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gnu: nomad-optimizer: Update to 4.3.1.
* gnu/packages/maths.scm (nomad-optimizer): Update to 4.3.1. [native-inputs]: Remove python-wrapper and python-cython. Add openmpi. [arguments]: Use G-expressions. Remove #:imported-modules and #:modules. <#:configure-flags>: Remove -DBUILD_INTERFACE_PYTHON=ON. <#:phases>: Remove 'fix-sources-for-build' phase. Rename 'fix-sources-for-tests' phase to 'fix-tests' and update it. Add 'mpi-setup' phase. Signed-off-by: Christopher Baines <mail@cbaines.net>
This commit is contained in:
Paul A. Patience
Christopher Baines
parent
67dcc64110
commit
33cbb0ca8d
1 changed files with 101 additions and 156 deletions
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@ -2421,7 +2421,7 @@ (define-public ipopt
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(define-public nomad-optimizer
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(package
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(name "nomad-optimizer")
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(version "4.2.0")
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(version "4.3.1")
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(source
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(origin
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(method git-fetch)
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@ -2430,164 +2430,109 @@ (define-public nomad-optimizer
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(commit (string-append "v." version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"1r4ygy3xn83dnppsw1451ynklsxpb238g5gk57inn84ghmdk08mj"))))
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(base32 "08bxdvx8p5qzdw331xa5irc1896as4q5hajsid7f3qcxjm4nq4v3"))))
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(build-system cmake-build-system)
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(native-inputs
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(list python-wrapper python-cython))
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(list openmpi))
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(arguments
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`(#:imported-modules ((guix build python-build-system)
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,@%cmake-build-system-modules)
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#:modules (((guix build python-build-system)
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#:select (python-version site-packages))
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(guix build cmake-build-system)
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(guix build utils))
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#:configure-flags
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'("-DBUILD_INTERFACE_C=ON"
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"-DBUILD_INTERFACE_PYTHON=ON"
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"-DBUILD_TESTS=ON")
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'fix-sources-for-build
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(lambda* (#:key outputs #:allow-other-keys)
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(substitute* "CMakeLists.txt"
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;; CMAKE_INSTALL_PREFIX is accidentally hardcoded.
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(("set\\(CMAKE_INSTALL_PREFIX .* FORCE\\)") "")
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;; Requiring GCC version 8 or later is unwarranted.
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(("message\\(FATAL_ERROR \"GCC version < 8")
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"message(STATUS \"GCC version < 8"))
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(let ((out (assoc-ref outputs "out")))
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(substitute* "interfaces/PyNomad/CMakeLists.txt"
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;; We don't want to build in-place, and anyway the install
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;; command further below runs build_ext as a prerequisite.
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(("COMMAND python setup_PyNomad\\.py .* build_ext --inplace\n")
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"")
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;; Don't install locally.
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(("COMMAND python (setup_PyNomad\\.py .* install) --user\n"
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_ args)
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(string-append "COMMAND ${CMAKE_COMMAND} -E env"
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" CC=" ,(cc-for-target)
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" CXX=" ,(cxx-for-target)
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" " (which "python")
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" " args
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" --prefix=" out
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"\n")))
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;; Fix erroneous assumptions about the paths of the include and
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;; library directories.
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(substitute* "interfaces/PyNomad/setup_PyNomad.py"
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(("^( +os_include_dirs = ).*" _ prefix)
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(string-append prefix "[\"../../src\"]\n"))
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(("^(installed_lib_dir1 = ).*" _ prefix)
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(string-append prefix "\"" out "/lib\"\n"))
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(("^installed_lib_dir2 = .*") "")
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(("^ +link_args\\.append\\(\"-Wl,-rpath,\" \\+ installed_lib_dir2\\)\n")
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"")))))
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;; Fix the tests so they run in out-of-source builds.
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;;
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;; TODO: Add support for examples/basic/batch/single_obj_MPIparallel,
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;; by adding openmpi to native-inputs and adjusting the example's
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;; BB_EXE parameter.
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(add-after 'fix-sources-for-build 'fix-sources-for-tests
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(lambda _
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(substitute* "examples/CMakeLists.txt"
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;; This test passes only sometimes.
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;; See https://github.com/bbopt/nomad/issues/72.
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(("^ +add_subdirectory\\(\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/advanced/library/PSDMads\\)\n")
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"")
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;; examples/basic/batch/example3 is accidentally omitted.
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(("^(add_subdirectory\\(\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/basic/batch/example)2(\\)\n)"
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_ prefix suffix)
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(string-append prefix "2" suffix
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prefix "3" suffix))
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;; The generated runExampleTest.sh script runs the test as part
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;; of a pipeline and incorrectly (because pipefail is unset)
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;; relies on the value of the exit status immediately after the
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;; pipeline.
