Commit bf5a5603 authored by Dion Haefner's avatar Dion Haefner

merge with old repo

parent ff8f324c
# CMake generated Testfile for
# Source directory: /home/dion/codes/dorie/dorie/cmake/modules
# Build directory: /home/dion/codes/dorie/dorie/cmake/modules
#
# This file includes the relevant testing commands required for
# testing this directory and lists subdirectories to be tested as well.
# File for module specific CMake tests. # File for module specific CMake tests.
# find all required packages # find all required packages
FIND_PACKAGE(HDF5 REQUIRED COMPONENTS C) FIND_PACKAGE (HDF5 REQUIRED)
FIND_PACKAGE(FFTW REQUIRED) FIND_PACKAGE (FFTW REQUIRED)
FIND_PACKAGE(SuperLU REQUIRED) FIND_PACKAGE (SuperLU REQUIRED)
FIND_PACKAGE(MPI REQUIRED) FIND_PACKAGE (MPI REQUIRED)
FIND_PACKAGE(UG REQUIRED) FIND_PACKAGE (METIS REQUIRED)
FIND_PACKAGE (ParMETIS REQUIRED)
FIND_PACKAGE(METIS) FIND_PACKAGE (UG REQUIRED)
FIND_PACKAGE(ParMETIS)
include_directories(${FFTW_INCLUDES}) include_directories(${FFTW_INCLUDES})
include_directories(${HDF5_INCLUDE_DIRS}) include_directories(${HDF5_INCLUDE_DIRS})
......
#.rst:
# FindHDF5
# --------
#
# 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.
#
# 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_VERSION - HDF5 version in format Major.Minor.Release
# 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 2015 Axel Huebl, Helmholtz-Zentrum Dresden - Rossendorf
# Copyright 2009 Kitware, Inc.
#
# Distributed under the OSI-approved BSD License (the "License");
# see accompanying file Copyright.txt for details.
#
# 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.)
# This module is maintained by Will Dicharry <wdicharry@stellarscience.com>.
include(${CMAKE_ROOT}/Modules/SelectLibraryConfigurations.cmake)
include(${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake)
# List of the valid HDF5 components
set( HDF5_VALID_COMPONENTS
C
CXX
Fortran
HL
Fortran_HL
)
# 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 ${component} )
endif()
endforeach()
endif()
# try to find the HDF5 wrapper compilers
find_program( HDF5_C_COMPILER_EXECUTABLE
NAMES hp5cc #h5cc
HINTS ENV HDF5_ROOT
PATH_SUFFIXES bin Bin
DOC "HDF5 Wrapper compiler. Used only to detect HDF5 compile flags." )
mark_as_advanced( HDF5_C_COMPILER_EXECUTABLE )
find_program( HDF5_CXX_COMPILER_EXECUTABLE
NAMES h5c++ h5pc++
HINTS ENV HDF5_ROOT
PATH_SUFFIXES bin Bin
DOC "HDF5 C++ Wrapper compiler. Used only to detect HDF5 compile flags." )
mark_as_advanced( HDF5_CXX_COMPILER_EXECUTABLE )
find_program( HDF5_Fortran_COMPILER_EXECUTABLE
NAMES h5fc h5pfc
HINTS ENV HDF5_ROOT
PATH_SUFFIXES bin Bin
DOC "HDF5 Fortran Wrapper compiler. Used only to detect HDF5 compile flags." )
mark_as_advanced( HDF5_Fortran_COMPILER_EXECUTABLE )
find_program( HDF5_DIFF_EXECUTABLE
NAMES h5diff
HINTS ENV HDF5_ROOT
PATH_SUFFIXES bin Bin
DOC "HDF5 file differencing tool." )
mark_as_advanced( HDF5_DIFF_EXECUTABLE )
# Invoke the HDF5 wrapper compiler. The compiler return value is stored to the
# return_value argument, the text output is stored to the output variable.
macro( _HDF5_invoke_compiler language output return_value )
if( HDF5_${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( 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( 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 ${_list_name} )
endmacro()
if( HDF5_INCLUDE_DIRS )
_remove_duplicates_from_beginning( HDF5_INCLUDE_DIRS )
endif()
if( HDF5_LIBRARY_DIRS )
_remove_duplicates_from_beginning( HDF5_LIBRARY_DIRS )
endif()
# If the HDF5 include directory was found, open H5pubconf.h to determine if
# HDF5 was compiled with parallel IO support
set( HDF5_IS_PARALLEL FALSE )
set( HDF5_VERSION "" )
foreach( _dir IN LISTS HDF5_INCLUDE_DIRS )
foreach(_hdr "${_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
)
