;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2013, 2014
, 2015 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>
+;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
+;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
+;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
+;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;;
;;; This file is part of GNU Guix.
;;;
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages maths)
+ #:use-module (ice-9 regex)
#:use-module (gnu packages)
- #:use-module ((guix licenses)
- #:renamer (symbol-prefix-proc 'license:))
+ #:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
+ #:use-module (guix svn-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 check)
#:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
#:use-module (gnu packages curl)
#: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 tbb)
#:use-module (gnu packages tcsh)
+ #:use-module (gnu packages tcl)
#:use-module (gnu packages texinfo)
#:use-module (gnu packages texlive)
- #:use-module (gnu packages xml))
+ #:use-module (gnu packages wxwidgets)
+ #:use-module (gnu packages xml)
+ #:use-module (gnu packages zip))
(define-public units
(package
(license license:gpl3+)
(home-page "http://www.gnu.org/software/units/")))
+(define-public double-conversion
+ (package
+ (name "double-conversion")
+ (version "1.1.5")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/floitsch/double-conversion/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83"))))
+ (build-system cmake-build-system)
+ (arguments
+ '(#:test-target "test"
+ #:configure-flags '("-DBUILD_SHARED_LIBS=ON"
+ "-DBUILD_TESTING=ON")))
+ (home-page "https://github.com/floitsch/double-conversion")
+ (synopsis "Conversion routines for IEEE doubles")
+ (description
+ "The double-conversion library provides binary-decimal and decimal-binary
+routines for IEEE doubles. The library consists of efficient conversion
+routines that have been extracted from the V8 JavaScript engine.")
+ (license license:bsd-3)))
+
+(define-public dionysus
+ (package
+ (name "dionysus")
+ (version "1.3.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://gnu/dionysus/dionysus-" version
+ ".tar.gz"))
+ (sha256
+ (base32
+ "1aqnvw6z33bzqgd1ga571pnx6vq2zrkckm1cz91grv45h4jr9vgs"))))
+ (build-system gnu-build-system)
+ (inputs `(("tcl" ,tcl))) ;for 'tclsh'
+ (synopsis "Local search for universal constants and scientific values")
+ (description
+ "GNU Dionysus is a convenient system for quickly retrieving the values of
+mathematical constants used in science and engineering. Values can be
+searched using a simple command-line tool, choosing from three databases:
+universal constants, atomic numbers, and constants related to
+semiconductors.")
+ (license license:gpl3+)
+ (home-page "http://www.gnu.org/software/dionysus/")))
+
(define-public gsl
(package
(name "gsl")
version ".tar.gz"))
(sha256
(base32
- "0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))))
+ "0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))
+ (patches (map search-patch '("gsl-poly-test-fix-pt1.patch"
+ "gsl-poly-test-fix-pt2.patch")))))
(build-system gnu-build-system)
(arguments
`(#:parallel-tests? #f
(define-public glpk
(package
(name "glpk")
- (version "4.54")
+ (version "4.55")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "18gr2anv8gyps6j9f22k7li6w07glvww666sdqblvlq2hh3whwmb"))))
+ "1rqx5fzj1mhkifilip5mkxybpj2wkniq5qcn8h1w2vkr2rzhs29p"))))
(build-system gnu-build-system)
(inputs
`(("gmp" ,gmp)))
(define-public pspp
(package
(name "pspp")
- (version "0.8.3")
+ (version "0.8.4")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "0vri2pzvmm38qaihfvwlry30f40lcnps4blg59ixic4q20ldxf5d"))))
+ "0b65q45x05ps95pph6glbg7ymdr638nfb0rk9x5x9qm5k073pk5z"))))
(build-system gnu-build-system)
(inputs
`(("cairo" ,cairo)
("gtksourceview" ,gtksourceview)
("zlib" ,zlib)))
(native-inputs
- `(("perl" ,perl)
+ `(("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.")
