mirror of
https://github.com/openmc-dev/openmc.git
synced 2026-07-28 14:15:42 -04:00
Rely on FindHDF5 rather than h5fc and h5pfc scripts
The FindHDF5.cmake packaged with CMake is broken in a number of respects. The HL components don't work (debian has a patch in cmake-data). It's also impossible to prefer a parallel installation if both h5fc and h5pfc appear on your PATH. Finally, hdf5_hl is not included in the list of libraries needed for the Fortran_HL component. A local version of FindHDF5 is used here which fixes all these issues. This enables one to compile OpenMC with MPI + serial HDF5 if needed by introducing the PHDF5 preprocessor flag.
This commit is contained in:
Paul Romano
parent
4db5ff01bd
commit
3c1ba76f95
5 changed files with 508 additions and 53 deletions
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@ -7,6 +7,9 @@ set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
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set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
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set(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/include)
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# Set module path
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set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules)
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# Make sure Fortran module directory is included when building
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include_directories(${CMAKE_BINARY_DIR}/include)
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@ -35,14 +38,12 @@ set(maxcoord 10 CACHE STRING "Maximum number of nested coordinate levels")
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add_definitions(-DMAX_COORD=${maxcoord})
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#===============================================================================
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# MPI for distributed-memory parallelism / HDF5 for binary output
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# MPI for distributed-memory parallelism
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#===============================================================================
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set(MPI_ENABLED FALSE)
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if($ENV{FC} MATCHES "h5fc$")
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message("-- Detected HDF5 wrapper: $ENV{FC}")
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elseif($ENV{FC} MATCHES "h5pfc$")
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message("-- Detected parallel HDF5 wrapper: $ENV{FC}")
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if($ENV{FC} MATCHES "mpi[^/]*$")
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message("-- Detected MPI wrapper: $ENV{FC}")
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add_definitions(-DMPI)
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set(MPI_ENABLED TRUE)
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endif()
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@ -53,6 +54,33 @@ if(MPI_ENABLED AND mpif08)
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add_definitions(-DMPIF08)
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endif()
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#===============================================================================
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# HDF5 for binary output
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#===============================================================================
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# Unfortunately FindHDF5.cmake will always prefer a serial HDF5 installation
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# over a parallel installation if both appear on the user's PATH. To get around
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# this, we check for the environment variable HDF5_ROOT and if it exists, use it
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# to check whether its a parallel version.
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if(DEFINED ENV{HDF5_ROOT} AND EXISTS $ENV{HDF5_ROOT}/bin/h5pcc)
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set(HDF5_PREFER_PARALLEL TRUE)
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else()
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set(HDF5_PREFER_PARALLEL FALSE)
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endif()
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find_package(HDF5 COMPONENTS Fortran_HL)
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if(NOT HDF5_FOUND)
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message(FATAL_ERROR "Could not find HDF5")
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endif()
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if(HDF5_IS_PARALLEL)
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if(NOT MPI_ENABLED)
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message(FATAL_ERROR "Parallel HDF5 must be used with MPI.")
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endif()
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add_definitions(-DPHDF5)
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message("-- Using parallel HDF5")
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endif()
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#===============================================================================
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# Set compile/link flags based on which compiler is being used
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#===============================================================================
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@ -212,6 +240,14 @@ set(program "openmc")
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file(GLOB source src/*.F90 src/xml/openmc_fox.F90)
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add_executable(${program} ${source})
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# target_include_directories was added in CMake 2.8.11 and is the recommended
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# way to set include directories. For lesser versions, we revert to set_property
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if(CMAKE_VERSION VERSION_LESS 2.8.11)
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include_directories(${HDF5_INCLUDE_DIRS})
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else()
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target_include_directories(${program} PUBLIC ${HDF5_INCLUDE_DIRS})
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endif()
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# target_compile_options was added in CMake 2.8.12 and is the recommended way to
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# set compile flags. Note that this sets the COMPILE_OPTIONS property (also
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# available only in 2.8.12+) rather than the COMPILE_FLAGS property, which is
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@ -225,7 +261,7 @@ endif()
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# target_link_libraries treats any arguments starting with - but not -l as
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# linker flags. Thus, we can pass both linker flags and libraries together.
