diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 211 |
1 files changed, 128 insertions, 83 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index ecb85642ec..fcd9c5482f 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -19,7 +19,7 @@ ;;; Copyright © 2017 Nikita <nikita@n0.is> ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org> -;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net> +;;; Copyright © 2017, 2019, 2022 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Dave Love <me@fx@gnu.org> ;;; Copyright © 2018, 2019, 2020, 2021 Jan (janneke) Nieuwenhuizen <janneke@gnu.org> @@ -45,7 +45,7 @@ ;;; Copyright © 2021 Gerd Heber <gerd.heber@gmail.com> ;;; Copyright © 2021 Franck Pérignon <franck.perignon@univ-grenoble-alpes.fr> ;;; Copyright © 2021 Philip McGrath <philip@philipmcgrath.com> -;;; Copyright © 2021 Paul A. Patience <paul@apatience.com> +;;; Copyright © 2021, 2022 Paul A. Patience <paul@apatience.com> ;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru> ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me> ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net> @@ -533,6 +533,14 @@ precision floating point numbers.") #:phases (modify-phases %standard-phases ,@(cond + ((and (target-riscv64?) + (%current-target-system)) + '((add-after 'unpack 'force-bootstrap + (lambda _ + ;; gsl ships with an old configure script that does not + ;; support riscv64. Regenerate it. + (delete-file "configure"))))) + ((or (string-prefix? "aarch64" system) (string-prefix? "powerpc" system)) ;; Some sparse matrix tests are failing on AArch64 and PowerPC: @@ -568,6 +576,11 @@ precision floating point numbers.") (string-append "exit (77);\n" all))))))) (else '())))))) + (native-inputs + (if (and (target-riscv64?) + (%current-target-system)) + (list autoconf automake libtool) + '())) (home-page "https://www.gnu.org/software/gsl/") (synopsis "Numerical library for C and C++") (description @@ -730,7 +743,7 @@ computing convex hulls.") (define-public lrslib (package (name "lrslib") - (version "7.1") + (version "7.2") (source (origin (method url-fetch) @@ -739,7 +752,7 @@ computing convex hulls.") (string-delete #\. version) ".tar.gz")) (sha256 (base32 - "05kq3hzam31dlmkccv3v358r478kpvx76mw37ka12c6ypwv5dsnk")))) + "1w1jsnfgny8cihndr5gfm99pvwp48qsvxkqfsi2q87gd3m57aj7w")))) (build-system gnu-build-system) (inputs (list gmp)) @@ -1079,14 +1092,14 @@ in the terminal or with an external viewer.") (define-public gnuplot (package (name "gnuplot") - (version "5.4.2") + (version "5.4.3") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" version "/gnuplot-" version ".tar.gz")) (sha256 - (base32 "1fp7rbhjmz2w63r72kicf8lfszzimz2csfx868fracw167hpaz75")))) + (base32 "112dplskbkdbaqi935m2xlk1xsw8s5l568wm7xad75hgp6x9py2i")))) (build-system gnu-build-system) (inputs (list readline cairo pango gd lua)) (native-inputs @@ -1924,21 +1937,20 @@ interfaces.") (define-public nomad-optimizer (package (name "nomad-optimizer") - (version "4.1.0") + (version "4.2.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/bbopt/nomad/") - (commit (string-append "v" version)))) + (commit (string-append "v." version)))) (file-name (git-file-name name version)) (sha256 (base32 - "0w386d8r5ldbvnv0c0g7vz95pfpvwdxis26vaalk2amsa5akl775")))) + "1r4ygy3xn83dnppsw1451ynklsxpb238g5gk57inn84ghmdk08mj")))) (build-system cmake-build-system) (native-inputs - `(("python" ,python-wrapper) - ("python-cython" ,python-cython))) + (list python-wrapper python-cython)) (arguments `(#:imported-modules ((guix build python-build-system) ,@%cmake-build-system-modules) @@ -1947,7 +1959,8 @@ interfaces.") (guix build cmake-build-system) (guix build utils)) #:configure-flags - '("-DBUILD_INTERFACES=ON" + '("-DBUILD_INTERFACE_C=ON" + "-DBUILD_INTERFACE_PYTHON=ON" "-DBUILD_TESTS=ON") #:phases (modify-phases %standard-phases @@ -1981,13 +1994,38 @@ interfaces.") (substitute* "interfaces/PyNomad/setup_PyNomad.py" (("^( +os_include_dirs = ).*" _ prefix) (string-append prefix "[\"../../src\"]\n")) - (("^(installed_lib_dir = ).