;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2013, 2014, 2015 Andreas Enge <andreas@enge.fr>
+;;; Copyright © 2013, 2014, 2015
, 2016 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
-;;; Copyright © 2014 John Darrington <jmd@gnu.org>
-;;; Copyright © 2014, 2015 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2016 John Darrington <jmd@gnu.org>
+;;; Copyright © 2014, 2015, 2016 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, 2016 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2015 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
+;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
+;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org>
+;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;;
;;; This file is part of GNU Guix.
;;;
#: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 utils)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
+ #:use-module (guix build-system r)
#:use-module (gnu packages algebra)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
#:use-module (gnu packages curl)
+ #:use-module (gnu packages cyrus-sasl)
+ #:use-module (gnu packages documentation)
#:use-module (gnu packages elf)
#:use-module (gnu packages flex)
#:use-module (gnu packages fltk)
#:use-module (gnu packages gcc)
#:use-module (gnu packages gd)
#:use-module (gnu packages ghostscript)
- #:use-module (gnu packages glib)
+ #:use-module (gnu packages graphviz)
#:use-module (gnu packages gtk)
#:use-module (gnu packages image)
#:use-module (gnu packages less)
#:use-module (gnu packages lisp)
+ #:use-module (gnu packages logging)
#:use-module (gnu packages gnome)
+ #:use-module (gnu packages guile)
#: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 netpbm)
#:use-module (gnu packages pcre)
#:use-module (gnu packages popt)
#:use-module (gnu packages perl)
#:use-module (gnu packages python)
#:use-module (gnu packages readline)
#:use-module (gnu packages tbb)
- #:use-module (gnu packages tcsh)
+ #:use-module (gnu packages shells)
#:use-module (gnu packages tcl)
#:use-module (gnu packages texinfo)
- #:use-module (gnu packages texlive)
+ #:use-module (gnu packages tex)
+ #:use-module (gnu packages tls)
#:use-module (gnu packages wxwidgets)
#:use-module (gnu packages xml)
#:use-module (gnu packages zip)
#:use-module (srfi srfi-1))
+(define-public c-graph
+ (package
+ (name "c-graph")
+ (version "2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://gnu/c-graph/c-graph-" version
+ ".tar.gz"))
+ (sha256 (base32
+ "1hlvpzrh7hzzf533diyfiabzskddi8zx92av9hwkjw3l46z7qv01"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("fortran" ,gfortran)))
+ (synopsis "Visualizing and demonstrating convolution")
+ (description
+ "GNU C-Graph is a tool for demonstrating the theory of convolution.
+Thus, it can serve as an excellent aid to students of signal and systems
+theory in visualizing the convolution process. Rather than forcing the
+student to write code, the program offers an intuitive interface with
+interactive dialogs to guide them.")
+ (license license:gpl3+)
+ (home-page "http://www.gnu.org/software/c-graph/")))
+
(define-public units
(package
(name "units")
- (version "2.12")
+ (version "2.13")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/units/units-" version
".tar.gz"))
(sha256 (base32
- "1jxvjknz2jhq773jrwx9gc1df3gfy73yqmkjkygqxzpi318yls3q"))))
+ "1awhjw9zjlfb8s5g3yyx63f7ddfcr1sanlbxpqifmrgq24ql198b"))))
(build-system gnu-build-system)
(synopsis "Conversion between thousands of scales")
(description
(define-public glpk
(package
(name "glpk")
- (version "4.57")
+ (version "4.60")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "0p17jj1ixd2m9lnsvx8nywmfmnplfk5gvw25r1gy84qzrjkv48vk"))))
+ "15z2ymzqhxwss6wgdj5f7vkyqlqdsjgrvm0x871kmlx0n0664mhk"))))
(build-system gnu-build-system)
(inputs
`(("gmp" ,gmp)))
LP/MIP solver is included in the package.")
(license license:gpl3+)))
-(define-public pspp
+(define-public 4ti2
(package
- (name "pspp")
- (version "0.8.5")
+ (name "4ti2")
+ (version "1.6.7")
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://gnu/pspp/pspp-"
- version ".tar.gz"))
+ (uri (string-append "http://www.4ti2.de/version_" version
+ "/4ti2-" version ".tar.gz"))
(sha256
(base32
- "0c8326yykidi94xi7jn27j8iqxc38vc07d4wf5zyk0l8lpzx5vz7"))))
+ "1frix3rnm9ffr93alqzw4cavxbfpf524l8rfbmcpyhwd3n1km0yl"))))
(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-2)
- ("zlib" ,zlib)))
(native-inputs
- `(("glib" ,glib "bin") ;for glib-genmarshal
- ("perl" ,perl)
- ("texinfo" ,texinfo)
- ("pkg-config" ,pkg-config)))
- (home-page "http://www.gnu.org/software/pspp/")
- (synopsis "Statistical analysis")
+ `(("which" ,(@ (gnu packages base) which)))) ; for the tests
+ (inputs
+ `(("glpk" ,glpk)
+ ("gmp" ,gmp)))
+ (home-page "http://www.4ti2.de/")
+ (synopsis "Mathematical tool suite for problems on linear spaces")
(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+)))
+ "4ti2 implements algorithms for solving algebraic, geometric and
+combinatorial problems on linear spaces. Among others, it solves systems
+of linear equations, computes extreme rays of polyhedral cones, solves
+integer programming problems and computes Markov bases for statistics.")
