rdbisme
commented
2 years ago Ehi @anfuso1193, the problem might be related to the cmake script of stagline. Could you please provide a link to the code such that I can inspect it?
Closed anfuso1193 closed 2 years ago
rdbisme
commented
2 years ago Ehi @anfuso1193, the problem might be related to the cmake script of stagline. Could you please provide a link to the code such that I can inspect it?
anfuso1193
commented
2 years ago Hi Ruben, have you recieved my email with all the info you asked for?
rdbisme
commented
2 years ago @anfuso1193 I don't think I have. But I'd very much prefer you to put that info here in the issue such that everybody in the future could eventually stumble on this issue and learn something.
anfuso1193
commented
2 years ago Yeah sure, sorry for that. Here's the file:
# Basic setup of project and minimum required CMake version
cmake_minimum_required(VERSION 2.6)
project(VKI_Stagnation_Line)
enable_language(Fortran)
# Library options
option(GOTO_BLAS "compile the GOTO BLAS library" OFF)
option(NITROGEN_PARK "include support for the Nitrogen chemistry library of Park" OFF)
option(NITROGEN_NASA "include support for the Nitrogen chemistry library of NASA" OFF)
option(NITROGEN_BARI "include support for the Nitrogen chemistry library of Bari" OFF)
option(NITROGEN_FHO "include support for the Nitrogen FHO chemistry library" OFF)
option(NITROGEN_TTLTH "include support for the Nitrogen TTLTH chemistry library" OFF)
option(NITROGEN_DSMC "include support for the Nitrogen DSMC chemistry library" OFF)
option(ARGON_CR "include support for the Argon CR library" OFF)
option(POLYAT_GAS_WCU "include support for the POLYAT_GAS_WCU chemistry library" OFF)
option(MUTATIONPP "include support for the Mutation++ library" ON)
option(CARBONABLA "include support for the ablative boundary conditions" ON)
# Descend into the src directory to build all targets and libraries
add_subdirectory(src)
# Mutation++ directories
set(MPP_INSTALL_DIR "" CACHE PATH "Mutation++ installation directory")
if (${MUTATIONPP} MATCHES "ON")
# if (NOT ${MPP_INSTALL_DIR} MATCHES "")
include_directories(${MPP_INSTALL_DIR}/include/mutation++)
include_directories(${MPP_INSTALL_DIR}/include/)
link_directories(${MPP_INSTALL_DIR}/lib)
# endif()
endif()
# Main executable
get_property(stagline_SRCS GLOBAL PROPERTY stagline_SRCS)
set_source_files_properties(${stagline_SRCS} PROPERTIES COMPILE_FLAGS -cpp)
add_executable(stagline ${stagline_SRCS})
if (${MUTATIONPP} MATCHES "ON")
target_link_libraries(stagline -lmutation++_fortran)
endif()
# BLAS
set (BLASS_LIB_PATH "" CACHE FILEPATH "The BLAS library file")
if (${GOTO_BLAS} MATCHES "ON")
target_link_libraries(stagline ${BLASS_LIB_PATH})
endif()
# Installation
set(CMAKE_INSTALL_PREFIX ${CMAKE_CURRENT_SOURCE_DIR})
install(TARGETS stagline DESTINATION bin)
# Doxygen generated documentation
option (BUILD_DOCUMENTATION
"Use Doxygen to create the HTML based API documentation" OFF)
if (BUILD_DOCUMENTATION)
FIND_PACKAGE(Doxygen)
if (NOT DOXYGEN_FOUND)
message(FATAL_ERROR
"Doxygen is needed to build the documentation. Please install it
correctly")
endif()
# Configure the Template Doxyfile for our specific project
configure_file(Doxyfile.in
${PROJECT_BINARY_DIR}/Doxyfile @ONLY IMMEDIATE)
# Add a custom target to run Doxygen when ever the project is built
add_custom_target (docs
COMMAND ${DOXYGEN_EXECUTABLE} ${PROJECT_BINARY_DIR}/Doxyfile
SOURCES ${PROJECT_BINARY_DIR}/Doxyfile)
endif()
Let me know if you have any troubles with the drive. I know other people didn’t have any problems installing and make it works. I think the problem is my machine. Thanks a lot!
rdbisme
commented
2 years ago I took the liberty to edit your message and add the actual code in the message to make sure it stays there for future reference (the Google Drive will expire).