*" _ prefix) - (string-append prefix "\"" out "/lib\"\n")))) - #t)) + (("^(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 @@ -1998,58 +2036,74 @@ interfaces.") '("FixedVariable" "NMonly" "PSDMads" "Restart" "c_api/example1" "c_api/example2" "exampleSuggestAndObserve")))) - ;; The built examples are assumed to be in the source tree - ;; (which isn't the case here). + ;; 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")) - ;; 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). - (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" - "single_obj" "single_obj_parallel" - "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 "))) + (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 " $" + builddir "/" dir "/")))))) (for-each - (lambda (f) (fix-exe-path dir f)) - '("param1.txt" "param2.txt" "param3.txt" "param10.txt")))) - #t)) + (lambda (dir) + (let ((dir (string-append "examples/" dir))) + (substitute* (string-append dir "/CMakeLists.txt") + ;; The install phase has not yet run. + (("COMMAND \\$\\{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"))))))) ;; The information in the .egg-info file is not kept up to date. (add-after 'install 'delete-superfluous-egg-info @@ -2058,8 +2112,7 @@ interfaces.") (site-packages inputs outputs) "/PyNomad-0.0.0-py" (python-version (assoc-ref inputs "python")) - ".egg-info")) - #t))))) + ".egg-info"))))))) (home-page "https://www.gerad.ca/nomad/") (synopsis "Nonlinear optimization by mesh-adaptive direct search") (description @@ -2801,7 +2854,7 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") (define-public gmsh (package (name "gmsh") - (version "4.8.4") + (version "4.9.5") (source (origin (method git-fetch) @@ -2812,7 +2865,7 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") (string-replace-substring version "." "_"))))) (file-name (git-file-name name version)) (sha256 - (base32 "07mi6ja3b9libgcdp2b4dwnkap1b9ha2wi2zdn9mhmwvp3g1pxhp")) + (base32 "0asd9p64ng5l2zk5glc33x3ynnvdpndlflg3q9mr0jxr7y9x0lrm")) (modules '((guix build utils))) (snippet '(begin @@ -6063,22 +6116,21 @@ and comparisons are supported.") (define-public sundials (package (name "sundials") - (version "3.1.1") + (version "6.1.1") (source (origin (method url-fetch) - (uri (string-append "https://computation.llnl.gov/projects/sundials/download/" + (uri (string-append "https://github.com/LLNL/sundials/releases/download/v6.1.1/" "sundials-" version ".tar.gz")) (sha256 (base32 - "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2")))) + "0327a1fy8rilwc4brsqqb71jd1ymb7mqgxsylab06crcg5xn7byg")))) (build-system cmake-build-system) (native-inputs - `(("python" ,python-2))) ;for tests; syntax incompatible with python 3 + (list python-2)) ;for tests; syntax incompatible with python 3 (inputs - `(("fortran" ,gfortran) ;for fcmix - ("blas" ,openblas) - ("suitesparse" ,suitesparse))) ;TODO: Add hypre + (list gfortran ;for fcmix + openblas petsc suitesparse)) ;TODO: Add hypre (arguments `(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon" "-DEXAMPLES_ENABLE_C:BOOL=ON" @@ -6107,24 +6159,17 @@ easily be incorporated into existing simulation codes.") (license license:bsd-3))) (define-public sundials-openmpi - (package (inherit sundials) + (package + (inherit sundials) (name "sundials-openmpi") (inputs - `(("mpi" ,openmpi) - ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI - ,@(package-inputs sundials))) + (modify-inputs (package-inputs sundials) + (delete "petsc") + (prepend openmpi petsc-openmpi))) ;support in SUNDIALS requires MPI (arguments (substitute-keyword-arguments (package-arguments sundials) ((#:configure-flags flags '()) - `(cons* "-DMPI_ENABLE:BOOL=ON" - "-DPETSC_ENABLE:BOOL=ON" - (string-append "-DPETSC_INCLUDE_DIR=" - (assoc-ref %build-inputs "petsc") - "/include") - (string-append "-DPETSC_LIBRARY_DIR=" - (assoc-ref %build-inputs "petsc") - "/lib") - ,flags)) + `(cons* "-DENABLE_MPI:BOOL=ON" ,flags)) ((#:phases phases '%standard-phases) `(modify-phases ,phases (add-before 'check 'mpi-setup |