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Guilhem Lavaux 2017-01-16 13:34:50 +01:00
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415
FindHDF5.cmake
View File

@ -1,351 +1,86 @@
# - Find HDF5, a library for reading and writing self describing array data.
#
# This module invokes the HDF5 wrapper compiler that should be installed
# alongside HDF5. Depending upon the HDF5 Configuration, the wrapper compiler
# is called either h5cc or h5pcc. If this succeeds, the module will then call
# the compiler with the -show argument to see what flags are used when compiling
# an HDF5 client application.
# To be used by projects that make use of Cmakeified hdf5-1.8.17
#
# The module will optionally accept the COMPONENTS argument. If no COMPONENTS
# are specified, then the find module will default to finding only the HDF5 C
# library. If one or more COMPONENTS are specified, the module will attempt to
# find the language bindings for the specified components. The only valid
# components are C, CXX, Fortran, HL, and Fortran_HL. If the COMPONENTS
# argument is not given, the module will attempt to find only the C bindings.
#
# On UNIX systems, this module will read the variable HDF5_USE_STATIC_LIBRARIES
# to determine whether or not to prefer a static link to a dynamic link for HDF5
# and all of it's dependencies. To use this feature, make sure that the
# HDF5_USE_STATIC_LIBRARIES variable is set before the call to find_package.
#
# To provide the module with a hint about where to find your HDF5 installation,
# you can set the environment variable HDF5_ROOT. The Find module will then
# look in this path when searching for HDF5 executables, paths, and libraries.
#
# In addition to finding the includes and libraries required to compile an HDF5
# client application, this module also makes an effort to find tools that come
# with the HDF5 distribution that may be useful for regression testing.
#
# This module will define the following variables:
# HDF5_INCLUDE_DIRS - Location of the hdf5 includes
# HDF5_INCLUDE_DIR - Location of the hdf5 includes (deprecated)
# HDF5_DEFINITIONS - Required compiler definitions for HDF5
# HDF5_C_LIBRARIES - Required libraries for the HDF5 C bindings.
# HDF5_CXX_LIBRARIES - Required libraries for the HDF5 C++ bindings
# HDF5_Fortran_LIBRARIES - Required libraries for the HDF5 Fortran bindings
# HDF5_HL_LIBRARIES - Required libraries for the HDF5 high level API
# HDF5_Fortran_HL_LIBRARIES - Required libraries for the high level Fortran
# bindings.
# HDF5_LIBRARIES - Required libraries for all requested bindings
# HDF5_FOUND - true if HDF5 was found on the system
# HDF5_LIBRARY_DIRS - the full set of library directories
# HDF5_IS_PARALLEL - Whether or not HDF5 was found with parallel IO support
# HDF5_C_COMPILER_EXECUTABLE - the path to the HDF5 C wrapper compiler
# HDF5_CXX_COMPILER_EXECUTABLE - the path to the HDF5 C++ wrapper compiler
# HDF5_Fortran_COMPILER_EXECUTABLE - the path to the HDF5 Fortran wrapper compiler
# HDF5_DIFF_EXECUTABLE - the path to the HDF5 dataset comparison tool
#=============================================================================
# Copyright 2009 Kitware, Inc.
#
# Distributed under the OSI-approved BSD License (the "License");
# see accompanying file Copyright.txt for details.
# 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.
#
# This software is distributed WITHOUT ANY WARRANTY; without even the
# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the License for more information.
#=============================================================================
# (To distribute this file outside of CMake, substitute the full
# License text for the above reference.)
# 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
# This module is maintained by Will Dicharry <wdicharry@stellarscience.com>.
include (SelectLibraryConfigurations)
include (FindPackageHandleStandardArgs)
include(SelectLibraryConfigurations)
include(FindPackageHandleStandardArgs)
# List of the valid HDF5 components
set( HDF5_VALID_COMPONENTS
C
CXX
Fortran
HL
Fortran_HL
# 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
)
# Validate the list of find components.
if( NOT HDF5_FIND_COMPONENTS )
set( HDF5_LANGUAGE_BINDINGS "C" )
else()