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target_link_libraries(${program} ${ldflags} ${libraries} fox_dom)
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target_link_libraries(${program} ${ldflags} ${HDF5_LIBRARIES} fox_dom)
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#===============================================================================
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# Install executable, scripts, manpage, license
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407
cmake/Modules/FindHDF5.cmake
Normal file
407
cmake/Modules/FindHDF5.cmake
Normal file
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@ -0,0 +1,407 @@
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#.rst:
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# FindHDF5
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# --------
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#
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# Find HDF5, a library for reading and writing self describing array data.
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#
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#
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#
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# This module invokes the HDF5 wrapper compiler that should be installed
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# alongside HDF5. Depending upon the HDF5 Configuration, the wrapper
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# compiler is called either h5cc or h5pcc. If this succeeds, the module
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# will then call the compiler with the -show argument to see what flags
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# are used when compiling an HDF5 client application.
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#
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# The module will optionally accept the COMPONENTS argument. If no
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# COMPONENTS are specified, then the find module will default to finding
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# only the HDF5 C library. If one or more COMPONENTS are specified, the
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# module will attempt to find the language bindings for the specified
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# components. The only valid components are C, CXX, Fortran, HL, and
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# Fortran_HL. If the COMPONENTS argument is not given, the module will
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# attempt to find only the C bindings.
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#
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# On UNIX systems, this module will read the variable
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# HDF5_USE_STATIC_LIBRARIES to determine whether or not to prefer a
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# static link to a dynamic link for HDF5 and all of it's dependencies.
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# To use this feature, make sure that the HDF5_USE_STATIC_LIBRARIES
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# variable is set before the call to find_package.
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#
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# To provide the module with a hint about where to find your HDF5
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# installation, you can set the environment variable HDF5_ROOT. The
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# Find module will then look in this path when searching for HDF5
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# executables, paths, and libraries.
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#
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# In addition to finding the includes and libraries required to compile
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# an HDF5 client application, this module also makes an effort to find
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# tools that come with the HDF5 distribution that may be useful for
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# regression testing.
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#
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# This module will define the following variables:
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#
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# ::
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#
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# HDF5_INCLUDE_DIRS - Location of the hdf5 includes
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# HDF5_INCLUDE_DIR - Location of the hdf5 includes (deprecated)
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# HDF5_DEFINITIONS - Required compiler definitions for HDF5
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# HDF5_C_LIBRARIES - Required libraries for the HDF5 C bindings.
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# HDF5_CXX_LIBRARIES - Required libraries for the HDF5 C++ bindings
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# HDF5_Fortran_LIBRARIES - Required libraries for the HDF5 Fortran bindings
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# HDF5_HL_LIBRARIES - Required libraries for the HDF5 high level API
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# HDF5_Fortran_HL_LIBRARIES - Required libraries for the high level Fortran
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# bindings.
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# HDF5_LIBRARIES - Required libraries for all requested bindings
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# HDF5_FOUND - true if HDF5 was found on the system
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# HDF5_VERSION - HDF5 version in format Major.Minor.Release
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# HDF5_LIBRARY_DIRS - the full set of library directories
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# HDF5_IS_PARALLEL - Whether or not HDF5 was found with parallel IO support
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# HDF5_C_COMPILER_EXECUTABLE - the path to the HDF5 C wrapper compiler
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# HDF5_CXX_COMPILER_EXECUTABLE - the path to the HDF5 C++ wrapper compiler
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# HDF5_Fortran_COMPILER_EXECUTABLE - the path to the HDF5 Fortran wrapper compiler
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# HDF5_DIFF_EXECUTABLE - the path to the HDF5 dataset comparison tool
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#=============================================================================
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# Copyright 2015 Axel Huebl, Helmholtz-Zentrum Dresden - Rossendorf
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# Copyright 2009 Kitware, Inc.