# This cmake module provides macros that install python packages into the virtualenv
# that is shared by all dune modules that depend on dune-python.
#
# .. cmake_function:: dune_install_python_package
#
# .. cmake_param:: PATH
# :required:
# :single:
#
# Relative path to the given python package source code.
#
# .. cmake_param:: MAJOR_VERSION
# :single:
#
# Set to "2" or "3" if your python package only works with
# python2 or python3. This will restrict the installation process to that
# python version.
#
# .. cmake_param:: NO_PIP
# :option:
#
# Instead of :code:`pip -e`, `python setup.py develop` will be used as
# the installation command.
#
# .. cmake_param:: NO_EDIT
# :option:
#
# Will drop :code:`pip`s :code:`-e` option (or switch :code:`develop` to :code:`install`).
# Only use this option if your package is incompatible with :code:`-e`.
#
# Installs the python package located at path into the virtualenv used by dune-python
# The package at the given location is expected to be a pip installable package.
# Also marks the given python package for global installation during :code:`make install`.
# By default, the python package will then be installed into the system-wide site-packages
# location. If you do not want to install it there, or you do not have permission to,
# you may optionally set :ref:`DUNE_PYTHON_INSTALL_USER` to a username. The
# packages will then be installed in the home directory of that user.
# This is done through pips :code:`--user` option. Installation in arbitrary locations is not
# supported to minimize :code:`PYTHONPATH` issues.
#
# .. cmake_variable:: DUNE_PYTHON_INSTALL_USER
#
# dune-python only supports two ways of globally installing python packages during
# :code:`make install`:
#
# * Into standard system paths (default)
# * Into the standard python path of a users home directory (through :code:`pip --user`)
#
# Set this variable to a username to use the latter.
#
include(CheckPythonPackage)
function(dorie_install_python_package)
# Parse Arguments
set(OPTION NO_PIP NO_EDIT QUIET)
set(SINGLE PATH MAJOR_VERSION)
set(MULTI)
include(CMakeParseArguments)
cmake_parse_arguments(PYINST "${OPTION}" "${SINGLE}" "${MULTI}" ${ARGN})
if(PYINST_UNPARSED_ARGUMENTS)
message(WARNING "Unparsed arguments in dune_install_python_package: This often indicates typos!")
endif()
# apply defaults
if(NOT PYINST_MAJOR_VERSION)
set(PYINST_MAJOR_VERSION 2 3)
endif()
# check for available pip packages
check_python_package(PACKAGE pip
INTERPRETER ${PYTHON2_EXECUTABLE}
RESULT PIP2_FOUND)
check_python_package(PACKAGE pip
INTERPRETER ${PYTHON3_EXECUTABLE}
RESULT PIP3_FOUND)
# Construct the installation command strings from the given options
if(PYINST_NO_PIP)
if(PYINST_NO_EDIT)
set(INST_COMMAND install)
else()
set(INST_COMMAND develop)
endif()
set(VENV_INSTALL_COMMAND python setup.py ${INST_COMMAND})
else()
set(EDIT_OPTION)
if(NOT PYINST_NO_EDIT)
set(EDIT_OPTION -e)
endif()
if(PYINST_QUIET)
set(EDIT_OPTION "-q ${EDIT_OPTION}")
endif()
set(VENV_INSTALL_COMMAND python -m pip install ${EDIT_OPTION} .)
endif()
# Construct the interpreter options for global installation
if(PYINST_NO_PIP)
set(SYSTEM_INSTALL_OPTIONS setup.py install)
if(DUNE_PYTHON_INSTALL_USER)
message("Error message: Incompatible options - NO_PIP and DUNE_PYTHON_INSTALL_USER")
endif()
else()
set(USER_STRING "")
if(DUNE_PYTHON_INSTALL_USER)
set(USER_STRING --user ${DUNE_PYTHON_INSTALL_USER})
endif()
set(SYSTEM_INSTALL_OPTIONS -m pip install ${USER_STRING} .)
endif()
# iterate over the given interpreters
foreach(version ${PYINST_MAJOR_VERSION})
# install the package into the virtual env
execute_process(COMMAND ${CMAKE_BINARY_DIR}/dune-env-${version} ${VENV_INSTALL_COMMAND}
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/${PYINST_PATH})
# define a rule on how to install the package during make install
if(PIP${version}_FOUND)
install(CODE "execute_process(COMMAND ${PYTHON${version}_EXECUTABLE} ${SYSTEM_INSTALL_OPTIONS}
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/${PYINST_PATH})
")
else()
install(CODE "message(FATAL_ERROR \"You need the python${version} package pip installed on the host system to install a module that contains python code\")")
endif()
endforeach()
endfunction()
# CMAKE generated file: DO NOT EDIT!
# Generated by "Unix Makefiles" Generator, CMake Version 3.5
# Default target executed when no arguments are given to make.
default_target: all
.PHONY : default_target
# Allow only one "make -f Makefile2" at a time, but pass parallelism.
.NOTPARALLEL:
#=============================================================================
# Special targets provided by cmake.
# Disable implicit rules so canonical targets will work.
.SUFFIXES:
# Remove some rules from gmake that .SUFFIXES does not remove.
SUFFIXES =
.SUFFIXES: .hpux_make_needs_suffix_list
# Suppress display of executed commands.
$(VERBOSE).SILENT:
# A target that is always out of date.
cmake_force:
.PHONY : cmake_force
#=============================================================================
# Set environment variables for the build.
# The shell in which to execute make rules.
SHELL = /bin/sh
# The CMake executable.
CMAKE_COMMAND = /usr/bin/cmake
# The command to remove a file.
RM = /usr/bin/cmake -E remove -f