# add the extra specified components, ensuring that they are valid.
foreach( component ${HDF5_FIND_COMPONENTS} )
list( FIND HDF5_VALID_COMPONENTS ${component} component_location )
if( ${component_location} EQUAL -1 )
message( FATAL_ERROR
"\"${component}\" is not a valid HDF5 component." )
else()
list( APPEND HDF5_LANGUAGE_BINDINGS ${component} )
endif()
endforeach()
endif()
# try to find the HDF5 wrapper compilers
find_program( HDF5_C_COMPILER_EXECUTABLE
NAMES h5cc h5pcc
HINTS ENV HDF5_ROOT
PATH_SUFFIXES bin Bin
DOC "HDF5 Wrapper compiler. Used only to detect HDF5 compile flags." )
mark_as_advanced( HDF5_C_COMPILER_EXECUTABLE )
find_program( HDF5_CXX_COMPILER_EXECUTABLE
NAMES h5c++ h5pc++
HINTS ENV HDF5_ROOT
PATH_SUFFIXES bin Bin
DOC "HDF5 C++ Wrapper compiler. Used only to detect HDF5 compile flags." )
mark_as_advanced( HDF5_CXX_COMPILER_EXECUTABLE )
find_program( HDF5_Fortran_COMPILER_EXECUTABLE
NAMES h5fc h5pfc
HINTS ENV HDF5_ROOT
PATH_SUFFIXES bin Bin
DOC "HDF5 Fortran Wrapper compiler. Used only to detect HDF5 compile flags." )
mark_as_advanced( HDF5_Fortran_COMPILER_EXECUTABLE )
find_program( HDF5_DIFF_EXECUTABLE
NAMES h5diff
HINTS ENV HDF5_ROOT
PATH_SUFFIXES bin Bin
DOC "HDF5 file differencing tool." )
mark_as_advanced( HDF5_DIFF_EXECUTABLE )
# Invoke the HDF5 wrapper compiler. The compiler return value is stored to the
# return_value argument, the text output is stored to the output variable.
macro( _HDF5_invoke_compiler language output return_value )
if( HDF5_${language}_COMPILER_EXECUTABLE )
exec_program( ${HDF5_${language}_COMPILER_EXECUTABLE}
ARGS -show
OUTPUT_VARIABLE ${output}
RETURN_VALUE ${return_value}
)
if( ${${return_value}} EQUAL 0 )
# do nothing
else()
message( STATUS
"Unable to determine HDF5 ${language} flags from HDF5 wrapper." )
endif()
endif()
endmacro()
# Parse a compile line for definitions, includes, library paths, and libraries.
macro( _HDF5_parse_compile_line
compile_line_var
include_paths
definitions
library_paths
libraries )
# Match the include paths
string( REGEX MATCHALL "-I([^\" ]+)" include_path_flags
"${${compile_line_var}}"
)
foreach( IPATH ${include_path_flags} )
string( REGEX REPLACE "^-I" "" IPATH ${IPATH} )
string( REGEX REPLACE "//" "/" IPATH ${IPATH} )
list( APPEND ${include_paths} ${IPATH} )
endforeach()
# Match the definitions
string( REGEX MATCHALL "-D[^ ]*" definition_flags "${${compile_line_var}}" )
foreach( DEF ${definition_flags} )
list( APPEND ${definitions} ${DEF} )
endforeach()
# Match the library paths
string( REGEX MATCHALL "-L([^\" ]+|\"[^\"]+\")" library_path_flags
"${${compile_line_var}}"
)
foreach( LPATH ${library_path_flags} )
string( REGEX REPLACE "^-L" "" LPATH ${LPATH} )
string( REGEX REPLACE "//" "/" LPATH ${LPATH} )
list( APPEND ${library_paths} ${LPATH} )
endforeach()
# now search for the library names specified in the compile line (match -l...)
# match only -l's preceded by a space or comma
# this is to exclude directory names like xxx-linux/
string( REGEX MATCHALL "[, ]-l([^\", ]+)" library_name_flags
"${${compile_line_var}}" )
# strip the -l from all of the library flags and add to the search list
foreach( LIB ${library_name_flags} )
string( REGEX REPLACE "^[, ]-l" "" LIB ${LIB} )
list( APPEND ${libraries} ${LIB} )
endforeach()
endmacro()
# Try to find HDF5 using an installed hdf5-config.cmake
if( NOT HDF5_FOUND )
find_package( HDF5 QUIET NO_MODULE )
if( HDF5_FOUND )
set( HDF5_INCLUDE_DIRS ${HDF5_INCLUDE_DIR} )
set( HDF5_LIBRARIES )
set( HDF5_C_TARGET hdf5 )
set( HDF5_CXX_TARGET hdf5_cpp )
