871 lines
33 KiB
Scheme
871 lines
33 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
|
;;; 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.
|
|
;;;
|
|
;;; GNU Guix is free software; you can redistribute it and/or modify it
|
|
;;; under the terms of the GNU General Public License as published by
|
|
;;; the Free Software Foundation; either version 3 of the License, or (at
|
|
;;; your option) any later version.
|
|
;;;
|
|
;;; GNU Guix is distributed in the hope that it will be useful, but
|
|
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
|
|
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
|
;;; GNU General Public License for more details.
|
|
;;;
|
|
;;; You should have received a copy of the GNU General Public License
|
|
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
|
|
|
|
(define-module (gnu packages maths)
|
|
#:use-module (gnu packages)
|
|
#:use-module ((guix licenses)
|
|
#: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)
|
|
#:use-module (gnu packages gcc)
|
|
#:use-module (gnu packages gd)
|
|
#:use-module (gnu packages ghostscript)
|
|
#:use-module (gnu packages glib)
|
|
#:use-module (gnu packages gtk)
|
|
#:use-module (gnu packages less)
|
|
#:use-module (gnu packages lisp)
|
|
#:use-module (gnu packages gnome)
|
|
#:use-module (gnu packages xorg)
|
|
#:use-module (gnu packages gl)
|
|
#:use-module (gnu packages m4)
|
|
#: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))
|
|
|
|
(define-public units
|
|
(package
|
|
(name "units")
|
|
(version "2.11")
|
|
(source (origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://gnu/units/units-" version
|
|
".tar.gz"))
|
|
(sha256 (base32
|
|
"1gjs3wc212aaiq4r76hx9nl1h3fa39n0ljwl9420d6ixl3rdmdjk"))))
|
|
(build-system gnu-build-system)
|
|
(synopsis "Conversion between thousands of scales")
|
|
(description
|
|
"GNU Units converts numeric quantities between units of measure. It
|
|
can handle scale changes through adaptive usage of standard scale prefixes
|
|
(micro-, kilo-, etc.). It can also handle nonlinear conversions such as
|
|
Fahrenheit to Celsius. Its interpreter is powerful enough to be used
|
|
effectively as a scientific calculator.")
|
|
(license license:gpl3+)
|
|
(home-page "http://www.gnu.org/software/units/")))
|
|
|
|
(define-public gsl
|
|
(package
|
|
(name "gsl")
|
|
(version "1.16")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://gnu/gsl/gsl-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:parallel-tests? #f
|
|
#:phases
|
|
(alist-replace
|
|
'configure
|
|
(lambda* (#:key target system outputs #:allow-other-keys #:rest args)
|
|
(let ((configure (assoc-ref %standard-phases 'configure)))
|
|
;; disable numerically unstable test on i686, see thread at
|
|
;; http://lists.gnu.org/archive/html/bug-gsl/2011-11/msg00019.html
|
|
(if (string=? (or target system) "i686-linux")
|
|
(substitute* "ode-initval2/Makefile.in"
|
|
(("TESTS = \\$\\(check_PROGRAMS\\)") "TESTS =")))
|
|
(apply configure args)))
|
|
%standard-phases)))
|
|
(home-page "http://www.gnu.org/software/gsl/")
|
|
(synopsis "Numerical library for C and C++")
|
|
(description
|
|
"The GNU Scientific Library is a library for numerical analysis in C
|
|
and C++. It includes a wide range of mathematical routines, with over 1000
|
|
functions in total. Subject areas covered by the library include:
|
|
differential equations, linear algebra, Fast Fourier Transforms and random
|
|
numbers.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public glpk
|
|
(package
|
|
(name "glpk")
|
|
(version "4.54")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://gnu/glpk/glpk-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"18gr2anv8gyps6j9f22k7li6w07glvww666sdqblvlq2hh3whwmb"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("gmp" ,gmp)))
|
|