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;; (The patch-shebangs phase runs later than this one, so no
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;; need to update the path to bash here.)
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(("#!/bin/bash") "#!/bin/bash\nset -o pipefail"))
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(substitute*
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(map (lambda (d) (string-append "examples/" d "/CMakeLists.txt"))
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(append
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(map (lambda (d) (string-append "basic/library/" d))
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'("example1" "example2" "example3"
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"single_obj_parallel"))
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(map (lambda (d) (string-append "advanced/library/" d))
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'("FixedVariable" "NMonly" "PSDMads" "Restart"
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"c_api/example1" "c_api/example2"
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"exampleSuggestAndObserve"))))
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;; The runExampleTest.sh script is run with WORKING_DIRECTORY
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;; set to CMAKE_CURRENT_SOURCE_DIR.
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;; Other scripts invoked by that script (for example
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;; examples/advanced/batch/SuggestAndObserve/loopSuggestAndObserve.sh)
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;; are in that same directory, but compiled examples are
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;; located in CMAKE_CURRENT_BINARY_DIR.
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(("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)"
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_ command test)
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(string-append command "${CMAKE_CURRENT_BINARY_DIR}" test)))
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;; The examples/basic/batch/example3 executable is already named
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;; bb3.exe.
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(substitute* "examples/basic/batch/single_obj_parallel/CMakeLists.txt"
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(("bb3.exe") "bb_parallel.exe"))
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;; (Unrelated to support for out-of-source testing.)
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(make-file-writable
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"examples/advanced/library/exampleSuggestAndObserve/cache0.txt")
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(let ((builddir (string-append (getcwd) "/../build")))
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(let ((dir "examples/advanced/library/FixedVariable"))
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(substitute* (string-append dir "/fixedVariable.cpp")
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(("^( +std::string sExe = ).*" _ prefix)
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(string-append prefix "\"" builddir "/" dir "/ufl.exe" "\";\n"))))
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;; The BB_EXE and SURROGATE_EXE paths are interpreted relative
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;; to the configuration file provided to NOMAD.
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;; However, the configuration files are all in the source tree
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;; rather than in the build tree (unlike the compiled
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;; executables).
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(let ((fix-exe-path (lambda* (dir #:optional
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(file "param.txt")
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(exe-opt "BB_EXE"))
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(substitute* (string-append dir "/" file)
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(((string-append "^" exe-opt " +"))
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;; The $ prevents NOMAD from prefixing
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;; the executable with the path of the
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;; parent directory of the configuration
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;; file NOMAD was provided with as
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;; argument (param.txt or some such).
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(string-append exe-opt " $"
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builddir "/" dir "/"))))))
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(for-each
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(lambda (dir)
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(let ((dir (string-append "examples/" dir)))
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(substitute* (string-append dir "/CMakeLists.txt")
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;; The install phase has not yet run.
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(("COMMAND \\$\\{CMAKE_INSTALL_PREFIX\\}/bin/nomad ")
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"COMMAND ${CMAKE_BINARY_DIR}/src/nomad "))
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(fix-exe-path dir)
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(when (equal? dir "examples/basic/batch/surrogate_sort")
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(fix-exe-path dir "param.txt" "SURROGATE_EXE"))))
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(append (map (lambda (d) (string-append "basic/batch/" d))
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'("example1" "example2" "example3"
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"single_obj"
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"single_obj_parallel"
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;; "single_obj_MPIparallel"
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"surrogate_sort"))
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'("advanced/batch/LHonly")))
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(let ((dir "examples/advanced/batch/FixedVariable"))
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(substitute* (string-append dir "/runFixed.sh")
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;; Hardcoded path to NOMAD executable.
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(("^\\.\\./\\.\\./\\.\\./\\.\\./bin/nomad ")
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(string-append builddir "/src/nomad ")))
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(for-each
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(lambda (f) (fix-exe-path dir f))
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'("param1.txt" "param2.txt" "param3.txt" "param10.txt"))))))))))
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(list
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;; Cannot build Python interface because it is incompatible with OpenMP
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;; support, which is enabled by default.
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#:configure-flags
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#~(list "-DBUILD_TESTS=ON"
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"-DBUILD_INTERFACE_C=ON")
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'fix-tests
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(lambda _
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(substitute* "examples/CMakeLists.txt"
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;; This test passes only sometimes.
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;; See https://github.com/bbopt/nomad/issues/72.
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(("^ +add_subdirectory\\(\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/advanced/library/PSDMads\\)\n")
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""))
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(make-file-writable
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"examples/advanced/library/exampleSuggestAndObserve/cache0.txt")
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;; Fix the tests so they run in out-of-source builds.
