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Merge pull request #443 from GEOS-ESM/develop
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‎CHANGELOG.md‎

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@@ -17,6 +17,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### Deprecated
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## [4.15.0] - 2025-04-24
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### Changed
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- Added a timeout to `mepo status` to prevent it from hanging indefinitely. The timeout is set to 60 seconds
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- Modified the f2py and f2py3 codes for meson+MPT support
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- It was found that when an f2py code uses MPI, with meson+MPT we need to run with `LD_PRELOAD=/path/to/mpt/libmpi.so`
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## [4.14.2] - 2025-04-22
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### Fixed

‎esma_support/esma_mepo_status.cmake‎

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@@ -21,6 +21,7 @@ function(esma_capture_mepo_status)
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OUTPUT_FILE "${OUTPUT_FILE}"
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RESULT_VARIABLE MEPO_STATUS_RESULT
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ERROR_QUIET
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TIMEOUT 60
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)
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if(NOT MEPO_STATUS_RESULT EQUAL 0)

‎python/.gitignore‎

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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share/python-wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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MANIFEST
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.nox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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*.py,cover
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.hypothesis/
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.pytest_cache/
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cover/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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db.sqlite3
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db.sqlite3-journal
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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# For a library or package, you might want to ignore these files since the code is
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# intended to run in multiple environments; otherwise, check them in:
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# .python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# UV
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# Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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#uv.lock
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# poetry
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# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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# This is especially recommended for binary packages to ensure reproducibility, and is more
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# commonly ignored for libraries.
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# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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#poetry.lock
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# pdm
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# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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#pdm.lock
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# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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# in version control.
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# https://pdm.fming.dev/latest/usage/project/#working-with-version-control
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.pdm.toml
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.pdm-python
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.pdm-build/
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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ENV/
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env.bak/
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venv.bak/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# PyCharm
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# JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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# Ruff stuff:
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.ruff_cache/
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# PyPI configuration file
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.pypirc

‎python/f2py/esma_add_f2py_module.cmake‎

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add_f2py_module (${name} ${ARGN})
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set(options USE_MPI)
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cmake_parse_arguments (esma_add_f2py_module "${options}" "" "" ${ARGN})
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# If one of the arguments is USE_MPI we need to
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# do something special on MPT systems.
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# First this only matters if we are on Python 3.12 or higher
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if (Python_VERSION VERSION_GREATER_EQUAL 3.12)
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message(DEBUG "[F2PY]: Python version is 3.12 or higher, so meson is our backend")
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message(DEBUG "[F2PY]: MPI_STACK: ${MPI_STACK}")
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# Next, check if we are using MPI and our stack is 'mpt'
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message(DEBUG "[F2PY]: Checking for USE_MPI and MPI_STACK=mpt")
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if(esma_add_f2py_module_USE_MPI AND MPI_STACK STREQUAL "mpt")
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message(DEBUG "[F2PY]: MPI_Fortran_LIBRARIES: ${MPI_Fortran_LIBRARIES}")
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# Now we need LD_PRELOAD the libmpi.so found in MPI_Fortran_LIBRARIES
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# But MPI_Fortran_LIBRARIES is a list, so we need to find the one
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# that ends with 'libmpi.so'
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foreach (mpi_lib ${MPI_Fortran_LIBRARIES})
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if (mpi_lib MATCHES "libmpi.so$")
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message(DEBUG "[F2PY]: Found libmpi.so: ${mpi_lib}")
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set(F2PY_PRELOAD "LD_PRELOAD=${mpi_lib}")
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message(STATUS "[F2PY3]: USE_MPI found and using MPT. Testing will add ${F2PY_PRELOAD}")
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break()
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endif()
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endforeach()
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endif()
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endif()
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set(UNIT_TEST test_${name})
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add_test (
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NAME ${UNIT_TEST}
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COMMAND ${CMAKE_COMMAND} -E env "LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib:$ENV{LD_LIBRARY_PATH}" ${Python_EXECUTABLE} -c "import ${name}"
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COMMAND ${CMAKE_COMMAND} -E env "LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib:$ENV{LD_LIBRARY_PATH}" "${F2PY_PRELOAD}" ${Python_EXECUTABLE} -c "import ${name}"
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)
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add_custom_command(
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TARGET ${name}
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COMMENT "Running Python import test on ${name}"
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POST_BUILD
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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COMMAND ${CMAKE_COMMAND} -E env "LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib:$ENV{LD_LIBRARY_PATH}" ${Python_EXECUTABLE} -c "import ${name}"
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COMMAND ${CMAKE_COMMAND} -E env "LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib:$ENV{LD_LIBRARY_PATH}" "${F2PY_PRELOAD}" ${Python_EXECUTABLE} -c "import ${name}"
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)
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endmacro ()

‎python/f2py3/esma_add_f2py3_module.cmake‎

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add_f2py3_module (${name} ${ARGN})
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set(options USE_MPI)
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cmake_parse_arguments (esma_add_f2py3_module "${options}" "" "" ${ARGN})
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# If one of the arguments is USE_MPI we need to
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# do something special on MPT systems.
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# First this only matters if we are on Python 3.12 or higher
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if (Python3_VERSION VERSION_GREATER_EQUAL 3.12)
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message(DEBUG "[F2PY3]: Python version is 3.12 or higher, so meson is our backend")
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message(DEBUG "[F2PY3]: MPI_STACK: ${MPI_STACK}")
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# Next, check if we are using MPI and our stack is 'mpt'
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message(DEBUG "[F2PY3]: Checking for USE_MPI and MPI_STACK=mpt")
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if(esma_add_f2py3_module_USE_MPI AND MPI_STACK STREQUAL "mpt")
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message(DEBUG "[F2PY3]: MPI_Fortran_LIBRARIES: ${MPI_Fortran_LIBRARIES}")
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# Now we need LD_PRELOAD the libmpi.so found in MPI_Fortran_LIBRARIES
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# But MPI_Fortran_LIBRARIES is a list, so we need to find the one
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# that ends with 'libmpi.so'
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foreach (mpi_lib ${MPI_Fortran_LIBRARIES})
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if (mpi_lib MATCHES "libmpi.so$")
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message(DEBUG "[F2PY3]: Found libmpi.so: ${mpi_lib}")
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set(F2PY3_PRELOAD "LD_PRELOAD=${mpi_lib}")
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message(STATUS "[F2PY3]: USE_MPI found and using MPT. Testing will add ${F2PY3_PRELOAD}")
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break()
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endif()
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endforeach()
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endif()
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endif()
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set(UNIT_TEST test_${name})
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add_test (
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NAME ${UNIT_TEST}
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COMMAND ${CMAKE_COMMAND} -E env "LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib:$ENV{LD_LIBRARY_PATH}" ${Python3_EXECUTABLE} -c "import ${name}"
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COMMAND ${CMAKE_COMMAND} -E env "LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib:$ENV{LD_LIBRARY_PATH}" "${F2PY3_PRELOAD}" ${Python3_EXECUTABLE} -c "import ${name}"
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add_custom_command(
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TARGET ${name}
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COMMENT "Running Python3 import test on ${name}"
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POST_BUILD
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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COMMAND ${CMAKE_COMMAND} -E env "LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib:$ENV{LD_LIBRARY_PATH}" ${Python3_EXECUTABLE} -c "import ${name}"
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COMMAND ${CMAKE_COMMAND} -E env "LD_LIBRARY_PATH=${CMAKE_BINARY_DIR}/lib:$ENV{LD_LIBRARY_PATH}" "${F2PY3_PRELOAD}" ${Python3_EXECUTABLE} -c "import ${name}"
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)
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endmacro ()

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