diff options
| -rw-r--r-- | gnu/packages/maths.scm | 257 |
1 files changed, 101 insertions, 156 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e9c77a2061..683acd96e1 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2421,7 +2421,7 @@ interfaces.") (define-public nomad-optimizer (package (name "nomad-optimizer") - (version "4.2.0") + (version "4.3.1") (source (origin (method git-fetch) @@ -2430,164 +2430,109 @@ interfaces.") (commit (string-append "v." version)))) (file-name (git-file-name name version)) (sha256 - (base32 - "1r4ygy3xn83dnppsw1451ynklsxpb238g5gk57inn84ghmdk08mj")))) + (base32 "08bxdvx8p5qzdw331xa5irc1896as4q5hajsid7f3qcxjm4nq4v3")))) (build-system cmake-build-system) (native-inputs - (list python-wrapper python-cython)) + (list openmpi)) (arguments - `(#:imported-modules ((guix build python-build-system) - ,@%cmake-build-system-modules) - #:modules (((guix build python-build-system) - #:select (python-version site-packages)) - (guix build cmake-build-system) - (guix build utils)) - #:configure-flags - '("-DBUILD_INTERFACE_C=ON" - "-DBUILD_INTERFACE_PYTHON=ON" - "-DBUILD_TESTS=ON") - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'fix-sources-for-build - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "CMakeLists.txt" - ;; CMAKE_INSTALL_PREFIX is accidentally hardcoded. - (("set\\(CMAKE_INSTALL_PREFIX .* FORCE\\)") "") - ;; Requiring GCC version 8 or later is unwarranted. - (("message\\(FATAL_ERROR \"GCC version < 8") - "message(STATUS \"GCC version < 8")) - - (let ((out (assoc-ref outputs "out"))) - (substitute* "interfaces/PyNomad/CMakeLists.txt" - ;; We don't want to build in-place, and anyway the install - ;; command further below runs build_ext as a prerequisite. - (("COMMAND python setup_PyNomad\\.py .* build_ext --inplace\n") - "") - ;; Don't install locally. - (("COMMAND python (setup_PyNomad\\.py .* install) --user\n" - _ args) - (string-append "COMMAND ${CMAKE_COMMAND} -E env" - " CC=" ,(cc-for-target) - " CXX=" ,(cxx-for-target) - " " (which "python") - " " args - " --prefix=" out - "\n"))) - ;; Fix erroneous assumptions about the paths of the include and - ;; library directories. - (substitute* "interfaces/PyNomad/setup_PyNomad.py" - (("^( +os_include_dirs = ).*" _ prefix) - (string-append prefix "[\"../../src\"]\n")) - (("^(installed_lib_dir1 = ).*" _ prefix) - (string-append prefix "\"" out "/lib\"\n")) - (("^installed_lib_dir2 = .*") "") - (("^ +link_args\\.append\\(\"-Wl,-rpath,\" \\+ installed_lib_dir2\\)\n") - ""))))) - - ;; Fix the tests so they run in out-of-source builds. - ;; - ;; TODO: Add support for examples/basic/batch/single_obj_MPIparallel, - ;; by adding openmpi to native-inputs and adjusting the example's - ;; BB_EXE parameter. - (add-after 'fix-sources-for-build 'fix-sources-for-tests - (lambda _ - (substitute* "examples/CMakeLists.txt" - ;; This test passes only sometimes. - ;; See https://github.com/bbopt/nomad/issues/72. - (("^ +add_subdirectory\\(\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/advanced/library/PSDMads\\)\n") - "") - ;; examples/basic/batch/example3 is accidentally omitted. - (("^(add_subdirectory\\(\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/basic/batch/example)2(\\)\n)" - _ prefix suffix) - (string-append prefix "2" suffix - prefix "3" suffix)) - - ;; The generated runExampleTest.sh script runs the test as part - ;; of a pipeline and incorrectly (because pipefail is unset) - ;; relies on the value of the exit status immediately after the - ;; pipeline. - ;; (The patch-shebangs phase runs later than this one, so no - ;; need to update the path to bash here.) - (("#!/bin/bash") "#!