Cmakeified hdf5-1.8.17
#
#
# Find the HDF5 includes and get all installed hdf5 library settings from
# HDF5-config.cmake file : Requires a CMake compatible hdf5-1.8.5 or later
# for this feature to work. The following vars are set if hdf5 is found.
#
# HDF5_FOUND - True if found, otherwise all other vars are undefined
# HDF5_INCLUDE_DIR - The include dir for main *.h files
# HDF5_FORTRAN_INCLUDE_DIR - The include dir for fortran modules and headers
# HDF5_VERSION_STRING - full version (e.g. 1.8.17)
# HDF5_VERSION_MAJOR - major part of version (e.g. 1.8)
# HDF5_VERSION_MINOR - minor part (e.g. 17)
#
# The following boolean vars will be defined
# HDF5_ENABLE_PARALLEL - 1 if HDF5 parallel supported
# HDF5_BUILD_FORTRAN - 1 if HDF5 was compiled with fortran on
# HDF5_BUILD_CPP_LIB - 1 if HDF5 was compiled with cpp on
# HDF5_BUILD_TOOLS - 1 if HDF5 was compiled with tools on
# HDF5_BUILD_HL_LIB - 1 if HDF5 was compiled with high level on
# HDF5_BUILD_HL_CPP_LIB - 1 if HDF5 was compiled with high level and cpp on
#
# Target names that are valid (depending on enabled options)
# will be the following
#
# hdf5 : HDF5 C library
# hdf5_tools : the tools library
# hdf5_f90cstub : used by Fortran to C interface
# hdf5_fortran : Fortran HDF5 library
# hdf5_cpp : HDF5 cpp interface library
# hdf5_hl : High Level library
# hdf5_hl_f90cstub : used by Fortran to C interface to High Level library
# hdf5_hl_fortran : Fortran High Level library
# hdf5_hl_cpp : High Level cpp interface library
#
# To aid in finding HDF5 as part of a subproject set
# HDF5_ROOT_DIR_HINT to the location where hdf5-config.cmake lies
include (SelectLibraryConfigurations)
include (FindPackageHandleStandardArgs)
# The HINTS option should only be used for values computed from the system.
set (_HDF5_HINTS
$ENV{HOME}/.local
$ENV{HDF5_ROOT}
$ENV{HDF5_ROOT_DIR_HINT}
)
# Hard-coded guesses should still go in PATHS. This ensures that the user
# environment can always override hard guesses.
set (_HDF5_PATHS
$ENV{HOME}/.local
$ENV{HDF5_ROOT}
$ENV{HDF5_ROOT_DIR_HINT}
/usr/lib/hdf5
/usr/share/hdf5
/usr/local/hdf5
/usr/local/hdf5/share
)
FIND_PATH (HDF5_ROOT_DIR "hdf5-config.cmake"
HINTS ${_HDF5_HINTS}
PATHS ${_HDF5_PATHS}
PATH_SUFFIXES
cmake/hdf5
lib/cmake/hdf5
share/cmake/hdf5
)
FIND_PATH (HDF5_INCLUDE_DIRS "H5public.h"
HINTS ${_HDF5_HINTS}
PATHS ${_HDF5_PATHS}
PATH_SUFFIXES
include
Include
)
# For backwards compatibility we set HDF5_INCLUDE_DIR to the value of
# HDF5_INCLUDE_DIRS
set ( HDF5_INCLUDE_DIR "${HDF5_INCLUDE_DIRS}" )
if (HDF5_INCLUDE_DIR)
set (HDF5_FOUND "YES")
include (${HDF5_ROOT_DIR}/hdf5-config.cmake)
endif (HDF5_INCLUDE_DIR)

