;;; Copyright © 2013, 2014, 2015, 2016, 2019, 2020 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
-;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Eric Bavier <bavier@posteo.net>
+;;; Copyright © 2014-2022 Eric Bavier <bavier@posteo.net>
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
-;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015–2021 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2015, 2018 Mark H Weaver <mhw@netris.org>
;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
;;; Copyright © 2016 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016, 2018, 2020, 2021 Kei Kebreau <kkebreau@posteo.net>
-;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016-2022 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be>
;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
;;; Copyright © 2018 Eric Brown <brown@fastmail.com>
;;; Copyright © 2018, 2021 Julien Lepiller <julien@lepiller.eu>
;;; Copyright © 2018 Amin Bandali <bandali@gnu.org>
-;;; Copyright © 2019, 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2019, 2021, 2022 Nicolas Goaziou <mail@nicolasgoaziou.fr>
;;; Copyright © 2019 Steve Sprang <scs@stevesprang.com>
;;; Copyright © 2019 Robert Smith <robertsmith@posteo.net>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
-;;; Copyright © 2020, 2021 Felix Gruber <felgru@posteo.net>
+;;; Copyright © 2020–2022 Felix Gruber <felgru@posteo.net>
;;; Copyright © 2020 R Veera Kumar <vkor@vkten.in>
;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com>
;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz>
;;; Copyright © 2021 Paul A. Patience <paul@apatience.com>
;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru>
;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me>
+;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
+ #:use-module (guix gexp)
#:use-module (guix utils)
#:use-module ((guix build utils) #:select (alist-replace))
#:use-module (guix build-system cmake)
#:use-module (guix build-system glib-or-gtk)
#:use-module (guix build-system gnu)
+ #:use-module (guix build-system meson)
#:use-module (guix build-system ocaml)
+ #:use-module (guix build-system perl)
#:use-module (guix build-system python)
#: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 bash)
#:use-module (gnu packages bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages coq)
#:use-module (gnu packages curl)
#:use-module (gnu packages cyrus-sasl)
+ #:use-module (gnu packages datamash)
#:use-module (gnu packages dbm)
#:use-module (gnu packages documentation)
#:use-module (gnu packages elf)
#:use-module (gnu packages m4)
#:use-module (gnu packages mpi)
#:use-module (gnu packages multiprecision)
+ #:use-module (gnu packages ncurses)
#:use-module (gnu packages netpbm)
#:use-module (gnu packages ocaml)
#:use-module (gnu packages onc-rpc)
+ #:use-module (gnu packages parallel)
#:use-module (gnu packages pcre)
#:use-module (gnu packages popt)
#:use-module (gnu packages perl)
#:use-module (gnu packages ruby)
#:use-module (gnu packages tbb)
#:use-module (gnu packages scheme)
+ #:use-module (gnu packages serialization)
#:use-module (gnu packages shells)
#:use-module (gnu packages sphinx)
#:use-module (gnu packages tcl)
(sha256 (base32
"1q1887ryqdr9sn0522hc7p16kqwlxxyz5dkmma8ar2nxplhgll7q"))))
(build-system gnu-build-system)
- (inputs `(("gtk+" ,gtk+)
- ("libxml2" ,libxml2)))
- (native-inputs `(("pkg-config" ,pkg-config)))
+ (inputs (list gtk+ libxml2))
+ (native-inputs (list pkg-config))
+ (arguments
+ `(#:configure-flags '("CFLAGS=-O2 -g -fcommon")))
(synopsis "Natural deduction first-order logic interface")
(description "Aris is a program for performing logical proofs. It supports
propositional and predicate logic, as well as Boolean algebra and
(license license:gpl3+)
(home-page "https://www.gnu.org/software/aris/")))
+(define-public bitwise
+ (package
+ (name "bitwise")
+ (version "0.42")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/mellowcandle/bitwise"
+ "/releases/download/v" version
+ "/bitwise-v" version ".tar.gz"))
+ (sha256
+ (base32 "1lniw4bsb5qs5ybf018qllf95pzixb1q3lvybzl4k3xz8zpkrm6k"))))
+ (build-system gnu-build-system)
+ (inputs
+ (list ncurses readline))
+ (native-inputs
+ (list cunit pkg-config))
+ (synopsis "Terminal based bit manipulator in ncurses")
+ (description "Bitwise is a multi base interactive calculator supporting
+dynamic base conversion and bit manipulation. It's a handy tool for low level
+hackers, kernel developers and device drivers developers.
+
+Some of the features include:
+@itemize
+@item Interactive ncurses interface.
+@item Command line calculator supporting all bitwise operations.
+@item Individual bit manipulator.
+@item Bitwise operations such as NOT, OR, AND, XOR, and shifts.
+@end itemize")
+ (license license:gpl3+)
+ (home-page "https://github.com/mellowcandle/bitwise/")))
+
(define-public c-graph
(package
(name "c-graph")
"092412jzxy6wdvpk96pfj499hpmaww8xllavbvlqspfpr7ips9id"))))
(build-system gnu-build-system)
(inputs
- `(("fortran" ,gfortran)))
+ (list gfortran))
(synopsis "Visualizing and demonstrating convolution")
(description
"GNU C-Graph is a tool for demonstrating the theory of convolution.
(arguments
'(#:configure-flags '("--with-hdf4" "--with-hdf5" "--enable-python"
"LIBS= -lz -lpcre -lexpat")))
- (synopsis "A common interface to various earth observation data formats")
+ (synopsis "Common interface to various earth observation data formats")
(description
"The Common Data Access toolbox (CODA) provides a set of interfaces for
reading remote sensing data from earth observation data files. It consists of
(define-public python-cvxopt
(package
(name "python-cvxopt")
- (version "1.2.3")
+ (version "1.2.7")
(source (origin
(method git-fetch)
(uri (git-reference
(file-name (git-file-name name version))
(sha256
(base32
- "1kiy2m62xgs2d5id6dnnwy4vap85cd70p7pgkb9nh23qf9xnak7b"))))
+ "114z34wwx1bsv4q6xj9p5q99dffgnj9s4i4arx10g191xq9q8i5y"))))
(build-system python-build-system)
(arguments
`(#:phases
(setenv "CVXOPT_BUILD_GSL" "1")
#t)))))
(inputs
- `(("fftw" ,fftw)
- ("glpk" ,glpk)
- ("gsl" ,gsl)
- ("lapack" ,lapack)
- ("openblas" ,openblas)
- ("suitesparse" ,suitesparse)))
+ (list fftw
+ glpk
+ gsl
+ lapack
+ openblas
+ suitesparse))
(home-page "https://www.cvxopt.org")
(synopsis "Python library for convex optimization")
(description
programming language.")
(license license:gpl3+)))
-(define-public python2-cvxopt
- (package-with-python2 python-cvxopt))
-
(define-public units
(package
(name "units")
(base32
"194pzs1mlsj4ww6v37qq3961h5hckm5h805cv0r14xj3g9wfx2sk"))))
(build-system gnu-build-system)
- (inputs `(("tcl" ,tcl))) ;for 'tclsh'
+ (inputs (list tcl)) ;for 'tclsh'
(synopsis "Local search for universal constants and scientific values")
(description
"GNU Dionysus is a convenient system for quickly retrieving the values of
(substitute* "linalg/test.c"
((".*gsl_test\\(test_LU_decomp.*") "\n")
((".*gsl_test\\(test_LUc_decomp.*") "\n")
+ ((".*gsl_test\\(test_QR_decomp_r.*") "\n")
((".*gsl_test\\(test_cholesky_decomp.*") "\n")
+ ((".*gsl_test\\(test_pcholesky_solve.*") "\n")
((".*gsl_test\\(test_COD_lssolve2.*") "\n"))
(substitute* "spmatrix/test.c"
((".*test_all.*") "\n")
((".*test_float.*") "\n")
- ((".*test_complex.*") "\n"))))))
+ ((".*test_complex.*") "\n"))
+
+ ;; XXX: These tests abort with:
+ ;; gsl: cholesky.c:645: ERROR: matrix is not positive definite
+ (substitute* '("multifit_nlinear/test.c"
+ "multilarge_nlinear/test.c")
+ (("gsl_ieee_env_setup.*" all)
+ (string-append "exit (77);\n" all)))))))
(else '()))))))
(home-page "https://www.gnu.org/software/gsl/")
functions in total. Subject areas covered by the library include:
differential equations, linear algebra, Fast Fourier Transforms and random
numbers.")
+
+ ;; Linear algebra routines should benefit from SIMD optimizations.
+ (properties `((tunable? . #t)))
+
(license license:gpl3+)))
+;; TODO: Merge back into the gsl package as a separate output.
+(define-public gsl-static
+ (package/inherit gsl
+ (name "gsl-static")
+ (arguments
+ `(,@(package-arguments gsl)
+ #:configure-flags (list "--disable-shared")
+ #:make-flags (list "CFLAGS=-fPIC")))))
+
(define-public sleef
(package
(name "sleef")
(for-each make-file-writable (find-files "."))
#t)))))
(inputs
- `(("fftw" ,fftw)
- ("gmp" ,gmp)
- ("mpfr" ,mpfr)
- ("openssl" ,openssl)))
+ (list fftw gmp mpfr openssl))
(home-page "https://sleef.org/")
(synopsis "SIMD library for evaluating elementary functions and DFT")
(description
"05bgxidxj8d9xdp82niy7cy36w181cxq7p8vc3y2ixshpgp1642a"))))
(build-system gnu-build-system)
(inputs
- `(("gmp" ,gmp)))
+ (list gmp))
(arguments
`(#:configure-flags '("--with-gmp"
"--disable-static")))
(base32 "0rj92x6p9m3la5gasjbj7sa569im527ffmka5y2sv1amgd3fflrh"))))
(build-system gnu-build-system)
(native-inputs
- `(("which" ,(@ (gnu packages base) which)))) ; for the tests
+ (list (@ (gnu packages base) which))) ; for the tests
(inputs
- `(("glpk" ,glpk)
- ("gmp" ,gmp)))
+ (list glpk gmp))
(home-page "http://www.4ti2.de/")
(synopsis "Mathematical tool suite for problems on linear spaces")
(description
"00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
(build-system gnu-build-system)
(inputs
- `(("gmp" ,gmp)))
+ (list 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
"05kq3hzam31dlmkccv3v358r478kpvx76mw37ka12c6ypwv5dsnk"))))
(build-system gnu-build-system)
(inputs
- `(("gmp" ,gmp)))
+ (list gmp))
(arguments
`(#:tests? #f ; no check phase
#:make-flags `("CC=gcc"
(base32 "1ic2q7kvxpqmgxlishygvx8d00i4wn51vkq4fyac44ahhf6c3kwd"))))
(build-system cmake-build-system)
(native-inputs
- `(("perl" ,perl)))
+ (list perl))
(home-page "https://jugit.fz-juelich.de/mlz/libcerf")
(synopsis "Library for complex error functions")
(description
"1aq0qc1y27iw9grhgnyji3290wwfznsrk3sg6ynqpxwjdda53h4m"))))
(build-system gnu-build-system)
(inputs
- `(("lrslib" ,lrslib)))
+ (list lrslib))
(arguments
`(#:tests? #f ; no check phase
#:phases
"0l7as5z6xvbxly8alam9s4kws70952qq35a6vkljzayi4b9gbklx"))))
(build-system gnu-build-system)
(native-inputs
- `(("autoconf" ,autoconf)
- ("automake" ,automake)
- ("libtool" ,libtool)
- ("pkg-config" ,pkg-config)))
+ (list autoconf automake libtool pkg-config))
(inputs
- `(("eigen" ,eigen)
- ("lapack" ,lapack)
- ("fortran" ,gfortran)))
+ (list eigen lapack gfortran))
(synopsis "Fortran subroutines for solving eigenvalue problems")
(description
"ARPACK-NG is a collection of Fortran77 subroutines designed to solve
"0nnap9q1mv14g57dl3vkvxrdr10k5w7zzyxs6rgxhia8q8mphgqb"))))
(build-system cmake-build-system)
(arguments
- `(#:phases
+ `(#:configure-flags '("-DCMAKE_C_FLAGS=-fcommon -O2")
+ #:phases
(modify-phases %standard-phases
;; These tests use a lot of stack variables and segfault without
;; lifting resource limits.
