diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 545 |
1 files changed, 511 insertions, 34 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 68c326752c..8ef4f44f5a 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -1,7 +1,8 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2013 Andreas Enge <andreas@enge.fr> +;;; Copyright © 2013, 2014 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org> ;;; Copyright © 2014 John Darrington <jmd@gnu.org> +;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org> ;;; ;;; This file is part of GNU Guix. ;;; @@ -24,11 +25,16 @@ #:renamer (symbol-prefix-proc 'license:)) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix utils) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) + #:use-module (gnu packages algebra) + #:use-module (gnu packages bison) + #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages curl) #:use-module (gnu packages elf) + #:use-module (gnu packages flex) #:use-module (gnu packages fltk) #:use-module (gnu packages fontutils) #:use-module (gnu packages gettext) @@ -37,14 +43,18 @@ #:use-module (gnu packages ghostscript) #:use-module (gnu packages gtk) #:use-module (gnu packages less) + #:use-module (gnu packages gnome) #:use-module (gnu packages xorg) #:use-module (gnu packages gl) + #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) #:use-module (gnu packages pcre) + #:use-module (gnu packages popt) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages readline) + #:use-module (gnu packages tcsh) #:use-module (gnu packages texinfo) #:use-module (gnu packages texlive) #:use-module (gnu packages xml)) @@ -137,7 +147,7 @@ LP/MIP solver is included in the package.") (define-public pspp (package (name "pspp") - (version "0.8.2") + (version "0.8.3") (source (origin (method url-fetch) @@ -145,7 +155,7 @@ LP/MIP solver is included in the package.") version ".tar.gz")) (sha256 (base32 - "1w7h3dglgx0jlq1wb605b8pgfsk2vr1q2q2rj7bsajh9ihbcsixr")))) + "0vri2pzvmm38qaihfvwlry30f40lcnps4blg59ixic4q20ldxf5d")))) (build-system gnu-build-system) (inputs `(("cairo" ,cairo) @@ -190,43 +200,14 @@ output in text, PostScript, PDF or HTML.") (inputs `(("fortran" ,gfortran-4.8) ("python" ,python-2))) (arguments - `(#:modules ((guix build cmake-build-system) - (guix build utils) - (guix build rpath) - (srfi srfi-1)) - #:imported-modules ((guix build cmake-build-system) - (guix build gnu-build-system) - (guix build utils) - (guix build rpath)) - #:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES") + `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES") #:phases (alist-cons-before 'check 'patch-python (lambda* (#:key inputs #:allow-other-keys) (let ((python (assoc-ref inputs "python"))) (substitute* "lapack_testing.py" (("/usr/bin/env python") python)))) - (alist-cons-after - 'strip 'add-libs-to-runpath - (lambda* (#:key inputs outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (fortran (assoc-ref inputs "fortran")) - (libc (assoc-ref inputs "libc")) - (rpaths `(,(string-append fortran "/lib64") - ,(string-append fortran "/lib") - ,(string-append libc "/lib") - ,(string-append out "/lib")))) - ;; Set RUNPATH for all libraries - (with-directory-excursion out - (for-each - (lambda (lib) - (let ((lib-rpaths (file-rpath lib))) - (for-each - (lambda (dir) - (or (member dir lib-rpaths) - (augment-rpath lib dir))) - rpaths))) - (find-files "lib" ".