;;; Copyright © 2014, 2015, 2016, 2017, 2018 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
-;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015, 2016, 2017, 2018 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2018 Kei Kebreau <kkebreau@posteo.net>
-;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2017, 2018, 2019 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
-;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com>
+;;; Copyright © 2017
, 2018 Paul Garlick <pgarlick@tourbillion-technology.com>
;;; Copyright © 2017 Nils Gillmann <ng0@n0.is>
;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com>
;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org>
-;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
+;;; Copyright © 2017
, 2019 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2017 Dave Love <me@fx@gnu.org>
;;; Copyright © 2018 Jan Nieuwenhuizen <janneke@gnu.org>
;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com>
;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com>
;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
+;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
+;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
;;;
;;; This file is part of GNU Guix.
;;;
(define-module (gnu packages maths)
#:use-module (ice-9 regex)
+ #:use-module (ice-9 match)
#:use-module (gnu packages)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix utils)
- #:use-module (guix build utils)
+ #:use-module ((guix build utils) #:select (alist-replace))
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
- #:use-module (guix build-system ocaml)
#:use-module (guix build-system python)
#:use-module (guix build-system r)
#:use-module (guix build-system ruby)
#:use-module (gnu packages algebra)
#:use-module (gnu packages audio)
#:use-module (gnu packages autotools)
+ #:use-module (gnu packages base)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages mpi)
#:use-module (gnu packages multiprecision)
#:use-module (gnu packages netpbm)
- #:use-module (gnu packages ocaml)
#:use-module (gnu packages pcre)
#:use-module (gnu packages popt)
#:use-module (gnu packages perl)
#:use-module (gnu packages pulseaudio)
#:use-module (gnu packages python)
#:use-module (gnu packages python-web)
+ #:use-module (gnu packages python-xyz)
#:use-module (gnu packages qt)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
(define-public coda
(package
(name "coda")
- (version "2.18.3")
+ (version "2.19")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/stcorp/coda/releases/download/"
version "/coda-" version ".tar.gz"))
(sha256
- (base32 "1zlzgcvwmmjm8mw8w4rg2rqy0pjilz7kyyxm0y4p8cbljbbjxxz0"))
+ (base32 "1fbxd2afm7dshd92p10yy8dwbr9gc1h1fmnnnmr7d0c5lnw80245"))
(patches (search-patches "coda-use-system-libs.patch"))
(modules '((guix build utils)))
(snippet
(license (license:non-copyleft "file://COPYING.txt"
"See COPYING in the distribution."))))
+(define-public python-cvxopt
+ (package
+ (name "python-cvxopt")
+ (version "1.2.1")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/cvxopt/cvxopt.git")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "05mnjil9palaa48xafdfh4f5pr4z7aqjr995rwl08qfyxs8y0crf"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'find-libraries
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "CVXOPT_BLAS_LIB" "openblas")
+ (setenv "CVXOPT_BUILD_FFTW" "1")
+ (setenv "CVXOPT_BUILD_GLPK" "1")
+ (setenv "CVXOPT_BUILD_GSL" "1")
+ #t)))))
+ (inputs
+ `(("fftw" ,fftw)
+ ("glpk" ,glpk)
+ ("gsl" ,gsl)
+ ("lapack" ,lapack)
+ ("openblas" ,openblas)
+ ("suitesparse" ,suitesparse)))
+ (home-page "https://www.cvxopt.org")
+ (synopsis "Python library for convex optimization")
+ (description
+ "CVXOPT is a package for convex optimization based on the Python
+programming language. Its main purpose is to make the development of software
+for convex optimization applications straightforward by building on Python’s
+extensive standard library and on the strengths of Python as a high-level
+programming language.")
+ (license license:gpl3+)))
+
+(define-public python2-cvxopt
+ (package-with-python2 python-cvxopt))
+
(define-public units
(package
(name "units")
- (version "2.17")
+ (version "2.18")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/units/units-" version
".tar.gz"))
(sha256 (base32
- "1n2xzpnxfn475zkd8rzs5gg58xszjbr4bdbgvk6hryzimvwwj0qz"))))
+ "0y26kj349i048y4z3xrk90bvciw2j6ds3rka7r7yn3183hirr5b4"))))
(build-system gnu-build-system)
(inputs
`(("readline" ,readline)
(define-public double-conversion
(package
(name "double-conversion")
- (version "3.0.0")
+ (version "3.1.0")
(home-page "https://github.com/google/double-conversion")
(source (origin
- (method url-fetch)
- (uri (string-append home-page "/archive/v" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference (url home-page) (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "059r1czs28ljjd388pn6l3njg1ghbf1cv3q9nkxv3dj2a8siabqm"))))
+ "123rb2p4snqagrybw66vnapchqdwn2rfpr1wcq0ya9gwbyl7xccx"))))
(build-system cmake-build-system)
(arguments
'(#:test-target "test"
numbers.")
(license license:gpl3+)))
-(define-public ocaml-gsl
- (package
- (name "ocaml-gsl")
- (version "1.19.3")
- (source
- (origin
- (method url-fetch)
- (uri
- (string-append
- "https://github.com/mmottl/gsl-ocaml/releases/download/v"
- version"/gsl-ocaml-" version ".tar.gz"))
- (sha256
- (base32
- "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh"))))
- (build-system ocaml-build-system)
- (inputs
- `(("gsl" ,gsl)))
- (home-page "https://mmottl.github.io/gsl-ocaml")
- (synopsis "Bindings to the GNU Scientific Library")
- (description
- "GSL-OCaml is an interface to the @dfn{GNU scientific library} (GSL) for
-the OCaml language.")
