Package: guix-patches;
Reported by: "Paul A. Patience" <paul <at> apatience.com>
Date: Tue, 10 Oct 2023 17:29:02 UTC
Severity: normal
Tags: patch
Done: Christopher Baines <mail <at> cbaines.net>
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guix-patches <at> gnu.org:bug#66449; Package guix-patches.
(Tue, 10 Oct 2023 17:29:02 GMT) Full text and rfc822 format available."Paul A. Patience" <paul <at> apatience.com>:guix-patches <at> gnu.org.
(Tue, 10 Oct 2023 17:29:02 GMT) Full text and rfc822 format available.Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):
From: "Paul A. Patience" <paul <at> apatience.com> To: guix-patches <at> gnu.org Cc: "Paul A. Patience" <paul <at> apatience.com> Subject: [PATCH] gnu: nomad-optimizer: Update to 4.3.1. Date: Tue, 10 Oct 2023 17:27:45 +0000
* 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.
---
gnu/packages/maths.scm | 257 ++++++++++++++++-------------------------
1 file changed, 101 insertions(+), 156 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 928e169e95..f3ee861811 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2420,7 +2420,7 @@ (define-public ipopt
(define-public nomad-optimizer
(package
(name "nomad-optimizer")
- (version "4.2.0")
+ (version "4.3.1")
(source
(origin
(method git-fetch)
@@ -2429,164 +2429,109 @@ (define-public nomad-optimizer
(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
base-commit: f4e8baf3806e79d7111d2943859865ae4ee0b59d
--
2.41.0
guix-patches <at> gnu.org:bug#66449; Package guix-patches.
(Tue, 17 Oct 2023 10:10:02 GMT) Full text and rfc822 format available.Message #8 received at submit <at> debbugs.gnu.org (full text, mbox):
From: Christopher Baines <mail <at> cbaines.net> To: "Paul A. Patience" <paul <at> apatience.com> Cc: 66449-done <at> debbugs.gnu.org, guix-patches <at> gnu.org Subject: Re: [bug#66449] [PATCH] gnu: nomad-optimizer: Update to 4.3.1. Date: Tue, 17 Oct 2023 11:08:32 +0100
[Message part 1 (text/plain, inline)]
"Paul A. Patience" <paul <at> apatience.com> writes: > * 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. > --- > gnu/packages/maths.scm | 257 ++++++++++++++++------------------------- > 1 file changed, 101 insertions(+), 156 deletions(-) Thanks for the patch, I've pushed this to master as 33cbb0ca8dd9edb28a12fbfdf0c430899813a737. Chris
[signature.asc (application/pgp-signature, inline)]
Christopher Baines <mail <at> cbaines.net>:"Paul A. Patience" <paul <at> apatience.com>:Debbugs Internal Request <help-debbugs <at> gnu.org>
to internal_control <at> debbugs.gnu.org.
(Tue, 14 Nov 2023 12:24:09 GMT) Full text and rfc822 format available.
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