(arguments
|
|
`(#:configure-flags '("--with-gmp")))
|
|
(home-page "http://www.gnu.org/software/glpk/")
|
|
(synopsis "GNU Linear Programming Kit, supporting the MathProg language")
|
|
(description
|
|
"GLPK is a C library for solving large-scale linear programming (LP),
|
|
mixed integer programming (MIP), and other related problems. It supports the
|
|
GNU MathProg modeling language, a subset of the AMPL language, and features a
|
|
translator for the language. In addition to the C library, a stand-alone
|
|
LP/MIP solver is included in the package.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public pspp
|
|
(package
|
|
(name "pspp")
|
|
(version "0.8.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://gnu/pspp/pspp-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0vri2pzvmm38qaihfvwlry30f40lcnps4blg59ixic4q20ldxf5d"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("cairo" ,cairo)
|
|
("fontconfig" ,fontconfig)
|
|
("gettext" ,gnu-gettext)
|
|
("gsl" ,gsl)
|
|
("libxml2" ,libxml2)
|
|
("pango" ,pango)
|
|
("readline" ,readline)
|
|
("gtk" ,gtk+-2)
|
|
("gtksourceview" ,gtksourceview)
|
|
("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("glib" ,glib "bin") ;for glib-genmarshal
|
|
("perl" ,perl)
|
|
("pkg-config" ,pkg-config)))
|
|
(home-page "http://www.gnu.org/software/pspp/")
|
|
(synopsis "Statistical analysis")
|
|
(description
|
|
"GNU PSPP is a statistical analysis program. It can perform
|
|
descriptive statistics, T-tests, linear regression and non-parametric tests.
|
|
It features both a graphical interface as well as command-line input. PSPP is
|
|
designed to interoperate with Gnumeric, LibreOffice and OpenOffice. Data can
|
|
be imported from spreadsheets, text files and database sources and it can be
|
|
output in text, PostScript, PDF or HTML.")
|
|
(license license:gpl3+)))
|
|
|
|
(define-public lapack
|
|
(package
|
|
(name "lapack")
|
|
(version "3.5.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://www.netlib.org/lapack/lapack-"
|
|
version ".tgz"))
|
|
(sha256
|
|
(base32
|
|
"0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s"))))
|
|
(build-system cmake-build-system)
|
|
(home-page "http://www.netlib.org/lapack/")
|
|
(native-inputs `(("patchelf" ,patchelf))) ;for augment-rpath
|
|
(inputs `(("fortran" ,gfortran-4.8)
|
|
("python" ,python-2)))
|
|
(arguments
|
|
`(#: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))))
|
|
%standard-phases)))
|
|
(synopsis "Library for numerical linear algebra")
|
|
(description
|
|
"LAPACK is a Fortran 90 library for solving the most commonly occurring
|
|
problems in numerical linear algebra.")
|
|
(license (license:bsd-style "file://LICENSE"
|
|
"See LICENSE in the distribution."))))
|
|
|
|
(define-public gnuplot
|
|
(package
|
|
(name "gnuplot")
|
|
(version "4.6.3")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
|
|
version "/gnuplot-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"1xd7gqdhlk7k1p9yyqf9vkk811nadc7m4si0q3nb6cpv4pxglpyz"))))
|
|
(build-system gnu-build-system)
|
|
(inputs `(("readline" ,readline)
|
|
("cairo" ,cairo)
|
|
("pango" ,pango)
|
|
("gd" ,gd)))
|
|
(native-inputs `(("texlive" ,texlive)
|
|
("pkg-config" ,pkg-config)))
|
|
(home-page "http://www.gnuplot.info")
|
|
(synopsis "Command-line driven graphing utility")
|
|
(description "Gnuplot is a portable command-line driven graphing
|
|
utility. It was originally created to allow scientists and students to
|
|
visualize mathematical functions and data interactively, but has grown to
|
|
support many non-interactive uses such as web scripting. It is also used as a
|
|
plotting engine by third-party applications like Octave.")
|
|
;; X11 Style with the additional restriction that derived works may only be
|
|
;; distributed as patches to the original.