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(substitute*
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'("examples/basic/library/COCO/CMakeLists.txt"
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"examples/basic/library/example1/CMakeLists.txt"
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"examples/basic/library/example2/CMakeLists.txt"
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"examples/basic/library/example3/CMakeLists.txt"
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"examples/basic/library/example4/CMakeLists.txt"
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"examples/basic/library/single_obj_parallel/CMakeLists.txt"
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"examples/advanced/library/FixedVariable/CMakeLists.txt"
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"examples/advanced/library/NMonly/CMakeLists.txt"
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"examples/advanced/library/PSDMads/CMakeLists.txt"
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"examples/advanced/library/Restart/CMakeLists.txt"
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"examples/advanced/library/Restart_VNS/CMakeLists.txt"
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"examples/advanced/library/c_api/example1/CMakeLists.txt"
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"examples/advanced/library/c_api/example2/CMakeLists.txt"
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"examples/advanced/library/exampleSuggestAndObserve/CMakeLists.txt")
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;; The runExampleTest.sh script is run with WORKING_DIRECTORY
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;; set to CMAKE_CURRENT_SOURCE_DIR.
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;; Other scripts invoked by that script (for example
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;; examples/advanced/batch/SuggestAndObserve/loopSuggestAndObserve.sh)
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;; are in that same directory, but compiled examples are
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;; located in CMAKE_CURRENT_BINARY_DIR.
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(("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)"
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_ command test)
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(string-append command "${CMAKE_CURRENT_BINARY_DIR}" test)))
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(let ((builddir (string-append (getcwd) "/../build")))
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(let ((dir "examples/advanced/library/FixedVariable"))
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(substitute* (string-append dir "/fixedVariable.cpp")
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(("^( +std::string sExe = ).*" _ prefix)
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(string-append prefix "\"" builddir "/" dir "/ufl.exe" "\";\n"))))
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;; The BB_EXE and SURROGATE_EXE paths are interpreted relative
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;; to the configuration file provided to NOMAD.
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;; However, the configuration files are all in the source tree
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;; rather than in the build tree (unlike the compiled
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;; executables).
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(let ((fix-exe-path (lambda* (dir #:optional
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(file "param.txt")
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(exe-opt "BB_EXE"))
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(substitute* (string-append dir "/" file)
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(((string-append "^" exe-opt " +"))
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;; The $ prevents NOMAD from prefixing
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;; the executable with the path of the
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;; parent directory of the configuration
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;; file NOMAD was provided with as
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;; argument (param.txt or some such).
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(string-append exe-opt " $"
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builddir "/" dir "/"))))))
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(for-each
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(lambda (dir)
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(substitute* (string-append dir "/CMakeLists.txt")
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;; The install phase has not yet run.
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(("(COMMAND.*)\\$\\{CMAKE_INSTALL_PREFIX\\}/bin/nomad\\b"
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_ prefix)
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(string-append prefix "${CMAKE_BINARY_DIR}/src/nomad")))
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(if (equal? dir "examples/basic/batch/single_obj_MPIparallel")
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(substitute* (string-append dir "/param.txt")
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(("^BB_EXE +'\\$.*mpirun \\$-np \\$4 ")
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(string-append "BB_EXE '$" (which "mpirun") " $"
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builddir "/" dir "/")))
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(fix-exe-path dir))
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(when (equal? dir "examples/basic/batch/surrogate_sort")
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(fix-exe-path dir "param.txt" "SURROGATE_EXE"))
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(when (equal? dir "examples/advanced/batch/FixedVariable")
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(fix-exe-path dir "param1.txt")
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(fix-exe-path dir "param2.txt")
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(fix-exe-path dir "param3.txt")
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(fix-exe-path dir "param10.txt")))
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'("examples/basic/batch/coco_bbob-constrained"
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"examples/basic/batch/example1"
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"examples/basic/batch/example2"
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"examples/basic/batch/example3"
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"examples/basic/batch/multi_obj"
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"examples/basic/batch/multi_obj2"
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"examples/basic/batch/single_obj"
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"examples/basic/batch/single_obj_MPIparallel"
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"examples/basic/batch/single_obj_parallel"
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"examples/basic/batch/surrogate_sort"
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"examples/advanced/batch/FixedVariable"
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"examples/advanced/batch/LHonly"))))))
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(add-before 'configure 'mpi-setup
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#$%openmpi-setup))))
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(home-page "https://www.gerad.ca/nomad/")
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(synopsis "Nonlinear optimization by mesh-adaptive direct search")
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(description
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