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WIP: Patches for clean Fedora RPM builds that pass unit tests #123

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91 changes: 60 additions & 31 deletions CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -7,32 +7,33 @@ cmake_policy(VERSION 3.13)

option( USE_NATIVE_ARCH "build for native cpu architecture" ON)

option( USE_GUI "build with GUI" ON )
option( USE_PYTHON "build with python interface" ON )
option( USE_MPI "enable mpi parallelization" OFF )
option( USE_MPI4PY "enable mpi4py interface" ON )
option( USE_OCC "build with OpenCascade geometry kernel interface" OFF)
option( USE_STLGEOM "build with STL geometry support" ON)
option( USE_CSG "build with CSG kernel" ON)
option( USE_INTERFACE "build nginterface" ON)
option( USE_GEOM2D "build 2d geometry kernels" ON)
option( USE_JPEG "enable snapshots using library libjpeg" OFF )
option( USE_MPEG "enable video recording with FFmpeg, uses libavcodec" OFF )
option( USE_CGNS "enable CGNS file read/write support" OFF )
option( USE_NUMA "compile with NUMA-aware code")
option( INTEL_MIC "cross compile for intel xeon phi")
option( USE_GUI "build with GUI" ON )
option( USE_PYTHON "build with python interface" ON )
option( USE_MPI "enable mpi parallelization" OFF )
option( USE_MPI4PY "enable mpi4py interface" ON )
option( USE_OCC "build with OpenCascade geometry kernel interface" OFF)
option( USE_STLGEOM "build with STL geometry support" ON)
option( USE_CSG "build with CSG kernel" ON)
option( USE_INTERFACE "build nginterface" ON)
option( USE_GEOM2D "build 2d geometry kernels" ON)
option( USE_JPEG "enable snapshots using library libjpeg" OFF )
option( USE_MPEG "enable video recording with FFmpeg, uses libavcodec" OFF )
option( USE_CGNS "enable CGNS file read/write support" OFF )
option( USE_NUMA "compile with NUMA-aware code" OFF )
option( INTEL_MIC "cross compile for intel xeon phi" OFF )
option( INSTALL_PROFILES "install environment variable settings to /etc/profile.d" OFF )
option( USE_CCACHE "use ccache")
option( USE_CCACHE "use ccache" OFF )
option( USE_INTERNAL_TCL "Compile tcl files into the code and don't install them" ON)
option( ENABLE_UNIT_TESTS "Enable Catch unit tests")
option( USE_INTERNAL_PYBIND11 "Use internally bundled version of Pybind11" ON)
option( ENABLE_UNIT_TESTS "Enable Catch unit tests" OFF)
option( ENABLE_CPP_CORE_GUIDELINES_CHECK "Enable cpp core guideline checks on ngcore" OFF)
option( USE_SPDLOG "Enable spd log logging" OFF)
option( DEBUG_LOG "Enable more debug output (may increase computation time) - only works with USE_SPDLOG=ON" OFF)
option( CHECK_RANGE "Check array range access, automatically enabled if built in debug mode" OFF)
option( USE_SPDLOG "Enable spd log logging" OFF)
option( DEBUG_LOG "Enable more debug output (may increase computation time) - only works with USE_SPDLOG=ON" OFF)
option( CHECK_RANGE "Check array range access, automatically enabled if built in debug mode" OFF)
option( BUILD_STUB_FILES "Build stub files for better autocompletion" ON)
option( BUILD_FOR_CONDA "Link python libraries only to executables" OFF)
option( BUILD_FOR_CONDA "Link python libraries only to executables" OFF)

option( USE_SUPERBUILD "build dependencies automatically" ON)
option( USE_SUPERBUILD "build dependencies automatically" ON)
option( TRACE_MEMORY "Enable memory tracing" OFF)

set(NG_COMPILE_FLAGS "" CACHE STRING "Additional compile flags")
Expand Down Expand Up @@ -76,19 +77,20 @@ if (USE_SUPERBUILD)
# execute the superbuild (this script will be invoked again without the
# USE_SUPERBUILD option this time)
include (cmake/SuperBuild.cmake)
return() # stop processing this file further
else()
project(Netgen)
if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
set(CMAKE_INSTALL_PREFIX "${INSTALL_DIR_DEFAULT}" CACHE PATH "Install directory" FORCE)
endif()
return() # stop processing this file further
endif()

