;;; 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>
+;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
+;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.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 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 gettext)
- #:renamer (symbol-prefix-proc 'gnu:))
+ #: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 tcl)
+ #:use-module (gnu packages texinfo)
+ #:use-module (gnu packages texlive)
#:use-module (gnu packages xml))
(define-public units
(package
(name "units")
- (version "2.01")
+ (version "2.11")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/units/units-" version
".tar.gz"))
(sha256 (base32
- "1wl8kaxgk4l5jgc1f71mx1rwa6ib84krjmzyzn2f987z1g3i52qk"))))
+ "1gjs3wc212aaiq4r76hx9nl1h3fa39n0ljwl9420d6ixl3rdmdjk"))))
(build-system gnu-build-system)
(synopsis "Conversion between thousands of scales")
(description
- "GNU Units converts quantities expressed in various systems of
-measurement to their equivalents in other systems of measurement. Like
-many similar programs, it can handle multiplicative scale changes. It can
-also handle nonlinear conversions such as Fahrenheit to Celsius or wire
-gauge, and it can convert from and to sums of units, such as converting
-between meters and feet plus inches.
-
-Beyond simple unit conversions, GNU Units can be used as a general-purpose
-scientific calculator that keeps track of units in its calculations. You
-can form arbitrary complex mathematical expressions of dimensions including
-sums, products, quotients, powers, and even roots of dimensions. Thus you
-can ensure accuracy and dimensional consistency when working with long
-expressions that involve many different units that may combine in complex
-ways.
-
-The units are defined in an external data file. You can use the extensive
-data file that comes with this program, or you can provide your own data
-file to suit your needs. You can also use your own data file to supplement
-the standard data file.")
+ "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 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 "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 "4.55")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://gnu/glpk/glpk-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1rqx5fzj1mhkifilip5mkxybpj2wkniq5qcn8h1w2vkr2rzhs29p"))))
+ (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 "0.8.0a")
+ (version "0.8.4")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "1pgkb3z8b4wk4gymnafclhkrqq7n05wq83mra3v53jdl6bnllmyq"))))
+ "0b65q45x05ps95pph6glbg7ymdr638nfb0rk9x5x9qm5k073pk5z"))))
(build-system gnu-build-system)
(inputs
- `(("gettext" ,gnu:gettext)
+ `(("cairo" ,cairo)
+ ("fontconfig" ,fontconfig)
+ ("gettext" ,gnu-gettext)
("gsl" ,gsl)
("libxml2" ,libxml2)
+ ("pango" ,pango)
("readline" ,readline)
+ ("gtk" ,gtk+-2)
+ ("gtksourceview" ,gtksourceview)
("zlib" ,zlib)))
(native-inputs
- `(("perl" ,perl)
+ `(("glib" ,glib "bin") ;for glib-genmarshal
+ ("perl" ,perl)
("pkg-config" ,pkg-config)))
- (arguments
- `(#:configure-flags
- `("--without-cairo" ; FIXME: tests currently fail for lack of font
- "--without-gui"))) ; FIXME: package missing dependencies
(home-page "http://www.gnu.org/software/pspp/")
(synopsis "Statistical analysis")
(description
- "PSPP is a program for statistical analysis of sampled data. It is a
-free replacement for the proprietary program SPSS, and appears very similar
-to it.
-
-PSPP can perform descriptive statistics, T-tests, anova, linear and logistic
-regression, cluster analysis, factor analysis, non-parametric tests and
-more. Its backend is designed to perform its analyses as fast as possible,
-regardless of the size of the input data. You can use PSPP with its
-graphical interface or the more traditional syntax commands.")
+ "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)
+ (location (source-properties->location (current-source-location)))
+ (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 "5.34.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/maxima/Maxima-source/"
+ version "-source/" name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1dw9vfzldpj7lv303xbw0wpyn6ra6i2yzwlrjbcx7j0jm5n43ji0"))))
+ (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-5.34.1', which doesn't exist. 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 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-4.8)
+ ("lapack-tar" ,(package-source lapack))))
+ (outputs '("out" "doc"))
+ (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)))
HCoop / jackhill / guix / guix.git / blobdiff