(add-after 'unpack 'disable-broken-tests
(lambda _
(substitute* "TESTING/CMakeLists.txt"
- (("add_lapack_test.* xeigtstz\\)") ""))
- #t))
+ (("add_lapack_test.* xeigtstz\\)") ""))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
"\\.h$")))
(copy-recursively (string-append "../clapack-"
,version "-CMAKE/INCLUDE")
- (string-append out "/include"))
- #t))))))
+ (string-append out "/include"))))))))
(home-page "https://www.netlib.org/clapack/")
(synopsis "Numerical linear algebra library for C")
(description
(define-public scalapack
(package
(name "scalapack")
- (version "2.0.2")
+ (version "2.1.0")
(source
(origin
(method url-fetch)
version ".tgz"))
(sha256
(base32
- "0p1r61ss1fq0bs8ynnx7xq4wwsdvs32ljvwjnx6yxr8gd6pawx0c"))
- (patches (search-patches "scalapack-blacs-mpi-deprecations.patch"))))
+ "19i0h9vdc3zsy58r6fy1vs2kz2l7amifkz0cf926j90xz1n23nb1"))
+ (patches (search-patches "scalapack-gcc-10-compilation.patch"))))
(build-system cmake-build-system)
(inputs
`(("mpi" ,openmpi)
`(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES")
#:phases (modify-phases %standard-phases
(add-before 'check 'mpi-setup
- ,%openmpi-setup))))
+ ,%openmpi-setup)
+ (add-after 'unpack 'skip-faulty-test
+ (lambda _
+ ;; FIXME: Skip these two tests that fail to complete for
+ ;; unknown reasons:
+ ;; <https://github.com/Reference-ScaLAPACK/scalapack/issues/43>.
+ (substitute* "TESTING/CMakeLists.txt"
+ (("^add_test\\(x[sd]hseqr.*" all)
+ (string-append "# " all "\n"))))))))
(home-page "http://www.netlib.org/scalapack/")
(synopsis "Library for scalable numerical linear algebra")
(description
(license (license:non-copyleft "file://LICENSE"
"See LICENSE in the distribution."))))
+(define-public feedgnuplot
+ (package
+ (name "feedgnuplot")
+ (version "1.60")
+ (home-page "https://github.com/dkogan/feedgnuplot")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url home-page)
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0403hwlian2s431m36qdzcczhvfjvh7128m64hmmwbbrgh0n7md7"))))
+ (build-system perl-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'check 'adjust-tests
+ (lambda _
+ (substitute* "t/plots.t"
+ ;; XXX: The vnlog tests uses 'echo' with escaped strings,
+ ;; but does not enable escape interpretation.
+ (("echo -n ")
+ "echo -ne "))))
+ (add-after 'install 'install-documentation
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (doc (string-append out "/share/doc/feedgnuplot")))
+ (mkdir-p doc)
+ (invoke "pod2html" "--title=feedgnuplot" "bin/feedgnuplot"
+ "--outfile" (string-append doc "/feedgnuplot.html")))))
+ (add-after 'install 'wrap
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (gnuplot (search-input-file inputs "/bin/gnuplot"))
+ ;; XXX: We need List::MoreUtils as well as its supporting
+ ;; (propagated) modules; for now just refer to labels.
+ (modules '("perl-list-moreutils" "perl-exporter-tiny"))
+ (PERL5LIB (string-join
+ (map (lambda (input)
+ (string-append (assoc-ref inputs input)
+ "/lib/perl5/site_perl"))
+ modules)
+ ":")))
+ (wrap-program (string-append out "/bin/feedgnuplot")
+ `("PERL5LIB" ":" suffix (,PERL5LIB))
+ `("PATH" ":" suffix (,(dirname gnuplot))))))))))
+ (inputs
+ (list gnuplot perl-list-moreutils vnlog))
+ (native-inputs
+ ;; For tests.
+ (list perl-ipc-run perl-string-shellquote))
+ (synopsis "Pipe-oriented plotting tool")
+ (description
+ "@command{feedgnuplot} is a tool to plot realtime and stored data
+from the command line, using @command{gnuplot}. It can read data from
+a pipe or file, make a variety of transformations, and render the result
+in the terminal or with an external viewer.")
+ (license license:gpl1+))) ;any version
+
(define-public gnuplot
(package
(name "gnuplot")
(sha256
(base32 "1fp7rbhjmz2w63r72kicf8lfszzimz2csfx868fracw167hpaz75"))))
(build-system gnu-build-system)
- (inputs `(("readline" ,readline)
- ("cairo" ,cairo)
- ("pango" ,pango)
- ("gd" ,gd)
- ("lua" ,lua)))
+ (inputs (list readline cairo pango gd lua))
(native-inputs
`(("pkg-config" ,pkg-config)
("texlive" ,texlive-tiny)))
(sha256
(base32 "11wqmd443b4nksdbzp1msdws3av948nmwq1xz80w6hka3ss2aigd"))))
(native-inputs
- `(("fortran" ,gfortran)))
+ (list gfortran))
(build-system gnu-build-system)
(synopsis "General Cartographic Transformation Package (GCTP)")
(description
"hdf4-tirpc.patch"))))
(build-system gnu-build-system)
(native-inputs
- `(("gfortran" ,gfortran)
- ("bison" ,bison)
- ("flex" ,flex)))
+ (list gfortran bison flex))
(inputs
`(("zlib" ,zlib)
("libjpeg" ,libjpeg-turbo)
(arguments
`(#:parallel-tests? #f
#:configure-flags (list "--enable-shared"
+ "FCFLAGS=-fallow-argument-mismatch"
+ "FFLAGS=-fallow-argument-mismatch"
(string-append "CPPFLAGS=-I"
(assoc-ref %build-inputs "libtirpc")
"/include/tirpc"))
;; .so-files. We truncate the hashes to avoid
;; unnecessary store references to those compilers:
(substitute* "libhdf4.settings"
- (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
+ (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash)
(string-append prefix (string-take hash 10) "...")))
#t))
(add-after 'install 'provide-absolute-libjpeg-reference
(patches (search-patches "hdf5-config-date.patch"))))
(build-system gnu-build-system)
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(native-inputs
- `(("gfortran" ,gfortran)
- ("perl" ,perl))) ;part of the test machinery needs Perl
+ (list gfortran perl)) ;part of the test machinery needs Perl
(outputs '("out" ; core library
"fortran")) ; fortran interface
(arguments
(define-public hdf5-1.12
(package
(inherit hdf5-1.8)
- (version "1.12.0")
+ (version "1.12.1")
(source
(origin
(method url-fetch)
(take (string-split version #\.) 2))
"/src/hdf5-" version ".tar.bz2")))
(sha256
- (base32 "0qazfslkqbmzg495jafpvqp0khws3jkxa0z7rph9qvhacil6544p"))
+ (base32 "074g3z504xf77ff38igs30i1aqxpm508p7yw78ykva7dncrgbyda"))
(patches (search-patches "hdf5-config-date.patch"))))))
(define-public hdf5
#:make-flags
(list (string-append "HDFLIB=" (assoc-ref %build-inputs "hdf4") "/lib")
(string-append "HDF5LIB=" (assoc-ref %build-inputs "hdf5") "/lib")
- (string-append "ZLIB=" (assoc-ref %build-inputs "zlib") "/lib/libz.so")
+ (string-append "ZLIB=" (search-input-file %build-inputs "/lib/libz.so"))
(string-append "JPEGLIB="
- (assoc-ref %build-inputs "libjpeg") "/lib/libjpeg.so")
+ (search-input-file %build-inputs "/lib/libjpeg.so"))
"LLEXT=so")
#:phases
"hdf/hdf5lib/exceptions/Makefile.in"
"hdf/hdflib/Makefile.in")
(("\\$\\(TOP\\)/lib/slf4j-api-1\\.7\\.5\\.jar")
- (search-input-file inputs "/share/java/slf4j-api.jar")))
+ ;; 'slf4j-api-X.Y.Z.jar' is installed in a Maven-style
+ ;; directory, so use 'find-files' to find it.
+ (car (find-files (assoc-ref inputs "slf4j-api")
+ "^slf4j-api.*\\.jar$"))))
;; Replace outdated config.sub and config.guess:
(with-directory-excursion "config"
(for-each (lambda (file)
(testjars
(append
(map (lambda (i)
- (string-append (assoc-ref inputs i)
- "/share/java/" i ".jar"))
+ (car (find-files (assoc-ref inputs i)
+ (string-append "^" i
+ ".*\\.jar$"))))
'("slf4j-api" "slf4j-simple"))
(list
(car (find-files (assoc-ref inputs "junit") "jar$"))
"hdf-eos2-fortrantests.patch"))))
(build-system gnu-build-system)
(native-inputs
- `(("gfortran" ,gfortran)))
+ (list gfortran))
(inputs
`(("hdf4" ,hdf4-alt) ; assume most HDF-EOS2 users won't use the HDF4 netCDF API
;; XXX: These inputs are really dependencies of hdf4.
"hdf-eos5-fix-szip.patch"
"hdf-eos5-fortrantests.patch"))))
(native-inputs
- `(("gfortran" ,gfortran)))
+ (list gfortran))
(build-system gnu-build-system)
(inputs
- `(("hdf5" ,hdf5-1.8)
- ("zlib" ,zlib)
- ("gctp" ,gctp)))
+ (list hdf5-1.8 zlib gctp))
(arguments
`(#:configure-flags '("--enable-install-include" "--enable-shared"
"CC=h5cc -Df2cFortran" "LIBS=-lgctp")
(("ExternalProject_Add\\(project_blosc") "message("))
#t)))))
(inputs
- `(("c-blosc" ,c-blosc)
- ("hdf5" ,hdf5-1.10)))
+ (list c-blosc hdf5-1.10))
(home-page "https://github.com/Blosc/hdf5-blosc")
(synopsis "Filter for HDF5 using the Blosc compressor")
(description "This is a filter for HDF5 that uses the Blosc compressor; by
(base32
"1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj"))))
(build-system gnu-build-system)
- (inputs `(("hdf5" ,hdf5-1.8))) ;h5cc for tests
+ (inputs (list hdf5-1.8)) ;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
"14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm"))))
(build-system cmake-build-system)
(arguments `(#:tests? #f)) ; Tests require googletest *sources*
- (inputs `(("lapack" ,lapack)
- ("fftw" ,fftw)))
+ (inputs (list lapack fftw))
;; FIXME: Even though the fonts are available dvips complains:
;; "Font cmmi10 not found; characters will be left blank."
(native-inputs
(sha256
(base32
"1a2fpp15a2rl1m50gcvvzd9y6bavl6vjf9zzf63sz5gdmq06yiqf"))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Make sure this variable is defined only once. Failing to do so
+ ;; would break builds of 'netcdf-parallel-openmpi' with a
+ ;; multiple-definition link error with GCC 10.
+ '(substitute* "ncdump/ocprint.c"
+ (("^int ocdebug") "static int ocdebug")))
(patches (search-patches "netcdf-date-time.patch"))))
(build-system gnu-build-system)
(native-inputs
- `(("m4" ,m4)
- ("doxygen" ,doxygen)
- ("graphviz" ,graphviz)))
+ (list m4 doxygen graphviz))
(inputs
`(("hdf4" ,hdf4-alt)
("hdf5" ,hdf5)
;; filenames to avoid unnecessary references to the corresponding
;; store items.