61
external/external_build.cmake vendored
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@ -3,7 +3,7 @@ include(FindOpenMP)
OPTION(ENABLE_OPENMP "Set to Yes if Healpix and/or you need openMP" OFF)
SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE URL "URL to download FFTW from")
SET(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.1.4.tar.gz" CACHE URL "URL to download Eigen from")
SET(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz" CACHE URL "URL to download Eigen from")
SET(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACHE STRING "URL to download gengetopt from")
SET(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/current18/src/hdf5-1.8.18.tar.bz2" CACHE STRING "URL to download HDF5 from")
SET(NETCDF_URL "http://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-4.1.3.tar.gz" CACHE STRING "URL to download NetCDF from")
@ -12,6 +12,25 @@ SET(GSL_URL "ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz" CACHE STRING "URL to dow
mark_as_advanced(FFTW_URL EIGEN_URL HDF5_URL NETCDF_URL BOOST_URL GSL_URL)
MACRO(CHECK_CHANGE_STATE VAR)
IF (DEFINED _PREVIOUS_${VAR})
IF (NOT ${_PREVIOUS_${VAR}} EQUAL ${${VAR}})
foreach(loopvar ${ARGN})
UNSET(${loopvar} CACHE)
endforeach()
ENDIF (NOT ${_PREVIOUS_${VAR}} EQUAL ${${VAR}})
ENDIF (DEFINED _PREVIOUS_${VAR})
SET(_PREVIOUS_${VAR} ${${VAR}} CACHE INTERNAL "Internal value")
ENDMACRO(CHECK_CHANGE_STATE)
CHECK_CHANGE_STATE(INTERNAL_BOOST Boost_LIBRARIES Boost_INCLUDE_DIRS)
CHECK_CHANGE_STATE(INTERNAL_EIGEN EIGEN3_INCLUDE_DIRS)
CHECK_CHANGE_STATE(INTERNAL_GSL GSL_LIBRARY GSL_CBLAS_LIBRARY GSL_INCLUDE)
CHECK_CHANGE_STATE(INTERNAL_HDF5
HDF5_INCLUDE_DIR HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_DIR
HDF5_C_STATIC_LIBRARY HDF5_HL_STATIC_LIBRARY HDF5_CXX_STATIC_LIBRARY)
CHECK_CHANGE_STATE(INTERNAL_DLIB DLIB_INCLUDE_DIR DLIB_LIBRARIES)
IF(ENABLE_OPENMP)
IF (NOT OPENMP_FOUND)
@ -75,24 +94,35 @@ if (INTERNAL_HDF5)
set(HDF5_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5.a CACHE STRING "HDF5 lib" FORCE)
set(HDF5_HL_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_hl.a CACHE STRING "HDF5 HL lib" FORCE)
set(HDF5_CXX_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_cpp.a CACHE STRING "HDF5 C++ lib" FORCE)
SET(HDF5_INCLUDE_DIR ${HDF5_BIN_DIR}/include CACHE STRING "HDF5 include path" FORCE)
mark_as_advanced(HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_INCLUDE_DIR)
SET(HDF5_INCLUDE_DIRS ${HDF5_BIN_DIR}/include CACHE STRING "HDF5 include path" FORCE)
mark_as_advanced(HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_INCLUDE_DIRS)
MESSAGE(STATUS "Internal HDF5 directory: $ENV{HDF5_ROOT}")
MESSAGE(STATUS "Libs: ${HDF5_LIBRARIES}")
SET(HDF5_FOUND TRUE)
else (INTERNAL_HDF5)
mark_as_advanced(CLEAR HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_INCLUDE_DIR)
mark_as_advanced(CLEAR HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_INCLUDE_DIRS)
if(HDF5_ROOTDIR)
SET(ENV{HDF5_ROOT} ${HDF5_ROOTDIR})
endif(HDF5_ROOTDIR)
find_package(HDF5 COMPONENTS C CXX HL static)
set(HDF5_LIBRARIES ${HDF5_C_STATIC_LIBRARY} CACHE STRING "HDF5 lib" FORCE)
set(HDF5_HL_LIBRARIES ${HDF5_HL_STATIC_LIBRARY} CACHE STRING "HDF5 HL lib" FORCE)
set(HDF5_CXX_LIBRARIES ${HDF5_CXX_STATIC_LIBRARY} CACHE STRING "HDF5 C++ lib" FORCE)
find_package(HDF5 COMPONENTS C CXX HL CONFIG QUIET)
if (NOT HDF5_FOUND)
cmessage(CWARNING "Could not find HDF5 cmake config. Try classical exploration")
find_package(HDF5 COMPONENTS C CXX HL)
cmessage(STATUS "HDF5 lib: ${HDF5_LIBRARIES}")
cmessage(STATUS "HDF5 includes: ${HDF5_INCLUDE_DIRS}")
get_filename_component(HDF5_BIN_DIR ${HDF5_C_LIBRARY_hdf5} DIRECTORY)
cmessage(STATUS "HDF5 libpath: ${HDF5_BIN_DIR}")
else()
set(HDF5_LIBRARIES ${HDF5_C_STATIC_LIBRARY} CACHE STRING "HDF5 lib" FORCE)
set(HDF5_HL_LIBRARIES ${HDF5_HL_STATIC_LIBRARY} CACHE STRING "HDF5 HL lib" FORCE)
set(HDF5_CXX_LIBRARIES ${HDF5_CXX_STATIC_LIBRARY} CACHE STRING "HDF5 C++ lib" FORCE)
get_filename_component(HDF5_BIN_DIR ${HDF5_C_STATIC_LIBRARY} DIRECTORY)
endif()
SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${HDF5_BIN_DIR}")
endif (INTERNAL_HDF5)
foreach(include_dir ${HDF5_INCLUDE_DIR})
foreach(include_dir ${HDF5_INCLUDE_DIRS})
SET(CONFIGURE_CPP_FLAGS "${CONFIGURE_CPP_FLAGS} -I${include_dir}")
endforeach(include_dir)
@ -161,8 +191,11 @@ if (INTERNAL_BOOST)
set(Boost_DEP boost)
ELSE (INTERNAL_BOOST)
find_package(Boost 1.53)
find_package(Boost 1.53 QUIET)
set(Boost_DEP)
if (NOT Boost_FOUND)
cmessage(CWARNING "Boost >= 1.53 was not found")
endif()
endif (INTERNAL_BOOST)
mark_as_advanced(Boost_INCLUDE_DIRS Boost_LIBRARIES)
@ -248,13 +281,17 @@ ENDIF(INTERNAL_FFTW)
IF (INTERNAL_EIGEN)
ExternalProject_Add(eigen
URL ${EIGEN_URL}
URL_HASH SHA256=04f8a4fa4afedaae721c1a1c756afeea20d3cdef0ce3293982cf1c518f178502
PREFIX ${BUILD_PREFIX}/eigen-prefix
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL}
)
SET(EIGEN_INCLUDE_PATH ${EXT_INSTALL}/include/eigen3)
SET(EIGEN3_INCLUDE_DIRS ${EXT_INSTALL}/include/eigen3)
ELSE (INTERNAL_EIGEN)
pkg_check_modules(EIGEN3 eigen3)
pkg_check_modules(EIGEN3 QUIET eigen3 )
if (NOT EIGEN3_FOUND)
cmessage(CWARNING "Eigen library not found")
endif()
ENDIF(INTERNAL_EIGEN)