+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 arpack-ng
+ (package
+ (name "arpack-ng")
+ (version "3.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/opencollab/arpack-ng/archive/"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1fwch6vipms1ispzg2djvbzv5wag36f1dmmr3xs3mbp6imfyhvff"))))
+ (build-system gnu-build-system)
+ (home-page "https://github.com/opencollab/arpack-ng")
+ (inputs
+ `(("lapack" ,lapack)
+ ("fortran" ,gfortran)))
+ (synopsis "Fortran subroutines for solving eigenvalue problems")
+ (description
+ "ARPACK-NG is a collection of Fortran77 subroutines designed to solve
+large scale eigenvalue problems.")
+ (license (license:non-copyleft "file://COPYING"
+ "See COPYING in the distribution."))))
+
(define-public lapack
(package
(name "lapack")
"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)
+ (inputs `(("fortran" ,gfortran)
("python" ,python-2)))
(arguments
`(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES")
(description
"LAPACK is a Fortran 90 library for solving the most commonly occurring
problems in numerical linear algebra.")
- (license (license:bsd-style "file://LICENSE"
+ (license (license:non-copyleft "file://LICENSE"
"See LICENSE in the distribution."))))
(define-public gnuplot
(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
+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
+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.
(source
(origin
(method url-fetch)
- (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-"
+ (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)
+ (inputs
+ `(("zlib" ,zlib)))
(arguments
`(#:phases
(alist-cons-before
(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")
+ (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
(define-public octave
(package
(name "octave")
- (version "3.8.0")
+ (version "3.8.2")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "0ks9pr154syw0vb3jn6xsnrkkrbvf9y7i7gaxa28rz6ngxbxvq9l"))))
+ "05slz8yx8k91fqlnfr1f0vni95iq9qmchz41c7nf4isn3b2fjn7j"))))
(build-system gnu-build-system)
(inputs
`(("lapack" ,lapack)
("readline" ,readline)
("glpk" ,glpk)
+ ("fftw" ,fftw)
+ ("fftwf" ,fftwf)
+ ("arpack" ,arpack-ng)
("curl" ,curl)
("pcre" ,pcre)
("fltk" ,fltk)
("fontconfig" ,fontconfig)
("freetype" ,freetype)
- ("hdf5-lib" ,hdf5 "lib")
- ("hdf5-include" ,hdf5 "include")
+ ("hdf5" ,hdf5)
("libxft" ,libxft)
("mesa" ,mesa)
+ ("glu" ,glu)
("zlib" ,zlib)))
(native-inputs
- `(("gfortran" ,gfortran-4.8)
+ `(("gfortran" ,gfortran)
("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
+ ;; 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)
"/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.")
+ (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
;; 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)
+ ("gfortran" ,gfortran)
("gmp" ,gmp)
- ("hdf5-lib" ,hdf5 "lib")
- ("hdf5-include" ,hdf5 "include")
+ ("hdf5" ,hdf5)
("lapack" ,lapack)
("mesa" ,mesa)
+ ("glu" ,glu)
("libx11" ,libx11)
("libxext" ,libxext)))
(arguments
`(("python" ,python-2)
("perl" ,perl)))
(inputs
- `(("gfortran" ,gfortran-4.8)
+ `(("gfortran" ,gfortran)
("lapack" ,lapack)
("superlu" ,superlu)
;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
"conf/uninstall.py"))))
%standard-phases)))))
(home-page "http://www.mcs.anl.gov/petsc")
- (synopsis "Library to solve ODEs and algebraic equations")
+ (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
+ (license (license:non-copyleft
"http://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
(define-public petsc-complex
(substitute-keyword-arguments (package-arguments petsc)
((#:configure-flags cf)
`(cons "--with-scalar-type=complex" ,cf))))
- (description
- (string-append (package-description petsc)
- " Complex scalar type version."))))
