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gnu: nomad-optimizer: Update to 4.3.1.

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* 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 2023-10-10 17:27:45 +00:00 committed by Christopher Baines
parent 67dcc64110
commit 33cbb0ca8d
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1 changed files with 101 additions and 156 deletions
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@ -2421,7 +2421,7 @@ (define-public ipopt
(define-public nomad-optimizer (define-public nomad-optimizer
(package (package
(name "nomad-optimizer") (name "nomad-optimizer")
(version "4.2.0") (version "4.3.1")
(source (source
(origin (origin
(method git-fetch) (method git-fetch)
@ -2430,164 +2430,109 @@ (define-public nomad-optimizer
(commit (string-append "v." version)))) (commit (string-append "v." version))))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32 "08bxdvx8p5qzdw331xa5irc1896as4q5hajsid7f3qcxjm4nq4v3"))))
"1r4ygy3xn83dnppsw1451ynklsxpb238g5gk57inn84ghmdk08mj"))))
(build-system cmake-build-system) (build-system cmake-build-system)
(native-inputs (native-inputs
(list python-wrapper python-cython)) (list openmpi))
(arguments (arguments
`(#:imported-modules ((guix build python-build-system) (list
,@%cmake-build-system-modules) ;; Cannot build Python interface because it is incompatible with OpenMP
#:modules (((guix build python-build-system) ;; support, which is enabled by default.
#:select (python-version site-packages)) #:configure-flags
(guix build cmake-build-system) #~(list "-DBUILD_TESTS=ON"
(guix build utils)) "-DBUILD_INTERFACE_C=ON")
#:configure-flags #:phases
'("-DBUILD_INTERFACE_C=ON" #~(modify-phases %standard-phases
"-DBUILD_INTERFACE_PYTHON=ON" (add-after 'unpack 'fix-tests
"-DBUILD_TESTS=ON") (lambda _
#:phases (substitute* "examples/CMakeLists.txt"
(modify-phases %standard-phases ;; This test passes only sometimes.
(add-after 'unpack 'fix-sources-for-build ;; See https://github.com/bbopt/nomad/issues/72.
(lambda* (#:key outputs #:allow-other-keys) (("^ +add_subdirectory\\(\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/advanced/library/PSDMads\\)\n")
(substitute* "CMakeLists.txt" ""))
;; CMAKE_INSTALL_PREFIX is accidentally hardcoded. (make-file-writable
(("set\\(CMAKE_INSTALL_PREFIX .* FORCE\\)") "") "examples/advanced/library/exampleSuggestAndObserve/cache0.txt")
;; Requiring GCC version 8 or later is unwarranted. ;; Fix the tests so they run in out-of-source builds.
(("message\\(FATAL_ERROR \"GCC version < 8") (substitute*
"message(STATUS \"GCC version < 8")) '("examples/basic/library/COCO/CMakeLists.txt"
"examples/basic/library/example1/CMakeLists.txt"
(let ((out (assoc-ref outputs "out"))) "examples/basic/library/example2/CMakeLists.txt"
(substitute* "interfaces/PyNomad/CMakeLists.txt" "examples/basic/library/example3/CMakeLists.txt"
;; We don't want to build in-place, and anyway the install "examples/basic/library/example4/CMakeLists.txt"
;; command further below runs build_ext as a prerequisite. "examples/basic/library/single_obj_parallel/CMakeLists.txt"
(("COMMAND python setup_PyNomad\\.py .* build_ext --inplace\n") "examples/advanced/library/FixedVariable/CMakeLists.txt"
"") "examples/advanced/library/NMonly/CMakeLists.txt"
;; Don't install locally. "examples/advanced/library/PSDMads/CMakeLists.txt"
(("COMMAND python (setup_PyNomad\\.py .* install) --user\n" "examples/advanced/library/Restart/CMakeLists.txt"
_ args) "examples/advanced/library/Restart_VNS/CMakeLists.txt"
(string-append "COMMAND ${CMAKE_COMMAND} -E env" "examples/advanced/library/c_api/example1/CMakeLists.txt"
" CC=" ,(cc-for-target) "examples/advanced/library/c_api/example2/CMakeLists.txt"
" CXX=" ,(cxx-for-target) "examples/advanced/library/exampleSuggestAndObserve/CMakeLists.txt")
" " (which "python") ;; The runExampleTest.sh script is run with WORKING_DIRECTORY
" " args ;; set to CMAKE_CURRENT_SOURCE_DIR.
" --prefix=" out ;; Other scripts invoked by that script (for example
"\n"))) ;; examples/advanced/batch/SuggestAndObserve/loopSuggestAndObserve.sh)
;; Fix erroneous assumptions about the paths of the include and ;; are in that same directory, but compiled examples are
;; library directories. ;; located in CMAKE_CURRENT_BINARY_DIR.