- (license license:gpl3+)))
-
-(define-public ocaml4.01-gsl
- (package-with-ocaml4.01 ocaml-gsl))
-
(define-public glpk
(package
(name "glpk")
(define-public cddlib
(package
(name "cddlib")
- (version "0.94h")
+ (version "0.94i")
(source
(origin
(method url-fetch)
(string-delete #\. version) ".tar.gz"))
(sha256
(base32
- "1dasasscwfg793q8fwzgwf64xwj7w62yfvszpr8x8g38jka08vgy"))))
+ "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
(build-system gnu-build-system)
(inputs
`(("gmp" ,gmp)))
(define-public arpack-ng
(package
(name "arpack-ng")
- (version "3.5.0")
+ (version "3.6.3")
(home-page "https://github.com/opencollab/arpack-ng")
- (source
- (origin
- (method url-fetch)
- (uri (string-append home-page "/archive/" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
- (sha256
- (base32
- "0f8jx3fifmj9qdp289zr7r651y1q48k1jya859rqxq62mvis7xsh"))))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference (url home-page) (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y"))))
(build-system gnu-build-system)
- (arguments
- '(#:phases (modify-phases %standard-phases
- (add-after 'unpack 'autoreconf
- (lambda _
- (invoke "autoreconf" "-vfi"))))))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
(arguments
(substitute-keyword-arguments (package-arguments arpack-ng)
((#:configure-flags _ '())
- ''("--enable-mpi"))))
+ ''("--enable-mpi"))
+ ((#:phases phases '%standard-phases)
+ `(modify-phases ,phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
(synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
(define-public lapack
(arguments
`(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
#:phases (modify-phases %standard-phases
- (add-before 'check 'set-test-environment
- (lambda _
- ;; By default, running the test suite would fail because
- ;; 'ssh' could not be found in $PATH. Define this
- ;; variable to placate Open MPI without adding a
- ;; dependency on OpenSSH (the agent isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
- #t)))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(home-page "http://www.netlib.org/scalapack/")
(synopsis "Library for scalable numerical linear algebra")
(description
(define-public gnuplot
(package
(name "gnuplot")
- (version "5.2.2")
+ (version "5.2.4")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
version ".tar.gz"))
(sha256
(base32
- "18diyy7aib9mn098x07g25c7jij1x7wbfpicz0z8gwxx08px45m4"))))
+ "1jvh8xmd2cvrhlsg88kxwh55wkwx31sg50v1n59slfippl0g058m"))))
(build-system gnu-build-system)
(inputs `(("readline" ,readline)
("cairo" ,cairo)
(mkdir-p flib)
(mkdir-p finc)
(mkdir-p fex)
- (rename-file (string-append bin "/h5fc")
- (string-append fbin "/h5fc"))
+ ;; Note: When built with --enable-parallel, the 'h5fc' file
+ ;; doesn't exist, hence this condition.
+ (when (file-exists? (string-append bin "/h5fc"))
+ (rename-file (string-append bin "/h5fc")
+ (string-append fbin "/h5fc")))
(for-each (lambda (file)
(rename-file file
(string-append flib "/" (basename file))))
(license (license:x11-style
"http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
+(define-public hdf5-1.10
+ (package (inherit hdf5)
+ (version "1.10.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/"
+ "hdf5-" (version-major+minor version)
+ "/hdf5-" version "/src/hdf5-"
+ version ".tar.bz2")
+ (string-append "https://support.hdfgroup.org/ftp/HDF5/"
+ "current"
+ (apply string-append
+ (take (string-split version #\.) 2))
+ "/src/hdf5-" version ".tar.bz2")))
+ (sha256
+ (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj"))
+ (patches (list (search-patch "hdf5-config-date.patch")))))))
+
(define-public hdf-java
(package
(name "hdf-java")
`(("mpi" ,openmpi)
,@(package-inputs hdf5)))
(arguments
- (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
- ,@(package-arguments hdf5))
+ (substitute-keyword-arguments (package-arguments hdf5)
+ ((#:configure-flags flags)
+ ``("--enable-parallel" ,@(delete "--enable-cxx" ,flags)))
((#:phases phases)
`(modify-phases ,phases
+ (add-after 'build 'mpi-setup
+ ,%openmpi-setup)
(add-before 'check 'patch-tests
(lambda _
;; OpenMPI's mpirun will exit with non-zero status if it
@end enumerate\n")
(license license:bsd-3)))
-;; For a fully featured Octave, users are strongly recommended also to install
+;; For a fully featured Octave, users are strongly recommended also to install
;; the following packages: less, ghostscript, gnuplot.
-(define-public octave
+(define-public octave-cli
(package
- (name "octave")
- (version "4.4.0")
+ (name "octave-cli")
+ (version "4.4.1")
(source
(origin
(method url-fetch)
version ".tar.lz"))
(sha256
(base32
- "0nm766737gbkq9wqry54a026k3dg7rb1065kngfpwgjz8b544xbp"))))
+ "0jsdgizlv02an2ppfjwk5qf209zpwi3317yb7jvlsjzxnir3lvhy"))))
(build-system gnu-build-system)
(inputs
`(("lapack" ,lapack)
("less" ,less)
("ghostscript" ,ghostscript)
("gnuplot" ,gnuplot)))
+ ;; Octave code uses this variable to detect directories holding multiple CA
+ ;; certificates to verify peers with. This is required for the networking
+ ;; functions that require encryption to work properly.