+ (synopsis "Library to solve PDEs (with complex scalars)")))
(define-public petsc-openmpi
(package (inherit petsc)
,(string-append "--with-mpi-dir="
(assoc-ref %build-inputs "openmpi"))
,@(delete "--with-mpi=0" ,cf)))))
- (description
- (string-append (package-description petsc)
- " With OpenMPI parallelism support."))))
+ (synopsis "Library to solve PDEs (with MPI support)")))
(define-public petsc-complex-openmpi
(package (inherit petsc-complex)
,(string-append "--with-mpi-dir="
(assoc-ref %build-inputs "openmpi"))
,@(delete "--with-mpi=0" ,cf)))))
- (description
- (string-append (package-description petsc-complex)
- " With OpenMPI parallelism support."))))
+ (synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
(define-public superlu
(package
`(("tcsh" ,tcsh)))
(inputs
`(("lapack" ,lapack)
- ("gfortran" ,gfortran-4.8)))
+ ("gfortran" ,gfortran)))
(arguments
`(#:parallel-build? #f
#:tests? #f ;tests are run as part of `make all`
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)))
+ (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")
+ (version "6.0.4")
(source
(origin
(method url-fetch)
- (uri (string-append "https://gforge.inria.fr/frs/download.php/31831/"
+ (uri (string-append "https://gforge.inria.fr/frs/download.php/34618/"
"scotch_" version ".tar.gz"))
(sha256
- (base32 "0yfqf9lk7chb3h42777x42x4adx0v3n0b41q0cdqrdmscp4iczp5"))
- (patches (list (search-patch "scotch-test-threading.patch")))))
+ (base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
+ (patches (list (search-patch "scotch-test-threading.patch")
+ (search-patch "pt-scotch-build-parallelism.patch")))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)
("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 "
+ (modify-phases %standard-phases
+ (add-after
+ 'unpack 'chdir-to-src
+ (lambda _ (chdir "src")))
+ (replace
+ 'configure
+ (lambda _
+ (call-with-output-file "Makefile.inc"
+ (lambda (port)
+ (format port "
EXE =
LIB = .a
OBJ = .o
MAKE = make
AR = ar
ARFLAGS = -ruv
+CAT = cat
CCS = gcc
CCP = mpicc
CCD = gcc
CPPFLAGS =~{ -D~a~}
-CFLAGS = -O2 -g $(CPPFLAGS)
+CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
LDFLAGS = -lz -lm -lrt -lpthread
CP = cp
LEX = flex -Pscotchyy -olex.yy.c
RANLIB = ranlib
YACC = bison -pscotchyy -y -b y
"
- '("COMMON_FILE_COMPRESS_GZ"
- "COMMON_PTHREAD"
- "COMMON_RANDOM_FIXED_SEED"
- ;; TODO: Define once our MPI supports
- ;; MPI_THREAD_MULTIPLE
- ;; "SCOTCH_PTHREAD"
- ;; "SCOTCH_PTHREAD_NUMBER=2"
- "restrict=__restrict")))))
- (alist-replace
+ '("COMMON_FILE_COMPRESS_GZ"
+ "COMMON_PTHREAD"
+ "COMMON_RANDOM_FIXED_SEED"
+ ;; Prevents symbolc clashes with libesmumps
+ "SCOTCH_RENAME"
+ ;; XXX: Causes invalid frees in superlu-dist tests
+ ;; "SCOTCH_PTHREAD"
+ ;; "SCOTCH_PTHREAD_NUMBER=2"
+ "restrict=__restrict"))))))
+ (add-after
+ 'build 'build-esmumps
+ (lambda _
+ (zero? (system* "make"
+ (format #f "-j~a" (parallel-job-count))
+ "esmumps"))))
+ (replace
'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(mkdir out)
(zero? (system* "make"
(string-append "prefix=" out)
- "install"))))
- %standard-phases)))))
+ "install"))
+ ;; esmumps files are not installed with the above
+ (for-each (lambda (f)
+ (copy-file f (string-append out "/include/" f)))
+ (find-files "../include" ".*esmumps.h$"))
+ (for-each (lambda (f)
+ (copy-file f (string-append out "/lib/" f)))
+ (find-files "../lib" "^lib.*esmumps.*"))))))))
(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
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)
+ `(modify-phases ,scotch-phases
+ (replace
+ 'build
+ (lambda _
+ (and