# Versioning variables come in from the configuration include, need them now.
set(CMAKE_EXPORT_COMPILE_COMMANDS ON)

include (${CMAKE_CURRENT_LIST_DIR}/cmake/generate_version_file.cmake)
set(CPACK_PACKAGE_VERSION "${NETGEN_VERSION}")
set(PACKAGE_VERSION "${NETGEN_VERSION}")

project(Netgen VERSION "${NETGEN_VERSION_SHORT}")
if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
set(CMAKE_INSTALL_PREFIX "${INSTALL_DIR_DEFAULT}" CACHE PATH "Install directory" FORCE)
endif()

#######################################################################
if(USE_CCACHE)
Expand Down Expand Up @@ -131,7 +133,7 @@ if(USE_PYTHON)
file(TO_CMAKE_PATH ${PYTHON_PACKAGES_INSTALL_DIR} PYTHON_PACKAGES_INSTALL_DIR)
endif(USE_PYTHON)

set(NG_INSTALL_SUFFIX netgen CACHE STRING "Suffix appended to install directories (project name)")
set(NG_INSTALL_SUFFIX netgen-mesher CACHE STRING "Suffix appended to install directories (project name)")

if(APPLE)
set(NG_INSTALL_DIR_BIN_DEFAULT Contents/MacOS)
Expand Down Expand Up @@ -230,11 +232,20 @@ endif(WIN32)
if(APPLE)
set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -undefined dynamic_lookup")
endif(APPLE)
if (CMAKE_CXX_COMPILER_ID MATCHES "GNU")
add_compile_options(-Wno-deprecated -Wno-sign-compare -Wno-unused-variable -Wno-unused-but-set-variable)
add_compile_options(-Wno-cpp -Wno-unused -Wno-parentheses)
# Uncomment below to run sanitizers
#add_compile_options(-g3 -O0 -fno-inline -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address -fno-common)
#add_link_options(-g3 -O0 -fno-inline -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address -fno-common)

endif()
#######################################################################
add_library(nglib ${NGLIB_LIBRARY_TYPE})
set_target_properties(nglib PROPERTIES VERSION "${NETGEN_LIBRARY_VERSION}")
if(USE_GUI)
add_library(nggui ${NGGUI_LIBRARY_TYPE})
set_target_properties(nggui PROPERTIES VERSION "${NETGEN_LIBRARY_VERSION}")
if(WIN32)
set_target_properties( nggui PROPERTIES OUTPUT_NAME "libnggui")
endif(WIN32)
Expand Down Expand Up @@ -302,7 +313,13 @@ else()
endif()

if (USE_PYTHON)
add_subdirectory(external_dependencies/pybind11)
if (USE_INTERNAL_PYBIND11)
message(STATUS "Checking for bundled Pybind11...")
add_subdirectory(external_dependencies/pybind11)
else()
message(STATUS "Looking for external Pybind11...")
include(cmake/pybind11Tools.cmake)
endif()
find_path(PYBIND_INCLUDE_DIR pybind11/pybind11.h HINTS ${PYTHON_INCLUDE_DIR})
if( PYBIND_INCLUDE_DIR )
message(STATUS "Found Pybind11: ${PYBIND_INCLUDE_DIR}")
Expand Down Expand Up @@ -427,11 +444,23 @@ if (USE_MPEG)
endif (USE_MPEG)