*so$"))))) - %standard-phases)))) + %standard-phases))) (synopsis "Library for numerical linear algebra") (description "LAPACK is a Fortran 90 library for solving the most commonly occurring @@ -349,3 +330,499 @@ applications and it provides great support for visualizing results. Work may be performed both at the interactive command-line as well as via script files.") (license license:gpl3+))) + +(define-public gmsh + (package + (name "gmsh") + (version "2.8.4") + (source + (origin + (method url-fetch) + (uri (string-append "http://www.geuz.org/gmsh/src/gmsh-" + version "-source.tgz")) + (sha256 + (base32 "0jv2yvk28w86rx5mvjkb0w12ff2jxih7axnpvznpd295lg5jg7hr")) + (modules '((guix build utils))) + (snippet + ;; Remove non-free METIS code + '(delete-file-recursively "contrib/Metis")))) + (build-system cmake-build-system) + (native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath + (propagated-inputs + `(("fltk" ,fltk) + ("gfortran" ,gfortran-4.8) + ("gmp" ,gmp) + ("hdf5-lib" ,hdf5 "lib") + ("hdf5-include" ,hdf5 "include") + ("lapack" ,lapack) + ("mesa" ,mesa) + ("libx11" ,libx11) + ("libxext" ,libxext))) + (arguments + `(#:configure-flags `("-DENABLE_METIS:BOOL=OFF" + "-DENABLE_BUILD_SHARED:BOOL=ON" + "-DENABLE_BUILD_DYNAMIC:BOOL=ON"))) + (home-page "http://www.geuz.org/gmsh/") + (synopsis "3D finite element grid generator") + (description "Gmsh is a 3D finite element grid generator with a built-in +CAD engine and post-processor. Its design goal is to provide a fast, light +and user-friendly meshing tool with parametric input and advanced +visualization capabilities. Gmsh is built around four modules: geometry, +mesh, solver and post-processing. The specification of any input to these +modules is done either interactively using the graphical user interface or in +ASCII text files using Gmsh's own scripting language.") + (license license:gpl2+))) + +(define-public petsc + (package + (name "petsc") + (version "3.4.4") + (source + (origin + (method url-fetch) + ;; The *-lite-* tarball does not contain the *large* documentation + (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" + "petsc-lite-" version ".tar.gz")) + (sha256 + (base32 "0v5dg6dhdjpi5ianvd4mm6hsvxzv1bsxwnh9f9myag0a0d9xk9iv")) + (patches + (list (search-patch "petsc-fix-threadcomm.patch"))))) + (build-system gnu-build-system) + (native-inputs + `(("python" ,python-2) + ("perl" ,perl))) + (inputs + `(("gfortran" ,gfortran-4.8) + ("lapack" ,lapack) + ("superlu" ,superlu) + ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi + ;; leaving out opengl, as configuration seems to only be for mac + )) + (arguments + `(#:test-target "test" + #:parallel-build? #f + #:configure-flags + `("--with-mpi=0" + "--with-openmp=1" + "--with-superlu=1" + ,(string-append "--with-superlu-include=" + (assoc-ref %build-inputs "superlu") "/include") + ,(string-append "--with-superlu-lib=" + (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a")) + #:phases + (alist-replace + 'configure + ;; PETSc's configure script is actually a python script, so we can't + ;; run it with bash. + (lambda* (#:key outputs (configure-flags '()) + #:allow-other-keys) + (let* ((prefix (assoc-ref outputs "out")) + (flags `(,(string-append "--prefix=" prefix) + ,@configure-flags))) + (format #t "build directory: ~s~%" (getcwd)) + (format #t "configure flags: ~s~%" flags) + (zero? (apply system* "./configure" flags)))) + (alist-cons-after + 'configure 'clean-local-references + ;; Try to keep build directory names from leaking into compiled code + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (substitute* (find-files "." "^petsc(conf|machineinfo).h$") + (((getcwd)) out)))) + (alist-cons-after + 'install 'clean-install + ;; Try to keep installed files from leaking build directory names. + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (fortran (assoc-ref inputs "gfortran"))) + (substitute* (map (lambda (file) + (string-append out "/" file)) + '("conf/petscvariables" + "conf/PETScConfig.cmake")) + (((getcwd)) out)) + ;; Make compiler references point to the store + (substitute* (string-append out "/conf/petscvariables") + (("= g(cc|\\+\\+|fortran)" _ suffix) + (string-append "= " fortran "/bin/g" suffix))) + ;; PETSc installs some build logs, which aren't necessary. + (for-each (lambda (file) + (let ((f (string-append out "/" file))) + (when (file-exists? f) + (delete-file f)))) + '("conf/configure.log" + "conf/make.log" + "conf/test.log" + "conf/error.log" + "conf/RDict.db" + ;; Once installed, should uninstall with Guix + "conf/uninstall.py")))) + %standard-phases))))) + (home-page "http://www.mcs.anl.gov/petsc") + (synopsis "Library to solve PDEs") + (description "PETSc, pronounced PET-see (the S is silent), is a suite of +data structures and routines for the scalable (parallel) solution of +scientific applications modeled by partial differential equations.") + (license (license:bsd-style + "http://www.mcs.anl.gov/petsc/documentation/copyright.html")))) + +(define-public petsc-complex + (package (inherit petsc) + (name "petsc-complex") + (arguments + (substitute-keyword-arguments (package-arguments petsc) + ((#:configure-flags cf) + `(cons "--with-scalar-type=complex" ,cf)))) + (synopsis "Library to solve PDEs (with complex scalars)"))) + +(define-public petsc-openmpi + (package (inherit petsc) + (name "petsc-openmpi") + (inputs + `(("openmpi" ,openmpi) + ,@(package-inputs petsc))) + (arguments + (substitute-keyword-arguments (package-arguments petsc) + ((#:configure-flags cf) + ``("--with-mpiexec=mpirun" + ,(string-append "--with-mpi-dir=" + (assoc-ref %build-inputs "openmpi")) + ,@(delete "--with-mpi=0" ,cf))))) + (synopsis "Library to solve PDEs (with MPI support)"))) + +(define-public petsc-complex-openmpi + (package (inherit petsc-complex) + (name "petsc-complex-openmpi") + (inputs + `(("openmpi" ,openmpi) + ,@(package-inputs petsc-complex))) + (arguments + (substitute-keyword-arguments (package-arguments petsc-complex) + ((#:configure-flags cf) + ``("--with-mpiexec=mpirun" + ,(string-append "--with-mpi-dir=" + (assoc-ref %build-inputs "openmpi")) + ,@(delete "--with-mpi=0" ,cf))))) + (synopsis "Library to solve PDEs (with complex scalars and MPI support)"))) + +(define-public superlu + (package + (name "superlu") + (version "4.3") + (source + (origin + (method url-fetch) + (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" + "superlu_" version ".tar.gz")) + (sha256 + (base32 "10b785s9s4x0m9q7ihap09275pq4km3k2hk76jiwdfdr5qr2168n")))) + (build-system gnu-build-system) + (native-inputs + `(("tcsh" ,tcsh))) + (inputs + `(("lapack" ,lapack) + ("gfortran" ,gfortran-4.8))) + (arguments + `(#:parallel-build? #f + #:tests? #f ;tests are run as part of `make all` + #:phases + (alist-replace + 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (call-with-output-file "make.inc" + (lambda (port) + (format port " +PLAT = +SuperLUroot = ~a +SUPERLULIB = ~a/lib/libsuperlu.a +TMGLIB = libtmglib.a +BLASDEF = -DUSE_VENDOR_BLAS +BLASLIB = -L~a/lib -lblas +LIBS = $(SUPERLULIB) $(BLASLIB) +ARCH = ar +ARCHFLAGS = cr +RANLIB = ranlib +CC = gcc +PIC = -fPIC +CFLAGS = -O3 -DPRNTlevel=0 $(PIC) +NOOPTS = -O0 $(PIC) +FORTRAN = gfortran +FFLAGS = -O2 $(PIC) +LOADER = $(CC) +CDEFS = -DAdd_" + (getcwd) + (assoc-ref outputs "out") + (assoc-ref inputs "lapack"))))) + (alist-cons-before + 'build 'create-install-directories + (lambda* (#:key outputs #:allow-other-keys) + (for-each + (lambda (dir) + (mkdir-p (string-append (assoc-ref outputs "out") + "/" dir))) + '("lib" "include"))) + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + ;; Library is placed in lib during the build phase. Copy over + ;; headers to include. + (let* ((out (assoc-ref outputs "out")) + (incdir (string-append out "/include"))) + (for-each (lambda (file) + (let ((base (basename file))) + (format #t "installing `~a' to `~a'~%" + base incdir) + (copy-file file + (string-append incdir "/" base)))) + (find-files "SRC" ".