+ (zero? (system* "make"
+ (format #f "-j~a" (parallel-job-count))
+ "ptscotch" "ptesmumps"))
+ ;; Install the serial metis compatibility library
+ (zero? (system* "make" "-C" "libscotchmetis" "install")))))
+ (replace
+ 'check
+ (lambda _ (zero? (system* "make" "ptcheck"))))))))
+ (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 "5.36.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
+ version "-source/" name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0x1rk659sn3cq0n5c90848ilzr1gb1wf0072fl6jhkdq00qgh2s0"))
+ (patches (list (search-patch "maxima-defsystem-mkdir.patch")))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("gcl" ,gcl)
+ ("gnuplot" ,gnuplot) ;for plots
+ ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
+ (native-inputs
+ `(("texinfo" ,texinfo)
+ ("perl" ,perl)))
+ (arguments
+ `(#:configure-flags
+ (list "--enable-gcl"
+ (string-append "--with-posix-shell="
+ (assoc-ref %build-inputs "bash")
+ "/bin/sh")
+ (string-append "--with-wish="
+ (assoc-ref %build-inputs "tk")
+ "/bin/wish"
+ (let ((v ,(package-version tk)))
+ (string-take v (string-index-right v #\.)))))
+ ;; By default Maxima attempts to write temporary files to
+ ;; '/tmp/nix-build-maxima-*', which won't exist at run time.
+ ;; Work around that.
+ #:make-flags (list "TMPDIR=/tmp")
+ #:phases (alist-cons-before
+ 'check 'pre-check
+ (lambda _
+ (chmod "src/maxima" #o555))
+ ;; Make sure the doc and emacs files are found in the
+ ;; standard location. Also configure maxima to find gnuplot
+ ;; without having it on the PATH.
+ (alist-cons-after
+ 'install 'post-install
+ (lambda* (#:key outputs inputs #:allow-other-keys)
+ (let* ((gnuplot (assoc-ref inputs "gnuplot"))
+ (out (assoc-ref outputs "out"))
+ (datadir (string-append out "/share/maxima/" ,version)))
+ (with-directory-excursion out
+ (mkdir-p "share/emacs")
+ (mkdir-p "share/doc")
+ (symlink
+ (string-append datadir "/emacs/")
+ (string-append out "/share/emacs/site-lisp"))
+ (symlink
+ (string-append datadir "/doc/")
+ (string-append out "/share/doc/maxima"))
+ (with-atomic-file-replacement
+ (string-append datadir "/share/maxima-init.lisp")
+ (lambda (in out)
+ (format out "~a ~s~a~%"
+ "(setf $gnuplot_command "
+ (string-append gnuplot "/bin/gnuplot") ")")
+ (dump-port in out))))))
+ %standard-phases))))
+ (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)))
+
+(define-public wxmaxima
+ (package
+ (name "wxmaxima")
+ (version "15.04.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/wxmaxima/wxMaxima/"
+ version "/" name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1fm47ah4aw5qdjqhkz67w5fwhy8yfffa5z896crp0d3hk2bh4180"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("wxwidgets" ,wxwidgets)
+ ("maxima" ,maxima)))
+ (arguments
+ `(#:phases (modify-phases %standard-phases
+ (add-after
+ 'install 'wrap-program
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (wrap-program (string-append (assoc-ref outputs "out")
+ "/bin/wxmaxima")
+ `("PATH" ":" prefix
+ (,(string-append (assoc-ref inputs "maxima")
+ "/bin"))))
+ #t)))))
+ (home-page "https://andrejv.github.io/wxmaxima/")
+ (synopsis "Graphical user interface for the Maxima computer algebra system")
+ (description
+ "wxMaxima is a graphical user interface for the Maxima computer algebra
+system. It eases the use of Maxima by making most of its commands available
+through a menu system and by providing input dialogs for commands that require
+more than one argument. It also implements its own display engine that
+outputs mathematical symbols directly instead of depicting them with ASCII
+characters.