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#
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# Distributed under the OSI-approved BSD License (the "License");
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# see accompanying file Copyright.txt for details.
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#
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# This software is distributed WITHOUT ANY WARRANTY; without even the
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# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
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# See the License for more information.
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#=============================================================================
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# (To distribute this file outside of CMake, substitute the full
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# License text for the above reference.)
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# This module is maintained by Will Dicharry <wdicharry@stellarscience.com>.
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include(SelectLibraryConfigurations)
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include(FindPackageHandleStandardArgs)
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# List of the valid HDF5 components
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set( HDF5_VALID_COMPONENTS
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C
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CXX
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Fortran
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HL
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Fortran_HL
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)
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# Validate the list of find components.
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if( NOT HDF5_FIND_COMPONENTS )
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set( HDF5_LANGUAGE_BINDINGS "C" )
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else()
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# add the extra specified components, ensuring that they are valid.
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foreach( component ${HDF5_FIND_COMPONENTS} )
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list( FIND HDF5_VALID_COMPONENTS ${component} component_location )
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if( ${component_location} EQUAL -1 )
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message( FATAL_ERROR
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"\"${component}\" is not a valid HDF5 component." )
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else()
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list( APPEND HDF5_LANGUAGE_BINDINGS ${component} )
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endif()
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endforeach()
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endif()
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if(HDF5_PREFER_PARALLEL)
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# try to find the HDF5 wrapper compilers
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find_program( HDF5_C_COMPILER_EXECUTABLE
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NAMES h5pcc h5cc
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HINTS ENV HDF5_ROOT
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PATH_SUFFIXES bin Bin
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DOC "HDF5 Wrapper compiler. Used only to detect HDF5 compile flags." )
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mark_as_advanced( HDF5_C_COMPILER_EXECUTABLE )
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find_program( HDF5_CXX_COMPILER_EXECUTABLE
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NAMES h5pc++ h5c++
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HINTS ENV HDF5_ROOT
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PATH_SUFFIXES bin Bin
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DOC "HDF5 C++ Wrapper compiler. Used only to detect HDF5 compile flags." )
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mark_as_advanced( HDF5_CXX_COMPILER_EXECUTABLE )
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find_program( HDF5_Fortran_COMPILER_EXECUTABLE
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NAMES h5pfc h5fc
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HINTS ENV HDF5_ROOT
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PATH_SUFFIXES bin Bin
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DOC "HDF5 Fortran Wrapper compiler. Used only to detect HDF5 compile flags." )
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mark_as_advanced( HDF5_Fortran_COMPILER_EXECUTABLE )
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else()
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# try to find the HDF5 wrapper compilers
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find_program( HDF5_C_COMPILER_EXECUTABLE
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NAMES h5cc h5pcc
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HINTS ENV HDF5_ROOT
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PATH_SUFFIXES bin Bin
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DOC "HDF5 Wrapper compiler. Used only to detect HDF5 compile flags." )
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mark_as_advanced( HDF5_C_COMPILER_EXECUTABLE )
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find_program( HDF5_CXX_COMPILER_EXECUTABLE
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NAMES h5c++ h5pc++
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HINTS ENV HDF5_ROOT
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PATH_SUFFIXES bin Bin
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DOC "HDF5 C++ Wrapper compiler. Used only to detect HDF5 compile flags." )
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mark_as_advanced( HDF5_CXX_COMPILER_EXECUTABLE )
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find_program( HDF5_Fortran_COMPILER_EXECUTABLE
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NAMES h5fc h5pfc
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HINTS ENV HDF5_ROOT
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PATH_SUFFIXES bin Bin
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DOC "HDF5 Fortran Wrapper compiler. Used only to detect HDF5 compile flags." )
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mark_as_advanced( HDF5_Fortran_COMPILER_EXECUTABLE )
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endif()
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find_program( HDF5_DIFF_EXECUTABLE
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NAMES h5diff
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HINTS ENV HDF5_ROOT
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PATH_SUFFIXES bin Bin
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DOC "HDF5 file differencing tool." )
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mark_as_advanced( HDF5_DIFF_EXECUTABLE )
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# Invoke the HDF5 wrapper compiler. The compiler return value is stored to the
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# return_value argument, the text output is stored to the output variable.