*\\.h$")))) + %standard-phases))))) + (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/") + (synopsis "Supernodal direct solver for sparse linear systems") + (description + "SuperLU is a general purpose library for the direct solution of large, +sparse, nonsymmetric systems of linear equations on high performance machines. +The library is written in C and is callable from either C or Fortran. The +library routines perform an LU decomposition with partial pivoting and +triangular system solves through forward and back substitution. The library +also provides threshold-based ILU factorization preconditioners.") + (license license:bsd-3))) + +(define-public superlu-dist + (package + (name "superlu-dist") + (version "3.3") + (source + (origin + (method url-fetch) + (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" + "superlu_dist_" version ".tar.gz")) + (sha256 + (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj")) + (patches (list (search-patch "superlu-dist-scotchmetis.patch"))))) + (build-system gnu-build-system) + (native-inputs + `(("tcsh" ,tcsh))) + (inputs + `(("gfortran" ,gfortran-4.8))) + (propagated-inputs + `(("openmpi" ,openmpi) ;headers include MPI heades + ("lapack" ,lapack) ;required to link with output library + ("pt-scotch" ,pt-scotch))) ;same + (arguments + `(#:parallel-build? #f ;race conditions using ar + #:phases + (alist-replace + 'configure + (lambda* (#:key inputs outputs #:allow-other-keys) + (call-with-output-file "make.inc" + (lambda (port) + (format port " +PLAT = +DSuperLUroot = ~a +DSUPERLULIB = ~a/lib/libsuperlu_dist.a +BLASDEF = -DUSE_VENDOR_BLAS +BLASLIB = -L~a/lib -lblas +PARMETISLIB = -L~a/lib \ + -lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \ + -lscotch -lscotcherr -lscotcherrexit +METISLIB = -L~:*~a/lib \ + -lscotchmetis -lscotch -lscotcherr -lscotcherrexit +LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB) +ARCH = ar +ARCHFLAGS = cr +RANLIB = ranlib +CC = mpicc +PIC = -fPIC +CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC) +NOOPTS = -O0 -g $(PIC) +FORTRAN = mpifort +FFLAGS = -O2 -g $(PIC) +LOADER = $(CC) +CDEFS = -DAdd_" + (getcwd) + (assoc-ref outputs "out") + (assoc-ref inputs "lapack") + (assoc-ref inputs "pt-scotch"))))) + (alist-cons-after + 'unpack 'remove-broken-symlinks + (lambda _ + (for-each delete-file + (find-files "MAKE_INC" "\\.#make\\..*"))) + (alist-cons-before + 'build 'create-install-directories + (lambda* (#:key outputs #:allow-other-keys) + (for-each + (lambda (dir) + (mkdir-p (string-append (assoc-ref outputs "out") + "/" dir))) + '("lib" "include"))) + (alist-replace + 'check + (lambda _ + (with-directory-excursion "EXAMPLE" + (and + (zero? (system* "mpirun" "-n" "2" + "./pddrive" "-r" "1" "-c" "2" "g20.rua")) + (zero? (system* "mpirun" "-n" "2" + "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))))) + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + ;; Library is placed in lib during the build phase. Copy over + ;; headers to include. + (let* ((out (assoc-ref outputs "out")) + (incdir (string-append out "/include"))) + (for-each (lambda (file) + (let ((base (basename file))) + (format #t "installing `~a' to `~a'~%" + base incdir) + (copy-file file + (string-append incdir "/" base)))) + (find-files "SRC" ".*\\.h$")))) + %standard-phases))))))) + (home-page (package-home-page superlu)) + (synopsis "Parallel supernodal direct solver") + (description + "SuperLU_DIST is a parallel extension to the serial SuperLU library. +It is targeted for distributed memory parallel machines. SuperLU_DIST is +implemented in ANSI C, and MPI for communications.") + (license license:bsd-3))) + +(define-public scotch + (package + (name "scotch") + (version "6.0.