#######################################################################
add_custom_target(ng_generate_version_file
${CMAKE_COMMAND}
# When not building directly from git source, version will need to be
# set explicitly--- but still get it from git!
if (NETGEN_VERSION_GIT)
add_custom_target(ng_generate_version_file
${CMAKE_COMMAND}
-DNETGEN_VERSION_GIT=${NETGEN_VERSION_GIT}
-DBDIR=${CMAKE_CURRENT_BINARY_DIR}
-P ${CMAKE_CURRENT_LIST_DIR}/cmake/generate_version_file.cmake
)
else()
add_custom_target(ng_generate_version_file
${CMAKE_COMMAND}
-DBDIR=${CMAKE_CURRENT_BINARY_DIR}
-P ${CMAKE_CURRENT_LIST_DIR}/cmake/generate_version_file.cmake
)
endif()

#######################################################################
if(INSTALL_PROFILES)
file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/netgen.sh "#!/bin/sh\n")
Expand Down
202 changes: 202 additions & 0 deletions cmake/cmake_modules/FindPythonLibsNew.cmake
Original file line number Diff line number Diff line change
@@ -0,0 +1,202 @@
# - Find python libraries
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Please, no vendored and totally outdated cmake stuff.
Pybind11 supports cmake config mode for ages, and does not require any external helpers.

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@xiphmont xiphmont Jul 6, 2022

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This is a patch that has been making the rounds for years as part of distro-packaged netgen-- I agree, it's pretty heavy/ugly. I used it only because I knew it worked. I'll do something better.

The general problem with CMake is that it is mostly unaware that RedHat distributions exist at all, and there does not seem to be any release testing against RH distros. A lot of the trouble is RedHat's own fault, of course, and CMake authors have been very responsive to suggested fixes. But that does mean that a bleeding-edge CMake is needed to build things, so I have generally opted for workarounds if they're not too awful.

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See #127

# This module finds the libraries corresponding to the Python interpreter
# FindPythonInterp provides.
# This code sets the following variables:
#
# PYTHONLIBS_FOUND - have the Python libs been found
# PYTHON_PREFIX - path to the Python installation
# PYTHON_LIBRARIES - path to the python library
# PYTHON_INCLUDE_DIRS - path to where Python.h is found
# PYTHON_MODULE_EXTENSION - lib extension, e.g. '.so' or '.pyd'
# PYTHON_MODULE_PREFIX - lib name prefix: usually an empty string
# PYTHON_SITE_PACKAGES - path to installation site-packages
# PYTHON_IS_DEBUG - whether the Python interpreter is a debug build
#
# Thanks to talljimbo for the patch adding the 'LDVERSION' config
# variable usage.

#=============================================================================
# Copyright 2001-2009 Kitware, Inc.
# Copyright 2012 Continuum Analytics, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
#
# * Neither the names of Kitware, Inc., the Insight Software Consortium,
# nor the names of their contributors may be used to endorse or promote
# products derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#=============================================================================

# Checking for the extension makes sure that `LibsNew` was found and not just `Libs`.
if(PYTHONLIBS_FOUND AND PYTHON_MODULE_EXTENSION)
return()
endif()

# Use the Python interpreter to find the libs.
if(PythonLibsNew_FIND_REQUIRED)
find_package(PythonInterp ${PythonLibsNew_FIND_VERSION} REQUIRED)
else()
find_package(PythonInterp ${PythonLibsNew_FIND_VERSION})
endif()

if(NOT PYTHONINTERP_FOUND)
set(PYTHONLIBS_FOUND FALSE)
set(PythonLibsNew_FOUND FALSE)
return()
endif()