+ (license license:gpl2+)))
+
+(define-public cddlib
+ (package
+ (name "cddlib")
+ (version "0.94h")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "ftp://ftp.ifor.math.ethz.ch/pub/fukuda/cdd/cddlib-"
+ (string-delete #\. version) ".tar.gz"))
+ (sha256
+ (base32
+ "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("gmp" ,gmp)))
+ (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
+ (synopsis "Library for convex hulls and extreme rays of polyhedra")
+ (description
+ "The C-library cddlib implements the Double Description Method of
+Motzkin et al. for generating all vertices (i.e. extreme points) and extreme
+rays of a general convex polyhedron given by a system of linear inequalities
+in arbitrary dimension. It can also be used for the converse operation of
+computing convex hulls.")
+ (license license:gpl2+)))
(define-public arpack-ng
(package
(inputs `(("fortran" ,gfortran)
("python" ,python-2)))
(arguments
- `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES")
+ `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
+ "-DLAPACKE=ON")
#:phases (alist-cons-before
'check 'patch-python
(lambda* (#:key inputs #:allow-other-keys)
"See LICENSE in the distribution."))))
(define-public gnuplot
- (package
- (name "gnuplot")
- (version "5.0.1")
- (source
- (origin
- (method url-fetch)
- (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
- version "/gnuplot-" version ".tar.gz"))
- (sha256
- (base32
- "0irwig94w3f8bn4a444hrjnp7w55vqwv8gqj42jiwn6zf5z5bg3w"))))
- (build-system gnu-build-system)
- (inputs `(("readline" ,readline)
- ("cairo" ,cairo)
- ("pango" ,pango)
- ("gd" ,gd)))
- (native-inputs `(("pkg-config" ,pkg-config)
- ;; Need 'tex', 'latex', 'pdflatex', 'kpsexand', and
- ;; 'texhash' binaries.
- ("texlive" ,texlive-bin)))
- (home-page "http://www.gnuplot.info")
- (synopsis "Command-line driven graphing utility")
- (description "Gnuplot is a portable command-line driven graphing
+ ;; Gnuplot version 5.0.4 was updated in-place, resulting in a hash mismatch.
+ ;; This can be removed at the next version update.
+ (let ((upstream-version "5.0.4")
+ (guix-revision "1"))
+ (package
+ (name "gnuplot")
+ (version (string-append upstream-version "-" guix-revision))
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
+ upstream-version "/gnuplot-"
+ upstream-version ".tar.gz"))
+ (sha256
+ (base32
+ "07n3w12dkcxjnhsvsliaqnkhajhi818v6q8mkpmpbplbf92vh70m"))))
+ (build-system gnu-build-system)
+ (inputs `(("readline" ,readline)
+ ("cairo" ,cairo)
+ ("pango" ,pango)
+ ("gd" ,gd)))
+ (native-inputs `(("pkg-config" ,pkg-config)
+ ("texlive" ,texlive-minimal)))
+ (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"))))
+ ;; 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")
+ (version "1.8.17")
(source
(origin
(method url-fetch)
version "/src/hdf5-"
version ".tar.bz2"))
(sha256
- (base32 "0f9n0v3p3lwc7564791a39c6cn1d3dbrn7d1j3ikqsi27a8hy23d"))))
+ (base32 "0sj8x0gfs5fb28gipnynb9wpkz113h8wq9sva9mxx66kv27xsdgw"))
+ (patches (list (search-patch "hdf5-config-date.patch")))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)))
(arguments
`(#:phases
- (alist-cons-before
- 'configure 'patch-configure
- (lambda _
- (substitute* "configure"
- (("/bin/mv") "mv")))
- %standard-phases)))
+ (modify-phases %standard-phases
+ (add-before 'configure 'patch-configure
+ (lambda _
+ (substitute* "configure"
+ (("/bin/mv") "mv"))
+ #t))
+ (add-after 'install 'patch-references
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+ (zlib (assoc-ref inputs "zlib")))
+ (substitute* (find-files bin "h5p?cc")
+ (("-lz" lib)
+ (string-append "-L" zlib "/lib " lib)))
+ #t))))))
(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
(license (license:x11-style
"http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
+(define-public hdf5-parallel-openmpi
+ (package (inherit hdf5)
+ (name "hdf5-parallel-openmpi")
+ (inputs
+ `(("mpi" ,openmpi)
+ ,@(package-inputs hdf5)))
+ (arguments
+ (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
+ ,@(package-arguments hdf5))
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-before 'check 'patch-tests
+ (lambda _
+ ;; OpenMPI's mpirun will exit with non-zero status if it
+ ;; detects an "abnormal termination", i.e. any process not
+ ;; calling MPI_Finalize(). Since the test is explicitely
+ ;; avoiding MPI_Finalize so as not to have at_exit and thus
+ ;; H5C_flush_cache from being called, mpirun will always
+ ;; complain, so turn this test off.