4
python/cosmotool/fftw.py
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@ -12,8 +12,8 @@ class CubeFT(object):
self.max_cpu = multiprocessing.cpu_count() if max_cpu < 0 else max_cpu
self._dhat = pyfftw.n_byte_align_empty((self.N,self.N,self.N/2+1), self.align, dtype='complex64')
self._density = pyfftw.n_byte_align_empty((self.N,self.N,self.N), self.align, dtype='float32')
self._irfft = pyfftw.FFTW(self._dhat, self._density, axes=(0,1,2), direction='FFTW_BACKWARD', threads=self.max_cpu, normalize_idft=False)
self._rfft = pyfftw.FFTW(self._density, self._dhat, axes=(0,1,2), threads=self.max_cpu, normalize_idft=False)
self._irfft = pyfftw.FFTW(self._dhat, self._density, axes=(0,1,2), direction='FFTW_BACKWARD', threads=self.max_cpu)#, normalize_idft=False)
self._rfft = pyfftw.FFTW(self._density, self._dhat, axes=(0,1,2), threads=self.max_cpu) #, normalize_idft=False)
def rfft(self):
return ne.evaluate('c*a', out=self._dhat, local_dict={'c':self._rfft(normalise_idft=False),'a':(self.L/self.N)**3}, casting='unsafe')

1
src/CMakeLists.txt
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@ -76,7 +76,6 @@ if(YORICK_SUPPORT)
include_directories(${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH})
endif(YORICK_SUPPORT)
message(STATUS "HDF5 ? ${HDF5_FOUND}")
if (HDF5_FOUND)
set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_CXX_LIBRARIES} ${ZLIB})
include_directories(${HDF5_INCLUDE_DIRS})

8
src/fortran.cpp
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@ -136,8 +136,9 @@ void UnformattedRead::endCheckpoint(bool autodrop)
{
if (checkPointRef != checkPointAccum)
{
if (!autodrop || checkPointAccum > checkPointRef)
if (!autodrop || checkPointAccum > checkPointRef) {
throw InvalidUnformattedAccess();
}
f->seekg(checkPointRef-checkPointAccum, ios::cur);
}
@ -145,10 +146,11 @@ void UnformattedRead::endCheckpoint(bool autodrop)
checkPointRef = (cSize == Check_32bits) ? 4 : 8;
checkPointAccum = 0;
checkPointRef = (cSize == Check_32bits) ? readInt32() : readInt64();
checkPointRef = (cSize == Check_32bits) ? readUint32() : readInt64();
if (oldCheckPoint != checkPointRef)
if (oldCheckPoint != checkPointRef) {
throw InvalidUnformattedAccess();
}
checkPointAccum = checkPointRef = 0;
}

3
src/fortran.hpp
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@ -46,6 +46,9 @@ namespace CosmoTool
{
class InvalidUnformattedAccess : public Exception
{
public:
InvalidUnformattedAccess()
: Exception("Invalid unformatted fortran file format") {}
};
class FortranTypes

4
src/loadGadget.cpp
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@ -146,14 +146,14 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id,
if (GadgetFormat == 2) {
int64_t startBlock = 0;
char block[5];
int32_t blocksize;
uint32_t blocksize;
try {
while (true) {
f->beginCheckpoint();
f->readOrderedBuffer(block, 4);
block[4] = 0;
blocksize = f->readInt32();
blocksize = f->readUint32();
f->endCheckpoint();
blockTable[block].position = f->position();
blockTable[block].size = blocksize;