+
+wxMaxima also features 2D and 3D inline plots, simple animations, mixing of
+text and mathematical calculations to create documents, exporting of input and
+output to TeX, and a browser for Maxima's manual including command index and
+full text searching.")
+ (license license:gpl2+)))
+
+(define-public muparser
+ (package
+ (name "muparser")
+ (version "2.2.5")
+ (source
+ (origin
+ (method svn-fetch)
+ (uri (svn-reference
+ (url "http://muparser.googlecode.com/svn/trunk/")
+ (revision 34)))
+ (sha256
+ (base32
+ "1d6bdbhx9zj3srwj3m7c9hvr18gnx1fx43h6d25my7q85gicpcwn"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:configure-flags '("--enable-samples=no")
+ #:tests? #f)) ;no "check" target
+ (home-page "http://muparser.beltoforion.de/")
+ (synopsis "Fast parser library for mathematical expressions")
+ (description
+ "muParser is an extensible high performance math parser library. It is
+based on transforming an expression into a bytecode and precalculating
+constant parts of it.")
+ (license license:expat)))
+
+(define-public openblas
+ (package
+ (name "openblas")
+ (version "0.2.14")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
+ version))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0av3pd96j8rx5i65f652xv9wqfkaqn0w4ma1gvbyz73i6j2hi9db"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ;no "check" target
+ ;; DYNAMIC_ARCH is not supported on MIPS. When it is disabled,
+ ;; OpenBLAS will tune itself to the build host, so we need to disable
+ ;; substitutions.
+ #:substitutable? ,(not (string-prefix? "mips" (%current-system)))
+ #:make-flags
+ (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
+ "SHELL=bash"
+ "NO_LAPACK=1"
+ ;; 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 MIPS.
+ ,@(if (string-prefix? "mips" (%current-system))
+ '()
+ '("DYNAMIC_ARCH=1")))
+ ;; no configure script
+ #:phases (alist-delete 'configure %standard-phases)))
+ (inputs
+ `(("fortran" ,gfortran)))
+ (native-inputs
+ `(("cunit" ,cunit)
+ ("perl" ,perl)))
+ (home-page "http://www.openblas.net/")
+ (synopsis "Optimized BLAS library based on GotoBLAS")
+ (description
+ "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
+ (license license:bsd-3)))
+
+(define-public openlibm
+ (package
+ (name "openlibm")
+ (version "0.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/JuliaLang/openlibm/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0cwqqqlblj3kzp9aq1wnpfs1fl0qd1wp1xzm5shb09w06i4rh9nn"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:make-flags
+ (list (string-append "prefix=" (assoc-ref %outputs "out")))
+ #:phases
+ ;; no configure script
+ (alist-delete 'configure %standard-phases)
+ #:tests? #f)) ;the tests are part of the default target
+ (home-page "http://openlibm.org/")
+ (synopsis "Portable C mathematical library (libm)")
+ (description
+ "OpenLibm is an effort to have a high quality, portable, standalone C
+mathematical library (libm). It can be used standalone in applications and
+programming language implementations. The project was born out of a need to
+have a good libm for the Julia programming langage that worked consistently
+across compilers and operating systems, and in 32-bit and 64-bit
+environments.")
+ ;; See LICENSE.md for details.