+ (substitute* "testpar/Makefile"
+ (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
+ (string-append front back "\n")))
+ (substitute* "tools/h5diff/testph5diff.sh"
+ (("/bin/sh") (which "sh")))
+ #t))))))
+ (synopsis "Management suite for data with parallel IO support")))
+
+(define-public h5check
+ (package
+ (name "h5check")
+ (version "2.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/"
+ "h5check/src/h5check-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
+ (build-system gnu-build-system)
+ (inputs `(("hdf5" ,hdf5))) ;h5cc for tests
+ (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html")
+ (synopsis "HDF5 format checker")
+ (description "@code{h5check} is a validation tool for verifying that an
+HDF5 file is encoded according to the HDF File Format Specification.")
+ (license (license:x11-style "file://COPYING"))))
+
+(define-public netcdf
+ (package
+ (name "netcdf")
+ (version "4.4.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/"
+ "netcdf-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0y6gdcplarwqqnrav2xg1xd6ih732rzzbmdw78v3rl5b8mwcnh0d"))
+ (patches (list (search-patch "netcdf-config-date.patch")))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("m4" ,m4)
+ ("doxygen" ,doxygen)
+ ("graphviz" ,graphviz)))
+ (inputs
+ `(("hdf5" ,hdf5)
+ ("zlib" ,zlib)))
+ (arguments
+ `(#:configure-flags '("--enable-doxygen" "--enable-dot")
+ #:parallel-tests? #f)) ;various race conditions
+ (home-page "http://www.unidata.ucar.edu/software/netcdf/")
+ (synopsis "Library for scientific data")
+ (description "NetCDF is an interface for scientific data access and a
+software library that provides an implementation of the interface. The netCDF
+library defines a machine-independent format for representing scientific data.
+Together, the interface, library, and format support the creation, access, and
+sharing of scientific data.")
+ (license (license:x11-style "file://COPYRIGHT"))))
+
+(define-public netcdf-parallel-openmpi
+ (package (inherit netcdf)
+ (name "netcdf-parallel-openmpi")
+ (inputs
+ `(("mpi" ,openmpi)
+ ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi)
+ (package-inputs netcdf))))
+ ;; TODO: Replace pkg-config references in nc-config with absolute references
+ (arguments
+ (substitute-keyword-arguments (package-arguments netcdf)
+ ((#:configure-flags flags)
+ `(cons* "CC=mpicc" "CXX=mpicxx"
+ "--enable-parallel-tests"
+ ;; Shared libraries not supported with parallel IO.
+ "--disable-shared" "--with-pic"
+ ,flags))))))
+
+(define-public nlopt
+ (package
+ (name "nlopt")
+ (version "2.4.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-"
+ version ".tar.gz"))
+ (sha256
+ (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(;; Shared libraries are not built by default. They are required to
+ ;; build the Guile, Octave, and Python bindings.
+ #:configure-flags '("--enable-shared")
+
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'set-libnlopt-file-name
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Make sure the Scheme module refers to the library by its
+ ;; absolute file name (we cannot do that from a snippet
+ ;; because the expansion of @libdir@ contains
+ ;; ${exec_prefix}.)
+ (let ((out (assoc-ref outputs "out")))
+ (substitute* "swig/nlopt.scm.in"
+ (("libnlopt")
+ (string-append out "/lib/libnlopt")))
+ #t))))))
+ (inputs `(("guile" ,guile-2.0)))
+ (native-inputs `(("pkg-config" ,pkg-config)))
+ (home-page "http://ab-initio.mit.edu/wiki/")
+ (synopsis "Library for nonlinear optimization")
+ (description "NLopt is a library for nonlinear optimization, providing a
+common interface for a number of different free optimization routines available
+online as well as original implementations of various other algorithms.")
+ (license license:lgpl2.1+)))
+
+(define-public ipopt
+ (package
+ (name "ipopt")
+ (version "3.12.5")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "http://www.coin-or.org/download/source/Ipopt/Ipopt-"
+ version".tgz"))
+ (sha256
+ (base32
+ "09bk2hqy2vgi4yi76xng9zxakddwqy3wij9nx7wf2vfbxxpazrsk"))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Make sure we don't use the bundled software.
+ '(delete-file-recursively "ThirdParty"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:phases (modify-phases %standard-phases
+ (add-after 'install 'add--L-flags-in-ipopt.pc
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; The '.pc' file lists '-llapack -lblas' in "Libs";
+ ;; move it to "Libs.private" where it belongs, and add a
+ ;; '-L' flag for LAPACK.
+ (let ((out (assoc-ref outputs "out"))
+ (lapack (assoc-ref inputs "lapack")))
+ (substitute* (string-append out "/lib/pkgconfig/"
+ "ipopt.pc")
+ (("Libs: (.*)-llapack -lblas(.*)$" _ before after)
+ (string-append "Libs: " before " " after "\n"
+ "Libs.private: " before
+ "-L" lapack "/lib -llapack -lblas "
+ after "\n")))
+ #t))))))
+ (native-inputs
+ `(("gfortran" ,gfortran)))
+ (inputs
+ ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
+ `(("lapack" ,lapack))) ;for both libblas and liblapack
+ (home-page "http://www.coin-or.org")
+ (synopsis "Large-scale nonlinear optimizer")
+ (description
+ "The Interior Point Optimizer (IPOPT) is a software package for
+large-scale nonlinear optimization. It provides C++, C, and Fortran
+interfaces.")