# According to http://stackoverflow.com/questions/646518/python-how-to-detect-debug-interpreter
# testing whether sys has the gettotalrefcount function is a reliable, cross-platform
# way to detect a CPython debug interpreter.
#
# The library suffix is from the config var LDVERSION sometimes, otherwise
# VERSION. VERSION will typically be like "2.7" on unix, and "27" on windows.
execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
"from distutils import sysconfig as s;import sys;import struct;
print('.'.join(str(v) for v in sys.version_info));
print(sys.prefix);
print(s.get_python_inc(plat_specific=True));
print(s.get_python_lib(plat_specific=True));
print(s.get_config_var('SO'));
print(hasattr(sys, 'gettotalrefcount')+0);
print(struct.calcsize('@P'));
print(s.get_config_var('LDVERSION') or s.get_config_var('VERSION'));
print(s.get_config_var('LIBDIR') or '');
print(s.get_config_var('MULTIARCH') or '');
"
RESULT_VARIABLE _PYTHON_SUCCESS
OUTPUT_VARIABLE _PYTHON_VALUES
ERROR_VARIABLE _PYTHON_ERROR_VALUE)

if(NOT _PYTHON_SUCCESS MATCHES 0)
if(PythonLibsNew_FIND_REQUIRED)
message(FATAL_ERROR
"Python config failure:\n${_PYTHON_ERROR_VALUE}")
endif()
set(PYTHONLIBS_FOUND FALSE)
set(PythonLibsNew_FOUND FALSE)
return()
endif()

# Convert the process output into a list
if(WIN32)
string(REGEX REPLACE "\\\\" "/" _PYTHON_VALUES ${_PYTHON_VALUES})
endif()
string(REGEX REPLACE ";" "\\\\;" _PYTHON_VALUES ${_PYTHON_VALUES})
string(REGEX REPLACE "\n" ";" _PYTHON_VALUES ${_PYTHON_VALUES})
list(GET _PYTHON_VALUES 0 _PYTHON_VERSION_LIST)
list(GET _PYTHON_VALUES 1 PYTHON_PREFIX)
list(GET _PYTHON_VALUES 2 PYTHON_INCLUDE_DIR)
list(GET _PYTHON_VALUES 3 PYTHON_SITE_PACKAGES)
list(GET _PYTHON_VALUES 4 PYTHON_MODULE_EXTENSION)
list(GET _PYTHON_VALUES 5 PYTHON_IS_DEBUG)
list(GET _PYTHON_VALUES 6 PYTHON_SIZEOF_VOID_P)
list(GET _PYTHON_VALUES 7 PYTHON_LIBRARY_SUFFIX)
list(GET _PYTHON_VALUES 8 PYTHON_LIBDIR)
list(GET _PYTHON_VALUES 9 PYTHON_MULTIARCH)

# Make sure the Python has the same pointer-size as the chosen compiler
# Skip if CMAKE_SIZEOF_VOID_P is not defined
if(CMAKE_SIZEOF_VOID_P AND (NOT "${PYTHON_SIZEOF_VOID_P}" STREQUAL "${CMAKE_SIZEOF_VOID_P}"))
if(PythonLibsNew_FIND_REQUIRED)
math(EXPR _PYTHON_BITS "${PYTHON_SIZEOF_VOID_P} * 8")
math(EXPR _CMAKE_BITS "${CMAKE_SIZEOF_VOID_P} * 8")
message(FATAL_ERROR
"Python config failure: Python is ${_PYTHON_BITS}-bit, "
"chosen compiler is ${_CMAKE_BITS}-bit")
endif()
set(PYTHONLIBS_FOUND FALSE)
set(PythonLibsNew_FOUND FALSE)
return()
endif()

# The built-in FindPython didn't always give the version numbers
string(REGEX REPLACE "\\." ";" _PYTHON_VERSION_LIST ${_PYTHON_VERSION_LIST})
list(GET _PYTHON_VERSION_LIST 0 PYTHON_VERSION_MAJOR)
list(GET _PYTHON_VERSION_LIST 1 PYTHON_VERSION_MINOR)
list(GET _PYTHON_VERSION_LIST 2 PYTHON_VERSION_PATCH)

# Make sure all directory separators are '/'
string(REGEX REPLACE "\\\\" "/" PYTHON_PREFIX ${PYTHON_PREFIX})
string(REGEX REPLACE "\\\\" "/" PYTHON_INCLUDE_DIR ${PYTHON_INCLUDE_DIR})
string(REGEX REPLACE "\\\\" "/" PYTHON_SITE_PACKAGES ${PYTHON_SITE_PACKAGES})

if(CMAKE_HOST_WIN32 AND NOT (MSYS OR MINGW))
set(PYTHON_LIBRARY
"${PYTHON_PREFIX}/libs/Python${PYTHON_LIBRARY_SUFFIX}.lib")