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macro( _HDF5_invoke_compiler language output return_value )
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if( HDF5_${language}_COMPILER_EXECUTABLE )
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exec_program( ${HDF5_${language}_COMPILER_EXECUTABLE}
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ARGS -show
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OUTPUT_VARIABLE ${output}
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RETURN_VALUE ${return_value}
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)
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if( ${${return_value}} EQUAL 0 )
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# do nothing
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else()
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message( STATUS
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"Unable to determine HDF5 ${language} flags from HDF5 wrapper." )
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endif()
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endif()
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endmacro()
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# Parse a compile line for definitions, includes, library paths, and libraries.
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macro( _HDF5_parse_compile_line
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compile_line_var
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include_paths
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definitions
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library_paths
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libraries )
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# Match the include paths
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string( REGEX MATCHALL "-I([^\" ]+)" include_path_flags
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"${${compile_line_var}}"
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)
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foreach( IPATH ${include_path_flags} )
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string( REGEX REPLACE "^-I" "" IPATH ${IPATH} )
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string( REPLACE "//" "/" IPATH ${IPATH} )
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list( APPEND ${include_paths} ${IPATH} )
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endforeach()
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# Match the definitions
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string( REGEX MATCHALL "-D[^ ]*" definition_flags "${${compile_line_var}}" )
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foreach( DEF ${definition_flags} )
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list( APPEND ${definitions} ${DEF} )
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endforeach()
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# Match the library paths
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string( REGEX MATCHALL "-L([^\" ]+|\"[^\"]+\")" library_path_flags
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"${${compile_line_var}}"
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)
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foreach( LPATH ${library_path_flags} )
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string( REGEX REPLACE "^-L" "" LPATH ${LPATH} )
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string( REPLACE "//" "/" LPATH ${LPATH} )
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list( APPEND ${library_paths} ${LPATH} )
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endforeach()
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# now search for the library names specified in the compile line (match -l...)
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# match only -l's preceded by a space or comma
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# this is to exclude directory names like xxx-linux/
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string( REGEX MATCHALL "[, ]-l([^\", ]+)" library_name_flags
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"${${compile_line_var}}" )
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# strip the -l from all of the library flags and add to the search list
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foreach( LIB ${library_name_flags} )
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string( REGEX REPLACE "^[, ]-l" "" LIB ${LIB} )
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list( APPEND ${libraries} ${LIB} )
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endforeach()
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endmacro()
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# Try to find HDF5 using an installed hdf5-config.cmake
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if( NOT HDF5_FOUND )