+ (license license:epl1.0)))
+
+(define-public ceres
+ (package
+ (name "ceres-solver")
+ (version "1.11.0")
+ (home-page "http://ceres-solver.org/")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append home-page "ceres-solver-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0i7qkbf8g6pd8arxzldppga26ckv93y8zldsfz6wbd4n6b1nqrjd"))))
+ (build-system cmake-build-system)
+ (arguments
+ ;; TODO: Build HTML user documentation and install separately.
+ '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
+ "-DBUILD_SHARED_LIBS=ON")
+
+ #:phases (modify-phases %standard-phases
+ (add-before 'configure 'set-library-directory
+ (lambda _
+ ;; Install libraries to lib/, not lib64/.
+ (substitute* "internal/ceres/CMakeLists.txt"
+ (("set\\(LIB_SUFFIX \"64\"\\)")
+ "set(LIB_SUFFIX \"\")"))
+ #t)))))
+ (native-inputs
+ `(("pkg-config" ,pkg-config)))
+ (propagated-inputs
+ `(("glog" ,glog))) ;for #include <glog/glog.h>
+ (inputs
+ `(("eigen" ,eigen)
+ ("blas" ,openblas)
+ ("lapack" ,lapack)
+ ("suitesparse" ,suitesparse)
+ ("gflags" ,gflags)))
+ (synopsis "C++ library for solving large optimization problems")
+ (description
+ "Ceres Solver is a C++ library for modeling and solving large,
+complicated optimization problems. It is a feature rich, mature and
+performant library which has been used in production since 2010. Ceres Solver
+can solve two kinds of problems:
+@enumerate
+@item non-linear least squares problems with bounds constraints;
+@item general unconstrained optimization problems.
+@end enumerate\n")
+ (license license:bsd-3)))
;; 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 "4.0.0")
+ (version "4.0.2")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "101jr9yck798586jz4vkjcgk36zksmxf1pxrzvipgn2xgyay0zjc"))))
+ "1hdxap3j88rpqjimnfhinym6z73wdi5dfa6fv85c13r1dk9qzk9r"))))
(build-system gnu-build-system)
(inputs
`(("lapack" ,lapack)
("arpack" ,arpack-ng)
("curl" ,curl)
("pcre" ,pcre)
+ ("cyrus-sasl" ,cyrus-sasl)
("fltk" ,fltk)
("fontconfig" ,fontconfig)
("freetype" ,freetype)
("libxft" ,libxft)
("mesa" ,mesa)
("glu" ,glu)
+ ("openssl" ,openssl)
("zlib" ,zlib)))
(native-inputs
`(("gfortran" ,gfortran)
("ghostscript" ,ghostscript)
("gnuplot" ,gnuplot)))
(arguments
- `(#:configure-flags (list (string-append "--with-shell="
- (assoc-ref %build-inputs "bash")
- "/bin/sh"))))
+ `(#: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
(define-public gmsh
(package
(name "gmsh")
- (version "2.8.4")
+ (version "2.11.0")
(source
(origin
(method url-fetch)
(uri (string-append "http://www.geuz.org/gmsh/src/gmsh-"
version "-source.tgz"))
(sha256
- (base32 "0jv2yvk28w86rx5mvjkb0w12ff2jxih7axnpvznpd295lg5jg7hr"))
+ (base32 "1ilplibvjgf7a905grpnclrvkmqy9fgrpl7xyp3w4yl1qc682v9b"))
(modules '((guix build utils)))
(snippet
;; Remove non-free METIS code
("glu" ,glu)
("libx11" ,libx11)
("libxext" ,libxext)))
+ (inputs
+ `(("fontconfig" ,fontconfig)
+ ("libxft" ,libxft)))
(arguments
`(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
"-DENABLE_BUILD_SHARED:BOOL=ON"
- "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
+ "-DENABLE_BUILD_DYNAMIC:BOOL=ON")
+ #:phases (modify-phases %standard-phases
+ (replace
+ 'check
+ (lambda _
+ (zero? (system* "make" "test"
+ ;; Disable this test. See
+ ;; https://geuz.org/trac/gmsh/ticket/271
+ "ARGS=-E component8_in_a_box")))))))
(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
(define-public petsc
(package
(name "petsc")
- (version "3.6.2")
+ (version "3.7.2")
(source
(origin
(method url-fetch)
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
"petsc-lite-" version ".tar.gz"))
(sha256
- (base32 "13h0m5f9xsdpps4lsp59iz2m7zkapwavq2zfkfvs3ab6sndla0l9"))))
+ (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)
,(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$")
- (((getcwd)) out))))
- (alist-cons-after
- 'install 'clean-install
+ (modify-phases %standard-phases
+ (replace 'configure
+ ;; PETSc's configure script is actually a python script, so we can't
+ ;; run it with bash.
+ (lambda* (#:key outputs (configure-flags '())
+ #:allow-other-keys)
+ (let* ((prefix (assoc-ref outputs "out"))
+ (flags `(,(string-append "--prefix=" prefix)
+ ,@configure-flags)))
+ (format #t "build directory: ~s~%" (getcwd))
+ (format #t "configure flags: ~s~%" flags)
+ (zero? (apply system* "./configure" flags)))))
+ (add-after 'configure 'clean-local-references
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
+ ;; Prevent build directory from leaking into compiled code
+ (((getcwd)) out)
+ ;; Scrub timestamp for reproducibility
+ ((".*Libraries compiled on.*") ""))
+ #t)))
+ (add-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")))
+ (let ((out (assoc-ref outputs "out")))
(substitute* (map (lambda (file)
(string-append out "/lib/petsc/conf/" file))
- '("petscvariables" "PETScConfig.cmake"))
+ '("petscvariables"))
(((getcwd)) out))
;; Make compiler references point to the store
(substitute* (string-append out "/lib/petsc/conf/petscvariables")
- (("= g(cc|\\+\\+|fortran)" _ suffix)
- (string-append "= " fortran "/bin/g" suffix)))
+ (("= (gcc|g\\+\\+|gfortran)" _ compiler)
+ (string-append "= " (which compiler))))
;; PETSc installs some build logs, which aren't necessary.