/bin/bash\nset -o pipefail")) - - (substitute* - (map (lambda (d) (string-append "examples/" d "/CMakeLists.txt")) - (append - (map (lambda (d) (string-append "basic/library/" d)) - '("example1" "example2" "example3" - "single_obj_parallel")) - (map (lambda (d) (string-append "advanced/library/" d)) - '("FixedVariable" "NMonly" "PSDMads" "Restart" - "c_api/example1" "c_api/example2" - "exampleSuggestAndObserve")))) - ;; The runExampleTest.sh script is run with WORKING_DIRECTORY - ;; set to CMAKE_CURRENT_SOURCE_DIR. - ;; Other scripts invoked by that script (for example - ;; examples/advanced/batch/SuggestAndObserve/loopSuggestAndObserve.sh) - ;; are in that same directory, but compiled examples are - ;; located in CMAKE_CURRENT_BINARY_DIR. - (("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)" - _ command test) - (string-append command "${CMAKE_CURRENT_BINARY_DIR}" test))) - - ;; The examples/basic/batch/example3 executable is already named - ;; bb3.exe. - (substitute* "examples/basic/batch/single_obj_parallel/CMakeLists.txt" - (("bb3.exe") "bb_parallel.exe")) - - ;; (Unrelated to support for out-of-source testing.) - (make-file-writable - "examples/advanced/library/exampleSuggestAndObserve/cache0.txt") - - (let ((builddir (string-append (getcwd) "/../build"))) - (let ((dir "examples/advanced/library/FixedVariable")) - (substitute* (string-append dir "/fixedVariable.cpp") - (("^( +std::string sExe = ).*" _ prefix) - (string-append prefix "\"" builddir "/" dir "/ufl.exe" "\";\n")))) - - ;; The BB_EXE and SURROGATE_EXE paths are interpreted relative - ;; to the configuration file provided to NOMAD. - ;; However, the configuration files are all in the source tree - ;; rather than in the build tree (unlike the compiled - ;; executables). - (let ((fix-exe-path (lambda* (dir #:optional - (file "param.txt") - (exe-opt "BB_EXE")) - (substitute* (string-append dir "/" file) - (((string-append "^" exe-opt " +")) - ;; The $ prevents NOMAD from prefixing - ;; the executable with the path of the - ;; parent directory of the configuration - ;; file NOMAD was provided with as - ;; argument (param.txt or some such). - (string-append exe-opt " $" - builddir "/" dir "/")))))) - (for-each - (lambda (dir) - (let ((dir (string-append "examples/" dir))) - (substitute* (string-append dir "/CMakeLists.txt") - ;; The install phase has not yet run. - (("COMMAND \\$\\{CMAKE_INSTALL_PREFIX\\}/bin/nomad ") - "COMMAND ${CMAKE_BINARY_DIR}/src/nomad ")) - (fix-exe-path dir) - (when (equal? dir "examples/basic/batch/surrogate_sort") - (fix-exe-path dir "param.txt" "SURROGATE_EXE")))) - (append (map (lambda (d) (string-append "basic/batch/" d)) - '("example1" "example2" "example3" - "single_obj" - "single_obj_parallel" - ;; "single_obj_MPIparallel" - "surrogate_sort")) - '("advanced/batch/LHonly"))) - - (let ((dir "examples/advanced/batch/FixedVariable")) - (substitute* (string-append dir "/runFixed.sh") - ;; Hardcoded path to NOMAD executable. - (("^\\.\\./\\.\\./\\.\\./\\.\\./bin/nomad ") - (string-append builddir "/src/nomad "))) - (for-each - (lambda (f) (fix-exe-path dir f)) - '("param1.txt" "param2.txt" "param3.txt" "param10.txt")))))))))) + (list + ;; Cannot build Python interface because it is incompatible with OpenMP + ;; support, which is enabled by default. + #:configure-flags + #~(list "-DBUILD_TESTS=ON" + "-DBUILD_INTERFACE_C=ON") + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'fix-tests + (lambda _ + (substitute* "examples/CMakeLists.txt" + ;; This test passes only sometimes. + ;; See https://github.com/bbopt/nomad/issues/72. + (("^ +add_subdirectory\\(\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/advanced/library/PSDMads\\)\n") + "")) + (make-file-writable + "examples/advanced/library/exampleSuggestAndObserve/cache0.txt") + ;; Fix the tests so they run