# when run in a venv, PYTHON_PREFIX points to it. But the libraries remain in the
# original python installation. They may be found relative to PYTHON_INCLUDE_DIR.
if(NOT EXISTS "${PYTHON_LIBRARY}")
get_filename_component(_PYTHON_ROOT ${PYTHON_INCLUDE_DIR} DIRECTORY)
set(PYTHON_LIBRARY
"${_PYTHON_ROOT}/libs/Python${PYTHON_LIBRARY_SUFFIX}.lib")
endif()

# raise an error if the python libs are still not found.
if(NOT EXISTS "${PYTHON_LIBRARY}")
message(FATAL_ERROR "Python libraries not found")
endif()

else()
if(PYTHON_MULTIARCH)
set(_PYTHON_LIBS_SEARCH "${PYTHON_LIBDIR}/${PYTHON_MULTIARCH}" "${PYTHON_LIBDIR}")
else()
set(_PYTHON_LIBS_SEARCH "${PYTHON_LIBDIR}")
endif()
#message(STATUS "Searching for Python libs in ${_PYTHON_LIBS_SEARCH}")
# Probably this needs to be more involved. It would be nice if the config
# information the python interpreter itself gave us were more complete.
find_library(PYTHON_LIBRARY
NAMES "python${PYTHON_LIBRARY_SUFFIX}"
PATHS ${_PYTHON_LIBS_SEARCH}
NO_DEFAULT_PATH)

# If all else fails, just set the name/version and let the linker figure out the path.
if(NOT PYTHON_LIBRARY)
set(PYTHON_LIBRARY python${PYTHON_LIBRARY_SUFFIX})
endif()
endif()

MARK_AS_ADVANCED(
PYTHON_LIBRARY
PYTHON_INCLUDE_DIR
)

# We use PYTHON_INCLUDE_DIR, PYTHON_LIBRARY and PYTHON_DEBUG_LIBRARY for the
# cache entries because they are meant to specify the location of a single
# library. We now set the variables listed by the documentation for this
# module.
SET(PYTHON_INCLUDE_DIRS "${PYTHON_INCLUDE_DIR}")
SET(PYTHON_LIBRARIES "${PYTHON_LIBRARY}")
SET(PYTHON_DEBUG_LIBRARIES "${PYTHON_DEBUG_LIBRARY}")

find_package_message(PYTHON
"Found PythonLibs: ${PYTHON_LIBRARY}"
"${PYTHON_EXECUTABLE}${PYTHON_VERSION}")

set(PYTHONLIBS_FOUND TRUE)
set(PythonLibsNew_FOUND TRUE)
5 changes: 3 additions & 2 deletions cmake/generate_version_file.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,8 @@ if(status AND NOT status EQUAL 0)
string(REGEX REPLACE "^netgen(.*)" "\\1" git_version_string "${git_version_string}")
endif()
else()
MESSAGE(WARNING "Could not determine git-version from source code - assuming 6.2.0.0")
set(git_version_string "v6.2.0.0")
MESSAGE(WARNING "Could not determine git-version from source code - assuming 6.99.2200-0-0")
set(git_version_string "v6.99.2200-0-0")
endif()
endif()
string(STRIP ${git_version_string} git_version_string)
Expand Down Expand Up @@ -57,6 +57,7 @@ if(NOT NETGEN_VERSION_PYTHON)
set(NETGEN_VERSION_PYTHON ${NETGEN_VERSION_TWEAK})
endif()

set(NETGEN_LIBRARY_VERSION "${NETGEN_VERSION_SHORT}")

set(version_file ${BDIR}/netgen_version.hpp)
set(new_version_file_string "\
Expand Down
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