(for-each (lambda (file)
(let ((f (string-append out "/lib/petsc/conf/" file)))
(delete-file f))))
'("configure.log" "make.log" "gmake.log"
"test.log" "error.log" "RDict.db"
+ "PETScBuildInternal.cmake"
;; Once installed, should uninstall with Guix
- "uninstall.py"))))
- %standard-phases)))))
+ "uninstall.py"))
+ #t))))))
(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
(define-public slepc
(package
(name "slepc")
- (version "3.6.2")
+ (version "3.7.1")
(source
(origin
(method url-fetch)
(uri (string-append "http://slepc.upv.es/download/download.php?"
"filename=slepc-" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1pv5iqz2kc8sj49zsabyz4arnfpana8mjrhq31vzgk16xldk3d1a"))))
+ "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)))
(assoc-ref %build-inputs "arpack") "/lib"))
#:phases
(modify-phases %standard-phases
- (replace
- 'configure
+ (replace 'configure
;; configure is a python script, so we can't run it with bash.
(lambda* (#:key inputs outputs (configure-flags '())
#:allow-other-keys)
(setenv "SLEPC_DIR" (getcwd))
(setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
(zero? (apply system* "./configure" flags)))))
- (add-after
- 'install 'delete-doc
+ (add-after 'install 'delete-doc
;; TODO: SLEPc installs HTML documentation alongside headers in
;; $out/include. We'd like to move them to share/doc, but delete
;; them for now, as they are incomplete and installing the complete
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")))
(for-each delete-file (find-files out "\\.html$")))))
- (add-after
- 'install 'clean-install
+ (add-after 'install 'clean-install
;; Clean up unnecessary build logs from installation.
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(sha256
(base32
"1820jfp3mbl7n85765v5mp6p0gzqpgr4d2lrnhwj4gl7cwp5ndah"))
- (patches (list (search-patch "mumps-build-parallelism.patch")))))
+ (patches (search-patches "mumps-build-parallelism.patch"))))
(build-system gnu-build-system)
(inputs
`(("fortran" ,gfortran)
(inputs
(alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
+(define-public r-pracma
+ (package
+ (name "r-pracma")
+ (version "1.8.8")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "pracma" version))
+ (sha256
+ (base32 "0ans9l5rrb7a38gyi4qx4258sd5r5668vyrk02yzjpg9k3h8l165"))))
+ (build-system r-build-system)
+ (home-page "http://cran.r-project.org/web/packages/pracma")
+ (synopsis "Practical numerical math functions")
+ (description "This package provides functions for numerical analysis and
+linear algebra, numerical optimization, differential equations, plus some
+special functions. It uses Matlab function names where appropriate to simplify
+porting.")
+ (license license:gpl3+)))
+
(define-public superlu
(package
(name "superlu")
- (version "4.3")
+ (version "5.2.1")
(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)
+ (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8"))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Replace the non-free implementation of MC64 with a stub adapted
+ ;; from Debian
+ '(begin
+ (use-modules (ice-9 regex)
+ (ice-9 rdelim))
+ (call-with-output-file "SRC/mc64ad.c"
+ (lambda (port)
+ (display "
+#include <stdio.h>
+#include <stdlib.h>
+void mc64id_(int *a) {
+ fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
+ abort ();
+}
+void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
+ int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
+ fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\");
+ abort ();
+}\n" port)))
+ ;; Remove the corresponding license verbiage. MC64 license follows
+ ;; a "------" line separator.