in out-of-source builds. + (substitute* + '("examples/basic/library/COCO/CMakeLists.txt" + "examples/basic/library/example1/CMakeLists.txt" + "examples/basic/library/example2/CMakeLists.txt" + "examples/basic/library/example3/CMakeLists.txt" + "examples/basic/library/example4/CMakeLists.txt" + "examples/basic/library/single_obj_parallel/CMakeLists.txt" + "examples/advanced/library/FixedVariable/CMakeLists.txt" + "examples/advanced/library/NMonly/CMakeLists.txt" + "examples/advanced/library/PSDMads/CMakeLists.txt" + "examples/advanced/library/Restart/CMakeLists.txt" + "examples/advanced/library/Restart_VNS/CMakeLists.txt" + "examples/advanced/library/c_api/example1/CMakeLists.txt" + "examples/advanced/library/c_api/example2/CMakeLists.txt" + "examples/advanced/library/exampleSuggestAndObserve/CMakeLists.txt") + ;; The runExampleTest.sh script is run with WORKING_DIRECTORY + ;; set to CMAKE_CURRENT_SOURCE_DIR. + ;; Other scripts invoked by that script (for example + ;; examples/advanced/batch/SuggestAndObserve/loopSuggestAndObserve.sh) + ;; are in that same directory, but compiled examples are + ;; located in CMAKE_CURRENT_BINARY_DIR. + (("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)" + _ command test) + (string-append command "${CMAKE_CURRENT_BINARY_DIR}" test))) + (let ((builddir (string-append (getcwd) "/../build"))) + (let ((dir "examples/advanced/library/FixedVariable")) + (substitute* (string-append dir "/fixedVariable.cpp") + (("^( +std::string sExe = ).*" _ prefix) + (string-append prefix "\"" builddir "/" dir "/ufl.exe" "\";\n")))) + ;; The BB_EXE and SURROGATE_EXE paths are interpreted relative + ;; to the configuration file provided to NOMAD. + ;; However, the configuration files are all in the source tree + ;; rather than in the build tree (unlike the compiled + ;; executables). + (let ((fix-exe-path (lambda* (dir #:optional + (file "param.txt") + (exe-opt "BB_EXE")) + (substitute* (string-append dir "/" file) + (((string-append "^" exe-opt " +")) + ;; The $ prevents NOMAD from prefixing + ;; the executable with the path of the + ;; parent directory of the configuration + ;; file NOMAD was provided with as + ;; argument (param.txt or some such). + (string-append exe-opt " $" + builddir "/" dir "/")))))) + (for-each + (lambda (dir) + (substitute* (string-append dir "/CMakeLists.txt") + ;; The install phase has not yet run. + (("(COMMAND.*)\\$\\{CMAKE_INSTALL_PREFIX\\}/bin/nomad\\b" + _ prefix) + (string-append prefix "${CMAKE_BINARY_DIR}/src/nomad"))) + (if (equal? dir "examples/basic/batch/single_obj_MPIparallel") + (substitute* (string-append dir "/param.txt") + (("^BB_EXE +'\\$.*mpirun \\$-np \\$4 ") + (string-append "BB_EXE '$" (which "mpirun") " $" + builddir "/" dir "/"))) + (fix-exe-path dir)) + (when (equal? dir "examples/basic/batch/surrogate_sort") + (fix-exe-path dir "param.txt" "SURROGATE_EXE")) + (when (equal? dir "examples/advanced/batch/FixedVariable") + (fix-exe-path dir "param1.txt") + (fix-exe-path dir "param2.txt") + (fix-exe-path dir "param3.txt") + (fix-exe-path dir "param10.txt"))) + '("examples/basic/batch/coco_bbob-constrained" + "examples/basic/batch/example1" + "examples/basic/batch/example2" + "examples/basic/batch/example3" + "examples/basic/batch/multi_obj" + "examples/basic/batch/multi_obj2" + "examples/basic/batch/single_obj" + "examples/basic/batch/single_obj_MPIparallel" + "examples/basic/batch/single_obj_parallel" + "examples/basic/batch/surrogate_sort" + "examples/advanced/batch/FixedVariable" + "examples/advanced/batch/LHonly")))))) + (add-before 'configure 'mpi-setup + #$%openmpi-setup)))) (home-page "https://www.gerad.ca/nomad/") (synopsis "Nonlinear optimization by mesh-adaptive direct search") (description |