diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 137 |
1 files changed, 110 insertions, 27 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 3b41d1bfd7..7f504fa52b 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -15,14 +15,14 @@ ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2016 Leo Famulari <leo@famulari.name> ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be> -;;; Copyright © 2017, 2018, 2019, 2020 Paul Garlick <pgarlick@tourbillion-technology.com> +;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com> ;;; 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, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Dave Love <me@fx@gnu.org> -;;; Copyright © 2018, 2019, 2020 Jan Nieuwenhuizen <janneke@gnu.org> +;;; Copyright © 2018, 2019, 2020, 2021 Jan (janneke) Nieuwenhuizen <janneke@gnu.org> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com> ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com> @@ -46,6 +46,7 @@ ;;; 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 Ivan Gankevich <i.gankevich@spbu.ru> ;;; ;;; This file is part of GNU Guix. ;;; @@ -960,14 +961,14 @@ singular value problems.") (define-public gnuplot (package (name "gnuplot") - (version "5.4.1") + (version "5.4.2") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" version "/gnuplot-" version ".tar.gz")) (sha256 - (base32 "03jrqs5lvxmbbz2c4g17dn2hrxqwd3hfadk9q8wbkbkyas2h8sbb")))) + (base32 "1fp7rbhjmz2w63r72kicf8lfszzimz2csfx868fracw167hpaz75")))) (build-system gnu-build-system) (inputs `(("readline" ,readline) ("cairo" ,cairo) @@ -2262,7 +2263,7 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") (define-public gmsh (package (name "gmsh") - (version "4.6.0") + (version "4.8.4") (source (origin (method git-fetch) @@ -2270,11 +2271,10 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") (url "https://gitlab.onelab.info/gmsh/gmsh.git") (commit (string-append "gmsh_" - (string-map (lambda (x) (if (eq? x #\.) #\_ x)) - version))))) + (string-replace-substring version "." "_"))))) (file-name (git-file-name name version)) (sha256 - (base32 "0m0pjxcy1bnr7a20i11lh0ih159pphq9wsvfjr3sfx4y3lginz5y")) + (base32 "07mi6ja3b9libgcdp2b4dwnkap1b9ha2wi2zdn9mhmwvp3g1pxhp")) (modules '((guix build utils))) (snippet '(begin @@ -2284,22 +2284,48 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") (propagated-inputs `(("fltk" ,fltk) ("gfortran" ,gfortran) + ("glu" ,glu) ("gmp" ,gmp) ("hdf5" ,hdf5) ("lapack" ,lapack) + ("libx11" ,libx11) + ("libxext" ,libxext) ("mesa" ,mesa) - ("glu" ,glu) ("metis" ,metis) - ("opencascade-occt" ,opencascade-occt) - ("libx11" ,libx11) - ("libxext" ,libxext))) + ("opencascade-occt" ,opencascade-occt))) (inputs `(("fontconfig" ,fontconfig) - ("libxft" ,libxft))) + ("libxft" ,libxft) + ("python" ,python))) (arguments `(#:configure-flags `("-DENABLE_SYSTEM_CONTRIB:BOOL=ON" "-DENABLE_BUILD_SHARED:BOOL=ON" - "-DENABLE_BUILD_DYNAMIC:BOOL=ON"))) + "-DENABLE_BUILD_DYNAMIC:BOOL=ON") + #:imported-modules (,@%cmake-build-system-modules + (guix build python-build-system)) + #:modules (((guix build python-build-system) #:select (site-packages)) + (guix build cmake-build-system) + (guix build utils)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-paths + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Use the standard Guix site-package path for + ;; installation of the Python API. + (substitute* "CMakeLists.txt" + (("include\\(GNUInstallDirs\\)\n") + (string-append "include(GNUInstallDirs)\n" + " set(GMSH_PY_LIB " + (site-packages inputs outputs) ")\n")) + (("\\$\\{GMSH\\_PY\\} DESTINATION \\$\\{GMSH\\_LIB\\}") + "${GMSH_PY} DESTINATION ${GMSH_PY_LIB}")) + ;; Find the shared library. + (let ((libgmsh (string-append (assoc-ref outputs "out") + "/lib/libgmsh.so"))) + (substitute* "api/gmsh.py" + (("find_library\\(\"gmsh\"\\)") + (simple-format #f "\"~a\"" libgmsh)))) + #t))))) (home-page "http://gmsh.info/") (synopsis "3D finite element grid generator") (description "Gmsh is a 3D finite element grid generator with a built-in @@ -3172,14 +3198,14 @@ implemented in ANSI C, and MPI for communications.") (define-public scotch (package (name "scotch") - (version "6.1.0") + (version "6.1.1") (source (origin (method url-fetch) (uri (string-append "https://gforge.inria.fr/frs/download.php/" "latestfile/298/scotch_" version ".tar.gz")) (sha256 - (base32 "1184fcv4wa2df8szb5lan6pjh0raarr45pk8ilpvbz23naikzg53")) + (base32 "04dkz24a2g20wq703fnyi4440ac4mwycy9gwrrllljj7zxcjy19r")) (patches (search-patches "scotch-build-parallelism.patch" "scotch-integer-declarations.patch")))) (build-system gnu-build-system) @@ -3187,7 +3213,8 @@ implemented in ANSI C, and MPI for communications.") `(("zlib" ,zlib))) (native-inputs `(("flex" ,flex) - ("bison" ,bison))) + ("bison" ,bison) + ("gfortran" ,gfortran))) (outputs '("out" "metis")) (arguments `(#:make-flags (list (string-append "prefix=" %output)) @@ -3212,6 +3239,7 @@ CAT = cat CCS = gcc CCP = mpicc CCD = gcc +FC = gfortran CPPFLAGS =~{ -D~a~} CFLAGS = -O2 -g -fPIC $(CPPFLAGS) LDFLAGS = -lz -lm -lrt -lpthread @@ -3255,6 +3283,8 @@ YACC = bison -pscotchyy -y -b y (find-files "../lib/" ".*metis\\..*")) #t)))))) (home-page "https://www.labri.fr/perso/pelegrin/scotch/") + (properties + `((release-monitoring-url . "https://gforge.inria.fr/frs/?group_id=248"))) (synopsis "Programs and libraries for graph algorithms") (description "SCOTCH is a set of programs and libraries which implement the static mapping and sparse matrix reordering algorithms developed within @@ -3291,6 +3321,7 @@ CAT = cat CCS = gcc CCP = mpicc CCD = gcc +FC = gfortran CPPFLAGS =~{ -D~a~} CFLAGS = -O2 -g -fPIC $(CPPFLAGS) LDFLAGS = -lz -lm -lrt -lpthread @@ -3345,6 +3376,7 @@ CAT = cat CCS = gcc CCP = mpicc CCD = gcc +FC = gfortran CPPFLAGS =~{ -D~a~} CFLAGS = -O2 -g -fPIC $(CPPFLAGS) $(RPATHFLAGS) CLIBFLAGS = -shared -fPIC @@ -3559,7 +3591,7 @@ to BMP, JPEG or PNG image formats.") (define-public maxima (package (name "maxima") - (version "5.45.0") + (version "5.45.1") (source (origin (method url-fetch) @@ -3567,7 +3599,7 @@ to BMP, JPEG or PNG image formats.") version "-source/" name "-" version ".tar.gz")) (sha256 (base32 - "1n6hc2d07d93hgc4yf3yqb9aqjqw6fskmvxggfxww1a8chr1yqy7")) + "1p77nk5sz1qfkn5zr97szpbi8ib4b22k8i52l4ag5gkhd4kid47y")) (patches (search-patches "maxima-defsystem-mkdir.patch")))) (build-system gnu-build-system) (inputs @@ -3658,7 +3690,7 @@ to BMP, JPEG or PNG image formats.") (wrap-program (string-append out "/bin/maxima") `("PATH" prefix (,binutils)))) #t))))) - (home-page "http://maxima.sourceforge.net") + (home-page "https://maxima.sourceforge.io") (synopsis "Numeric and symbolic expression manipulation") (description "Maxima is a system for the manipulation of symbolic and numerical expressions. It yields high precision numeric results by using @@ -3842,13 +3874,17 @@ parts of it.") ;; Build the library for all supported CPUs. This allows ;; switching CPU targets at runtime with the environment variable ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type. - ;; Unfortunately, this is not supported on non-x86 architectures, + ;; Unfortunately, this is not supported on all architectures, ;; where it leads to failed builds. ,@(let ((system (or (%current-target-system) (%current-system)))) (cond ((or (string-prefix? "x86_64" system) (string-prefix? "i686" system)) '("DYNAMIC_ARCH=1")) + ;; On some of these architectures the CPU can't be detected. + ((string-prefix? "powerpc64le" system) + '("DYNAMIC_ARCH=1" + "TARGET=GENERIC")) ;; On MIPS