Anyway, the way Mutation is included is not as reported in the documentation. Did you check it?
https://github.com/mutationpp/Mutationpp/blob/master/docs/coupling.md
rdbisme
commented
2 years ago Here's an example for the Fortran interface: https://github.com/mutationpp/Mutationpp/blob/master/examples/fortran/CMakeLists.txt.shared
anfuso1193
commented
2 years ago No, I didn't. I was following other instructions (Codes_101_BD.docs file inside the stagline folder). I will have a look at the documentation.
rdbisme
commented
2 years ago I guess that's historical for old versions of mutation. The new way is exactly aimed at avoid problems with wrong path because that information is included in the cmake target and doesn't have to be hard-coded by hand.
Let me know if you manage to make it work.😉
anfuso1193
commented
2 years ago Hi Ruben, sorry to bother you. I have tried to have a look at the docs but I am not familiar with the procedure so I guess I still need your help. Thanks a lot
rdbisme
commented
2 years ago Hello @anfuso1193, if you tell me what you tried and what problems you are encountering, I can help you troubleshoot. I'm afraid I have no time to support the build system of an external project right now, I'm sorry.
The starting point is this file: https://github.com/mutationpp/Mutationpp/blob/master/examples/fortran/CMakeLists.txt.shared. Adapt it to stagline cmake script file.
anfuso1193
commented
2 years ago Thanks, Ruben. The code seems to work now but the problem was not the CMake. Apparently, it was on my .zshrc file. Thanks for your time and help!
rdbisme
commented
2 years ago Hello @anfuso1193, good to know. I still think that the cmake script should be adapted to use cmake targets (as shown in the script I shared before) instead of retrieving paths. Also, the build script should be adapted to be independent of user environment configuration (your .zshrc). One way to do that, in addition to switching to targets to reduce problems with non-existent paths), is to configure the RPATH accordingly. More info here: https://gitlab.kitware.com/cmake/community/-/wikis/doc/cmake/RPATH-handling. The RPATH allows to bake information on where to find shared libraries directly in the binary, avoiding the need to set LD_LIBRARY_PATH or similar things.
I'm closing this now, feel free to get back here if you need more help with building.
OS Version: Catalina 10.15.7
**Cmake Version:** 3.21.0 **`uname -a` output**
``` TERM_PROGRAM_VERSION=433 TMPDIR=/var/folders/93/y0zzpfzj5pldqkpyldw0qyjr0000gn/T/ XPC_FLAGS=0x0 LANG=it_IT.UTF-8 TERM_PROGRAM=Apple_Terminal XPC_SERVICE_NAME=0 DISPLAY=/private/tmp/com.apple.launchd.gDkaxCGN8v/org.xquartz:0 TERM_SESSION_ID=50072EF3-177C-4C5E-8BA0-FA001A0FE177 SSH_AUTH_SOCK=/private/tmp/com.apple.launchd.cux2KAVo1B/Listeners TERM=xterm-256color SHELL=/bin/zsh HOME=/Users/enricoanfuso LOGNAME=enricoanfuso USER=enricoanfuso PATH=/Users/enricoanfuso/.rvm/gems/ruby-2.6.3/bin:/Users/enricoanfuso/.rvm/gems/ruby-2.6.3@global/bin:/Users/enricoanfuso/.rvm/rubies/ruby-2.6.3/bin:/Users/enricoanfuso/opt/anaconda3/condabin:/usr/local/texlive/2017/bin/x86_64-darwin:/Users/enricoanfuso/Documents/Enrico/VKI/Codes/stagline/bin:/Users/enricoanfuso/Documents/Enrico/VKI/Codes/Mutationpp/install/bin:/Users/enricoanfuso/Documents/Enrico/VKI/Codes/CodeRTE/RTE/rte1d_enrico//install/bin:/Users/enricoanfuso/Documents/Enrico/VKI/Codes/NEQAIR/NEQAIR-v15.0-update/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Library/TeX/texbin:/usr/local/share/dotnet:/opt/X11/bin:~/.dotnet/tools:/Library/Frameworks/Mono.framework/Versions/Current/Commands:/Applications/Xamarin