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://gforge.inria.fr/frs/download.php/31831/" + "scotch_" version ".tar.gz")) + (sha256 + (base32 "0yfqf9lk7chb3h42777x42x4adx0v3n0b41q0cdqrdmscp4iczp5")) + (patches (list (search-patch "scotch-test-threading.patch"))))) + (build-system gnu-build-system) + (inputs + `(("zlib" ,zlib) + ("flex" ,flex) + ("bison" ,bison))) + (arguments + `(#:phases + (alist-cons-after + 'unpack 'chdir-to-src + (lambda _ (chdir "src")) + (alist-replace + 'configure + (lambda _ + (call-with-output-file "Makefile.inc" + (lambda (port) + (format port " +EXE = +LIB = .a +OBJ = .o +MAKE = make +AR = ar +ARFLAGS = -ruv +CCS = gcc +CCP = mpicc +CCD = gcc +CPPFLAGS =~{ -D~a~} +CFLAGS = -O2 -g $(CPPFLAGS) +LDFLAGS = -lz -lm -lrt -lpthread +CP = cp +LEX = flex -Pscotchyy -olex.yy.c +LN = ln +MKDIR = mkdir +MV = mv +RANLIB = ranlib +YACC = bison -pscotchyy -y -b y +" + '("COMMON_FILE_COMPRESS_GZ" + "COMMON_PTHREAD" + "COMMON_RANDOM_FIXED_SEED" + ;; TODO: Define once our MPI supports + ;; MPI_THREAD_MULTIPLE + ;; "SCOTCH_PTHREAD" + ;; "SCOTCH_PTHREAD_NUMBER=2" + "restrict=__restrict"))))) + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (mkdir out) + (zero? (system* "make" + (string-append "prefix=" out) + "install")))) + %standard-phases))))) + (home-page "http://www.labri.fr/perso/pelegrin/scotch/") + (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 +the SCOTCH project. Its purpose is to apply graph theory, with a divide and +conquer approach, to scientific computing problems such as graph and mesh +partitioning, static mapping, and sparse matrix ordering, in application +domains ranging from structural mechanics to operating systems or +bio-chemistry.") + ;; See LICENSE_en.txt + (license license:cecill-c))) + +(define-public pt-scotch + (package (inherit scotch) + (name "pt-scotch") + (propagated-inputs + `(("openmpi" ,openmpi))) ;Headers include MPI headers + (arguments + (substitute-keyword-arguments (package-arguments scotch) + ((#:phases scotch-phases) + `(alist-replace + 'build + ;; TODO: Would like to add parallelism here + (lambda _ + (and + (zero? (system* "make" "ptscotch")) + ;; Install the serial metis compatibility library + (zero? (system* "make" "-C" "libscotchmetis" "install")))) + (alist-replace + 'check + (lambda _ (zero? (system* "make" "ptcheck"))) + (alist-replace + 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (mkdir out) + (zero? (system* "make" + (string-append "prefix=" out) + "install")))) + ,scotch-phases)))))) + (synopsis "Programs and libraries for graph algorithms (with MPI)"))) + +(define-public gsegrafix + (package + (name "gsegrafix") + (version "1.0.6") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://gnu/" name "/" name "-" + version ".tar.gz")) + (sha256 + (base32 + "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags '("LDFLAGS=-lm"))) + (inputs + `(("libgnomecanvas" ,libgnomecanvas) + ("libbonoboui" ,libbonoboui) + ("libgnomeui" ,libgnomeui) + ("libgnomeprintui" ,libgnomeprintui) + ("popt" ,popt))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (home-page "http://www.gnu.org/software/gsegrafix/") + (synopsis "GNOME application to create scientific and engineering plots") + (description "GSEGrafix is an application which produces high-quality graphical +plots for science and engineering. Plots are specified via simple ASCII +parameter files and data files and are presented in an anti-aliased GNOME +canvas. The program supports rectangular two-dimensional plots, histograms, +polar-axis plots and three-dimensional plots. Plots can be printed or saved +to BMP, JPEG or PNG image formats.") + (license license:gpl3+))) |