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find_package( HDF5 QUIET NO_MODULE )
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if( HDF5_FOUND )
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set( HDF5_INCLUDE_DIRS ${HDF5_INCLUDE_DIR} )
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set( HDF5_LIBRARIES )
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set( HDF5_C_TARGET hdf5 )
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set( HDF5_CXX_TARGET hdf5_cpp )
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set( HDF5_HL_TARGET hdf5_hl )
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set( HDF5_Fortran_TARGET hdf5_fortran )
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set( HDF5_Fortran_HL_TARGET hdf5_hl_fortran )
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foreach( _component ${HDF5_LANGUAGE_BINDINGS} )
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list( FIND HDF5_VALID_COMPONENTS ${_component} _component_location )
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get_target_property( _comp_location ${HDF5_${_component}_TARGET} LOCATION )
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if( _comp_location )
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set( HDF5_${_component}_LIBRARY ${_comp_location} CACHE PATH
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"HDF5 ${_component} library" )
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mark_as_advanced( HDF5_${_component}_LIBRARY )
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list( APPEND HDF5_LIBRARIES ${HDF5_${_component}_LIBRARY} )
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endif()
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endforeach()
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endif()
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endif()
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if( NOT HDF5_FOUND )
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_HDF5_invoke_compiler( C HDF5_C_COMPILE_LINE HDF5_C_RETURN_VALUE )
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_HDF5_invoke_compiler( CXX HDF5_CXX_COMPILE_LINE HDF5_CXX_RETURN_VALUE )
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_HDF5_invoke_compiler( Fortran HDF5_Fortran_COMPILE_LINE HDF5_Fortran_RETURN_VALUE )
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set(HDF5_HL_COMPILE_LINE ${HDF5_C_COMPILE_LINE})
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set(HDF5_Fortran_HL_COMPILE_LINE ${HDF5_Fortran_COMPILE_LINE})
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# seed the initial lists of libraries to find with items we know we need
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set( HDF5_C_LIBRARY_NAMES_INIT hdf5 )
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set( HDF5_HL_LIBRARY_NAMES_INIT hdf5_hl ${HDF5_C_LIBRARY_NAMES_INIT} )
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set( HDF5_CXX_LIBRARY_NAMES_INIT hdf5_cpp ${HDF5_C_LIBRARY_NAMES_INIT} )
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set( HDF5_Fortran_LIBRARY_NAMES_INIT hdf5_fortran
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${HDF5_C_LIBRARY_NAMES_INIT} )
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set( HDF5_Fortran_HL_LIBRARY_NAMES_INIT hdf5hl_fortran hdf5_hl
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${HDF5_Fortran_LIBRARY_NAMES_INIT} )
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foreach( LANGUAGE ${HDF5_LANGUAGE_BINDINGS} )
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if( HDF5_${LANGUAGE}_COMPILE_LINE )
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_HDF5_parse_compile_line( HDF5_${LANGUAGE}_COMPILE_LINE
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HDF5_${LANGUAGE}_INCLUDE_FLAGS
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HDF5_${LANGUAGE}_DEFINITIONS
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HDF5_${LANGUAGE}_LIBRARY_DIRS
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HDF5_${LANGUAGE}_LIBRARY_NAMES
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)
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# take a guess that the includes may be in the 'include' sibling
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# directory of a library directory.
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foreach( dir ${HDF5_${LANGUAGE}_LIBRARY_DIRS} )
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list( APPEND HDF5_${LANGUAGE}_INCLUDE_FLAGS ${dir}/../include )
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endforeach()
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endif()
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# set the definitions for the language bindings.
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list( APPEND HDF5_DEFINITIONS ${HDF5_${LANGUAGE}_DEFINITIONS} )
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||||
# find the HDF5 include directories
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if(${LANGUAGE} MATCHES "Fortran")