Workbooks.app/Contents/SharedSupport/path-bin:/Users/enricoanfuso/.rvm/bin SHLVL=1 PWD=/Users/enricoanfuso/Documents/Enrico/VKI/Codes/stagline/build OLDPWD=/Users/enricoanfuso/Documents/Enrico/VKI/Codes/stagline CLICOLOR=1export LSCOLORS=GxFxCxDxBxegedabagaced PS1=$ NEQAIR_DIRECTORY=/Users/enricoanfuso/Documents/Enrico/VKI/Codes/NEQAIR/NEQAIR-v15.0-update RAD_DIRECTORY=/Users/enricoanfuso/Documents/Enrico/VKI/Codes/CodeRTE/RTE/rte1d_enrico/ HTGR_DATA_DIRECTORY=/Users/enricoanfuso/Documents/Enrico/VKI/Codes/CodeRTE/RTE/rte1d_enrico//data MPP_DIRECTORY=/Users/enricoanfuso/Documents/Enrico/VKI/Codes/Mutationpp MPP_DATA_DIRECTORY=/Users/enricoanfuso/Documents/Enrico/VKI/Codes/Mutationpp/data ABLA_DATA_DIR=/Users/enricoanfuso/Documents/Enrico/VKI/Codes/stagline/src/ablation_modules/ablation_data SPyICP_DIRECTORY=/Users/enricoanfuso/Documents/Enrico/VKI/Project/Python/CodesClean/RtePlasmatron CONDA_EXE=/Users/enricoanfuso/opt/anaconda3/bin/conda _CE_M= _CE_CONDA= CONDA_PYTHON_EXE=/Users/enricoanfuso/opt/anaconda3/bin/python CONDA_SHLVL=0 rvm_prefix=/Users/enricoanfuso rvm_path=/Users/enricoanfuso/.rvm rvm_bin_path=/Users/enricoanfuso/.rvm/bin rvm_version=1.29.9 (latest) GEM_HOME=/Users/enricoanfuso/.rvm/gems/ruby-2.6.3 GEM_PATH=/Users/enricoanfuso/.rvm/gems/ruby-2.6.3:/Users/enricoanfuso/.rvm/gems/ruby-2.6.3@global MY_RUBY_HOME=/Users/enricoanfuso/.rvm/rubies/ruby-2.6.3 IRBRC=/Users/enricoanfuso/.rvm/rubies/ruby-2.6.3/.irbrc RUBY_VERSION=ruby-2.6.3 rvm_alias_expanded= rvm_bin_flag= rvm_docs_type= rvm_gemstone_package_file= rvm_gemstone_url= rvm_niceness= rvm_nightly_flag= rvm_only_path_flag= rvm_pretty_print_flag= rvm_proxy= rvm_quiet_flag= rvm_ruby_bits= rvm_ruby_file= rvm_ruby_make= rvm_ruby_make_install= rvm_ruby_mode= rvm_script_name= rvm_sdk= rvm_silent_flag= rvm_use_flag= rvm_hook= _=/usr/bin/env ``` **Mutation++ origin** Build from source - [ ] Package manager - [x] Build from source **Mutation++ build steps**envoutputStep git clone github.com/mutationpp/Mutationpp mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX:PATH=$(realpath ../install) .. make -j4 install
Step: modify the ~/.zshrc profile export MPP_DIRECTORY='/Users/enricoanfuso/Documents/Enrico/VKI/Codes/Mutationpp' export MPP_DATA_DIRECTORY=$MPP_DIRECTORY/data export PATH=$MPP_DIRECTORY/install/bin:$PATH export LD_LIBRARY_PATH=$MPP_DIRECTORY/install/lib:$LD_LIBRARY_PATH
Step ccmake .. BUILD_FORTRAN_WRAPPER --> ON
Step cd Mutationpp cd build make -j4 install
Step In "Mutationpp/install/include" I have drag&drop the "mutationpp.mod" file inside the "mutation++" folder
Mutation++ cmake output
``` CMake Warning (dev): Policy CMP0042 is not set: MACOSX_RPATH is enabled by default. Run "cmake --help-policy CMP0042" for policy details. Use the cmake_policy command to set the policy and suppress this warning. MACOSX_RPATH is not specified for the following targets: mutation++_fortran This warning is for project developers. Use -Wno-dev to suppress it. Generating done ``` **Mutation++ make output**Your software build steps
Steps to reproduce
When I try to run a test case of 'stagline' I get the following errors
" dyld: Library not loaded: libmutation++_fortran.dylib Referenced from: /Users/enricoanfuso/Documents/Enrico/VKI/Codes/stagline/bin/stagline Reason: image not found zsh: abort stagline "
Comments I checked in "/Users/enricoanfuso/Documents/Enrico/VKI/Codes/Mutationpp/install/lib" and both the files libmutation++_fortran.dylib, libmutation++.dylib are there