+ (license (list license:expat
+ license:isc
+ license:bsd-2
+ license:public-domain
+ license:lgpl2.1+))))
+
+(define-public openspecfun
+ (package
+ (name "openspecfun")
+ (version "0.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/JuliaLang/openspecfun/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0nsa3jjmlhcqkw5ba5ypbn3n0c8b6lc22zzlxnmxkxi9shhdx65z"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ;no "check" target
+ #:make-flags
+ (list (string-append "prefix=" (assoc-ref %outputs "out")))
+ ;; no configure script
+ #:phases (alist-delete 'configure %standard-phases)))
+ (inputs
+ `(("fortran" ,gfortran)))
+ (home-page "https://github.com/JuliaLang/openspecfun")
+ (synopsis "Collection of special mathematical functions")
+ (description
+ "Openspecfun provides AMOS and Faddeeva. AMOS (from Netlib) is a
+portable package for Bessel Functions of a Complex Argument and Nonnegative
+Order; it contains subroutines for computing Bessel functions and Airy
+functions. Faddeeva allows computing the various error functions of arbitrary
+complex arguments (Faddeeva function, error function, complementary error
+function, scaled complementary error function, imaginary error function, and
+Dawson function); given these, one can also easily compute Voigt functions,
+Fresnel integrals, and similar related functions as well.")
+ ;; Faddeeva is released under the Expat license; AMOS is included as
+ ;; public domain software.
+ (license (list license:expat license:public-domain))))
+
+(define-public suitesparse
+ (package
+ (name "suitesparse")
+ (version "4.4.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:parallel-build? #f ;cholmod build fails otherwise
+ #:tests? #f ;no "check" target
+ #:make-flags
+ (list "CC=gcc"
+ "BLAS=-lblas"
+ "TBB=-ltbb"
+ "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used
+ (string-append "INSTALL_LIB="
+ (assoc-ref %outputs "out") "/lib")
+ (string-append "INSTALL_INCLUDE="
+ (assoc-ref %outputs "out") "/include"))
+ #:phases
+ (alist-cons-before
+ 'install 'prepare-out
+ ;; README.txt states that the target directories must exist prior to
+ ;; running "make install".
+ (lambda _
+ (mkdir-p (string-append (assoc-ref %outputs "out") "/lib"))
+ (mkdir-p (string-append (assoc-ref %outputs "out") "/include")))
+ ;; no configure script
+ (alist-delete 'configure %standard-phases))))
+ (inputs
+ `(("tbb" ,tbb)
+ ("lapack" ,lapack)))
+ (home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
+ (synopsis "Suite of sparse matrix software")
+ (description
+ "SuiteSparse is a suite of sparse matrix algorithms, including: UMFPACK,
+multifrontal LU factorization; CHOLMOD, supernodal Cholesky; SPQR,
+multifrontal QR; KLU and BTF, sparse LU factorization, well-suited for circuit
+simulation; ordering methods (AMD, CAMD, COLAMD, and CCOLAMD); CSparse and
+CXSparse, a concise sparse Cholesky factorization package; and many other
+packages.")
+ ;; LGPLv2.1+:
+ ;; AMD, CAMD, BTF, COLAMD, CCOLAMD, CSparse, CXSparse, KLU, LDL
+ ;; GPLv2+:
+ ;; GPUQREngine, RBio, SuiteSparse_GPURuntime, SuiteSparseQR, UMFPACK
+ (license (list license:gpl2+ license:lgpl2.1+))))
+
+(define-public atlas
+ (package
+ (name "atlas")
+ (version "3.10.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/math-atlas/atlas"
+ version ".tar.bz2"))
+ (sha256
+ (base32
+ "0bqh4bdnjdyww4mcpg6kn0x7338mfqbdgysn97dzrwwb26di7ars"))))
+ (build-system gnu-build-system)
+ (home-page "http://math-atlas.sourceforge.net/")
+ (inputs `(("gfortran" ,gfortran)
+ ("lapack-tar" ,(package-source lapack))))
+ (outputs '("out" "doc"))
+ ;; For the moment we drop support for MIPS at it fails to compile. See
+ ;; https://lists.gnu.org/archive/html/guix-devel/2014-11/msg00516.html
+ (supported-systems (delete "mips64el-linux" %supported-systems))
+ (arguments
+ `(#:parallel-build? #f
+ #:parallel-tests? #f
+
+ ;; ATLAS tunes itself for the machine it is built on, as explained at
+ ;; <http://lists.gnu.org/archive/html/guix-devel/2014-10/msg00305.html>.