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set(HDF5_INCLUDE_FILENAME hdf5.mod)
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else()
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set(HDF5_INCLUDE_FILENAME hdf5.h)
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endif()
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find_path( HDF5_${LANGUAGE}_INCLUDE_DIR ${HDF5_INCLUDE_FILENAME}
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HINTS
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${HDF5_${LANGUAGE}_INCLUDE_FLAGS}
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ENV
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HDF5_ROOT
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PATHS
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$ENV{HOME}/.local/include
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PATH_SUFFIXES
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include
|
||||
Include
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||||
)
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mark_as_advanced( HDF5_${LANGUAGE}_INCLUDE_DIR )
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list( APPEND HDF5_INCLUDE_DIRS ${HDF5_${LANGUAGE}_INCLUDE_DIR} )
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||||
set( HDF5_${LANGUAGE}_LIBRARY_NAMES
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${HDF5_${LANGUAGE}_LIBRARY_NAMES_INIT}
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||||
${HDF5_${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 ${_list_name} )
|
||||
endmacro()
|
||||
|
||||
if( HDF5_INCLUDE_DIRS )
|
||||
_remove_duplicates_from_beginning( HDF5_INCLUDE_DIRS )
|
||||
endif()
|
||||
if( HDF5_LIBRARY_DIRS )
|
||||
_remove_duplicates_from_beginning( HDF5_LIBRARY_DIRS )
|
||||
endif()
|
||||
if( HDF5_LIBRARIES )
|
||||
_remove_duplicates_from_beginning( HDF5_LIBRARIES )
|
||||
endif()
|
||||
|
||||
# If the HDF5 include directory was found, open H5pubconf.h to determine if
|
||||
# HDF5 was compiled with parallel IO support
|
||||
set( HDF5_IS_PARALLEL FALSE )
|
||||
set( HDF5_VERSION "" )
|
||||
foreach( _dir IN LISTS HDF5_INCLUDE_DIRS )
|
||||
foreach(_hdr "${_dir}/H5pubconf.h" "${_dir}/H5pubconf-64.h" "${_dir}/H5pubconf-32.h")
|
||||
if( EXISTS "${_hdr}" )
|
||||
file( STRINGS "${_hdr}"
|
||||
HDF5_HAVE_PARALLEL_DEFINE
|
||||
REGEX "HAVE_PARALLEL 1" )
|
||||
if( HDF5_HAVE_PARALLEL_DEFINE )
|
||||
set( HDF5_IS_PARALLEL TRUE )
|
||||
endif()
|
||||
unset(HDF5_HAVE_PARALLEL_DEFINE)
|
||||
|
||||
file( STRINGS "${_hdr}"
|
||||
HDF5_VERSION_DEFINE
|
||||
REGEX "^[ \t]*#[ \t]*define[ \t]+H5_VERSION[ \t]+" )
|
||||
if( "${HDF5_VERSION_DEFINE}" MATCHES
|
||||
"H5_VERSION[ \t]+\"([0-9]+\\.[0-9]+\\.[0-9]+).*\"" )
|
||||
set( HDF5_VERSION "${CMAKE_MATCH_1}" )
|
||||
endif()
|
||||
unset(HDF5_VERSION_DEFINE)
|
||||
endif()
|
||||
endforeach()
|
||||
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
|
||||
REQUIRED_VARS HDF5_LIBRARIES HDF5_INCLUDE_DIRS
|
||||
VERSION_VAR HDF5_VERSION
|
||||
)
|
||||
|
|
@ -4,7 +4,7 @@ module hdf5_interface
|
|||
use h5lt
|
||||
use, intrinsic :: ISO_C_BINDING
|
||||
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
use message_passing, only: MPI_COMM_WORLD, MPI_INFO_NULL
|
||||
#endif
|
||||
|
||||
|
|
@ -36,7 +36,7 @@ module hdf5_interface
|
|||
module procedure hdf5_write_integer_4Darray
|
||||
module procedure hdf5_write_long
|
||||
module procedure hdf5_write_string
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
module procedure hdf5_write_double_parallel
|
||||
module procedure hdf5_write_double_1Darray_parallel
|
||||
module procedure hdf5_write_double_2Darray_parallel
|
||||
|
|
@ -66,7 +66,7 @@ module hdf5_interface
|
|||
module procedure hdf5_read_integer_4Darray
|
||||
module procedure hdf5_read_long
|
||||
module procedure hdf5_read_string
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
module procedure hdf5_read_double_parallel
|
||||
module procedure hdf5_read_double_1Darray_parallel
|
||||
module procedure hdf5_read_double_2Darray_parallel
|
||||
|
|
@ -134,7 +134,7 @@ contains
|
|||
|
||||
end subroutine hdf5_file_close
|
||||
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
|
||||
!===============================================================================
|
||||
! HDF5_FILE_CREATE_PARALLEL creates HDF5 file with parallel I/O
|
||||
|
|
@ -809,7 +809,7 @@ contains
|
|||
|
||||
end subroutine hdf5_write_attribute_string
|
||||
|
||||
# ifdef MPI
|
||||
#ifdef PHDF5
|
||||
|
||||
!===============================================================================
|
||||
! HDF5_WRITE_INTEGER_PARALLEL writes integer scalar data in parallel
|
||||
|
|
@ -1807,6 +1807,6 @@ contains
|
|||
|
||||
end subroutine hdf5_read_string_parallel
|
||||
|
||||
# endif
|
||||
#endif
|
||||
|
||||
end module hdf5_interface
|
||||
|
|
|
|||
|
|
@ -96,7 +96,7 @@ contains
|
|||
self % serial = .true.