(substitute* "libnetcdf.settings"
- (("(/gnu/store/)([a-Z0-9]*)" all prefix hash)
+ (("(/gnu/store/)([0-9A-Za-z]*)" all prefix hash)
(string-append prefix (string-take hash 10) "...")))
#t)))
"0x4acvfhbsx1q79dkkwrwbgfhm0w5ngnp4zj5kk92s1khihmqfhj"))))
(build-system gnu-build-system)
(arguments
- `(#:parallel-tests? #f))
+ `(#:configure-flags '("FCFLAGS=-fallow-argument-mismatch"
+ "FFLAGS=-fallow-argument-mismatch")
+ #:parallel-tests? #f))
(inputs
- `(("netcdf" ,netcdf)))
+ (list netcdf))
(native-inputs
- `(("gfortran" ,gfortran)))
+ (list gfortran))
(synopsis "Fortran interface for the netCDF library")
(description (package-description netcdf))
(home-page (package-home-page netcdf))
(("libnlopt")
(string-append out "/lib/libnlopt")))
#t))))))
- (inputs `(("guile" ,guile-2.0)))
- (native-inputs `(("pkg-config" ,pkg-config)))
+ (inputs (list guile-2.0))
+ (native-inputs (list 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
after "\n")))
#t))))))
(native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)))
+ (list gfortran pkg-config))
(inputs
;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL.
- `(("lapack" ,lapack))) ;for both libblas and liblapack
+ (list lapack)) ;for both libblas and liblapack
(home-page "https://www.coin-or.org")
(synopsis "Large-scale nonlinear optimizer")
(description
(lambda* (#:key inputs outputs #:allow-other-keys)
(delete-file (string-append
(site-packages inputs outputs)
- "PyNomad-0.0.0-py"
+ "/PyNomad-0.0.0-py"
(python-version (assoc-ref inputs "python"))
".egg-info"))
#t)))))
'(delete-file-recursively "ThirdParty"))))
(build-system gnu-build-system)
(native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)))
+ (list gfortran pkg-config))
(inputs
- `(("openblas" ,openblas)))
+ (list openblas))
(home-page "https://www.coin-or.org")
(synopsis "Branch-and-cut solver")
(description
#t))))
(build-system gnu-build-system)
(native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)))
+ (list gfortran pkg-config))
(inputs
- `(("openblas" ,openblas)))
+ (list openblas))
(home-page "https://www.coin-or.org")
(synopsis "Linear programming solver")
(description
and quadratic objectives using the Simplex algorithm.")
(license license:epl1.0)))
+(define-public gecode
+ (package
+ (name "gecode")
+ (version "6.2.0")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/Gecode/gecode")
+ (commit (string-append "release-" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0b1cq0c810j1xr2x9y9996p894571sdxng5h74py17c6nr8c6dmk"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; delete generated sources
+ (for-each delete-file
+ '("gecode/kernel/var-imp.hpp"
+ "gecode/kernel/var-type.hpp"))))))
+ (outputs '("out" "examples"))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:configure-flags
+ (list (string-append "GLDFLAGS=-Wl,-rpath="
+ (assoc-ref %outputs "out")
+ "/lib")
+ "--enable-examples=no")
+ #:modules ((guix build gnu-build-system)
+ (guix build utils)
+ (ice-9 rdelim)
+ (ice-9 popen))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'build 'build-examples
+ (lambda* (#:key outputs #:allow-other-keys)
+ (invoke "make" "compileexamples")))
+ ;; The Makefile disrespects GLDFLAGS for some reason, so we have to
+ ;; patch it ourselves... *sigh*
+ (add-after 'install 'fix-rpath
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((libdir (string-append (assoc-ref outputs "out") "/lib")))
+ (for-each
+ (lambda (file)
+ (let* ((pipe (open-pipe* OPEN_READ "patchelf"
+ "--print-rpath" file))
+ (line (read-line pipe)))
+ (and (zero? (close-pipe pipe))
+ (invoke "patchelf" "--set-rpath"
+ (string-append libdir ":" line)
+ file))))
+ (find-files libdir ".*\\.so$")))))
+ (add-after 'install 'install-examples
+ (lambda* (#:key outputs #:allow-other-keys)
+ (invoke "make" "installexamples"
+ (string-append "bindir=" (assoc-ref outputs "examples")
+ "/bin"))))
+ ;; Tests depend on installed libraries.
+ (delete 'check)
+ (add-after 'fix-rpath 'check
+ (assoc-ref %standard-phases 'check)))))
+ (native-inputs
+ (list patchelf perl sed))
+ (home-page "https://www.gecode.org")
+ (synopsis "Toolkit for developing constraint-based systems")
+ (description "Gecode is a C++ toolkit for developing constraint-based
+systems and applications. It provides a modular and extensible solver.")
+ (license license:expat)))
+
(define-public libflame
(package
(name "libflame")
(string-append static "/include"))
#t))))))
(inputs
- `(("gfortran" ,gfortran)))
+ (list gfortran))
(native-inputs
`(("lapack" ,lapack)
("openblas" ,openblas)
includes a complete LAPACK implementation.")
(license license:bsd-3)))
+(define-public libpotassco
+ ;; No public release, update together with clasp
+ (let ((revision "1")
+ (commit "2f9fb7ca2c202f1b47643aa414054f2f4f9c1821"))
+ (package
+ (name "libpotassco")
+ (version (git-version "0.0" revision commit))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/potassco/libpotassco")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1c32f9gqclf7qx07lpx8wd720vfhkjqhzc6nyy8mjmgwpmb3iyyn"))))
+ (arguments
+ `(#:configure-flags '("-DLIB_POTASSCO_BUILD_TESTS=on"
+ "-DLIB_POTASSCO_INSTALL_LIB=on"
+ "-DBUILD_SHARED_LIBS=on")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-cmake
+ (lambda _
+ (substitute* "CMakeLists.txt"
+ ;; clasp expects lowercase potassco and include directory is
+ ;; lowercase as well, so let's use that
+ (("\"cmake/Potassco\"") "\"cmake/potassco\"")
+ (("PotasscoConfig\\.cmake") "potassco-config.cmake")
+ (("PotasscoConfigVersion\\.cmake")
+ "potassco-config-version.cmake"))
+ (rename-file "cmake/PotasscoConfig.cmake.in"
+ "cmake/potassco-config.cmake.in"))))))
+ (build-system cmake-build-system)
+ (home-page "https://potassco.org/")
+ (synopsis "Utility library for Potassco's projects")
+ (description "@code{libpotassco} is a utility library providing functions
+and datatypes for
+@itemize
+@item parsing, writing, and converting logic programs in aspif and smodels
+format,
+@item passing information between a grounder and a solver,
+@item and defining and parsing command-line options and for creating
+command-line applications.
+@end itemize
+Furthermore, it comes with the tool @command{lpconvert} that converts either
+between aspif and smodels format or to a human-readable text format.")
+ (license license:expat))))
+
+(define-public clasp
+ (package
+ (name "clasp")
+ (version "3.3.6")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/potassco/clasp")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0rahqiq530jckvx717858h1q5p8znp1kb6sjm95p8blkr4n3pvmj"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:configure-flags '("-DCLASP_BUILD_TESTS=on"
+ "-DCLASP_INSTALL_LIB=on"
+ "-DCLASP_USE_LOCAL_LIB_POTASSCO=off"
+ "-DBUILD_SHARED_LIBS=on")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-cmake
+ (lambda _
+ (substitute* "CMakeLists.txt"
+ ;; Use lowercase to be consistent with libpotassco
+ (("\"cmake/Clasp\"") "\"cmake/clasp\"")
+ (("ClaspConfig\\.cmake") "clasp-config.cmake")
+ (("ClaspConfigVersion\\.cmake")
+ "clasp-config-version.cmake"))
+ (substitute* "cmake/ClaspConfig.cmake.in"
+ (("find_package\\(Potassco") "find_package(potassco"))
+ (rename-file "cmake/ClaspConfig.cmake.in"
+ "cmake/clasp-config.cmake.in"))))))
+ (inputs
+ (list libpotassco))
+ (home-page "https://potassco.org/")
+ (synopsis "Answer set solver")
+ (description "clasp is an answer set solver for (extended) normal and
+disjunctive logic programs. The primary algorithm of clasp relies on
+conflict-driven nogood learning, a technique that proved very successful for
+satisfiability checking (SAT).")
+ (license license:expat)))
+
+(define-public clingo
+ (package
+ (name "clingo")
+ (version "5.5.0")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/potassco/clingo")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0rfjwkcwm0mmf3r4i7asyjwb6cia4i7px7fn2kdbi9j85qvas4pb"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:configure-flags `("-DCLINGO_BUILD_TESTS=on"
+ "-DCLINGO_INSTALL_LIB=on"
+ "-DCLINGO_BUILD_STATIC=off"
+ "-DCLINGO_BUILD_SHARED=on"
+ ;; XXX: Clingo requries private headers and
+ ;; sources from clasp
+ ,(string-append
+ "-DCLASP_SOURCE_DIR="
+ (assoc-ref %build-inputs "clasp-src")))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-cmake
+ (lambda _
+ (substitute* "CMakeLists.txt"
+ (("add_subdirectory\\(clasp\\)")
+ "find_package(clasp REQUIRED)"))
+ (substitute* "libclingo/CMakeLists.txt"
+ (("\"cmake/Clingo\"") "\"cmake/clingo\"")
+ (("ClingoConfig\\.cmake") "clingo-config.cmake")
+ (("ClingoConfigVersion\\.cmake")
+ "clingo-config-version.cmake"))
+ (substitute* "cmake/ClingoConfig.cmake.in"
+ (("find_package\\(Clasp") "find_package(clasp"))
+ (rename-file "cmake/ClingoConfig.cmake.in"
+ "cmake/clingo-config.cmake.in")))
+ (add-after 'unpack 'skip-failing-tests
+ (lambda _
+ (with-directory-excursion "libclingo/tests"
+ (substitute* "CMakeLists.txt"
+ (("COMMAND test_clingo" all)
+ (string-append all
+ " -f "
+ "\"${CMAKE_CURRENT_SOURCE_DIR}/good.txt\"")))
+ (call-with-output-file "good.txt"
+ (lambda (port)
+ (for-each (lambda (test) (format port "~s~%" test))
+ '("parse-ast-v2" "add-ast-v2" "build-ast-v2"
+ "unpool-ast-v2" "parse_term"
+ "propagator" "propgator-sequence-mining"
+ "symbol" "visitor"))))))))))
+ (inputs
+ (list clasp libpotassco))
+ (native-inputs
+ `(("clasp-src" ,(package-source clasp))))
+ (home-page "https://potassco.org/")
+ (synopsis "Grounder and solver for logic programs")
+ (description "Clingo computes answer sets for a given logic program.")
+ (license license:expat)))
+
(define-public ceres
(package
(name "ceres-solver")
- (version "1.14.0")
+ (version "2.0.0")
(home-page "http://ceres-solver.org/")
(source (origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "13lfxy8x58w8vprr0nkbzziaijlh0vvqshgahvcgw0mrqdgh0i27"))))
+ "00vng9vnmdb1qga01m0why90m0041w7bn6kxa2h4m26aflfqla8h"))))
(build-system cmake-build-system)
(arguments
;; TODO: Build HTML user documentation and install separately.
(add-before 'configure 'set-library-directory
(lambda _
;; Install libraries to lib/, not lib64/.