+ (native-search-paths
+ (list (search-path-specification
+ (variable "CURLOPT_CAPATH")
+ (files '("etc/ssl/certs")))))
(arguments
`(#:configure-flags
(list (string-append "--with-shell="
(modify-phases %standard-phases
(add-after 'configure 'configure-makeinfo
(lambda* (#:key inputs #:allow-other-keys)
- (substitute* "libinterp/corefcn/help.cc"
- (("Vmakeinfo_program = \"makeinfo\"")
- (string-append "Vmakeinfo_program = \""
- (assoc-ref inputs "texinfo")
- "/bin/makeinfo\"")))
+ (substitute* "libinterp/corefcn/help.h"
+ (("\"makeinfo\"")
+ (string-append
+ "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\"")))
#t)))))
(home-page "https://www.gnu.org/software/octave/")
(synopsis "High-level language for numerical computation")
script files.")
(license license:gpl3+)))
-(define-public qtoctave
- (package (inherit octave)
- (name "qtoctave")
+(define-public octave
+ (package (inherit octave-cli)
+ (name "octave")
(source (origin
- (inherit (package-source octave))
- (patches (append (origin-patches (package-source octave))
- (search-patches
- "qtoctave-qt-5.11-fix.patch")))))
+ (inherit (package-source octave-cli))))
(inputs
`(("qscintilla" ,qscintilla)
("qt" ,qtbase)
- ,@(package-inputs octave)))
+ ,@(package-inputs octave-cli)))
(native-inputs
`(("qttools" , qttools) ;for lrelease
("texlive" ,texlive) ;for texi2dvi
- ,@(package-native-inputs octave)))
+ ,@(package-native-inputs octave-cli)))
(arguments
- (substitute-keyword-arguments (package-arguments octave)
+ (substitute-keyword-arguments (package-arguments octave-cli)
((#:phases phases)
`(modify-phases ,phases
(add-before 'configure 'patch-qscintilla-library-name
"qscintilla2_qt5"))
#t))))))))
+(define-public qtoctave
+ (deprecated-package "qtoctave" octave))
+
(define-public opencascade-oce
(package
(name "opencascade-oce")
(define-public petsc
(package
(name "petsc")
- (version "3.8.0")
+ (version "3.10.2")
(source
(origin
(method url-fetch)
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
"petsc-lite-" version ".tar.gz"))
(sha256
- (base32 "1lajbk3c29hnh83v6cbmm3a8wv6bdykh0p70kwrr4vrnizalk88s"))))
+ (base32 "0bl64pydak3rblnjffi482r8bin4xim9sb37ksl2jkcxf0i0irsi"))))
+ (outputs '("out" ;libraries and headers
+ "examples")) ;~30MiB of examples
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)))
#: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"))
+ "--with-superlu=1")
#:make-flags
;; Honor (parallel-job-count) for build. Do not use --with-make-np,
;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
"PETScBuildInternal.cmake"
;; Once installed, should uninstall with Guix
"uninstall.py"))
+ #t)))
+ (add-after 'install 'move-examples
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (examples (assoc-ref outputs "examples"))
+ (exdir (string-append out "/share/petsc/examples"))
+ (exdir' (string-append examples "/share/petsc/examples")))
+ (copy-recursively exdir exdir')
+ (delete-file-recursively exdir)
#t))))))
(home-page "http://www.mcs.anl.gov/petsc")
(synopsis "Library to solve PDEs")
(package (inherit petsc)
(name "petsc-openmpi")
(inputs
- `(("openmpi" ,openmpi)
+ `(("hdf5" ,hdf5-parallel-openmpi)
+ ("hypre" ,hypre-openmpi)
+ ("metis" ,metis)
+ ("mumps" ,mumps-openmpi)
+ ("openmpi" ,openmpi)
+ ("scalapack" ,scalapack)
+ ("scotch" ,pt-scotch32)
,@(package-inputs petsc)))
(arguments
(substitute-keyword-arguments (package-arguments petsc)
((#:configure-flags cf)
- ``("--with-mpiexec=mpirun"
+ ``("--with-hypre=1"
+ "--with-mpiexec=mpirun"
+ "--with-metis=1"
+ "--with-mumps=1"
+ "--with-scalapack=1"
+ "--with-ptscotch=1"
,(string-append "--with-mpi-dir="
(assoc-ref %build-inputs "openmpi"))
- ,@(delete "--with-mpi=0" ,cf)))))
- (synopsis "Library to solve PDEs (with MPI support)")))
+ ,(string-append "--with-hdf5-include="
+ (assoc-ref %build-inputs "hdf5") "/include")
+ ,(string-append "--with-hdf5-lib="
+ (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
+ ,@(delete "--with-mpi=0" ,cf)))
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-before 'configure 'mpi-setup
+ ,%openmpi-setup)))))
+ (synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
(define-public petsc-complex-openmpi
(package (inherit petsc-complex)
,@(delete "--with-mpi=0" ,cf)))))
(synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
+(define-public python-petsc4py
+ (package
+ (name "python-petsc4py")
+ (version "3.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "petsc4py" version))
+ (sha256
+ (base32
+ "0ch3g6dsvxl7qi984fcssv7cxfbif4bw04gkvxl2l1b8wrmvrm25"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'build 'pre-build
+ (lambda _
+ ;; Define path to PETSc installation.
+ (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
+ #t))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
+ (inputs
+ `(("petsc" ,petsc-openmpi)
+ ("python-numpy" ,python-numpy)))
+ (home-page "https://bitbucket.org/petsc/petsc4py/")
+ (synopsis "Python bindings for PETSc")
+ (description "PETSc, the Portable, Extensible Toolkit for
+Scientific Computation, is a suite of data structures and routines for
+the scalable (parallel) solution of scientific applications modeled by
+partial differential equations. It employs the MPI standard for all
+message-passing communication. @code{petsc4py} provides Python
+bindings to almost all functions of PETSc.")
+ (license license:bsd-3)))
(define-public python-kiwisolver
(package
(define-public slepc
(package
(name "slepc")
- (version "3.8.2")
+ (version "3.10.1")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "04zd48p43rnvg68p6cp28zll0px5whglc5v0sc3s6vdj1v920z8y"))))
+ "188j1a133q91h8pivpnzwcf78kz8dvz2nzf6ndnjygdbqb48fizn"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)))
(substitute-keyword-arguments (package-arguments slepc)
((#:phases phases '%standard-phases)
`(modify-phases ,phases
- (add-before 'check 'set-test-environment
- (lambda _
- ;; By default, running the test suite would fail because 'ssh'
- ;; could not be found in $PATH. Define this variable to
- ;; placate Open MPI without adding a dependency on OpenSSH (the
- ;; agent isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
- #t))))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
(inputs
`(("mpi" ,openmpi)
("arpack" ,arpack-ng-openmpi)
,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
(synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
+(define-public python-slepc4py
+ (package
+ (name "python-slepc4py")
+ (version "3.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "slepc4py" version))
+ (sha256
+ (base32
+ "0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j"))))
+ (build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'build 'pre-build
+ (lambda _
+ ;; Define path to PETSc installation.
+ (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc"))
+ ;; Define path to SLEPc installation.
+ (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc"))
+ #t))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
+ (inputs
+ `(("python-numpy" ,python-numpy)
+ ("python-petsc4py" ,python-petsc4py)
+ ("slepc" ,slepc-openmpi)))
+ (home-page "https://bitbucket.org/slepc/slepc4py/")
+ (synopsis "Python bindings for SLEPc")
+ (description "SLEPc, the Scalable Library for Eigenvalue Problem
+Computations, is based on PETSc, the Portable, Extensible Toolkit for
+Scientific Computation. It employs the MPI standard for all
+message-passing communication. @code{slepc4py} provides Python
+bindings to almost all functions of SLEPc.")
+ (license license:bsd-3)))
+
(define-public mumps
(package
(name "mumps")
(substitute-keyword-arguments (package-arguments mumps)
((#:phases phases)
`(modify-phases ,phases
- (add-before 'check 'set-test-environment
- (lambda _
- ;; By default, running the test suite would fail because 'ssh'
- ;; could not be found in $PATH. Define this variable to
- ;; placate Open MPI without adding a dependency on OpenSSH (the
- ;; agent isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
- #t))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)
(replace 'check
(lambda _
((assoc-ref ,phases 'check)
(define-public r-pracma
(package
(name "r-pracma")
- (version "2.1.4")
+ (version "2.2.2")
(source (origin
(method url-fetch)
(uri (cran-uri "pracma" version))
(sha256
- (base32 "1ygm81i7mqvh229dp9935djjyb120p3bqvaf4k572sa4q63fzjhc"))))
+ (base32 "18zhni05gwnxbphl6bmjjxmsgg5wwnnkwlb4g971cqyw3dsd83ki"))))
(build-system r-build-system)
- (propagated-inputs
- `(("r-quadprog" ,r-quadprog)))
- (home-page "https://cran.r-project.org/web/packages/pracma")
+ (home-page "https://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
(lambda _
(substitute* "spec/parser_spec.rb"
(("\\\\\"")
- "\"")))))))
+ "\""))
+ #t)))))
(native-inputs
`(("bundler" ,bundler)
("ruby-rspec" ,ruby-rspec)))
(define-public superlu-dist
(package
(name "superlu-dist")
- (version "5.3.0")
+ (version "6.1.0")
(source
(origin
(method url-fetch)
(uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
"superlu_dist_" version ".tar.gz"))
(sha256
- (base32 "0ja5ihqivkda1wd58y4lmzvmwssm9g91f70c5q0fzwhng6580h6y"))
+ (base32 "0pqgcgh1yxhfzs99fas3mggajzd5wca3nbyp878rziy74gfk03dl"))
(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_dist.c"
(lambda (port)
(display "
abort ();
}\n" port)))
(substitute* "SRC/util.c" ;adjust default algorithm
- (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
- "RowPerm = NOROWPERM"))
+ (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
+ ;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
+ ;; general (i.e. non-square) processor-grid support.
+ "RowPerm = NOROWPERM;"))
#t))
- (patches (search-patches "superlu-dist-scotchmetis.patch"))))
- (build-system gnu-build-system)
+ (patches (search-patches "superlu-dist-scotchmetis.patch"
+ "superlu-dist-awpm-grid.patch"))))
+ (build-system cmake-build-system)
(native-inputs
`(("tcsh" ,tcsh)))
(inputs
- `(("gfortran" ,gfortran)))
+ `(("gfortran" ,gfortran)
+ ("blas" ,openblas)
+ ("lapack" ,lapack)
+ ("combblas" ,combinatorial-blas)))
(propagated-inputs
- `(("openmpi" ,openmpi) ;headers include MPI heades
- ("lapack" ,lapack) ;required to link with output library
- ("pt-scotch" ,pt-scotch))) ;same
+ `(("mpi" ,openmpi) ;headers include MPI heades
+ ("parmetis" ,pt-scotch32 "metis")
+ ("pt-scotch" ,pt-scotch32)))
(arguments
- `(#:parallel-build? #f ;race conditions using ar
+ `(#:parallel-tests? #f ;tests use MPI and OpenMP
+ #:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
+ "-DTPL_ENABLE_COMBBLASLIB=YES"
+ "-DTPL_BLAS_LIBRARIES=-lopenblas"
+ "-DTPL_LAPACK_LIBRARIES=-llapack"
+ (string-append "-DTPL_PARMETIS_LIBRARIES="
+ (string-join
+ '("ptscotchparmetis" "ptscotch" "ptscotcherr"
+ "scotchmetis" "scotch" "scotcherr")
+ ";"))
+ (string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
+ (assoc-ref %build-inputs "parmetis")
+ "/include")
+ "-DTPL_ENABLE_COMBBLASLIB=ON"
+ (string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
+ (assoc-ref %build-inputs "combblas")
+ "/include/CombBLAS;"
+ (assoc-ref %build-inputs "combblas")
+ "/include/BipartiteMatchings")
+ "-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
#:phases
(modify-phases %standard-phases
- (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"))))
- #t))
- (add-after 'unpack 'remove-broken-symlinks
- (lambda _
- (for-each delete-file
- (find-files "MAKE_INC" "\\.#make\\..*"))
- #t))
- (add-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"))
- #t))
- (replace 'check
+ (add-before 'configure 'set-c++-standard
(lambda _
- ;; By default, running the test suite would fail because 'ssh'
- ;; could not be found in $PATH. Define this variable to placate
- ;; Open MPI without adding a dependency on OpenSSH (the agent
- ;; isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
- (with-directory-excursion "EXAMPLE"
- (invoke "mpirun" "-n" "2"
- "./pddrive" "-r" "1" "-c" "2" "g20.rua")
- (invoke "mpirun" "-n" "2"
- "./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))
- #t))
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- ;; Library is placed in lib during the build phase. Copy over
- ;; headers to include.
- (let* ((out (assoc-ref outputs "out"))
- (incdir (string-append out "/include")))
- (for-each (lambda (file)
- (let ((base (basename file)))
- (format #t "installing `~a' to `~a'~%"
- base incdir)
- (copy-file file
- (string-append incdir "/" base))))
- (find-files "SRC" ".*\\.h$")))
- #t)))))
+ (substitute* "CMakeLists.txt"
+ ;; AWPM headers require C++14
+ (("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)
+ (add-before 'check 'omp-setup
+ (lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
(home-page (package-home-page superlu))
(synopsis "Parallel supernodal direct solver")
(description
(define-public scotch
(package
(name "scotch")
- (version "6.0.5a")
+ (version "6.0.6")
(source
(origin
(method url-fetch)
(uri (string-append "https://gforge.inria.fr/frs/download.php/"
"latestfile/298/scotch_" version ".tar.gz"))
(sha256
- (base32 "0vsmgjz8qv80di3ljmc7hbdsizxxxwy2b9rgd2fl1mdc6dgbj8av"))
- (patches (search-patches "scotch-test-threading.patch"
- "scotch-build-parallelism.patch"
- "scotch-graph-induce-type-64.patch"
- "scotch-graph-diam-64.patch"))))
+ (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8"))
+ (patches (search-patches "scotch-build-parallelism.patch"
+ "scotch-integer-declarations.patch"))))
(build-system gnu-build-system)
(inputs
`(("zlib" ,zlib)
("flex" ,flex)
("bison" ,bison)))
+ (outputs '("out" "metis"))
(arguments
- `(#:phases
+ `(#:make-flags (list (string-append "prefix=" %output))
+ #:phases
(modify-phases %standard-phases
(add-after
'unpack 'chdir-to-src
'("COMMON_FILE_COMPRESS_GZ"
"COMMON_PTHREAD"
"COMMON_RANDOM_FIXED_SEED"
- "INTSIZE64" ;use 'long' instead of 'int'
+ "INTSIZE64" ;use 'int64_t'
;; Prevents symbolc clashes with libesmumps
"SCOTCH_RENAME"
;; XXX: Causes invalid frees in superlu-dist tests
;; "SCOTCH_PTHREAD_NUMBER=2"
"restrict=__restrict"))))
#t))
- (add-after
- 'build 'build-esmumps
+ (add-after 'build 'build-esmumps
(lambda _
- ;; By default, running the test suite would fail because 'ssh'
- ;; could not be found in $PATH. Define this variable to placate
- ;; Open MPI without adding a dependency on OpenSSH (the agent
- ;; isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
-
(invoke "make"
(format #f "-j~a" (parallel-job-count))
"esmumps")))
- (replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (mkdir out)
- (invoke "make"
- (string-append "prefix=" out)
- "install")
- ;; esmumps files are not installed with the above
- (for-each (lambda (f)
- (copy-file f (string-append out "/include/" f)))
- (find-files "../include" ".*esmumps.h$"))
- (for-each (lambda (f)
- (copy-file f (string-append out "/lib/" f)))
- (find-files "../lib" "^lib.*esmumps.*"))
- #t))))))
+ (add-before 'install 'make-install-dirs
+ (lambda* (#:key outputs #:allow-other-keys)
+ (mkdir (assoc-ref outputs "out"))))
+ (add-after 'install 'install-metis
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "metis")))
+ (mkdir out)
+ ;; metis files are not installed with 'make install'
+ (for-each (lambda (f)
+ (install-file f (string-append out "/include")))
+ (find-files "../include/" ".*metis\\.h"))
+ (for-each (lambda (f)
+ (install-file f (string-append out "/lib")))
+ (find-files "../lib/" ".*metis\\..*"))
+ #t))))))
(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
(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"))))))))
+ (invoke "make" (format #f "-j~a" (parallel-job-count))
+ "ptscotch" "ptesmumps")
+
+ ;; Install the serial metis compatibility library
+ (invoke "make" "-C" "libscotchmetis" "install")))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)
+ (replace 'check
+ (lambda _
+ (invoke "make" "ptcheck")))))))
(synopsis "Programs and libraries for graph algorithms (with MPI)")))
(define-public pt-scotch32
`(modify-phases ,scotch32-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")))))
+ (invoke "make" (format #f "-j~a" (parallel-job-count))
+ "ptscotch" "ptesmumps")
+ ;; Install the serial metis compatibility library
+ (invoke "make" "-C" "libscotchmetis" "install")))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)
(replace 'check
(lambda _
- (zero? (system* "make" "ptcheck"))))))))
+ (invoke "make" "ptcheck")))))))
(synopsis
"Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
(assoc-ref %build-inputs "lapack")
" -llapack"))
#:phases (modify-phases %standard-phases
- (add-before 'check 'set-test-environment
- (lambda _
- ;; By default, running the test suite would fail because
- ;; 'ssh' could not be found in $PATH. Define this
- ;; variable to placate Open MPI without adding a
- ;; dependency on OpenSSH (the agent isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
- #t)))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
(home-page "http://www.p4est.org")
(synopsis "Adaptive mesh refinement on forests of octrees")
(description
(define-public maxima
(package
(name "maxima")
- (version "5.41.0")
+ (version "5.42.1")
(source
(origin
(method url-fetch)
version "-source/" name "-" version ".tar.gz"))
(sha256
(base32
- "0x0n81z0s4pl8nwpf7ivlsbvsdphm9w42250g7qdkizl0132by6s"))
+ "1ka0xf70a55ndgmyrq7p5xxbd78pq7bfkqhgxsivaqdw6gn5lmcg"))
(patches (search-patches "maxima-defsystem-mkdir.patch"))))
(build-system gnu-build-system)
(inputs
(lambda _
(chmod "src/maxima" #o555)
#t))
+ (replace 'check
+ (lambda _
+ ;; This is derived from the testing code in the "debian/rules" file
+ ;; of Debian's Maxima package.
+ ;; If Maxima can successfully run this, the binary to be installed
+ ;; should be fine.
+ (zero?
+ (system
+ (string-append "./maxima-local "
+ "--lisp=gcl "
+ "--batch-string=\"run_testsuite();\" "
+ "| grep -q \"No unexpected errors found\"")))))
;; 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.
(define-public wxmaxima
(package
(name "wxmaxima")
- (version "18.02.0")
+ (version "18.11.4")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://github.com/andrejv/" name "/archive"
- "/Version-" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/wxMaxima-developers/wxmaxima.git")
+ (commit (string-append "Version-" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "03kr2rgfp4hcf3is8m8d8f9hj660c3xgrc50vrrfpixx4syh6wvj"))
- (patches
- (search-patches "wxmaxima-do-not-use-old-gnuplot-parameters.patch"))))
+ "1sz8n9v23q442l7yjj67pjh0dk78rl4cbcc3j8m1bm88anlfxl9r"))))
(build-system cmake-build-system)
(native-inputs
`(("gettext" ,gettext-minimal)))
(define-public armadillo
(package
(name "armadillo")
- (version "7.800.2")
+ (version "9.100.5")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/arma/armadillo-"
version ".tar.xz"))
(sha256
(base32
- "1qqzy7dp891j9v7062mv1599hdwr97vqzrd3j2fl8c3gmc00dmzg"))))
+ "1ka1vd9fcmvp12qkcm4888dkfqwnalvv00x04wy29f3nx3qwczby"))))
(build-system cmake-build-system)
- (arguments `(#:tests? #f)) ;no test target
+ (arguments `(#:tests? #f)) ; no test target
(inputs
`(("openblas" ,openblas)
("lapack" ,lapack)
(define-public openblas
(package
(name "openblas")
- (version "0.3.2")
+ (version "0.3.3")
(source
(origin
(method url-fetch)
- (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
- version))
+ (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20"
+ version "%20version.tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0b20km2jv7m6qiylrlvhq2vnmkmilb633mr8rhqmgbn1wqrp58jq"))))
+ "0cvlixnpc3cdvvn3f30phfvsgnqljqix6wn72ps9rj7xdhvw06jg"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
"OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
(license license:bsd-3)))
+(define-public openblas-ilp64
+ (package (inherit openblas)
+ (name "openblas-ilp64")
+ (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux"))
+ (arguments
+ (substitute-keyword-arguments (package-arguments openblas)
+ ((#:make-flags flags '())
+ `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64")
+ ,flags))))
+ (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)")
+ (license license:bsd-3)))
+
(define* (make-blis implementation #:optional substitutable?)
"Return a BLIS package with the given IMPLEMENTATION (see config/ in the
source tree for a list of implementations.)
(define-public glm
(package
(name "glm")
- (version "0.9.9.0")
+ (version "0.9.9.3")
(source
(origin
(method url-fetch)
version "/glm-" version ".zip"))
(sha256
(base32
- "0ihjadp2sb8w312a276skfjsljm3y41bjscbxf79wn23gi00giz1"))))
+ "0yqk5r3qh60d4r2iab5q7wq0fryn8p3pz6s28y1i7amqj1aqavj9"))))
(build-system cmake-build-system)
(native-inputs
`(("unzip" ,unzip)))
`(("unzip" ,unzip)))
(inputs
`(("hdf5" ,hdf5)
- ("octave" ,octave)
+ ("octave" ,octave-cli)
("python" ,python-2) ; print syntax
;; ("python2-numpy" ,python2-numpy) ; only required for the tests
("zlib" ,zlib)))
(define-public hypre
(package
(name "hypre")
- (version "2.11.0")
+ (version "2.14.0")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/LLNL/hypre/archive/"
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m"))
+ "0v515i73bvaz378h5465b1dy9v2gf924zy2q94cpq4qqarawvkqh"))
(modules '((guix build utils)))
(snippet
'(begin
;; substitute the tarball creation time.
(substitute* "src/utilities/HYPRE_utilities.h"
(("Date Compiled: .*$")
- "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n"))
+ "Date Compiled: Apr 11 2018 16:24:59 +0000\"\n"))
#t))))
(build-system gnu-build-system)
(outputs '("out" ;6.1 MiB of headers and libraries
`(("doc++" ,doc++)
("netpbm" ,netpbm)
("perl" ,perl) ;needed to run 'ppmquant' during tests
- ("texlive" ,texlive) ;full package required for fonts
+ ("texlive" ,(texlive-union (list texlive-generic-xypic
+ texlive-fonts-xypic
+ texlive-latex-hyperref
+ texlive-latex-oberdiek
+ texlive-generic-ifxetex
+ texlive-latex-url
+ texlive-bibtex)))
("ghostscript" ,ghostscript)))
(inputs
`(("blas" ,openblas)
"--with-blas")
#:phases
(modify-phases %standard-phases
+ (add-before 'build 'set-HOME
+ (lambda _
+ ;; FIXME: texlive-union does not find the built
+ ;; metafonts, so it tries to generate them in HOME.
+ (setenv "HOME" "/tmp")
+ #t))
(add-before 'configure 'chdir-src
(lambda _ (chdir "src")))
(replace 'configure
configure-flags)))))))
(add-after 'build 'build-docs
(lambda _
- (zero? (system* "make" "-Cdocs" "pdf" "html"))))
+ (invoke "make" "-Cdocs" "pdf" "html")))
(replace 'check
(lambda _
(setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib"))
,@(delete "--without-MPI" ,flags)))
((#:phases phases)
`(modify-phases ,phases
- (add-before 'check 'set-test-environment
- (lambda _
- ;; By default, running the test suite would fail because 'ssh'
- ;; could not be found in $PATH. Define this variable to
- ;; placate Open MPI without adding a dependency on OpenSSH (the
- ;; agent isn't used anyway.)
- (setenv "OMPI_MCA_plm_rsh_agent" (which "cat"))
- #t))))))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
(synopsis "Parallel solvers and preconditioners for linear equations")
(description
"HYPRE is a software library of high performance preconditioners and
(define-public z3
(package
(name "z3")
- (version "4.5.0")
+ (version "4.8.4")
+ (home-page "https://github.com/Z3Prover/z3")
(source (origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/Z3Prover/z3/archive/z3-"
- version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference (url home-page)
+ (commit (string-append "z3-" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf"))))
- (build-system cmake-build-system)
+ "014igqm5vwswz0yhz0cdxsj3a6dh7i79hvhgc3jmmmz3z0xm1gyn"))))
+ (build-system gnu-build-system)
(arguments
- `(#:configure-flags
- (list "-DBUILD_PYTHON_BINDINGS=true"
- "-DINSTALL_PYTHON_BINDINGS=true"
- (string-append "-DCMAKE_INSTALL_PYTHON_PKG_DIR="
- %output
- "/lib/python2.7/site-packages"))
- #:phases
+ `(#:phases
(modify-phases %standard-phases
+ (add-after 'unpack 'fix-compatability
+ ;; Versions after 4.8.3 have immintrin.h IFDEFed for Windows only.
+ (lambda _
+ (substitute* "src/util/mpz.cpp"
+ (("#include <immintrin.h>") ""))
+ #t))
(add-before 'configure 'bootstrap
(lambda _
(zero?
- (system* "python" "contrib/cmake/bootstrap.py" "create"))))
+ (system* "python" "scripts/mk_make.py"))))
+ ;; work around gnu-build-system's setting --enable-fast-install
+ ;; (z3's `configure' is a wrapper around the above python file,
+ ;; which fails when passed --enable-fast-install)
+ (replace 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (invoke "./configure"
+ (string-append "--prefix=" (assoc-ref outputs "out")))))
+ (add-after 'configure 'change-directory
+ (lambda _
+ (chdir "build")
+ #t))
(add-before 'check 'make-test-z3
(lambda _
;; Build the test suite executable.
;; Run all the tests that don't require arguments.
(zero? (system* "./test-z3" "/a")))))))
(native-inputs
- `(("python" ,python-2)))
+ `(("which" ,which)
+ ("python" ,python-wrapper)))
(synopsis "Theorem prover")
(description "Z3 is a theorem prover and @dfn{satisfiability modulo
theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
- (home-page "https://github.com/Z3Prover/z3")
(license license:expat)))
-(define-public cubicle
- (package
- (name "cubicle")
- (version "1.1.1")
- (source (origin
- (method url-fetch)
- (uri (string-append "http://cubicle.lri.fr/cubicle-"
- version ".tar.gz"))
- (sha256
- (base32
- "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h"))))
- (build-system gnu-build-system)
- (native-inputs
- `(("ocaml" ,ocaml)
- ("which" ,(@@ (gnu packages base) which))))
- (propagated-inputs
- `(("z3" ,z3)))
- (arguments
- `(#:configure-flags (list "--with-z3")
- #:tests? #f
- #:phases
- (modify-phases %standard-phases
- (add-before 'configure 'configure-for-release
- (lambda _
- (substitute* "Makefile.in"
- (("SVNREV=") "#SVNREV="))))
- (add-before 'configure 'fix-/bin/sh
- (lambda _
- (substitute* "configure"
- (("/bin/sh") (which "sh")))))
- (add-before 'configure 'fix-smt-z3wrapper.ml
- (lambda _
- (substitute* "Makefile.in"
- (("\\\\n") "")))))))
- (home-page "http://cubicle.lri.fr/")
- (synopsis "Model checker for array-based systems")
- (description "Cubicle is a model checker for verifying safety properties
-of array-based systems. This is a syntactically restricted class of
-parametrized transition systems with states represented as arrays indexed by
-an arbitrary number of processes. Cache coherence protocols and mutual
-exclusion algorithms are typical examples of such systems.")
- (license license:asl2.0)))
-
(define-public elemental
(package
(name "elemental")
(version "0.87.7")
(source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/elemental/Elemental/"
- "archive/v" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/elemental/Elemental.git")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
(sha256
(base32
- "1nfp82w22pi8x8fg9sc37z8kf84dqi1dhxp8bbk7571y4aygvv3v"))))
+ "1687xpjjzig27y2pnqv7hv09smpijyfdpz7qjgmcxf4shfajlfkc"))))
(build-system cmake-build-system)
(home-page "http://libelemental.org")
(native-inputs
"-DCMAKE_INSTALL_LIBDIR=lib"
"-DGFORTRAN_LIB=gfortran")
#:phases (modify-phases %standard-phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)
(add-before 'check 'setup-tests
(lambda _
;; Parallelism is done at the MPI layer.
;; Tests are installed, with no easy configuration
;; switch to prevent this, so delete them.
(delete-file-recursively
- (string-append (assoc-ref outputs "out") "/bin"))
+ (string-append (assoc-ref outputs "out") "/bin"))
#t)))))
(synopsis "Dense and sparse-direct linear algebra and optimization")
(description "Elemental is a modern C++ library for distributed-memory
state-space exploration and generation, and tools to optimise and analyse
specifications. Also, state spaces can be manipulated, visualised and
analysed.")
- (home-page "http://mcrl2.org")
+ (home-page "https://mcrl2.org")
(license license:boost1.0)))
(define-public r-subplex
be fed to @command{tcalc} through the command line.")
(home-page "https://sites.google.com/site/mohammedisam2000/tcalc")
(license license:gpl3+)))
+
+(define-public sundials
+ (package
+ (name "sundials")
+ (version "3.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://computation.llnl.gov/projects/sundials/download/"
+ "sundials-" version ".tar.gz"))
+ (sha256
+ (base32
+ "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2"))))
+ (build-system cmake-build-system)
+ (native-inputs
+ `(("python" ,python-2))) ;for tests; syntax incompatible with python 3
+ (inputs
+ `(("fortran" ,gfortran) ;for fcmix
+ ("blas" ,openblas)
+ ("suitesparse" ,suitesparse))) ;TODO: Add hypre
+ (arguments
+ `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
+ "-DEXAMPLES_ENABLE_CXX:BOOL=ON"
+ "-DEXAMPLES_ENABLE_F77:BOOL=ON"
+ "-DEXAMPLES_ENABLE_F90:BOOL=ON"
+ "-DEXAMPLES_INSTALL:BOOL=OFF"
+
+ "-DFCMIX_ENABLE:BOOL=ON"
+
+ "-DKLU_ENABLE:BOOL=ON"
+ ,(string-append "-DKLU_INCLUDE_DIR="
+ (assoc-ref %build-inputs "suitesparse")
+ "/include")
+ ,(string-append "-DKLU_LIBRARY_DIR="
+ (assoc-ref %build-inputs "suitesparse")
+ "/lib"))))
+ (home-page "https://computation.llnl.gov/projects/sundials")
+ (synopsis "Suite of nonlinear and differential/algebraic equation solvers")
+ (description "SUNDIALS is a family of software packages implemented with
+the goal of providing robust time integrators and nonlinear solvers that can
+easily be incorporated into existing simulation codes.")
+ (license license:bsd-3)))
+
+(define-public sundials-openmpi
+ (package (inherit sundials)
+ (name "sundials-openmpi")
+ (inputs
+ `(("mpi" ,openmpi)
+ ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI
+ ,@(package-inputs sundials)))
+ (arguments
+ (substitute-keyword-arguments (package-arguments sundials)
+ ((#:configure-flags flags '())
+ `(cons* "-DMPI_ENABLE:BOOL=ON"
+ "-DPETSC_ENABLE:BOOL=ON"
+ (string-append "-DPETSC_INCLUDE_DIR="
+ (assoc-ref %build-inputs "petsc")
+ "/include")
+ (string-append "-DPETSC_LIBRARY_DIR="
+ (assoc-ref %build-inputs "petsc")
+ "/lib")
+ ,flags))
+ ((#:phases phases '%standard-phases)
+ `(modify-phases ,phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)))))
+ (synopsis "SUNDIALS with OpenMPI support")))
+
+(define-public combinatorial-blas
+ (package
+ (name "combinatorial-blas")
+ (version "1.6.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/"
+ "CombBLAS_beta_"
+ (match (string-split version #\.)
+ ((major minor patch)
+ (string-append major minor "_" patch))) ;e.g. "16_2"
+ ".tgz"))
+ (sha256
+ (base32
+ "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
+ (patches (search-patches "combinatorial-blas-awpm.patch"
+ "combinatorial-blas-io-fix.patch"))))
+ (build-system cmake-build-system)
+ (inputs
+ `(("mpi" ,openmpi)
+ ("test-data" ,(origin
+ (method url-fetch)
+ (uri (string-append "https://people.eecs.berkeley.edu/~aydin/"
+ "CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
+ (sha256
+ (base32
+ "01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
+ (arguments
+ `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
+ "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
+ #:parallel-tests? #f ;tests use 'mpiexec -n4'
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)
+ (add-before 'check 'test-setup
+ (lambda* (#:key inputs #:allow-other-keys)
+ (setenv "OMP_NUM_THREADS" "2")
+ (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
+ (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/")
+ (synopsis "Linear algebra primitives for graph analytics")
+ (description "The Combinatorial BLAS (CombBLAS) is an extensible
+distributed-memory parallel graph library offering a small but powerful set of
+linear algebra primitives specifically targeting graph analytics.")
+ (license (list
+ license:gpl2+ ;include/psort/(funnel|sort)*.h
+ license:x11 ;usort and psort
+ license:bsd-3)))) ;CombBLAS and MersenneTwister.h
HCoop / jackhill / guix / guix.git / blobdiff