set( HDF5_HL_TARGET hdf5_hl )
set( HDF5_Fortran_TARGET hdf5_fortran )
set( HDF5_Fortran_HL_TARGET hdf5_hl_fortran )
foreach( _component ${HDF5_LANGUAGE_BINDINGS} )
list( FIND HDF5_VALID_COMPONENTS ${_component} _component_location )
get_target_property( _comp_location ${HDF5_${_component}_TARGET} LOCATION )
if( _comp_location )
set( HDF5_${_component}_LIBRARY ${_comp_location} CACHE PATH
"HDF5 ${_component} library" )
mark_as_advanced( HDF5_${_component}_LIBRARY )
list( APPEND HDF5_LIBRARIES ${HDF5_${_component}_LIBRARY} )
endif()
endforeach()
endif()
endif()
if( NOT HDF5_FOUND )
_HDF5_invoke_compiler( C HDF5_C_COMPILE_LINE HDF5_C_RETURN_VALUE )
_HDF5_invoke_compiler( CXX HDF5_CXX_COMPILE_LINE HDF5_CXX_RETURN_VALUE )
_HDF5_invoke_compiler( Fortran HDF5_Fortran_COMPILE_LINE HDF5_Fortran_RETURN_VALUE )
# seed the initial lists of libraries to find with items we know we need
set( HDF5_C_LIBRARY_NAMES_INIT hdf5 )
set( HDF5_HL_LIBRARY_NAMES_INIT hdf5_hl ${HDF5_C_LIBRARY_NAMES_INIT} )
set( HDF5_CXX_LIBRARY_NAMES_INIT hdf5_cpp ${HDF5_C_LIBRARY_NAMES_INIT} )
set( HDF5_Fortran_LIBRARY_NAMES_INIT hdf5_fortran
${HDF5_C_LIBRARY_NAMES_INIT} )
set( HDF5_Fortran_HL_LIBRARY_NAMES_INIT hdf5hl_fortran
${HDF5_Fortran_LIBRARY_NAMES_INIT} )
foreach( LANGUAGE ${HDF5_LANGUAGE_BINDINGS} )
if( HDF5_${LANGUAGE}_COMPILE_LINE )
_HDF5_parse_compile_line( HDF5_${LANGUAGE}_COMPILE_LINE
HDF5_${LANGUAGE}_INCLUDE_FLAGS
HDF5_${LANGUAGE}_DEFINITIONS
HDF5_${LANGUAGE}_LIBRARY_DIRS
HDF5_${LANGUAGE}_LIBRARY_NAMES
)
# take a guess that the includes may be in the 'include' sibling
# directory of a library directory.
foreach( dir ${HDF5_${LANGUAGE}_LIBRARY_DIRS} )
list( APPEND HDF5_${LANGUAGE}_INCLUDE_FLAGS ${dir}/../include )
endforeach()
endif()
# set the definitions for the language bindings.
list( APPEND HDF5_DEFINITIONS ${HDF5_${LANGUAGE}_DEFINITIONS} )
# find the HDF5 include directories
if(${LANGUAGE} MATCHES "Fortran.*")
set(HDF5_INCLUDE_FILENAME hdf5.mod)
else()
set(HDF5_INCLUDE_FILENAME hdf5.h)
endif()
find_path( HDF5_${LANGUAGE}_INCLUDE_DIR ${HDF5_INCLUDE_FILENAME}
HINTS
${HDF5_${LANGUAGE}_INCLUDE_FLAGS}
ENV
HDF5_ROOT
PATHS
$ENV{HOME}/.local/include
PATH_SUFFIXES
include
Include
)
mark_as_advanced( HDF5_${LANGUAGE}_INCLUDE_DIR )
list( APPEND HDF5_INCLUDE_DIRS ${HDF5_${LANGUAGE}_INCLUDE_DIR} )
set( HDF5_${LANGUAGE}_LIBRARY_NAMES
${HDF5_${LANGUAGE}_LIBRARY_NAMES_INIT}
${HDF5_${LANGUAGE}_LIBRARY_NAMES} )
# find the HDF5 libraries
foreach( LIB ${HDF5_${LANGUAGE}_LIBRARY_NAMES} )
if( UNIX AND HDF5_USE_STATIC_LIBRARIES )
# According to bug 1643 on the CMake bug tracker, this is the
# preferred method for searching for a static library.
# See http://www.cmake.org/Bug/view.php?id=1643. We search
# first for the full static library name, but fall back to a
# generic search on the name if the static search fails.
set( THIS_LIBRARY_SEARCH_DEBUG lib${LIB}d.a ${LIB}d )
set( THIS_LIBRARY_SEARCH_RELEASE lib${LIB}.a ${LIB} )
else()
set( THIS_LIBRARY_SEARCH_DEBUG ${LIB}d )
set( THIS_LIBRARY_SEARCH_RELEASE ${LIB} )
endif()
find_library( HDF5_${LIB}_LIBRARY_DEBUG
NAMES ${THIS_LIBRARY_SEARCH_DEBUG}
HINTS ${HDF5_${LANGUAGE}_LIBRARY_DIRS}
ENV HDF5_ROOT
PATH_SUFFIXES lib Lib )
find_library( HDF5_${LIB}_LIBRARY_RELEASE
NAMES ${THIS_LIBRARY_SEARCH_RELEASE}
HINTS ${HDF5_${LANGUAGE}_LIBRARY_DIRS}
ENV HDF5_ROOT
PATH_SUFFIXES lib Lib )
select_library_configurations( HDF5_${LIB} )
list(APPEND HDF5_${LANGUAGE}_LIBRARIES ${HDF5_${LIB}_LIBRARY})
endforeach()
list( APPEND HDF5_LIBRARY_DIRS ${HDF5_${LANGUAGE}_LIBRARY_DIRS} )