- (substitute* "internal/ceres/CMakeLists.txt"
+ (substitute* "CMakeLists.txt"
(("set\\(LIB_SUFFIX \"64\"\\)")
- "set(LIB_SUFFIX \"\")"))
- #t)))))
+ "set(LIB_SUFFIX \"\")")))))))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(propagated-inputs
- `(("glog" ,glog))) ;for #include <glog/glog.h>
+ (list glog)) ;for #include <glog/glog.h>
(inputs
- `(("eigen" ,eigen)
- ("blas" ,openblas)
- ("lapack" ,lapack)
- ("suitesparse" ,suitesparse)
- ("gflags" ,gflags)))
+ (list eigen
+ openblas
+ lapack
+ suitesparse
+ gflags))
(synopsis "C++ library for solving large optimization problems")
(description
"Ceres Solver is a C++ library for modeling and solving large,
@item non-linear least squares problems with bounds constraints;
@item general unconstrained optimization problems.
@end enumerate\n")
- (license license:bsd-3)))
+ (license license:bsd-3)
+
+ ;; Mark as tunable to take advantage of SIMD code in Eigen.
+ (properties `((tunable? . #t)))))
+
+(define-public ceres-solver-benchmarks
+ (package
+ (inherit ceres)
+ (name "ceres-solver-benchmarks")
+ (arguments
+ '(#:modules ((ice-9 popen)
+ (ice-9 rdelim)
+ (guix build utils)
+ (guix build cmake-build-system))
+
+ #:phases (modify-phases %standard-phases
+ (delete 'configure)
+ (replace 'build
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin")))
+ (define flags
+ (string-tokenize
+ (read-line (open-pipe* OPEN_READ
+ "pkg-config" "eigen3"
+ "--cflags"))))
+
+ (define (compile-file top-dir)
+ (lambda (file)
+ (let ((source (string-append file ".cc")))
+ (format #t "building '~a'...~%" file)
+ (apply invoke "c++" "-fopenmp" "-O2" "-g" "-DNDEBUG"
+ source "-lceres" "-lbenchmark" "-lglog"
+ "-pthread"
+ "-o" (string-append bin "/" file)
+ "-I" top-dir flags))))
+
+ (mkdir-p bin)
+ (with-directory-excursion "internal/ceres"
+ (for-each (compile-file "..")
+ '("schur_eliminator_benchmark"
+ "small_blas_gemm_benchmark"
+ "small_blas_gemv_benchmark"))
+ (with-directory-excursion "autodiff_benchmarks"
+ ((compile-file "../..") "autodiff_benchmarks"))))))
+ (delete 'check)
+ (delete 'install))))
+ (inputs (modify-inputs (package-inputs ceres)
+ (prepend googlebenchmark ceres)))
+ (synopsis "Benchmarks of the Ceres optimization problem solver")))
;; For a fully featured Octave, users are strongly recommended also to install
;; the following packages: less, ghostscript, gnuplot.
("texinfo" ,texinfo)
("zlib" ,zlib)))
(native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)
- ("perl" ,perl)
- ;; The following inputs are not actually used in the build process.
- ;; However, the ./configure gratuitously tests for their existence and
- ;; assumes that programs not present at build time are also not, and
- ;; can never be, available at run time! If these inputs are therefore
- ;; not present, support for them will be built out. However, Octave
- ;; will still run without them, albeit without the features they
- ;; provide.
- ("less" ,less)
- ("ghostscript" ,ghostscript)
- ("gnuplot" ,gnuplot)))
+ (list gfortran
+ pkg-config
+ perl
+ ;; The following inputs are not actually used in the build process.
+ ;; However, the ./configure gratuitously tests for their existence and
+ ;; assumes that programs not present at build time are also not, and
+ ;; can never be, available at run time! If these inputs are therefore
+ ;; not present, support for them will be built out. However, Octave
+ ;; will still run without them, albeit without the features they
+ ;; provide.
+ less
+ ghostscript
+ 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.
(assoc-ref %outputs "out"))
"-UCMAKE_INSTALL_RPATH")))
(inputs
- `(("freetype" ,freetype)
- ("glu" ,glu)
- ("libxmu" ,libxmu)
- ("mesa" ,mesa)
- ("tcl" ,tcl)
- ("tk" ,tk)))
+ (list freetype
+ glu
+ libxmu
+ mesa
+ tcl
+ tk))
(native-inputs
`(("python" ,python-wrapper)))
(home-page "https://github.com/tpaviot/oce")
(define-public opencascade-occt
(package
(name "opencascade-occt")
- (version "7.3.0p3")
+ (version "7.6.0")
(source
(origin
(method git-fetch)
version)))))
(file-name (git-file-name name version))
(sha256
- (base32 "0bdywwxb6mk0ykbiajlvsb37295akqjp0a60y672qjfa67k0ljv4"))
+ (base32 "1rcwm9fkx0j4wrsyikb6g7qd611kpry7dand5dzdjvs5vzd13zvd"))
(modules '((guix build utils)))
(snippet
'(begin
"-DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON"
"-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON"
"-UCMAKE_INSTALL_LIBDIR")))
+ (native-inputs (list fontconfig))
(inputs
- `(("doxygen" ,doxygen)
- ;("freeimage" ,freeimage)
- ("freetype" ,freetype)
- ("glu" ,glu)
- ("libxext" ,libxext)
- ("libxi" ,libxi)
- ("libxmu" ,libxmu)
- ("mesa" ,mesa)
- ("tbb" ,tbb)
- ("tcl" ,tcl)
- ("tk" ,tk)))
+ (list doxygen
+ ;("freeimage" ,freeimage)
+ freetype
+ glu
+ libxext
+ libxi
+ libxmu
+ mesa
+ tbb-2020
+ tcl
+ tk))
;; TODO: build Overview documentation and add 'doc' output.
(home-page "https://www.opencascade.com")
(synopsis "Libraries for 3D modeling and numerical simulation")
#t))))
(build-system cmake-build-system)
(propagated-inputs
- `(("fltk" ,fltk)
- ("gfortran" ,gfortran)
- ("glu" ,glu)
- ("gmp" ,gmp)
- ("hdf5" ,hdf5)
- ("lapack" ,lapack)
- ("libx11" ,libx11)
- ("libxext" ,libxext)
- ("mesa" ,mesa)
- ("metis" ,metis)
- ("opencascade-occt" ,opencascade-occt)))
+ (list fltk
+ gfortran
+ glu
+ gmp
+ hdf5
+ lapack
+ libx11
+ libxext
+ mesa
+ metis
+ opencascade-occt))
(inputs
`(("fontconfig" ,fontconfig)
("libxft" ,libxft)
,(list (string-append (assoc-ref inputs "qtsvg")
"/lib/qt5/plugins/"))))))))))
(native-inputs
- `(("pkg-config" ,pkg-config)
- ;;("python-astropy" ,python-astropy) ;; FIXME: Package this.
- ("qttools" ,qttools)
- ("python-sip" ,python-sip-4)))
+ (list pkg-config
+ ;;("python-astropy" ,python-astropy) ;; FIXME: Package this.
+ qttools python-sip-4))
(inputs
- `(("ghostscript" ,ghostscript) ;optional, for EPS/PS output
- ("python-dbus" ,python-dbus)
- ("python-h5py" ,python-h5py) ;optional, for HDF5 data
- ("python-pyqt" ,python-pyqt)
- ("qtbase" ,qtbase-5)
- ("qtsvg" ,qtsvg)))
+ (list ghostscript ;optional, for EPS/PS output
+ python-dbus
+ python-h5py ;optional, for HDF5 data
+ python-pyqt
+ qtbase-5
+ qtsvg))
(propagated-inputs
- `(("python-numpy" ,python-numpy)))
+ (list python-numpy))
(home-page "https://veusz.github.io/")
(synopsis "Scientific plotting package")
(description
(define-public petsc
(package
(name "petsc")
- (version "3.11.2")
+ (version "3.16.1")
(source
(origin
(method url-fetch)
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
"petsc-lite-" version ".tar.gz"))
(sha256
- (base32 "1645nwwcp9bcnfnxikk480mhbbacdvhsay2c401818hk97dqj5nx"))))
+ (base32 "0sm03vpg010q9icidiq587n325m0598cj6hab2rdv85nwyygg74h"))))
(outputs '("out" ; libraries and headers
"examples")) ; ~30MiB of examples
(build-system gnu-build-system)
(native-inputs
- `(("python" ,python-2)))
+ (list python which))
(inputs
- `(("gfortran" ,gfortran)
- ("openblas" ,openblas)
- ("superlu" ,superlu)
- ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
- ;; leaving out opengl, as configuration seems to only be for mac
- ))
+ (list gfortran openblas superlu
+ ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi
+ ;; leaving out opengl, as configuration seems to only be for mac
+ ))
(arguments
- `(#:test-target "test"
- #:parallel-build? #f ; build is parallel by default
- #:configure-flags
- `("--with-mpi=0"
- "--with-openmp=1"
- "--with-openblas=1"
- "--with-superlu=1")
- #:make-flags
- ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
- ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
- (list (format #f "MAKE_NP=~a" (parallel-job-count)))
- #:phases
- (modify-phases %standard-phases
- (replace 'configure
- ;; PETSc's configure script is actually a python script, so we can't
- ;; run it with bash.
- (lambda* (#:key outputs (configure-flags '())
- #:allow-other-keys)
- (let* ((prefix (assoc-ref outputs "out"))
- (flags `(,(string-append "--prefix=" prefix)
- ,@configure-flags)))
- (format #t "build directory: ~s~%" (getcwd))
- (format #t "configure flags: ~s~%" flags)
- (apply invoke "./configure" flags))))
- (add-after 'configure 'clean-local-references
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
- ;; Prevent build directory from leaking into compiled code
- (((getcwd)) out)
- ;; Scrub timestamp for reproducibility
- ((".*Libraries compiled on.*") ""))
- (substitute* (find-files "." "petscvariables")
- ;; Do not expose build machine characteristics, set to defaults.
- (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
- (("NPMAX = [:digit:]+") "NPMAX = 2"))
- #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")))
- (substitute* (map (lambda (file)
- (string-append out "/lib/petsc/conf/" file))
- '("petscvariables"))
- (((getcwd)) out))
- ;; Make compiler references point to the store
- (substitute* (string-append out "/lib/petsc/conf/petscvariables")
- (("= (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)))
- (when (file-exists? f)
- (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"))
- #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))))))
+ (list
+ #:test-target "test"
+ #:parallel-build? #f ; build is parallel by default
+ #:configure-flags
+ #~(list "--with-mpi=0"
+ "--with-openmp=1"
+ "--with-openblas=1"
+ (string-append "--with-openblas-dir="
+ #$(this-package-input "openblas"))
+ "--with-superlu=1")
+ #:make-flags
+ ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
+ ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
+ #~(list (format #f "MAKE_NP=~a" (parallel-job-count)))
+ #:phases
+ #~(modify-phases %standard-phases
+ (replace 'configure
+ ;; PETSc's configure script is actually a python script, so we can't
+ ;; run it with bash.
+ (lambda* (#:key outputs (configure-flags '())
+ #:allow-other-keys)
+ (let* ((prefix (assoc-ref outputs "out"))
+ (flags `(,(string-append "--prefix=" prefix)
+ ,@configure-flags)))
+ (format #t "build directory: ~s~%" (getcwd))
+ (format #t "configure flags: ~s~%" flags)
+ (apply invoke "./configure" flags)
+
+ ;; Generate test scripts with the right shebang.
+ (substitute* "config/example_template.py"
+ (("#!/usr/bin/env bash")
+ (string-append "#!" (which "bash")))))))
+ (add-after 'configure 'clean-local-references
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (substitute* (find-files "." "^petsc(conf|machineinfo).h$")
+ ;; Prevent build directory from leaking into compiled code
+ (((getcwd)) out)
+ ;; Scrub timestamp for reproducibility
+ ((".*Libraries compiled on.*") ""))
+ (substitute* (find-files "." "petscvariables")
+ ;; Do not expose build machine characteristics, set to defaults.