|
|
(license (license:fsf-free
|
|
"http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
|
|
|
|
(define-public hdf5
|
|
(package
|
|
(name "hdf5")
|
|
(version "1.8.12")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-"
|
|
version "/src/hdf5-"
|
|
version ".tar.bz2"))
|
|
(sha256
|
|
(base32 "0f9n0v3p3lwc7564791a39c6cn1d3dbrn7d1j3ikqsi27a8hy23d"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:phases
|
|
(alist-cons-before
|
|
'configure 'patch-configure
|
|
(lambda _
|
|
(substitute* "configure"
|
|
(("/bin/mv") "mv")))
|
|
%standard-phases)))
|
|
(outputs '("out" "bin" "lib" "include"))
|
|
(home-page "http://www.hdfgroup.org")
|
|
(synopsis "Management suite for extremely large and complex data")
|
|
(description "HDF5 is a suite that makes possible the management of
|
|
extremely large and complex data collections.")
|
|
(license (license:x11-style
|
|
"http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
|
|
|
|
|
|
;; For a fully featured Octave, users are strongly recommended also to install
|
|
;; the following packages: texinfo, less, ghostscript, gnuplot.
|
|
(define-public octave
|
|
(package
|
|
(name "octave")
|
|
(version "3.8.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://gnu/octave/octave-"
|
|
version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"0ks9pr154syw0vb3jn6xsnrkkrbvf9y7i7gaxa28rz6ngxbxvq9l"))))
|
|
(build-system gnu-build-system)
|
|
(inputs
|
|
`(("lapack" ,lapack)
|
|
("readline" ,readline)
|
|
("glpk" ,glpk)
|
|
("curl" ,curl)
|
|
("pcre" ,pcre)
|
|
("fltk" ,fltk)
|
|
("fontconfig" ,fontconfig)
|
|
("freetype" ,freetype)
|
|
("hdf5-lib" ,hdf5 "lib")
|
|
("hdf5-include" ,hdf5 "include")
|
|
("libxft" ,libxft)
|
|
("mesa" ,mesa)
|
|
("zlib" ,zlib)))
|
|
(native-inputs
|
|
`(("gfortran" ,gfortran-4.8)
|
|
("pkg-config" ,pkg-config)
|
|
("perl" ,perl)
|
|
;; The following inputs are not actually used in the build process. However, the
|
|
;; ./configure gratuitously tests for their existence and assumes that programs not
|
|
;; present at build time are also not, and can never be, available at run time!
|
|
;; If these inputs are therefore not present, support for them will be built out.
|
|
;; However, Octave will still run without them, albeit without the features they
|
|
;; provide.
|
|
("less" ,less)
|
|
("texinfo" ,texinfo)
|
|
("ghostscript" ,ghostscript)
|
|
("gnuplot" ,gnuplot)))
|
|
(arguments
|
|
`(#:configure-flags (list (string-append "--with-shell="
|
|
(assoc-ref %build-inputs "bash")
|
|
"/bin/sh"))))
|
|
(home-page "http://www.gnu.org/software/octave/")
|
|
(synopsis "High-level language for numerical computation")
|
|
(description "GNU Octave is a high-level interpreted language that is specialized
|
|
for numerical computations. It can be used for both linear and non-linear
|
|
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+)))
|
|
|
|
(define-public maxima
|
|
(package
|
|
(name "maxima")
|
|
(version "5.33.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
|
|
version "-source/" name "-" version ".tar.gz"))
|
|
(sha256
|
|
(base32
|
|
"13axm11xw0f3frx5b0qdidi7igkn1524fzz77s9rbpl2yy2nrbz2"))))
|
|
(build-system gnu-build-system)
|
|
(arguments
|
|
`(#:phases (alist-cons-before
|
|
'check 'pre-check
|
|
(lambda _
|
|
(chmod "src/maxima" #o555))
|
|
%standard-phases)))
|
|
(inputs
|
|
`(("gcl" ,gcl)))
|
|
(native-inputs
|
|
`(("texinfo" ,texinfo)
|
|
("perl" ,perl)))
|
|
(home-page "http://maxima.sourceforge.net")
|
|
(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
|
|
exact fractions, arbitrary precision integers, and variable precision floating
|
|
point numbers")
|
|
;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
|
|
;; Others simply say "GNU General Public License" without stating a
|
|
;; version (which implicitly means gpl1+).
|
|
;; At least one file (src/maxima.asd) says "version 2."
|
|
;; GPLv2 only is therefore the smallest subset.
|
|
(license license:gpl2)))
|