+ (with-atomic-file-replacement "License.txt"
+ (let ((rx (make-regexp "-{8}")))
+ (lambda (in out)
+ (let loop ()
+ (let ((line (read-line in 'concat)))
+ (unless (regexp-exec rx line)
+ (display line out)
+ (loop)))))))))))
+ (build-system cmake-build-system)
(native-inputs
`(("tcsh" ,tcsh)))
(inputs
- `(("lapack" ,lapack)
+ `(("blas" ,openblas)
("gfortran" ,gfortran)))
(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)))))
+ `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas
+ "-DTPL_BLAS_LIBRARIES=openblas"
+ "-DBUILD_SHARED_LIBS:BOOL=YES"
+ "-DCMAKE_INSTALL_LIBDIR=lib")))
(home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/")
(synopsis "Supernodal direct solver for sparse linear systems")
(description
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)))
+ (license (list license:bsd-3
+ license:gpl2+ ;EXAMPLE/*fgmr.c
+ (license:fsf-free "file://SRC/colamd.h")))))
(define-public superlu-dist
(package
"superlu_dist_" version ".tar.gz"))
(sha256
(base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj"))
- (patches (list (search-patch "superlu-dist-scotchmetis.patch")))))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Replace the non-free implementation of MC64 with a stub
+ '(begin
+ (use-modules (ice-9 regex)
+ (ice-9 rdelim))
+ (call-with-output-file "SRC/mc64ad.c"
+ (lambda (port)
+ (display "
+#include <stdio.h>
+#include <stdlib.h>
+void mc64id_(int *a) {
+ fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
+ abort ();
+}
+void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
+ int *h, int *i, int *j, int *k, double *l, int *m, int *n) {
+ fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\");
+ abort ();
+}\n" port)))
+ (delete-file "SRC/mc64ad.f.bak")
+ (substitute* "SRC/util.c" ;adjust default algorithm
+ (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
+ "RowPerm = NOROWPERM"))))
+ (patches (search-patches "superlu-dist-scotchmetis.patch"))))
(build-system gnu-build-system)
(native-inputs
`(("tcsh" ,tcsh)))
"scotch_" version ".tar.gz"))
(sha256
(base32 "1ir088mvrqggyqdkx9qfynmiaffqbyih5qfl5mga2nrlm1qlsgzm"))
- (patches (list (search-patch "scotch-test-threading.patch")
- (search-patch "pt-scotch-build-parallelism.patch")))))
+ (patches (search-patches "scotch-test-threading.patch"
+ "pt-scotch-build-parallelism.patch"))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)
(sha256
(base32
"0x1rk659sn3cq0n5c90848ilzr1gb1wf0072fl6jhkdq00qgh2s0"))
- (patches (list (search-patch "maxima-defsystem-mkdir.patch")))))
+ (patches (search-patches "maxima-defsystem-mkdir.patch"))))
(build-system gnu-build-system)
(inputs
`(("gcl" ,gcl)
(define-public wxmaxima
(package
(name "wxmaxima")
- (version "15.04.0")
+ (version "16.04.2")
(source
(origin
(method url-fetch)
version "/" name "-" version ".tar.gz"))
(sha256
(base32
- "1fm47ah4aw5qdjqhkz67w5fwhy8yfffa5z896crp0d3hk2bh4180"))))
+ "1fpqzk1921isiqrpgpf433ldq41924qs9sy99fl1zn5661b2l73n"))))
(build-system gnu-build-system)
(inputs
`(("wxwidgets" ,wxwidgets)
- ("maxima" ,maxima)))
+ ("maxima" ,maxima)
+ ;; Runtime support.
+ ("adwaita-icon-theme" ,adwaita-icon-theme)
+ ("gtk+" ,gtk+)
+ ("shared-mime-info" ,shared-mime-info)))
(arguments
`(#:phases (modify-phases %standard-phases
(add-after
"/bin/wxmaxima")
`("PATH" ":" prefix
(,(string-append (assoc-ref inputs "maxima")
- "/bin"))))
+ "/bin")))
+ ;; For GtkFileChooserDialog.
+ `("GSETTINGS_SCHEMA_DIR" =
+ (,(string-append (assoc-ref inputs "gtk+")
+ "/share/glib-2.0/schemas")))
+ `("XDG_DATA_DIRS" ":" prefix
+ (;; Needed by gdk-pixbuf to know supported icon formats.
+ ,(string-append
+ (assoc-ref inputs "shared-mime-info") "/share")
+ ;; The default icon theme of GTK+.
+ ,(string-append
+ (assoc-ref inputs "adwaita-icon-theme") "/share"))))
#t)))))
(home-page "https://andrejv.github.io/wxmaxima/")
(synopsis "Graphical user interface for the Maxima computer algebra system")
(define-public armadillo
(package
(name "armadillo")
- (version "6.400.3")
+ (version "6.700.7")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/arma/armadillo-"
version ".tar.gz"))
(sha256
(base32
- "0bsgrmldlx77w5x26n3axj1hg6iw6csyw0dwl1flrbdwl51f9701"))))
+ "0xbidcxrvbq33xf7iysg2nic2ai9a043psl33kiv6ifkk7p8hcra"))))
(build-system cmake-build-system)
(arguments `(#:tests? #f)) ;no test target
(inputs
(define-public armadillo-for-rcpparmadillo
(package (inherit armadillo)
- (version "6.200.2")
+ (version "6.700.6")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/arma/armadillo-"
version ".tar.gz"))
(sha256
(base32
- "1f69rlqhnf2wv8khyn2a8vi6gx1i72qgfy8b9b760ssk85dcl763"))))))
+ "1cdpjxb0fz5f28y5qrqgpw53s7qi8s2v3al9lfdldqxngb21vpx8"))))))
(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)))
+ ;; When switching download sites, muparser re-issued a 2.2.5 release with a
+ ;; different hash. In order to make `guix package --upgrade` work correctly,
+ ;; we set a Guix packaging revision.
+ ;; When the next version of muparser is released, we can remove
+ ;; UPSTREAM-VERSION and REVISION and use the plain VERSION.