we force the "SICORTEX" TARGET, as for the other ;; two available MIPS targets special extended instructions ;; for Loongson cores are used. @@ -3857,6 +3893,9 @@ parts of it.") ;; On aarch64 force the generic 'armv8-a' target ((string-prefix? "aarch64" system) '("TARGET=ARMV8")) + ;; Failed to detect CPU. + ((string-prefix? "armhf" system) + '("TARGET=ARMV7")) (else '())))) ;; no configure script #:phases @@ -4078,7 +4117,7 @@ Fresnel integrals, and similar related functions as well.") (define-public suitesparse (package (name "suitesparse") - (version "5.9.0") + (version "5.10.1") (source (origin (method git-fetch) @@ -4088,7 +4127,7 @@ Fresnel integrals, and similar related functions as well.") (file-name (git-file-name name version)) (sha256 (base32 - "1zhkix58afw92s7p291prljdm3yi0pjg1kbi3lczdb8rb14jkz5n")) + "19gx5wlgqnqpgz6mvam9lalyzpbfwgqhppps8z3np9sh0mgaiyw9")) (patches (search-patches "suitesparse-mongoose-cmake.patch")) (modules '((guix build utils))) (snippet @@ -4103,6 +4142,11 @@ Fresnel integrals, and similar related functions as well.") (list (string-append "CC=" ,(cc-for-target)) "TBB=-ltbb" "MY_METIS_LIB=-lmetis" + + ;; The default is to link against netlib lapack. Use OpenBLAS + ;; instead. + "BLAS=-lopenblas" "LAPACK=-lopenblas" + ;; Flags for cmake (required to build GraphBLAS and Mongoose) (string-append "CMAKE_OPTIONS=-DCMAKE_INSTALL_PREFIX=" (assoc-ref %outputs "out") @@ -4122,7 +4166,7 @@ Fresnel integrals, and similar related functions as well.") (delete 'configure)))) ;no configure script (inputs `(("tbb" ,tbb) - ("lapack" ,lapack) + ("openblas" ,openblas) ("gmp" ,gmp) ("mpfr" ,mpfr) ("metis" ,metis))) @@ -4268,6 +4312,9 @@ done in the BIOS, or, on GNU/Linux, with the following command: @end example Failure to do so will result in a library with poor performance.") + ;; The test suite is notoriously lengthy and routinely exceeds the default + ;; timeout of 21600 seconds on the not unbeefy berlin build nodes. + (properties '((timeout . 86400))) ; 1 day (license license:bsd-3))) (define-public cglm @@ -5180,7 +5227,7 @@ reduction.") (define-public mcrl2 (package (name "mcrl2") - (version "202006.0") + (version "202106.0") (source (origin (method url-fetch) (uri (string-append @@ -5188,7 +5235,7 @@ reduction.") version ".tar.gz")) (sha256 (base32 - "167ryrzk1a2j53c2j198jlxa98amcaym070gkcj730619gymv5zl")))) + "0db9wgy9spwm76mgfisnifrlg69y9cadjgxjr4gdwzfgg6wgqf6d")))) (inputs `(("boost" ,boost) ("glu" ,glu) @@ -6419,3 +6466,39 @@ to source-code analysis of C software. The Frama-C analyzers assist you in various source-code-related activities, from the navigation through unfamiliar projects up to the certification of critical software.") (license license:lgpl2.1+))) + +(define-public blitz + (package + (name "blitz") + (version "1.0.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/blitzpp/blitz") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0c88gc72j3zggyk4yrrip6i0v7xkx97l140vpy3xhxs2i7xy1461")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags '("-DBUILD_DOC=ON" + "-DBUILD_TESTING=ON") + ;; The default "check" target also includes examples and benchmarks. + #:test-target "check-testsuite" + #:phases + (modify-phases %standard-phases + (add-after 'build 'build-doc + (lambda _ + (invoke "make" "-j" (number->string (parallel-job-count)) + "blitz-doc")))))) + (native-inputs + `(("python" ,python) + ("texinfo" ,texinfo))) + (synopsis "C++ template class library for multidimensional arrays") + (description "Blitz++ is a C++ template class library that provides +high-performance multidimensional array containers for scientific computing.") + (home-page "https://github.com/blitzpp/blitz") + (license (list license:artistic2.0 + license:bsd-3 + license:lgpl3+)))) |