diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 242 |
1 files changed, 173 insertions, 69 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 879af45dc7..1f96ed907e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -12,7 +12,7 @@ ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de> ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016, 2018, 2020 Kei Kebreau <kkebreau@posteo.net> -;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ludovic Courtès <ludo@gnu.org> +;;; 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> @@ -34,7 +34,7 @@ ;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com> ;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> -;;; Copyright © 2020 Felix Gruber <felgru@posteo.net> +;;; Copyright © 2020, 2021 Felix Gruber <felgru@posteo.net> ;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in> ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com> ;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz> @@ -43,6 +43,8 @@ ;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Martin Becze <mjbecze@riseup.net> ;;; 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> ;;; ;;; This file is part of GNU Guix. ;;; @@ -2292,7 +2294,8 @@ ASCII text files using Gmsh's own scripting language.") (native-inputs `(("pkg-config" ,pkg-config) ;;("python-astropy" ,python-astropy) ;; FIXME: Package this. - ("qttools" ,qttools))) + ("qttools" ,qttools) + ("python-sip" ,python-sip-4))) (inputs `(("ghostscript" ,ghostscript) ;optional, for EPS/PS output ("python-dbus" ,python-dbus) @@ -3249,6 +3252,63 @@ YACC = bison -pscotchyy -y -b y (synopsis "Programs and libraries for graph algorithms (32-bit integers)"))) +(define-public scotch-shared + (package (inherit scotch) + (name "scotch-shared") + (native-inputs + `(("gcc" ,gcc) + ("flex" ,flex) + ("bison" ,bison))) + (arguments + (substitute-keyword-arguments (package-arguments scotch) + ((#:phases scotch-shared-phases) + `(modify-phases ,scotch-shared-phases + (replace + 'configure + (lambda _ + ;; Otherwise, the RUNPATH will lack the final path component. + (setenv "RPATHFLAGS" (string-append "-Wl,-rpath=" + (assoc-ref %outputs "out") "/lib")) + (call-with-output-file "Makefile.inc" + (lambda (port) + (format port " +EXE = +LIB = .so +OBJ = .o +MAKE = make +AR = gcc +ARFLAGS = -shared -o +CAT = cat +CCS = gcc +CCP = mpicc +CCD = gcc +CPPFLAGS =~{ -D~a~} +CFLAGS = -O2 -g -fPIC $(CPPFLAGS) $(RPATHFLAGS) +CLIBFLAGS = -shared -fPIC +LDFLAGS = -lz -lm -lrt -lpthread -Xlinker --no-as-needed +CP = cp +LEX = flex -Pscotchyy -olex.yy.c +LN = ln +MKDIR = mkdir +MV = mv +RANLIB = echo +YACC = bison -pscotchyy -y -b y +" + '("COMMON_FILE_COMPRESS_GZ" + "COMMON_PTHREAD" + "COMMON_RANDOM_FIXED_SEED" + "INTSIZE64" ;use 'int64_t' + ;; Prevents symbolc clashes with libesmumps + "SCOTCH_RENAME" + ;; XXX: Causes invalid frees in superlu-dist tests + ;; "SCOTCH_PTHREAD" + ;; "SCOTCH_PTHREAD_NUMBER=2" + "restrict=__restrict" + ))))#t)) + (delete 'check))))) + (synopsis + "Programs and libraries for graph algorithms (shared libraries version)"))) + (define-public pt-scotch (package (inherit scotch) (name "pt-scotch") @@ -3296,6 +3356,28 @@ YACC = bison -pscotchyy -y -b y (synopsis "Programs and libraries for graph algorithms (with MPI and 32-bit integers)"))) +(define-public pt-scotch-shared + (package (inherit scotch-shared) + (name "pt-scotch-shared") + (propagated-inputs + `(("openmpi" ,openmpi))) ;Headers include MPI headers + (arguments + (substitute-keyword-arguments (package-arguments scotch-shared) + ((#:phases scotch-shared-phases) + `(modify-phases ,scotch-shared-phases + (replace + 'build + (lambda _ + (invoke "make" (format #f "-j~a" (parallel-job-count)) + "ptscotch" "ptesmumps") + + ;; Install the serial metis compatibility library + (invoke "make" "-C" "libscotchmetis" "install"))) + (add-before 'check 'mpi-setup + ,%openmpi-setup))))) + (synopsis "Graph algorithms (shared libraries version, with MPI)"))) + + (define-public metis (package (name "metis") @@ -3308,6 +3390,9 @@ YACC = bison -pscotchyy -y -b y (sha256 (base32 "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn")))) + (properties + `((release-monitoring-url + . "http://glaros.dtc.umn.edu/gkhome/metis/metis/download"))) (build-system cmake-build-system) (inputs `(("blas" ,openblas))) @@ -3745,52 +3830,94 @@ parts of it.") (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)") (license license:bsd-3))) -(define* (make-blis implementation #:optional substitutable?) - "Return a BLIS package with the given IMPLEMENTATION (see config/ in the -source tree for a list of implementations.) - -SUBSTITUTABLE? determines whether the package is made available as a -substitute. - -Currently the specialization must be selected at configure-time, but work is -underway to allow BLIS to select the right optimized kernels at run time: -<https://github.com/flame/blis/issues/129>." +(define-public blis (package - (name (if (string=? implementation "reference") - "blis" - (string-append "blis-" implementation))) - (version "0.2.2") + (name "blis") + (version "0.8.1") (home-page "https://github.com/flame/blis") (source (origin (method git-fetch) (uri (git-reference (url home-page) (commit version))) (sha256 (base32 - "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh")) + "05ifil6jj9424sr8kmircl8k4bmxnl3y12a79vwj1kxxva5gz50g")) (file-name (git-file-name "blis" version)))) + (native-inputs + `(("python" ,python) + ("perl" ,perl))) (build-system gnu-build-system) (arguments - `(#:test-target "test" - - #:substitutable? ,substitutable? - - #:phases (modify-phases %standard-phases - (replace 'configure - (lambda* (#:key outputs #:allow-other-keys) - ;; This is a home-made 'configure' script. - (let ((out (assoc-ref outputs "out"))) - (invoke "./configure" "-p" out - "-d" "opt" - "--disable-static" - "--enable-shared" - "--enable-threading=openmp" - - ,implementation)))) - (add-before 'check 'show-test-output - (lambda _ - ;; By default "make check" is silent. Make it verbose. - (system "tail -F output.testsuite &") - #t))))) + `(#:modules + ((guix build gnu-build-system) + (guix build utils) + (srfi srfi-1)) + #:test-target "test" + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs + target + system + (configure-flags '()) + #:allow-other-keys) + ;; This is a home-made 'configure' script. + (let* ((out (assoc-ref outputs "out")) + ;; Guix-specific support for choosing the configuration + ;; via #:configure-flags: see below for details. + (config-flag-prefix "--blis-config=") + (maybe-config-flag (find + (lambda (s) + (string-prefix? config-flag-prefix s)) + configure-flags)) + (configure-flags (if maybe-config-flag + (delete maybe-config-flag + configure-flags) + configure-flags)) + ;; Select the "configuration" to build. + ;; The "generic" configuration is non-optimized but + ;; portable (no assembly). + ;; The "x86_64" configuration family includes + ;; sub-configurations for all supported + ;; x86_64 microarchitectures. + ;; BLIS currently lacks runtime hardware detection + ;; for other architectures: see + ;; <https://github.com/flame/blis/commit/c534da6>. + ;; Conservatively, we stick to "generic" on armhf, + ;; aarch64, and ppc64le for now. (But perhaps + ;; "power9", "cortexa9", and "cortexa57" might be + ;; general enough to use?) + ;; Another approach would be to use the "auto" + ;; configuration and make this package + ;; non-substitutable. + ;; The build is fairly intensive, though. + (blis-config + (cond + (maybe-config-flag + (substring maybe-config-flag + (string-length config-flag-prefix))) + ((string-prefix? "x86_64" (or target system)) + "x86_64") + (else + "generic"))) + (configure-args + `("-p" ,out + "-d" "opt" + "--disable-static" + "--enable-shared" + "--enable-threading=openmp" + "--enable-verbose-make" + ,@configure-flags + ,blis-config))) + (format #t "configure args: ~s~%" configure-args) + (apply invoke + "./configure" + configure-args) + #t))) + (add-before 'check 'show-test-output + (lambda _ + ;; By default "make check" is silent. Make it verbose. + (system "tail -F output.testsuite &") + #t))))) (synopsis "High-performance basic linear algebra (BLAS) routines") (description "BLIS is a portable software framework for instantiating high-performance @@ -3802,35 +3929,12 @@ it also includes a BLAS compatibility layer which gives application developers access to BLIS implementations via traditional BLAS routine calls.") (license license:bsd-3))) -(define-public blis - ;; This is the "reference" implementation, which is the non-optimized but - ;; portable variant (no assembly). - (make-blis "reference" #t)) +(define-public blis-sandybridge (deprecated-package "blis-sandybridge" blis)) +(define-public blis-haswell (deprecated-package "blis-haswell" blis)) +(define-public blis-knl (deprecated-package "blis-knl" blis)) (define ignorance blis) -(define-syntax-rule (blis/x86_64 processor) - "Expand to a package specialized for PROCESSOR." - (package - (inherit (make-blis processor)) - (supported-systems '("x86_64-linux")))) - -(define-public blis-sandybridge - ;; BLIS specialized for Sandy Bridge processors (launched 2011): - ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>. - (blis/x86_64 "sandybridge")) - -(define-public blis-haswell - ;; BLIS specialized for Haswell processors (launched 2013): - ;; <http://ark.intel.com/products/codename/42174/Haswell>. - (blis/x86_64 "haswell")) - -(define-public blis-knl - ;; BLIS specialized for Knights Landing processor (launched 2016): - ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>. - (blis/x86_64 "knl")) - - (define-public openlibm (package (name "openlibm") @@ -3911,7 +4015,7 @@ Fresnel integrals, and similar related functions as well.") (define-public suitesparse (package (name "suitesparse") - (version "5.8.1") + (version "5.9.0") (source (origin (method git-fetch) @@ -3921,7 +4025,7 @@ Fresnel integrals, and similar related functions as well.") (file-name (git-file-name name version)) (sha256 (base32 - "0qjlyfxs8s48rs63c2fzspisgq1kk4bwkgnhmh125hgkdhrq2w1c")) + "1zhkix58afw92s7p291prljdm3yi0pjg1kbi3lczdb8rb14jkz5n")) (patches (search-patches "suitesparse-mongoose-cmake.patch")) (modules '((guix build utils))) (snippet @@ -3931,9 +4035,9 @@ Fresnel integrals, and similar related functions as well.") #t)))) (build-system gnu-build-system) (arguments - '(#:tests? #f ;no "check" target + `(#:tests? #f ;no "check" target #:make-flags - (list "CC=gcc" + (list (string-append "CC=" ,(cc-for-target)) "TBB=-ltbb" "MY_METIS_LIB=-lmetis" ;; Flags for cmake (required to build GraphBLAS and Mongoose) |