+ (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
+ (("NPMAX = [:digit:]+") "NPMAX = 2")))))
+ (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")))
+ (substitute* (map (lambda (file)
+ (string-append out "/lib/petsc/conf/" file))
+ '("petscvariables"))
+ (((getcwd)) out))
+ ;; Make compiler references point to the store
+ (substitute* (string-append out "/lib/petsc/conf/petscvariables")
+ (("= (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)))
+ (when (file-exists? f)
+ (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")))))
+ (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)))))))
(home-page "https://www.mcs.anl.gov/petsc")
(synopsis "Library to solve PDEs")
(description "PETSc, pronounced PET-see (the S is silent), is a suite of
"https://www.mcs.anl.gov/petsc/documentation/copyright.html"))))
(define-public petsc-complex
- (package (inherit petsc)
+ (package
+ (inherit petsc)
(name "petsc-complex")
(arguments
(substitute-keyword-arguments (package-arguments petsc)
((#:configure-flags cf)
- `(cons "--with-scalar-type=complex" ,cf))))
+ #~(cons "--with-scalar-type=complex" #$cf))))
(synopsis "Library to solve PDEs (with complex scalars)")))
(define-public petsc-openmpi
- (package (inherit petsc)
+ (package
+ (inherit petsc)
(name "petsc-openmpi")
(inputs
`(("hdf5" ,hdf5-parallel-openmpi)
(arguments
(substitute-keyword-arguments (package-arguments petsc)
((#:configure-flags cf)
- ``("--with-hypre=1"
- "--with-mpiexec=mpirun"
- "--with-metis=1"
- "--with-mumps=1"
- "--with-scalapack=1"
- "--with-ptscotch=1"
- ,(string-append "--with-mpi-dir="
- (assoc-ref %build-inputs "openmpi"))
- ,(string-append "--with-hdf5-include="
- (assoc-ref %build-inputs "hdf5") "/include")
- ,(string-append "--with-hdf5-lib="
- (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a")
- ,@(delete "--with-mpi=0" ,cf)))
+ #~`("--with-hypre=1"
+ "--with-mpiexec=mpirun"
+ "--with-metis=1"
+ "--with-mumps=1"
+ "--with-scalapack=1"
+ "--with-ptscotch=1"
+ ,(string-append "--with-mpi-dir="
+ #$(this-package-input "openmpi"))
+ ,(string-append "--with-hdf5-include="
+ #$(this-package-input "hdf5") "/include")
+ ,(string-append "--with-hdf5-lib="
+ #$(this-package-input "hdf5") "/lib/libhdf5.a")
+ ,@(delete "--with-mpi=0" #$cf)))
((#:phases phases)
- `(modify-phases ,phases
- (add-before 'configure 'mpi-setup
- ,%openmpi-setup)))))
+ #~(modify-phases #$phases
+ (add-before 'configure 'mpi-setup
+ #$%openmpi-setup)))))
(synopsis "Library to solve PDEs (with MUMPS and MPI support)")))
(define-public petsc-complex-openmpi
- (package (inherit petsc-complex)
+ (package
+ (inherit petsc-complex)
(name "petsc-complex-openmpi")
(inputs
- `(("openmpi" ,openmpi)
- ,@(package-inputs petsc-complex)))
+ (modify-inputs (package-inputs petsc-complex)
+ (prepend openmpi)))
(arguments
(substitute-keyword-arguments (package-arguments petsc-complex)
((#:configure-flags cf)
- ``("--with-mpiexec=mpirun"
- ,(string-append "--with-mpi-dir="
- (assoc-ref %build-inputs "openmpi"))
- ,@(delete "--with-mpi=0" ,cf)))
+ #~`("--with-mpiexec=mpirun"
+ ,(string-append "--with-mpi-dir="
+ #$(this-package-input "openmpi"))
+ ,@(delete "--with-mpi=0" #$cf)))
((#:phases phases)
- `(modify-phases ,phases
- (add-before 'configure 'mpi-setup
- ,%openmpi-setup)))))
+ #~(modify-phases #$phases
+ (add-before 'configure 'mpi-setup
+ #$%openmpi-setup)))))
(synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
(define-public python-petsc4py
(package
(name "python-petsc4py")
- (version "3.11.0")
+ (version "3.16.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "petsc4py" version))
(sha256
(base32
- "1rm1qj5wlkhxl39by9n78lh3gbmii31wsnb8j1rr5hvfr5xgbx2q"))
+ "0pxr6qa7p0pmpq0av29lx8lzlrdcfdzj87ynixzr8dn42y13a662"))
(modules '((guix build utils)))
(snippet
'(begin
(add-before 'check 'mpi-setup
,%openmpi-setup))))
(native-inputs
- `(("python-cython" ,python-cython)))
+ (list python-cython))
(inputs
`(("petsc" ,petsc-openmpi)
("python-numpy" ,python-numpy)))
(define-public slepc
(package
(name "slepc")
- (version "3.11.1")
+ (version "3.16.1")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "1yq84q9wannc8xwapxpay4ypdd675picwi395hhsdvng9q6hf5j8"))))
+ "1ysfm77s5fcissv3q0k5d65mlp93zi4anqg62q3cd25dn66sva5i"))))
(build-system gnu-build-system)
(native-inputs
- `(("python" ,python-2)
+ `(("python" ,python)
+ ("which" ,which)
("petsc:examples" ,petsc "examples"))) ;for gmakegen.py script
(inputs
`(("arpack" ,arpack-ng)
("gfortran" ,gfortran)))
(propagated-inputs
- `(("petsc" ,petsc)))
+ (list petsc))
(arguments
`(#:parallel-build? #f ;build is parallel by default
#:configure-flags
The emphasis of the software is on methods and techniques appropriate for
problems in which the associated matrices are sparse, for example, those
arising after the discretization of partial differential equations.")
- (license license:bsd-2)))
+ (license license:bsd-2)
+ (properties
+ `((release-monitoring-url . "http://slepc.upv.es/download/")))))
(define-public slepc-complex
(package (inherit slepc)
,%openmpi-setup)))))
(inputs
`(("mpi" ,openmpi)
- ("arpack" ,arpack-ng-openmpi)
,@(alist-delete "arpack" (package-inputs slepc))))
(propagated-inputs
`(("petsc" ,petsc-openmpi)
+ ("arpack" ,arpack-ng-openmpi)
,@(alist-delete "petsc" (package-propagated-inputs slepc))))
(synopsis "Scalable library for eigenproblems (with MPI support)")))
(define-public python-slepc4py
(package
(name "python-slepc4py")
- (version "3.11.0")
+ (version "3.16.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "slepc4py" version))
(sha256
(base32
- "1ksp08kxf4wg408b9nn39z3qfhy643j22d4rfbl30vzxk2rxh4lq"))))
+ "0fq997y73ymvcvdrxycp450pxwdgnqaw62gv9rwncfgsfplkvs9w"))))
(build-system python-build-system)
(arguments
`(#:phases
(base32 "1s9hyknfvhj86g3giayyf3dxzg23iij0rs7bdvj075v9qbyhqn9b"))))
(build-system gnu-build-system)
(native-inputs
- `(("autoconf" ,autoconf)
- ("automake" ,automake)))
+ (list autoconf automake))
(home-page "http://us.metamath.org/")
(synopsis "Proof verifier based on a minimalistic formalism")
(description
book.")
(license license:gpl2+)))
+(define-public minizinc
+ (package
+ (name "minizinc")
+ (version "2.5.5")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/MiniZinc/libminizinc")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "10b2hsl1fx9psh0iagmp8ki3f60f3qg5hmvra5aczjlfmbl88ggp"))
+ (modules '((guix build utils)
+ (ice-9 ftw)
+ (srfi srfi-1)))
+ (snippet
+ '(begin
+ ;; Do not advertise proprietary solvers
+ (with-directory-excursion "cmake/targets"
+ (let ((targets '("libminizinc_fzn.cmake"
+ "libminizinc_gecode.cmake"
+ "libminizinc_mip.cmake"
+ "libminizinc_nl.cmake"
+ "libminizinc_osicbc.cmake"
+ "libminizinc_parser.cmake"
+ "libmzn.cmake"
+ "minizinc.cmake"
+ "mzn2doc.cmake")))
+ (for-each delete-file
+ (remove
+ (lambda (file)
+ (member file (cons* "." ".." targets)))
+ (scandir ".")))
+ (substitute* "libmzn.cmake"
+ (("include\\(cmake/targets/(.*)\\)" all target)
+ (if (member target targets) all "")))))
+ (with-directory-excursion "include/minizinc/solvers/MIP"
+ (for-each delete-file
+ (remove
+ (lambda (file)
+ (member file '("." ".."
+ "MIP_osicbc_solverfactory.hh"
+ "MIP_osicbc_wrap.hh"
+ "MIP_solverinstance.hh"
+ "MIP_solverinstance.hpp"
+ "MIP_wrap.hh")))
+ (scandir "."))))
+ (with-directory-excursion "solvers/MIP"
+ (for-each delete-file
+ (remove
+ (lambda (file)
+ (member file '("." ".."
+ "MIP_osicbc_solverfactory.cpp"
+ "MIP_osicbc_wrap.cpp"
+ "MIP_solverinstance.cpp"
+ "MIP_wrap.cpp")))
+ (scandir "."))))
+ (substitute* "CMakeLists.txt"
+ (("find_package\\(([^ ]*).*\\)" all pkg)
+ (if (member pkg '("Gecode" "OsiCBC" "Threads"))
+ all
+ "")))
+ ;; TODO: swap out miniz for zlib
+ #t))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:tests? #f ; no ‘check’ target
+ #:modules ((guix build cmake-build-system)
+ (guix build utils)
+ (srfi srfi-1))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'install 'install-solver-configs
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((gecode (assoc-ref inputs "gecode"))
+ (pkgdatadir (string-append (assoc-ref outputs "out")
+ "/share/minizinc")))
+ (call-with-output-file (string-append pkgdatadir
+ "/Preferences.json")
+ (lambda (port)
+ (display "\
+{
+ \"tagDefaults\": [
+ [\"\", \"org.gecode.gecode\"],
+ [\"gecode\", \"org.gecode.gecode\"]
+ ],
+ \"solverDefaults\": []
+}"
+ port)
+ (newline port)))
+
+ (mkdir-p (string-append pkgdatadir "/solvers"))
+ (call-with-output-file (string-append pkgdatadir
+ "/solvers/gecode.msc")
+ (lambda (port)
+ (format port
+ "\
+{
+ \"id\": \"org.gecode.gecode\",
+ \"name\": \"Gecode\",
+ \"description\": \"Gecode FlatZinc executable\",
+ \"version\": ~s,
+ \"mznlib\": ~s,
+ \"executable\": ~s,
+ \"supportsMzn\": false,
+ \"supportsFzn\": true,
+ \"needsSolns2Out\": true,
+ \"needsMznExecutable\": false,
+ \"needsStdlibDir\": false,
+ \"isGUIApplication\": false
+}"
+ (last (string-split gecode #\-))
+ (string-append gecode "/share/gecode/mznlib")
+ (string-append gecode "/bin/fzn-gecode"))
+ (newline port)))))))))
+ (native-inputs
+ (list bison flex))
+ (inputs
+ (list cbc gecode zlib))
+ (home-page "https://www.minizinc.org")
+ (synopsis "High-level constraint modeling language")
+ (description "MiniZinc is a high-level modeling language for constraint
+satisfaction and optimization problems. Models are compiled to FlatZinc, a
+language understood by many solvers.")
+ (license license:mpl2.0)))
+
(define-public mumps
(package
(name "mumps")
"mumps-shared-pord.patch"))))
(build-system gnu-build-system)
(inputs
- `(("fortran" ,gfortran)
- ;; These are required for linking against mumps, but we let the user
- ;; declare the dependency.