(substitute* "interfaces/PyNomad/setup_PyNomad.py" (("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)"
(("^( +os_include_dirs = ).*" _ prefix) _ command test)
(string-append prefix "[\"../../src\"]\n")) (string-append command "${CMAKE_CURRENT_BINARY_DIR}" test)))
(("^(installed_lib_dir1 = ).*" _ prefix) (let ((builddir (string-append (getcwd) "/../build")))
(string-append prefix "\"" out "/lib\"\n")) (let ((dir "examples/advanced/library/FixedVariable"))
(("^installed_lib_dir2 = .*") "") (substitute* (string-append dir "/fixedVariable.cpp")
(("^ +link_args\\.append\\(\"-Wl,-rpath,\" \\+ installed_lib_dir2\\)\n") (("^( +std::string sExe = ).*" _ prefix)
""))))) (string-append prefix "\"" builddir "/" dir "/ufl.exe" "\";\n"))))
;; The BB_EXE and SURROGATE_EXE paths are interpreted relative
;; Fix the tests so they run in out-of-source builds. ;; to the configuration file provided to NOMAD.
;; ;; However, the configuration files are all in the source tree
;; TODO: Add support for examples/basic/batch/single_obj_MPIparallel, ;; rather than in the build tree (unlike the compiled
;; by adding openmpi to native-inputs and adjusting the example's ;; executables).
;; BB_EXE parameter. (let ((fix-exe-path (lambda* (dir #:optional
(add-after 'fix-sources-for-build 'fix-sources-for-tests (file "param.txt")
(lambda _ (exe-opt "BB_EXE"))
(substitute* "examples/CMakeLists.txt" (substitute* (string-append dir "/" file)
;; This test passes only sometimes. (((string-append "^" exe-opt " +"))
;; See https://github.com/bbopt/nomad/issues/72. ;; The $ prevents NOMAD from prefixing
(("^ +add_subdirectory\\(\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/advanced/library/PSDMads\\)\n") ;; the executable with the path of the
"") ;; parent directory of the configuration
;; examples/basic/batch/example3 is accidentally omitted. ;; file NOMAD was provided with as
(("^(add_subdirectory\\(\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/basic/batch/example)2(\\)\n)" ;; argument (param.txt or some such).
_ prefix suffix) (string-append exe-opt " $"
(string-append prefix "2" suffix builddir "/" dir "/"))))))
prefix "3" suffix)) (for-each
(lambda (dir)
;; The generated runExampleTest.sh script runs the test as part (substitute* (string-append dir "/CMakeLists.txt")
;; of a pipeline and incorrectly (because pipefail is unset) ;; The install phase has not yet run.
;; relies on the value of the exit status immediately after the (("(COMMAND.*)\\$\\{CMAKE_INSTALL_PREFIX\\}/bin/nomad\\b"
;; pipeline. _ prefix)
;; (The patch-shebangs phase runs later than this one, so no (string-append prefix "${CMAKE_BINARY_DIR}/src/nomad")))
;; need to update the path to bash here.) (if (equal? dir "examples/basic/batch/single_obj_MPIparallel")
(("#!/bin/bash") "#!/bin/bash\nset -o pipefail")) (substitute* (string-append dir "/param.txt")
(("^BB_EXE +'\\$.*mpirun \\$-np \\$4 ")
(substitute* (string-append "BB_EXE '$" (which "mpirun") " $"
(map (lambda (d) (string-append "examples/" d "/CMakeLists.txt")) builddir "/" dir "/")))
(append (fix-exe-path dir))
(map (lambda (d) (string-append "basic/library/" d)) (when (equal? dir "examples/basic/batch/surrogate_sort")
'("example1" "example2" "example3" (fix-exe-path dir "param.txt" "SURROGATE_EXE"))
"single_obj_parallel")) (when (equal? dir "examples/advanced/batch/FixedVariable")
(map (lambda (d) (string-append "advanced/library/" d)) (fix-exe-path dir "param1.txt")
'("FixedVariable" "NMonly" "PSDMads" "Restart" (fix-exe-path dir "param2.txt")
"c_api/example1" "c_api/example2" (fix-exe-path dir "param3.txt")
"exampleSuggestAndObserve")))) (fix-exe-path dir "param10.txt")))
;; The runExampleTest.sh script is run with WORKING_DIRECTORY '("examples/basic/batch/coco_bbob-constrained"
;; set to CMAKE_CURRENT_SOURCE_DIR. "examples/basic/batch/example1"
;; Other scripts invoked by that script (for example "examples/basic/batch/example2"
;; examples/advanced/batch/SuggestAndObserve/loopSuggestAndObserve.sh) "examples/basic/batch/example3"
;; are in that same directory, but compiled examples are "examples/basic/batch/multi_obj"
;; located in CMAKE_CURRENT_BINARY_DIR. "examples/basic/batch/multi_obj2"
(("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)" "examples/basic/batch/single_obj"
_ command test) "examples/basic/batch/single_obj_MPIparallel"
(string-append command "${CMAKE_CURRENT_BINARY_DIR}" test))) "examples/basic/batch/single_obj_parallel"
"examples/basic/batch/surrogate_sort"
;; The examples/basic/batch/example3 executable is already named "examples/advanced/batch/FixedVariable"
;; bb3.exe. "examples/advanced/batch/LHonly"))))))
(substitute* "examples/basic/batch/single_obj_parallel/CMakeLists.txt" (add-before 'configure 'mpi-setup
(("bb3.exe") "bb_parallel.exe")) #$%openmpi-setup))))
;; (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"))))))))))
(home-page "https://www.gerad.ca/nomad/") (home-page "https://www.gerad.ca/nomad/")
(synopsis "Nonlinear optimization by mesh-adaptive direct search") (synopsis "Nonlinear optimization by mesh-adaptive direct search")
(description (description