+ (let ((upstream-version "2.2.5")
+ (revision "2"))
+ (package
+ (name "muparser")
+ (version (string-append upstream-version "-" revision))
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/beltoforion/muparser/archive/v"
+ upstream-version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6"))))
+ (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
(define-public openlibm
(package
(name "openlibm")
- (version "0.4.1")
+ (version "0.5.1")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0cwqqqlblj3kzp9aq1wnpfs1fl0qd1wp1xzm5shb09w06i4rh9nn"))))
+ "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
(define-public openspecfun
(package
(name "openspecfun")
- (version "0.4")
+ (version "0.5.2")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0nsa3jjmlhcqkw5ba5ypbn3n0c8b6lc22zzlxnmxkxi9shhdx65z"))))
+ "1y5b2h6f2k72536kym3vzy3li3bhpd23x463g7hdmjdi3cncavz1"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
(version "3.10.2")
(source (origin
(method url-fetch)
- (uri (string-append "mirror://sourceforge/math-atlas/atlas"
- version ".tar.bz2"))
+ (uri (string-append "mirror://sourceforge/math-atlas/Stable/"
+ version "/atlas" version ".tar.bz2"))
(sha256
(base32
"0bqh4bdnjdyww4mcpg6kn0x7338mfqbdgysn97dzrwwb26di7ars"))))
,(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
+ (modify-phases %standard-phases
+ (add-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" ".*")))))
+ (add-after 'check 'check-pt
+ (lambda _ (zero? (system* "make" "ptcheck"))))
+ ;; Fix files required to run configure.
+ (add-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)))))))
+ "sh"))))
+ ;; Fix /bin/sh in generated make files.
+ (add-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'.
+ (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))))))))
(synopsis "Automatically Tuned Linear Algebra Software")
(description
"ATLAS is an automatically tuned linear algebra software library
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:
+done in the BIOS, or, on GNU/Linux, with the following command:
-cpufreq-selector -g performance -c 0
-...
-cpufreq-selector -g performance -c N-1
+@example
+# cpupower --governor performance
+@end example
-where N is the number of cores of your CPU. Failure to do so will result in a
-library with poor performance.")
+Failure to do so will result in a library with poor performance.")
(license license:bsd-3)))
(define-public glm
(source
(origin
(method url-fetch)
- (uri (string-append "mirror://sourceforge/ogl-math/glm-"
- version ".zip"))
+ (uri (string-append "mirror://sourceforge/ogl-math/glm-" version
+ "/glm-" version ".zip"))
(sha256
(base32
"1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l"))))
;; 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=.*$") "PLATFORM=ux64\n")))))
+ (("^PLATFORM=.*$") "PLATFORM=ux64\n")
+
+ ;; The check for 'isnan' as it is written fails with
+ ;; "non-floating-point argument in call to function
+ ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro
+ ;; definition, which in turn leads to bad things. Fix the feature
+ ;; test.
+ (("isnan\\(0\\)") "isnan(0.)")))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no check target
(delete 'configure)
(replace 'build
(lambda _
- (with-directory-excursion "lpsolve55"
- (system* "bash" "ccc"))
- (with-directory-excursion "lp_solve"
- (system* "bash" "ccc"))
- #t))
+ (and (with-directory-excursion "lpsolve55"
+ (zero? (system* "bash" "ccc")))
+ (with-directory-excursion "lp_solve"
+ (zero? (system* "bash" "ccc"))))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(define-public dealii
(package
(name "dealii")
- (version "8.2.1")
+ (version "8.4.1")
(source
(origin
(method url-fetch)
"download/v" version "/dealii-" version ".tar.gz"))
(sha256
(base32
- "185jych0gdnpkjwxni7pd0dda149492zwq2457xdjg76bzj78mnp"))
- (patches (list (search-patch "dealii-p4est-interface.patch")))
+ "1bdksvvyp1rj37df1ndh8j3x9nzpc3sazw8nd0hzvnlw0qnyk800"))
(modules '((guix build utils)))
(snippet
;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
;; ("python2-numpy" ,python2-numpy) ; only required for the tests
("zlib" ,zlib)))
(arguments
- `(#:tests? #f)) ; The test data are downloaded from the Internet.
+ `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file
+ ;; taken 46 MiB unstripped, and 6 MiB stripped.
+ #:strip-directories '("lib" "lib64" "libexec"
+ "bin" "sbin" "share/flann/octave")
+
+ ;; Save 12 MiB by not installing .a files. Passing
+ ;; '-DBUILD_STATIC_LIBS=OFF' has no effect.
+ #:phases (modify-phases %standard-phases
+ (add-after 'install 'remove-static-libraries
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (lib (string-append out "/lib")))
+ (for-each delete-file
+ (find-files lib "\\.a$"))
+ #t))))
+
+ #:tests? #f)) ; The test data are downloaded from the Internet.
(home-page "http://www.cs.ubc.ca/research/flann/")
(synopsis "Library for approximate nearest neighbors computation")
(description "FLANN is a library for performing fast approximate
(source
(origin
(method url-fetch)
- (uri
- (string-append
- "mirror://sourceforge/w-calc/wcalc-" version ".tar.bz2"))
+ (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
+ "wcalc-" version ".tar.bz2"))
(sha256
(base32
"1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
(version "3.6")
(source (origin
(method url-fetch)
- (uri (string-append "mirror://sourceforge/xaos/xaos-"
- version ".tar.gz"))
+ (uri (string-append "mirror://sourceforge/xaos/XaoS/" version
+ "/xaos-" version ".tar.gz"))
(sha256
(base32
"15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
set.")