- ("blas" ,openblas)
- ("metis" ,metis)
- ("scotch" ,scotch)))
+ (list gfortran
+ ;; These are required for linking against mumps, but we let the user
+ ;; declare the dependency.
+ openblas
+ metis
+ scotch))
(arguments
`(#:modules ((ice-9 match)
(ice-9 popen)
LIBOTHERS = -pthread
CDEFS = -DAdd_
PIC = -fPIC
-OPTF = -O2 -DALLOW_NON_INIT $(PIC)
+OPTF = -O2 -DALLOW_NON_INIT -fallow-argument-mismatch $(PIC)
OPTL = -O2 $(PIC)
OPTC = -O2 $(PIC)
INCS = $(INCSEQ)
LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
IORDERINGSF = $(ISCOTCH)
IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
- (assoc-ref inputs "mpi")
- (assoc-ref inputs "blas")
+ (->bool (which "mpicc")) ;MPI support enabled?
+ (dirname
+ (dirname (search-input-file inputs "/include/cblas.h")))
(assoc-ref inputs "scalapack")
(assoc-ref inputs "metis")
(match (list (assoc-ref inputs "pt-scotch")
`((,scotch "" "-Dscotch")))
((ptscotch _)
`((,ptscotch
- "-lptesmumps -lptscotch -lptscotcherr "
+ "-lesmumps -lptscotch -lptscotcherr "
"-Dptscotch")))))))))
(replace 'build
;; By default only the d-precision library is built. Make with "all"
(license license:cecill-c)))
(define-public mumps-metis
- (package (inherit mumps)
+ (package
+ (inherit mumps)
(name "mumps-metis")
- (inputs
- (alist-delete "scotch" (package-inputs mumps)))))
+ (inputs (modify-inputs (package-inputs mumps)
+ (delete "scotch")))))
(define-public mumps-openmpi
- (package (inherit mumps)
+ (package
+ (inherit mumps)
(name "mumps-openmpi")
(inputs
- `(("mpi" ,openmpi)
- ("scalapack" ,scalapack)
- ("pt-scotch" ,pt-scotch)
- ,@(alist-delete "scotch" (package-inputs mumps))))
+ (modify-inputs (package-inputs mumps)
+ (delete "scotch")
+ (prepend openmpi scalapack pt-scotch)))
(arguments
(substitute-keyword-arguments (package-arguments mumps)
((#:phases phases)
(synopsis "Multifrontal sparse direct solver (with MPI)")))
(define-public mumps-metis-openmpi
- (package (inherit mumps-openmpi)
+ (package
+ (inherit mumps-openmpi)
(name "mumps-metis-openmpi")
- (inputs
- (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
+ (inputs (modify-inputs (package-inputs mumps-openmpi)
+ (delete "pt-scotch")))))
(define-public ruby-asciimath
(package
"1aapydwwkydbwgz07n7ma3a5jy9n3v0shy6q6j8mi4wr3crhx45a"))))
(build-system ruby-build-system)
(native-inputs
- `(("ruby-nokogiri" ,ruby-nokogiri)
- ("ruby-rspec" ,ruby-rspec)))
+ (list ruby-nokogiri ruby-rspec))
(synopsis "AsciiMath parsing and conversion library")
(description
"A pure Ruby AsciiMath parsing and conversion library. AsciiMath is an
(define-public superlu
(package
(name "superlu")
- (version "5.2.2")
+ (version "5.3.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://portal.nersc.gov/project/sparse/superlu/"
- "superlu_" version ".tar.gz"))
+ "superlu-" version ".tar.gz"))
(sha256
- (base32 "13520vk6fqspyl22cq4ak2jh3rlmhja4czq56j75fdx65fkk80s7"))
+ (base32 "0xvib7nk2rlbsiv1iwkwl9kxppkalkciv628bsyiiv0pv754n48q"))
(modules '((guix build utils)))
(snippet
;; Replace the non-free implementation of MC64 with a stub adapted
#t)))))))
(build-system cmake-build-system)
(native-inputs
- `(("tcsh" ,tcsh)))
+ (list tcsh))
(inputs
`(("blas" ,openblas)
("gfortran" ,gfortran)))
"superlu-dist-awpm-grid.patch"))))
(build-system cmake-build-system)
(native-inputs
- `(("tcsh" ,tcsh)))
+ (list tcsh))
(inputs
`(("gfortran" ,gfortran)
("blas" ,openblas)
(define-public scotch
(package
(name "scotch")
- (version "6.1.1")
+ (version "7.0.1")
(source
(origin
- (method url-fetch)
- (uri (string-append "https://gforge.inria.fr/frs/download.php/"
- "latestfile/298/scotch_" version ".tar.gz"))
- (sha256
- (base32 "04dkz24a2g20wq703fnyi4440ac4mwycy9gwrrllljj7zxcjy19r"))
- (patches (search-patches "scotch-build-parallelism.patch"
- "scotch-integer-declarations.patch"))))
- (build-system gnu-build-system)
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.inria.fr/scotch/scotch")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1fvgxd3ipl5xswswyadvxvlcgv6an8c229ispnlksgnlwphg10ig"))))
+ (build-system cmake-build-system)
(inputs
- `(("zlib" ,zlib)))
+ (list zlib))
(native-inputs
- `(("flex" ,flex)
- ("bison" ,bison)
- ("gfortran" ,gfortran)))
+ (list flex bison gfortran))
(outputs '("out" "metis"))
(arguments
- `(#:make-flags (list (string-append "prefix=" %output))
+ `(#:configure-flags '("-DBUILD_SHARED_LIBS=YES"
+ "-DBUILD_PTSCOTCH=OFF")
#:phases
(modify-phases %standard-phases
- (add-after
- 'unpack 'chdir-to-src
- (lambda _ (chdir "src") #t))
- (replace
- 'configure
- (lambda _
- (call-with-output-file "Makefile.inc"
- (lambda (port)
- (format port "
-EXE =
-LIB = .a
-OBJ = .o
-MAKE = make
-AR = ar
-ARFLAGS = -ruv
-CAT = cat
-CCS = gcc
-CCP = mpicc
-CCD = gcc
-FC = gfortran
-CPPFLAGS =~{ -D~a~}
-CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
-LDFLAGS = -lz -lm -lrt -lpthread
-CP = cp
-LEX = flex -Pscotchyy -olex.yy.c
-LN = ln
-MKDIR = mkdir
-MV = mv
-RANLIB = ranlib
-YACC = bison -pscotchyy -y -b y
-"
- '("COMMON_FILE_COMPRESS_GZ"
- "COMMON_PTHREAD"
- "COMMON_RANDOM_FIXED_SEED"
- "INTSIZE64" ;use 'int64_t'
- ;; Prevents symbol clashes with libesmumps
- "SCOTCH_RENAME"
- ;; XXX: Causes invalid frees in superlu-dist tests
- ;; "SCOTCH_PTHREAD"
- ;; "SCOTCH_PTHREAD_NUMBER=2"
- "restrict=__restrict"))))
- #t))
- (add-after 'build 'build-esmumps
- (lambda _
- (invoke "make"
- (format #f "-j~a" (parallel-job-count))
- "esmumps")))
- (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))))))
+ (let* ((out (assoc-ref outputs "out"))
+ (metis (assoc-ref outputs "metis"))
+ (prefix (string-length out)))
+ (for-each (lambda (file)
+ (let ((target (string-append
+ metis
+ (string-drop file prefix))))
+ (mkdir-p (dirname target))
+ (rename-file file target)))
+ (find-files out "metis"))))))))
(home-page "https://www.labri.fr/perso/pelegrin/scotch/")
(properties
- `((release-monitoring-url . "https://gforge.inria.fr/frs/?group_id=248")))
+ `((release-monitoring-url
+ . "https://gitlab.inria.fr/scotch/scotch/-/releases")))
(synopsis "Programs and libraries for graph algorithms")
(description "SCOTCH is a set of programs and libraries which implement
the static mapping and sparse matrix reordering algorithms developed within
(define-public scotch32
;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by
;; some applications.
- (package (inherit scotch)
+ (package
+ (inherit scotch)
(name "scotch32")
(arguments
(substitute-keyword-arguments (package-arguments scotch)
- ((#:phases scotch-phases)
- `(modify-phases ,scotch-phases
- (replace
- 'configure
- (lambda _
- (call-with-output-file "Makefile.inc"
- (lambda (port)
- (format port "
-EXE =
-LIB = .a
-OBJ = .o
-MAKE = make
-AR = ar
-ARFLAGS = -ruv
-CAT = cat
-CCS = gcc
-CCP = mpicc
-CCD = gcc
-FC = gfortran
-CPPFLAGS =~{ -D~a~}
-CFLAGS = -O2 -g -fPIC $(CPPFLAGS)
-LDFLAGS = -lz -lm -lrt -lpthread
-CP = cp
-LEX = flex -Pscotchyy -olex.yy.c
-LN = ln
-MKDIR = mkdir
-MV = mv
-RANLIB = ranlib
-YACC = bison -pscotchyy -y -b y
-"
- '("COMMON_FILE_COMPRESS_GZ"
- "COMMON_PTHREAD"
- "COMMON_RANDOM_FIXED_SEED"
- "INTSIZE32" ;use 32-bit integers. See INSTALL.txt
- ;; Prevents symbolc clashes with libesmumps
- "SCOTCH_RENAME"
- ;; XXX: Causes invalid frees in superlu-dist tests
- ;; "SCOTCH_PTHREAD"
- ;; "SCOTCH_PTHREAD_NUMBER=2"
- "restrict=__restrict"))))))))))
+ ((#:configure-flags flags ''())
+ ''("-DBUILD_SHARED_LIBS=YES" "-DBUILD_PTSCOTCH=OFF"
+ "-DCMAKE_C_FLAGS=-DINTSIZE32=1"))))
(synopsis
"Programs and libraries for graph algorithms (32-bit integers)")))
-(define-public scotch-shared
- (package (inherit scotch)
- (name "scotch-shared")
- (native-inputs
- `(("gcc" ,gcc)
- ("flex" ,flex)
- ("bison" ,bison)))
- (arguments
- (substitute-keyword-arguments (package-arguments scotch)
- ((#:phases scotch-shared-phases)
- `(modify-phases ,scotch-shared-phases
- (replace
- 'configure
- (lambda _
- ;; Otherwise, the RUNPATH will lack the final path component.