|
||||
end if
|
||||
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_file_create(filename, self % hdf5_fh)
|
||||
else
|
||||
|
|
@ -126,7 +126,7 @@ contains
|
|||
self % serial = .true.
|
||||
end if
|
||||
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_file_open(filename, self % hdf5_fh, mode)
|
||||
else
|
||||
|
|
@ -212,7 +212,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_write_double(self % hdf5_grp, name_, buffer)
|
||||
else
|
||||
|
|
@ -263,7 +263,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_read_double(self % hdf5_grp, name_, buffer)
|
||||
else
|
||||
|
|
@ -315,7 +315,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_write_double_1Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -368,7 +368,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_read_double_1Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -421,7 +421,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_write_double_2Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -474,7 +474,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_read_double_2Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -527,7 +527,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_write_double_3Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -580,7 +580,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_read_double_3Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -634,7 +634,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_write_double_4Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -689,7 +689,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_read_double_4Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -741,7 +741,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_write_integer(self % hdf5_grp, name_, buffer)
|
||||
else
|
||||
|
|
@ -792,7 +792,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_read_integer(self % hdf5_grp, name_, buffer)
|
||||
else
|
||||
|
|
@ -844,7 +844,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_write_integer_1Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -897,7 +897,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_read_integer_1Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -951,7 +951,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_write_integer_2Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -1004,7 +1004,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_read_integer_2Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -1057,7 +1057,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_write_integer_3Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -1110,7 +1110,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_read_integer_3Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -1164,7 +1164,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_write_integer_4Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -1218,7 +1218,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_read_integer_4Darray(self % hdf5_grp, name_, buffer, length)
|
||||
else
|
||||
|
|
@ -1270,7 +1270,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_write_long(self % hdf5_grp, name_, buffer, hdf5_integer8_t)
|
||||
else
|
||||
|
|
@ -1322,7 +1322,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_read_long(self % hdf5_grp, name_, buffer, hdf5_integer8_t)
|
||||
else
|
||||
|
|
@ -1378,7 +1378,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_write_string(self % hdf5_grp, name_, buffer, n)
|
||||
else
|
||||
|
|
@ -1434,7 +1434,7 @@ contains
|
|||
else
|
||||
self % hdf5_grp = self % hdf5_fh
|
||||
endif
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
if (self % serial) then
|
||||
call hdf5_read_string(self % hdf5_grp, name_, buffer, n)
|
||||
else
|
||||
|
|
@ -1579,11 +1579,11 @@ contains
|
|||
|
||||
class(BinaryOutput) :: self
|
||||
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
integer(8) :: offset(1) ! source data offset
|
||||
#endif
|
||||
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
|
||||