(home-page "http://www.gnu.org/software/xaos/")
(license license:gpl2+)))
+
+(define-public hypre
+ (package
+ (name "hypre")
+ (version "2.11.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/LLNL/hypre/archive/"
+ "v" version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Remove use of __DATE__ and __TIME__ for reproducibility;
+ ;; substitute the tarball creation time.
+ (substitute* "src/utilities/HYPRE_utilities.h"
+ (("Date Compiled: .*$")
+ "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
+ #t))))
+ (build-system gnu-build-system)
+ (outputs '("out" ;6.1 MiB of headers and libraries
+ "doc")) ;4.8 MiB of documentation
+ (native-inputs
+ `(("doc++" ,doc++)
+ ("netpbm" ,netpbm)
+ ("texlive" ,texlive) ;full package required for fonts
+ ("ghostscript" ,ghostscript)))
+ (inputs
+ `(("blas" ,openblas)
+ ("lapack" ,lapack)))
+ (arguments
+ `(#:modules ((srfi srfi-1)
+ ,@%gnu-build-system-modules)
+ #:configure-flags '("--enable-shared"
+ "--disable-fortran"
+ "--without-MPI"
+ "--with-openmp"
+ "--with-fei"
+ "--with-lapack"
+ "--with-blas")
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'chdir-src
+ (lambda _ (chdir "src")))
+ (replace 'configure
+ (lambda* (#:key build target configure-flags
+ #:allow-other-keys #:rest args)
+ (let* ((configure (assoc-ref %standard-phases 'configure)))
+ (apply configure
+ (append args
+ (list #:configure-flags
+ (cons (string-append
+ "--host=" (or target build))
+ configure-flags)))))))
+ (add-after 'build 'build-docs
+ (lambda _
+ (zero? (system* "make" "-Cdocs" "pdf" "html"))))
+ (replace 'check
+ (lambda _
+ (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
+ (setenv "PATH" (string-append "." ":" (getenv "PATH")))
+ (and (system* "make" "check" "CHECKRUN=")
+ (fold (lambda (filename result)
+ (and result
+ (let ((size (stat:size (stat filename))))
+ (when (not (zero? size))
+ (format #t "~a size ~d; error indication~%"
+ filename size))
+ (zero? size))))
+ #t
+ (find-files "test" ".*\\.err$")))))
+ (add-after 'install 'install-docs
+ (lambda* (#:key outputs #:allow-other-keys)
+ ;; Custom install because docs/Makefile doesn't honor ${docdir}.
+ (let* ((doc (assoc-ref outputs "doc"))
+ (docdir (string-append doc "/share/doc/hypre-" ,version)))
+ (mkdir-p docdir)
+ (with-directory-excursion "docs"
+ (for-each (lambda (base)
+ (install-file (string-append base ".pdf") docdir)
+ (copy-recursively base docdir)) ;html docs
+ '("HYPRE_usr_manual"
+ "HYPRE_ref_manual")))
+ #t))))))
+ (home-page "http://www.llnl.gov/casc/hypre/")
+ (synopsis "Library of solvers and preconditioners for linear equations")
+ (description
+ "HYPRE is a software library of high performance preconditioners and
+solvers for the solution of large, sparse linear systems of equations. It
+features multigrid solvers for both structured and unstructured grid
+problems.")
+ (license license:lgpl2.1)))
+
+(define-public hypre-openmpi
+ (package (inherit hypre)
+ (name "hypre-openmpi")
+ (inputs
+ `(("mpi" ,openmpi)
+ ,@(package-inputs hypre)))
+ (arguments
+ (substitute-keyword-arguments (package-arguments hypre)
+ ((#:configure-flags flags)
+ ``("--with-MPI"
+ ,@(delete "--without-MPI" ,flags)))))
+ (synopsis "Parallel solvers and preconditioners for linear equations")
+ (description
+ "HYPRE is a software library of high performance preconditioners and
+solvers for the solution of large, sparse linear systems of equations on
+parallel computers. It features parallel multigrid solvers for both
+structured and unstructured grid problems.")))
+
+(define-public matio
+ (package
+ (name "matio")
+ (version "1.5.6")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/matio/matio/" version "/"
+ "matio-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("zlib" ,zlib)
+ ("hdf5" ,hdf5)))
+ (home-page "http://matio.sourceforge.net/")
+ (synopsis "Library for reading and writing MAT files")
+ (description "Matio is a library for reading and writing MAT files. It
+supports compressed MAT files, as well as newer (version 7.3) MAT files.")
+ (license license:bsd-2)))
+
+(define-public libhilbert
+ (package
+ (name "libhilbert")
+ (version "0.2-1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://web.cs.dal.ca/~chamilto/hilbert/"
+ "libhilbert-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0v48x8405dj95gjn2saja4bzhw86d6zl6d3dg8h7dzac2qr97s34"))))
+ (build-system gnu-build-system)
+ (home-page "http://web.cs.dal.ca/~chamilto/hilbert")
+ (synopsis "Hilbert indices for multidimensional data")
+ (description "The libhilbert library can efficiently calculate Hilbert
+curves and order-preserving representations of Hilbert curve indices that use
+the same amount of space as the original point representation. This is useful
+when using the Gilbert curve as a space filling curve through a
+high-dimensional space where not all demensions have the same cardinality.")
+ (license license:lgpl2.1+)))
HCoop / jackhill / guix / guix.git / blobdiff