- (setenv "RPATHFLAGS" (string-append "-Wl,-rpath="
- (assoc-ref %outputs "out") "/lib"))
- (call-with-output-file "Makefile.inc"
- (lambda (port)
- (format port "
-EXE =
-LIB = .so
-OBJ = .o
-MAKE = make
-AR = gcc
-ARFLAGS = -shared -o
-CAT = cat
-CCS = gcc
-CCP = mpicc
-CCD = gcc
-FC = gfortran
-CPPFLAGS =~{ -D~a~}
-CFLAGS = -O2 -g -fPIC $(CPPFLAGS) $(RPATHFLAGS)
-CLIBFLAGS = -shared -fPIC
-LDFLAGS = -lz -lm -lrt -lpthread -Xlinker --no-as-needed
-CP = cp
-LEX = flex -Pscotchyy -olex.yy.c
-LN = ln
-MKDIR = mkdir
-MV = mv
-RANLIB = echo
-YACC = bison -pscotchyy -y -b y
-"
- '("COMMON_FILE_COMPRESS_GZ"
- "COMMON_PTHREAD"
- "COMMON_RANDOM_FIXED_SEED"
- "INTSIZE64" ;use 'int64_t'
- ;; Prevents symbolc clashes with libesmumps
- "SCOTCH_RENAME"
- ;; XXX: Causes invalid frees in superlu-dist tests
- ;; "SCOTCH_PTHREAD"
- ;; "SCOTCH_PTHREAD_NUMBER=2"
- "restrict=__restrict"
- ))))#t))
- (delete 'check)))))
- (synopsis
- "Programs and libraries for graph algorithms (shared libraries version)")))
-
(define-public pt-scotch
- (package (inherit scotch)
+ (package
+ (inherit scotch)
(name "pt-scotch")
(propagated-inputs
- `(("openmpi" ,openmpi))) ;Headers include MPI headers
+ (list openmpi)) ;headers include MPI headers
(arguments
(substitute-keyword-arguments (package-arguments scotch)
- ((#:phases scotch-phases)
- `(modify-phases ,scotch-phases
- (replace
- 'build
- (lambda _
- (invoke "make" (format #f "-j~a" (parallel-job-count))
- "ptscotch" "ptesmumps")
-
- ;; Install the serial metis compatibility library
- (invoke "make" "-C" "libscotchmetis" "install")))
+ ((#:configure-flags flags ''())
+ ''("-DBUILD_SHARED_LIBS=YES" "-DBUILD_PTSCOTCH=ON"))
+ ((#:phases phases '%standard-phases)
+ `(modify-phases ,phases
(add-before 'check 'mpi-setup
- ,%openmpi-setup)
- (replace 'check
- (lambda _
- (invoke "make" "ptcheck")))))))
+ ,%openmpi-setup)))))
(synopsis "Programs and libraries for graph algorithms (with MPI)")))
(define-public pt-scotch32
- (package (inherit scotch32)
+ (package
+ (inherit pt-scotch)
(name "pt-scotch32")
(propagated-inputs
- `(("openmpi" ,openmpi))) ;headers include MPI headers
+ (list openmpi)) ;headers include MPI headers
(arguments
- (substitute-keyword-arguments (package-arguments scotch32)
- ((#:phases scotch32-phases)
- `(modify-phases ,scotch32-phases
- (replace 'build
- (lambda _
- (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")))))))
+ (substitute-keyword-arguments (package-arguments pt-scotch)
+ ((#:configure-flags flags ''())
+ ''("-DBUILD_SHARED_LIBS=YES" "-DBUILD_PTSCOTCH=ON"
+ "-DCMAKE_C_FLAGS=-DINTSIZE32=1"))))
(synopsis
"Programs and libraries for graph algorithms (with MPI and 32-bit integers)")))
-(define-public pt-scotch-shared
- (package (inherit scotch-shared)
- (name "pt-scotch-shared")
- (propagated-inputs
- `(("openmpi" ,openmpi))) ;Headers include MPI headers
- (arguments
- (substitute-keyword-arguments (package-arguments scotch-shared)
- ((#:phases scotch-shared-phases)
- `(modify-phases ,scotch-shared-phases
- (replace
- 'build
- (lambda _
- (invoke "make" (format #f "-j~a" (parallel-job-count))
- "ptscotch" "ptesmumps")
+(define-public scotch-shared
+ ;; There used to be separate shared library variants while the default would
+ ;; provide .a files including PIC objects. With the switch to CMake, .a
+ ;; files contain non-PIC objects, which breaks some users, and switching to
+ ;; shared libraries by default seems to make more sense, as discussed here:
+ ;; <https://issues.guix.gnu.org/47619#2>.
+ (deprecated-package "scotch-shared" scotch))
- ;; Install the serial metis compatibility library
- (invoke "make" "-C" "libscotchmetis" "install")))
- (add-before 'check 'mpi-setup
- ,%openmpi-setup)))))
- (synopsis "Graph algorithms (shared libraries version, with MPI)")))
+(define-public pt-scotch-shared
+ (deprecated-package "pt-scotch-shared" pt-scotch))
(define-public metis
`(#:configure-flags
(list "--disable-static")))
(inputs
- `(("glib" ,glib)
- ("gtk+" ,gtk+)))
+ (list glib gtk+))
(native-inputs
- `(("pkg-config" ,pkg-config)))
+ (list pkg-config))
(home-page "https://www.gnu.org/software/gsegrafix/")
(synopsis "GNOME application to create scientific and engineering plots")
(description
(patches (search-patches "maxima-defsystem-mkdir.patch"))))
(build-system gnu-build-system)
(inputs
- `(("gcl" ,gcl)
+ `(("bash" ,bash-minimal)
("gnuplot" ,gnuplot) ;for plots
+ ("sbcl" ,sbcl)
("sed" ,sed)
("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima'
(native-inputs
- `(("texinfo" ,texinfo)
- ("perl" ,perl)
- ("python" ,python)))
+ (list texinfo perl python))
(arguments
`(#:configure-flags
- (list "--enable-gcl"
- (string-append "--with-posix-shell="
- (assoc-ref %build-inputs "bash")
- "/bin/sh")
- (string-append "--with-wish="
- (assoc-ref %build-inputs "tk")
- "/bin/wish"
- (let ((v ,(package-version tk)))
- (string-take v (string-index-right v #\.)))))
+ ,#~(list "--enable-sbcl"
+ (string-append "--with-sbcl=" #$sbcl "/bin/sbcl")
+ (string-append "--with-posix-shell=" #$bash-minimal "/bin/sh")
+ (string-append "--with-wish=" #$tk "/bin/wish"
+ #$(version-major+minor (package-version tk))))
;; By default Maxima attempts to write temporary files to
;; '/tmp/nix-build-maxima-*', which won't exist at run time.
;; Work around that.
(invoke "sh" "-c"
(string-append
"./maxima-local "
- "--lisp=gcl "
+ "--lisp=sbcl "
"--batch-string=\"run_testsuite();\" "
"| grep -q \"No unexpected errors found\""))))
;; Make sure the doc and emacs files are found in the
(native-inputs
`(("gettext" ,gettext-minimal)))
(inputs
- `(("wxwidgets" ,wxwidgets)
- ("maxima" ,maxima)
- ;; Runtime support.
- ("adwaita-icon-theme" ,adwaita-icon-theme)
- ("gtk+" ,gtk+)
- ("shared-mime-info" ,shared-mime-info)))
+ (list wxwidgets
+ maxima
+ ;; Runtime support.
+ adwaita-icon-theme
+ gtk+
+ shared-mime-info))
(arguments
`(#:tests? #f ; tests fail non-deterministically
#:phases
(define-public openblas
(package
(name "openblas")
- (version "0.3.13")
+ (version "0.3.18")
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "14jxh0v3jfbw4mfjx4mcz4dd51lyq7pqvh9k8dg94539ypzjr2lj"))))
+ "17zdd8asylz2w71hczrz5y344p6d5ds1jn4901maw7zcp3dbk63g"))))
(build-system gnu-build-system)
(arguments
`(#:test-target "test"
(list (string-append "PREFIX=" (assoc-ref %outputs "out"))
"SHELL=bash"
"MAKE_NB_JOBS=0" ;use jobserver for submakes
+ "NO_STATIC=1" ;avoid a 67 MiB static archive
;; This is the maximum number of threads OpenBLAS will ever use (that
;; is, if $OPENBLAS_NUM_THREADS is greater than that, then NUM_THREADS
,@(let ((system (or (%current-target-system) (%current-system))))
(cond
((or (string-prefix? "x86_64" system)
- (string-prefix? "i686" system))
- '("DYNAMIC_ARCH=1"))
- ;; On some of these architectures the CPU can't be detected.
- ((or (string-prefix? "powerpc64le" system)
+ (string-prefix? "i686" system)
+ (string-prefix? "powerpc64le" system)
(string-prefix? "aarch64" system))
- '("DYNAMIC_ARCH=1"
- "TARGET=GENERIC"))
+ ;; Dynamic older enables a few extra CPU architectures that
+ ;; were released before 2010.
+ '("DYNAMIC_ARCH=1" "DYNAMIC_OLDER=1" "TARGET=GENERIC"))
+ ;; On some of these architectures the CPU can't be detected.
;; On MIPS we force the "SICORTEX" TARGET, as for the other
;; two available MIPS targets special extended instructions
;; for Loongson cores are used.
;; Failed to detect CPU.
((string-prefix? "armhf" system)
'("TARGET=ARMV7"))
+ ((string-prefix? "riscv64" system)
+ '("TARGET=RISCV64_GENERIC"))
(else '()))))
;; no configure script
#:phases
;; Get libgfortran found when building in utest.
(setenv "FEXTRALIB"
(string-append "-L" (assoc-ref inputs "fortran-lib")
- "/lib"))
- #t)))))
+ "/lib")))))))
(inputs
`(("fortran-lib" ,gfortran "lib")))
(native-inputs
"05ifil6jj9424sr8kmircl8k4bmxnl3y12a79vwj1kxxva5gz50g"))
(file-name (git-file-name "blis" version))))
(native-inputs
- `(("python" ,python)
- ("perl" ,perl)))
+ (list python perl))
(build-system gnu-build-system)
(arguments
`(#:modules
(modify-phases %standard-phases
(delete 'configure)))) ;no configure script
(inputs
- `(("tbb" ,tbb)
- ("openblas" ,openblas)
- ("gmp" ,gmp)
- ("mpfr" ,mpfr)
- ("metis" ,metis)))
+ (list tbb openblas gmp mpfr metis))
(native-inputs
`(("cmake" ,cmake-minimal)
("m4" ,m4)))
(define-public cglm
(package
(name "cglm")
- (version "0.8.2")
+ (version "0.8.4")
(source
(origin
(method git-fetch)
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "1lcfl9ph4bnl3hckpx4hzwh8r4llnw94ik75igc5qy38wk468gmk"))))
- (build-system cmake-build-system)
+ (base32 "0zgckh56vcdar3a4n51r84wrizyd2ssqal4nsvxd4qdjm0rvb4h0"))))
+ (build-system meson-build-system)
(arguments
- `(#:configure-flags
- (list "-DCGLM_USE_TEST=ON")))
+ `(#:configure-flags '("-Dbuild_tests=true")))
(home-page "https://github.com/recp/cglm")
(synopsis "Mathematics C library for graphics programming")
(description
Cflags: -I${includedir}~%" out ,(version-prefix version 3)))))
#t))))))
(native-inputs
- `(("unzip" ,unzip)))
+ (list unzip))
(home-page "https://glm.g-truc.net/")
(synopsis "OpenGL Mathematics library")
(description "OpenGL Mathematics (GLM) is a header-only C++ mathematics
revised simplex and the branch-and-bound methods.")
(license license:lgpl2.1+)))
+;; Private Trilinos package for dealii-openmpi (similar to
+;; trilinos-serial-xyce and trilinos-parallel-xyce).
+;; This version is the latest known to be compatible with deal.II [1].
+;; Since the latest version of Trilinos is not necessarily supported by
+;; deal.II, it may be worth keeping this package even if and when Trilinos
+;; gets packaged separately for Guix (unless various versions of Trilinos are
+;; packaged).
+;;
+;; An insightful source of information for building Trilinos for deal.II lies
+;; in the Trilinos package for candi [2], which is a source-based installer
+;; for deal.II and its dependencies.
+;;
+;; [1]: https://www.dealii.org/current/external-libs/trilinos.html
+;; [2]: https://github.com/dealii/candi/blob/master/deal.II-toolchain/packages/trilinos.package
+(define trilinos-for-dealii-openmpi
+ (package
+ (name "trilinos-for-dealii-openmpi")
+ (version "12.18.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/trilinos/Trilinos/")
+ (commit
+ (string-append "trilinos-release-"
+ (string-replace-substring version "." "-")))))
+ (file-name (git-file-name "trilinos" version))
+ (sha256
+ (base32 "0fnwlhzsh85qj38cq3igbs8nm1b2jdgr2z734sapmyyzsy21mkgp"))))
+ (build-system cmake-build-system)
+ (native-inputs
+ `(("gfortran" ,gfortran)
+ ;; Trilinos's repository contains several C-shell scripts, but adding
+ ;; tcsh to the native inputs does not result in the check phase running
+ ;; any more tests than without it (nor is tcsh required to build
+ ;; Trilinos).