+ ;; For this reason, we want users to build it locally instead of using
+ ;; substitutes.
+ #:substitutable? #f
+
+ #:modules ((srfi srfi-26)
+ (srfi srfi-1)
+ (guix build gnu-build-system)
+ (guix build utils))
+ #:configure-flags
+ `(;; Generate position independent code suitable for dynamic libraries
+ ;; and use WALL timer to get more accurate timing.
+ "-Fa" "alg" "-fPIC" "-D" "c" "-DWALL"
+ ;; Set word width.
+ "-b"
+ ,,(if (string-match "64" (%current-system))
+ "64"
+ "32")
+ ;; Disable parallel build as it gives errors: atlas_pthread.h is
+ ;; needed to compile C files before it is generated.
+ "-Ss" "pmake" "make -j 1"
+ ;; Probe is failing for MIPS. We therefore define the system
+ ;; architecture explicitly by setting (-A) MACHINETYPE = 49
+ ;; 'MIPSR1xK' and (-V) ISA = 1 'none'.
+ ,,@(if (string-prefix? "mips" (%current-system))
+ (list "-A" "49" "-V" "1")
+ (list))
+ ;; Generate shared libraries.
+ "--shared"
+ ;; Build a full LAPACK library.
+ ,(string-append "--with-netlib-lapack-tarfile="
+ (assoc-ref %build-inputs "lapack-tar")))
+ #:phases
+ (alist-cons-after
+ 'install 'install-doc
+ (lambda* (#:key outputs inputs #:allow-other-keys)
+ (let ((doc (string-append (assoc-ref outputs "doc")
+ "/share/doc/atlas")))
+ (mkdir-p doc)
+ (fold (lambda (file previous)
+ (and previous (zero? (system* "cp" file doc))))
+ #t (find-files "../ATLAS/doc" ".*"))))
+ (alist-cons-after
+ 'check 'check-pt
+ (lambda _ (zero? (system* "make" "ptcheck")))
+ ;; Fix files required to run configure.
+ (alist-cons-before
+ 'configure 'fix-/bin/sh
+ (lambda _
+ ;; Use `sh', not `/bin/sh'.
+ (substitute* (find-files "." "Makefile|configure|SpewMakeInc\\.c")
+ (("/bin/sh")
+ "sh")))
+ ;; Fix /bin/sh in generated make files.
+ (alist-cons-after
+ 'configure 'fix-/bin/sh-in-generated-files
+ (lambda _
+ (substitute* (find-files "." "^[Mm]ake\\.inc.*")
+ (("/bin/sh")
+ "sh")))
+ ;; ATLAS configure program does not accepts the default flags
+ ;; passed by the 'gnu-build-system'.
+ (alist-replace
+ 'configure
+ (lambda* (#:key native-inputs inputs outputs
+ (configure-flags '())
+ #:allow-other-keys #:rest args)
+ (let* ((prefix (assoc-ref outputs "out"))
+ (bash (or (and=> (assoc-ref
+ (or native-inputs inputs) "bash")
+ (cut string-append <> "/bin/bash"))
+ "/bin/sh"))
+ (flags `(,(string-append "--prefix=" prefix)
+ ,@configure-flags))
+ (abs-srcdir (getcwd))
+ (srcdir (string-append "../" (basename abs-srcdir))))
+ (format #t "source directory: ~s (relative from build: ~s)~%"
+ abs-srcdir srcdir)
+ (mkdir "../build")
+ (chdir "../build")
+ (format #t "build directory: ~s~%" (getcwd))
+ (format #t "configure flags: ~s~%" flags)
+ (zero? (apply system* bash
+ (string-append srcdir "/configure")
+ flags))))
+ %standard-phases)))))))
+ (synopsis "Automatically Tuned Linear Algebra Software")
+ (description
+ "ATLAS is an automatically tuned linear algebra software library
+providing C and Fortran77 interfaces to a portably efficient BLAS
+implementation, as well as a few routines from LAPACK.