! Set size of total dataspace for all procs and rank
|
||||
dims1(1) = n_particles
|
||||
|
|
@ -1662,11 +1662,11 @@ contains
|
|||
|
||||
class(BinaryOutput) :: self
|
||||
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
integer(8) :: offset(1) ! offset of data
|
||||
#endif
|
||||
|
||||
#ifdef MPI
|
||||
#ifdef PHDF5
|
||||
|
||||
! Set size of total dataspace for all procs and rank
|
||||
dims1(1) = n_particles
|
||||
|
|
|
|||
|
|
@ -107,12 +107,13 @@ tests = OrderedDict()
|
|||
|
||||
class Test(object):
|
||||
def __init__(self, name, debug=False, optimize=False, mpi=False, openmp=False,
|
||||
valgrind=False, coverage=False):
|
||||
phdf5=False, valgrind=False, coverage=False):
|
||||
self.name = name
|
||||
self.debug = debug
|
||||
self.optimize = optimize
|
||||
self.mpi = mpi
|
||||
self.openmp = openmp
|
||||
self.phdf5 = phdf5
|
||||
self.valgrind = valgrind
|
||||
self.coverage = coverage
|
||||
self.success = True
|
||||
|
|
@ -125,9 +126,9 @@ class Test(object):
|
|||
|
||||
# Check for MPI
|
||||
if self.mpi:
|
||||
self.fc = PHDF5_DIR + '/bin/h5pfc'
|
||||
self.fc = os.path.join(MPI_DIR, 'bin', 'mpifort')
|
||||
else:
|
||||
self.fc = HDF5_DIR + '/bin/h5fc'
|
||||
self.fc = FC
|
||||
|
||||
# Sets the build name that will show up on the CDash
|
||||
def get_build_name(self):
|
||||
|
|
@ -159,6 +160,10 @@ class Test(object):
|
|||
os.environ['FC'] = self.fc
|
||||
if self.mpi:
|
||||
os.environ['MPI_DIR'] = MPI_DIR
|
||||
if self.phdf5:
|
||||
os.environ['HDF5_ROOT'] = PHDF5_DIR
|
||||
else:
|
||||
os.environ['HDF5_ROOT'] = HDF5_DIR
|
||||
rc = call(['ctest', '-S', 'ctestscript.run','-V'])
|
||||
if rc != 0:
|
||||
self.success = False
|
||||
|
|
@ -169,6 +174,10 @@ class Test(object):
|
|||
os.environ['FC'] = self.fc
|
||||
if self.mpi:
|
||||
os.environ['MPI_DIR'] = MPI_DIR
|
||||
if self.phdf5:
|
||||
os.environ['HDF5_ROOT'] = PHDF5_DIR
|
||||
else:
|
||||
os.environ['HDF5_ROOT'] = HDF5_DIR
|
||||
build_opts = self.build_opts.split()
|
||||
self.cmake += build_opts
|
||||
rc = call(self.cmake)
|
||||
|
|
@ -258,8 +267,8 @@ class Test(object):
|
|||
|
||||
# Simple function to add a test to the global tests dictionary
|
||||
def add_test(name, debug=False, optimize=False, mpi=False, openmp=False,\
|
||||
valgrind=False, coverage=False):
|
||||
tests.update({name: Test(name, debug, optimize, mpi, openmp,
|
||||
phdf5=False, valgrind=False, coverage=False):
|
||||
tests.update({name: Test(name, debug, optimize, mpi, openmp, phdf5,
|
||||
valgrind, coverage)})
|
||||
|
||||
# List of all tests that may be run. User can add -C to command line to specify
|
||||
|
|
@ -270,12 +279,15 @@ add_test('hdf5-optimize', optimize=True)
|
|||
add_test('omp-hdf5-normal', openmp=True)
|
||||
add_test('omp-hdf5-debug', openmp=True, debug=True)
|
||||
add_test('omp-hdf5-optimize', openmp=True, optimize=True)
|
||||
add_test('phdf5-normal', mpi=True)
|
||||
add_test('phdf5-debug', mpi=True, debug=True)
|
||||
add_test('phdf5-optimize', mpi=True, optimize=True)
|
||||
add_test('phdf5-omp-normal', mpi=True, openmp=True)
|
||||
add_test('phdf5-omp-debug', mpi=True, openmp=True, debug=True)
|
||||
add_test('phdf5-omp-optimize', mpi=True, openmp=True, optimize=True)
|
||||
add_test('mpi-hdf5-normal', mpi=True)
|
||||
add_test('mpi-hdf5-debug', mpi=True, debug=True)
|
||||
add_test('mpi-hdf5-optimize', mpi=True, optimize=True)
|
||||
add_test('phdf5-normal', mpi=True, phdf5=True)
|
||||
add_test('phdf5-debug', mpi=True, phdf5=True, debug=True)
|
||||
add_test('phdf5-optimize', mpi=True, phdf5=True, optimize=True)
|
||||
add_test('phdf5-omp-normal', mpi=True, phdf5=True, openmp=True)
|
||||
add_test('phdf5-omp-debug', mpi=True, phdf5=True, openmp=True, debug=True)
|
||||
add_test('phdf5-omp-optimize', mpi=True, phdf5=True, openmp=True, optimize=True)
|
||||
add_test('hdf5-debug_valgrind', debug=True, valgrind=True)
|
||||
add_test('hdf5-debug_coverage', debug=True, coverage=True)
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue