;;; Copyright © 2016, 2017, 2018 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 © 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>
;;;
;;; This file is part of GNU Guix.
;;;
(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 "1.1.5")
+ (version "3.1.0")
+ (home-page "https://github.com/google/double-conversion")
(source (origin
- (method url-fetch)
- (uri (string-append
- "https://github.com/floitsch/double-conversion/archive/v"
- version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference (url home-page) (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0cnr8xhyjfxijay8ymkqcph3672wp2lj23qhdmr3m4kia5kpdf83"))))
+ "123rb2p4snqagrybw66vnapchqdwn2rfpr1wcq0ya9gwbyl7xccx"))))
(build-system cmake-build-system)
(arguments
'(#:test-target "test"
#:configure-flags '("-DBUILD_SHARED_LIBS=ON"
"-DBUILD_TESTING=ON")))
- (home-page "https://github.com/floitsch/double-conversion")
(synopsis "Conversion routines for IEEE doubles")
(description
"The double-conversion library provides binary-decimal and decimal-binary
(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="
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 "2.1.8")
(source (origin
(method url-fetch)
(uri (cran-uri "pracma" version))
(sha256
- (base32 "1ygm81i7mqvh229dp9935djjyb120p3bqvaf4k572sa4q63fzjhc"))))
+ (base32 "0m8ladhrfyxwybblkcdgg4xv1mk5kibmwarpj2k0c2y34zzcix4z"))))
(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)))
"/" dir)))
'("lib" "include"))
#t))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup)
(replace 'check
(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")
;; "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
'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 openblas
(package
(name "openblas")
- (version "0.3.0")
+ (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
- "14a9vyvp2k5zpd0axbnqk0d3khc1v3cck10nb5fj7d2sgn8490ky"))))
+ "0cvlixnpc3cdvvn3f30phfvsgnqljqix6wn72ps9rj7xdhvw06jg"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
#:phases
(modify-phases %standard-phases
(delete 'configure)
- ;; Conditionally apply a patch on i686 to avoid rebuilding
- ;; all architectures. FIXME: This should be moved to the
- ;; (source (patches ...)) field in the next rebuild cycle.
- ,@(if (string-prefix? "i686" (or (%current-target-system)
- (%current-system)))
- `((add-after 'unpack 'fix-tests
- (lambda* (#:key inputs #:allow-other-keys)
- (invoke "patch" "-p1"
- "--input" (assoc-ref inputs "i686-fix-tests.patch")))))
- '())
(add-before 'build 'set-extralib
(lambda* (#:key inputs #:allow-other-keys)
;; Get libgfortran found when building in utest.
`(("fortran-lib" ,gfortran "lib")))
(native-inputs
`(("cunit" ,cunit)
- ,@(if (string-prefix? "i686" (or (%current-target-system)
- (%current-system)))
- `(("i686-fix-tests.patch"
- ,(search-patch "openblas-fix-tests-i686.patch")))
- '())
("fortran" ,gfortran)
("perl" ,perl)))
(home-page "http://www.openblas.net/")
"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 "4.8.1")
+ (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"))))
+ "1vr57bwx40sd5riijyrhy70i2wnv9xrdihf6y5zdz56yq88rl48f"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags
"/lib/python2.7/site-packages"))
#: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?
(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")
+ (version "1.1.2")
(source (origin
(method url-fetch)
(uri (string-append "http://cubicle.lri.fr/cubicle-"
version ".tar.gz"))
(sha256
(base32
- "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h"))))
+ "10kk80jdmpdvql88sdjsh7vqzlpaphd8vip2lp47aarxjkwjlz1q"))))
(build-system gnu-build-system)
(native-inputs
- `(("ocaml" ,ocaml)
+ `(("automake" ,automake)
+ ("ocaml" ,ocaml)
("which" ,(@@ (gnu packages base) which))))
(propagated-inputs
- `(("z3" ,z3)))
+ `(("ocaml-num" ,ocaml-num)
+ ("z3" ,z3)))
(arguments
`(#:configure-flags (list "--with-z3")
+ #:make-flags (list "QUIET=")
#:tests? #f
#:phases
(modify-phases %standard-phases
(add-before 'configure 'configure-for-release
(lambda _
(substitute* "Makefile.in"
- (("SVNREV=") "#SVNREV="))))
+ (("SVNREV=") "#SVNREV="))
+ #t))
(add-before 'configure 'fix-/bin/sh
(lambda _
(substitute* "configure"
- (("/bin/sh") (which "sh")))))
+ (("-/bin/sh") (string-append "-" (which "sh"))))
+ #t))
(add-before 'configure 'fix-smt-z3wrapper.ml
(lambda _
(substitute* "Makefile.in"
- (("\\\\n") "")))))))
+ (("\\\\n") ""))
+ #t))
+ (add-before 'configure 'fix-ocaml-num
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "Makefile.in"
+ (("= \\$\\(FUNCTORYLIB\\)")
+ (string-append "= -I "
+ (assoc-ref inputs "ocaml-num")
+ "/lib/ocaml/site-lib"
+ " $(FUNCTORYLIB)")))
+ #t)))))
(home-page "http://cubicle.lri.fr/")
(synopsis "Model checker for array-based systems")
(description "Cubicle is a model checker for verifying safety properties
(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")))
HCoop / jackhill / guix / guix.git / blobdiff