# Append the libraries for this language binding to the list of all
# required libraries.
list(APPEND HDF5_LIBRARIES ${HDF5_${LANGUAGE}_LIBRARIES})
endforeach()
# We may have picked up some duplicates in various lists during the above
# process for the language bindings (both the C and C++ bindings depend on
# libz for example). Remove the duplicates. It appears that the default
# CMake behavior is to remove duplicates from the end of a list. However,
# for link lines, this is incorrect since unresolved symbols are searched
# for down the link line. Therefore, we reverse the list, remove the
# duplicates, and then reverse it again to get the duplicates removed from
# the beginning.
macro( _remove_duplicates_from_beginning _list_name )
list( REVERSE ${_list_name} )
list( REMOVE_DUPLICATES ${_list_name} )
list( REVERSE ${_list_name} )
endmacro()
if( HDF5_INCLUDE_DIRS )
_remove_duplicates_from_beginning( HDF5_INCLUDE_DIRS )
endif()
if( HDF5_LIBRARY_DIRS )
_remove_duplicates_from_beginning( HDF5_LIBRARY_DIRS )
endif()
# If the HDF5 include directory was found, open H5pubconf.h to determine if
# HDF5 was compiled with parallel IO support
set( HDF5_IS_PARALLEL FALSE )
foreach( _dir IN LISTS HDF5_INCLUDE_DIRS )
if( EXISTS "${_dir}/H5pubconf.h" )
file( STRINGS "${_dir}/H5pubconf.h"
HDF5_HAVE_PARALLEL_DEFINE
REGEX "HAVE_PARALLEL 1" )
if( HDF5_HAVE_PARALLEL_DEFINE )
set( HDF5_IS_PARALLEL TRUE )
endif()
endif()
endforeach()
set( HDF5_IS_PARALLEL ${HDF5_IS_PARALLEL} CACHE BOOL
"HDF5 library compiled with parallel IO support" )
mark_as_advanced( HDF5_IS_PARALLEL )
# For backwards compatibility we set HDF5_INCLUDE_DIR to the value of
# HDF5_INCLUDE_DIRS
if( HDF5_INCLUDE_DIRS )
set( HDF5_INCLUDE_DIR "${HDF5_INCLUDE_DIRS}" )
endif()
endif()
find_package_handle_standard_args( HDF5 DEFAULT_MSG
HDF5_LIBRARIES
HDF5_INCLUDE_DIRS
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)

5
external/external_build.cmake vendored
View File

@ -86,7 +86,10 @@ else (INTERNAL_HDF5)
if(HDF5_ROOTDIR)
SET(ENV{HDF5_ROOT} ${HDF5_ROOTDIR})
endif(HDF5_ROOTDIR)
find_package(HDF5 COMPONENTS C CXX HL)
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)
endif (INTERNAL_HDF5)
foreach(include_dir ${HDF5_INCLUDE_DIR})

29
src/hdf5_array.hpp
View File

@ -202,6 +202,29 @@ namespace CosmoTool {
}
};
class hdf5_StringType
{
public:
H5::StrType type;
hdf5_StringType()
: type(0, H5T_VARIABLE)
{
}
static const hdf5_StringType *ctype()
{
static hdf5_StringType singleton;
return &singleton;
}
};
template<> struct get_hdf5_data_type<std::string> {
static H5::DataType type() {
return hdf5_StringType::ctype()->type;
}
};
class hdf5_BoolType
{
public:
@ -286,7 +309,7 @@ namespace CosmoTool {
template<typename ArrayType>
void hdf5_check_array(ArrayType& data, std::vector<hsize_t>& dims) {
for (long i = 0; i < data.num_dimensions(); i++) {
for (size_t i = 0; i < data.num_dimensions(); i++) {
if (data.shape()[i] != dims[i]) {
throw InvalidDimensions();
}
@ -295,7 +318,7 @@ namespace CosmoTool {
template<typename ArrayType>
void hdf5_weak_check_array(ArrayType& data, std::vector<hsize_t>& dims) {
for (long i = 0; i < data.num_dimensions(); i++) {
for (size_t i = 0; i < data.num_dimensions(); i++) {
if (data.index_bases()[i] < 0) {
// Negative indexes are not supported right now.
throw InvalidDimensions();
@ -326,7 +349,7 @@ namespace CosmoTool {
H5::DataSpace dataspace = dataset.getSpace();
std::vector<hsize_t> dimensions(data.num_dimensions());
if (dataspace.getSimpleExtentNdims() != data.num_dimensions())
if ((size_t)dataspace.getSimpleExtentNdims() != (size_t)data.num_dimensions())
{
throw InvalidDimensions();
}