+
+Optimization occurs at build time. For this reason, the library is built on
+the machine where it is installed, without resorting to pre-built substitutes.
+
+Before building the library, CPU throttling should be disabled. This can be
+done in the BIOS, or, on GNU/Linux, with the following commands:
+
+cpufreq-selector -g performance -c 0
+...
+cpufreq-selector -g performance -c N-1
+
+where N is the number of cores of your CPU. Failure to do so will result in a
+library with poor performance.")
+ (license license:bsd-3)))
+
+(define-public glm
+ (package
+ (name "glm")
+ (version "0.9.6.3")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/ogl-math/glm-"
+ version ".zip"))
+ (sha256
+ (base32
+ "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
+ (build-system cmake-build-system)
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (home-page "http://glm.g-truc.net")
+ (synopsis "OpenGL Mathematics library")
+ (description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
+library for graphics software based on the OpenGL Shading Language (GLSL)
+specifications.")
+ (license license:expat)))
+
+(define-public lpsolve
+ (package
+ (name "lpsolve")
+ (version "5.5.2.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/lpsolve/lpsolve/" version
+ "/lp_solve_" version "_source.tar.gz"))
+ (sha256
+ (base32
+ "176c7f023mb6b8bfmv4rfqnrlw88lsg422ca74zjh19i2h5s69sq"))
+ (modules '((guix build utils)))
+ (snippet
+ '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc")
+ (("^c=cc") "c=gcc")
+ ;; Pretend to be on a 64 bit platform to obtain a common directory
+ ;; name for the build results on all architectures; nothing else
+ ;; seems to depend on it.
+ (("^PLATFORM=.*$") "PLATFORM=ux64\n")))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; no check target
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'build
+ (lambda _
+ (with-directory-excursion "lpsolve55"
+ (system* "bash" "ccc"))
+ (with-directory-excursion "lp_solve"
+ (system* "bash" "ccc"))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (lib (string-append out "/lib"))
+ ;; This is where LibreOffice expects to find the header
+ ;; files, and where they are installed by Debian.
+ (include (string-append out "/include/lpsolve")))
+ (mkdir-p lib)
+ (copy-file "lpsolve55/bin/ux64/liblpsolve55.a"
+ (string-append lib "/liblpsolve55.a"))
+ (copy-file "lpsolve55/bin/ux64/liblpsolve55.so"
+ (string-append lib "/liblpsolve55.so"))
+ (mkdir-p bin)
+ (copy-file "lp_solve/bin/ux64/lp_solve"
+ (string-append bin "/lp_solve"))
+ (mkdir-p include)
+ ;; Install a subset of the header files as on Debian
+ ;; (plus lp_bit.h, which matches the regular expression).
+ (for-each
+ (lambda (name)
+ (copy-file name (string-append include "/" name)))
+ (find-files "." "lp_[HMSa-z].*\\.h$"))
+ (with-directory-excursion "shared"
+ (for-each
+ (lambda (name)
+ (copy-file name (string-append include "/" name)))
+ (find-files "." "\\.h$")))
+ #t))))))
+ (home-page "http://lpsolve.sourceforge.net/")
+ (synopsis "Mixed integer linear programming (MILP) solver")
+ (description
+ "lp_solve is a mixed integer linear programming solver based on the
+revised simplex and the branch-and-bound methods.")
+ (license license:lgpl2.1+)))
HCoop / jackhill / guix / guix.git / blobdiff