+ ;; It seems that Trilinos has replaced its use of C-shell test scripts
+ ;; with CMake's testing facilities.
+ ;; For example,
+ ;; packages/zoltan/doc/Zoltan_html/dev_html/dev_test_script.html [1]
+ ;; states that Zoltan's C-shell test script
+ ;; packages/zoltan/test/test_zoltan has been obsoleted by the tests now
+ ;; performed through CMake.
+ ;;
+ ;; Perl is required for some Zoltan tests and Python 2 for one ML test.
+ ;;
+ ;; [1]: https://cs.sandia.gov/zoltan/dev_html/dev_test_script.html
+ ("perl" ,perl)
+ ("python" ,python-2)))
+ (inputs
+ `(("blas" ,openblas)
+ ("lapack" ,lapack)
+ ("mumps" ,mumps-openmpi)
+ ("scalapack" ,scalapack)))
+ (propagated-inputs
+ `(("mpi" ,openmpi)))
+ (arguments
+ `(#:build-type "Release"
+ #:configure-flags
+ `("-DBUILD_SHARED_LIBS=ON"
+ ;; Obtain the equivalent of RelWithDebInfo but with -O3 (the Release
+ ;; default) rather than -O2 (the RelWithDebInfo default), to conform
+ ;; to candi's trilinos.package's compilation flags, which are -g -O3.
+ "-DCMAKE_C_FLAGS=-g"
+ "-DCMAKE_CXX_FLAGS=-g"
+ "-DCMAKE_Fortran_FLAGS=-g"
+
+ ;; Trilinos libraries that deal.II can interface with.
+ "-DTrilinos_ENABLE_Amesos=ON"
+ "-DTrilinos_ENABLE_AztecOO=ON"
+ "-DTrilinos_ENABLE_Epetra=ON"
+ "-DTrilinos_ENABLE_EpetraExt=ON"
+ "-DTrilinos_ENABLE_Ifpack=ON"
+ "-DTrilinos_ENABLE_ML=ON"
+ "-DTrilinos_ENABLE_MueLu=ON"
+ "-DTrilinos_ENABLE_ROL=ON"
+ ;; Optional; required for deal.II's GridIn::read_exodusii, but
+ ;; depends on netcdf.
+ ;; Enable if and when someone needs it.
+ ;;"-DTrilinos_ENABLE_SEACAS=ON"
+ "-DTrilinos_ENABLE_Sacado=ON"
+ "-DTrilinos_ENABLE_Teuchos=ON"
+ "-DTrilinos_ENABLE_Tpetra=ON"
+ "-DTrilinos_ENABLE_Zoltan=ON"
+
+ ;; Third-party libraries (TPLs) that Trilinos can interface with.
+ "-DBLAS_LIBRARY_NAMES=openblas"
+ "-DTPL_ENABLE_MPI=ON"
+ "-DTPL_ENABLE_MUMPS=ON"
+ "-DTPL_ENABLE_SCALAPACK=ON"
+
+ ;; Enable the tests but not the examples (which are enabled by
+ ;; default when enabling tests).
+ ;; Although some examples are run as tests, they are otherwise
+ ;; unnecessary since this is a private package meant for
+ ;; dealii-openmpi.
+ ;; Besides, some MueLu and ROL examples require a lot of memory to
+ ;; compile.
+ ;;
+ ;; (For future reference, note that some ROL and SEACAS examples
+ ;; require removing gfortran from CPLUS_INCLUDE_PATH as in the
+ ;; dune-istl, dune-localfunctions and dune-alugrid packages.)
+ "-DTrilinos_ENABLE_TESTS=ON"
+ "-DTrilinos_ENABLE_EXAMPLES=OFF"
+ ;; MueLu tests require considerably more time and memory to compile
+ ;; than the rest of the tests.
+ "-DMueLu_ENABLE_TESTS=OFF"
+
+ ;; The following options were gleaned from candi's trilinos.package.
+ ;; (We do not enable the complex instantiations, which are anyway
+ ;; provided only as an option in trilinos.package, because they are
+ ;; costly in compilation time and memory usage, and disk space [1].)
+ ;;
+ ;; [1]: https://www.docs.trilinos.org/files/TrilinosBuildReference.html#enabling-float-and-complex-scalar-types
+ "-DTrilinos_ENABLE_Ifpack2=OFF"
+ "-DTeuchos_ENABLE_FLOAT=ON"
+ "-DTpetra_INST_INT_LONG=ON"
+ "-DTPL_ENABLE_Boost=OFF")
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'configure 'fix-kokkos-config
+ (lambda _
+ ;; GNU Make 4.3 accidentally leaves the backslash preceding the
+ ;; number sign in strings containing a literal backslash–number
+ ;; sign (\#) [1, 2].
+ ;; This is still an issue in Trilinos 13.0.1, but should be fixed
+ ;; in the following version.
+ ;; (The latest versions of Kokkos incorporate the fix [2].)
+ ;;
+ ;; [1]: https://github.com/GEOSX/thirdPartyLibs/issues/136
+ ;; [2]: https://github.com/kokkos/kokkos/blob/3.4.00/Makefile.kokkos#L441
+ (substitute* "KokkosCore_config.h"
+ (("\\\\#") "#"))
+ #t))
+ (add-before 'check 'mpi-setup
+ ,%openmpi-setup))))
+ (home-page "https://trilinos.github.io/")
+ (synopsis "Algorithms for engineering and scientific problems")
+ (description
+ "The Trilinos Project is an effort to develop algorithms and enabling
+technologies within an object-oriented software framework for the solution of
+large-scale, complex multi-physics engineering and scientific problems.
+A unique design feature of Trilinos is its focus on packages.")
+ ;; The packages are variously licensed under more than just BSD-3 and
+ ;; LGPL-2.1+, but all the licenses are either BSD- or LGPL-compatible.
+ ;; See https://trilinos.github.io/license.html.
+ (license (list license:bsd-3 license:lgpl2.1+))))
+
(define-public dealii
(package
(name "dealii")
- (version "9.3.1")
+ (version "9.3.2")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/dealii/dealii/releases/"
"download/v" version "/dealii-" version ".tar.gz"))
(sha256
- (base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6"))
+ (base32 "1s0kawnljg24jj6nibwrif5gxdgg2daqfylhqqpl1lvmzmmxfhak"))
+ (patches (search-patches "dealii-fix-compiliation-with-boost-1.78.patch"
+ "dealii-fix-sundials.patch"))
(modules '((guix build utils)))
(snippet
'(begin
(outputs '("out" "doc"))
(native-inputs
;; Required to build the documentation.
- `(("dot" ,graphviz)
- ("doxygen" ,doxygen)
- ("perl" ,perl)))
+ (list graphviz doxygen perl))
(inputs
- `(("arpack" ,arpack-ng)
- ("blas" ,openblas)
- ("gfortran" ,gfortran)
- ("lapack" ,lapack)
- ("muparser" ,muparser)
- ("zlib" ,zlib)))
+ (list arpack-ng
+ openblas
+ gfortran
+ lapack
+ muparser
+ zlib))
(propagated-inputs
;; Some scripts are installed into share/deal.II/scripts that require
;; perl and python, but they are not executable (and some are missing the
;; Anyway, they are meant to be used at build time, so rather than adding
;; the interpreters here, any package depending on them should just add
;; the requisite interpreter to its native inputs.
- `(("boost" ,boost)
- ("hdf5" ,hdf5)
- ("suitesparse" ,suitesparse) ; For UMFPACK.
- ("tbb" ,tbb)))
+ (list boost hdf5 suitesparse ; For UMFPACK.
+ tbb))
(arguments
`(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease.
;; The tests take too long and must be explicitly enabled with "make
("p4est" ,p4est-openmpi)
("petsc" ,petsc-openmpi)
("slepc" ,slepc-openmpi)
+ ("trilinos" ,trilinos-for-dealii-openmpi)
,@(alist-delete "hdf5" (package-propagated-inputs dealii))))
(arguments
(substitute-keyword-arguments (package-arguments dealii)
(build-system cmake-build-system)
(outputs '("out"))
(native-inputs
- `(("unzip" ,unzip)))
+ (list unzip))
(inputs
`(("hdf5" ,hdf5)
;; FIXME: 'mkoctfile' fails with a linker error:
"1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
(build-system gnu-build-system)
(inputs
- `(("mpfr" ,mpfr)
- ("readline" ,readline)))
+ (list mpfr readline))
(home-page "http://w-calc.sourceforge.net/index.php")
(synopsis "Flexible command-line scientific calculator")
(description "Wcalc is a very capable calculator. It has standard functions
(native-inputs `(("gettext" ,gettext-minimal)
("qtbase" ,qtbase-5)
("qttools" ,qttools)))
- (inputs `(("libx11" ,libx11)
- ("zlib" ,zlib)
- ("libpng" ,libpng)
- ("gsl" ,gsl)))
+ (inputs (list libx11 zlib libpng gsl))
;; The upstream project file ("XaoS.pro") and the Makefile it generates are
;; not enough for this package to install properly. These phases fix that.
(arguments
("texlive" ,(texlive-updmap.cfg (list texlive-adjustbox
texlive-amsfonts
texlive-bibtex
+ texlive-capt-of
texlive-caption
texlive-cm
texlive-etoolbox
texlive-xcolor
texlive-xypic
texlive-generic-listofitems
- texlive-generic-ulem
- texlive-latex-capt-of
texlive-latex-cmap
texlive-latex-colortbl
texlive-latex-etoc
texlive-latex-framed
texlive-latex-geometry
texlive-latex-hanging
- texlive-latex-hyperref
+ texlive-hyperref
texlive-latex-multirow
texlive-latex-natbib
texlive-latex-needspace
texlive-latex-tocloft
texlive-latex-upquote
texlive-latex-varwidth
- texlive-latex-wasysym
+ texlive-ulem
+ texlive-wasysym
texlive-latex-wrapfig)))))
(inputs
`(("blas" ,openblas)
"0vr8c1mz1k6mz0sgh6n3scl5c3a71iqmy5fnydrgq504icj4vym4"))))
(build-system gnu-build-system)
(inputs
- `(("zlib" ,zlib)
- ("hdf5" ,hdf5-1.8)))
+ (list zlib hdf5-1.8))
(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
(define-public vc
(package
(name "vc")
- (version "1.4.1")
+ (version "1.4.2")
(source
(origin (method url-fetch)
(uri (string-append "https://github.com/VcDevel/Vc/releases/"
"download/" version "/Vc-" version ".tar.gz"))
(sha256
(base32
- "17qili8bf8r78cng65yf4qmgna8kiqjqbgcqbric6v9j6nkhkrk8"))))
+ "0lirdqzcxys9walz04bllsphydynk7973aimd5k1h1qbwi8z3lsh"))))
(build-system cmake-build-system)
(arguments
'(#:configure-flags
"1rllzcfwc042c336mhq262a8ha90x6afq30kvk60r7i4761j4yjm"))))
(build-system gnu-build-system)
(inputs
- `(("openlibm" ,openlibm)))
+ (list openlibm))
(arguments
`(#:tests? #f ; no tests
#:phases
(define-public jacal
(package
(name "jacal")
- (version "1c4")
+ (version "1c7")
(source (origin
(method url-fetch)
(uri (string-append
"http://groups.csail.mit.edu/mac/ftpdir/scm/jacal-"
version ".zip"))
- (sha256 (base32
- "055zrn12a1dmy0dqkwrkq3fklbhg3yir6vn0lacp4mvbg8573a3q"))
- (patches (search-patches "jacal-fix-texinfo.patch"))))
+ (sha256
+ (base32 "06a5sx9ikd62bpnd898g3yk818b020b1a27mk7dbfla2zizib4xz"))))
(build-system gnu-build-system)
(arguments
`(#:phases
(chmod wrapper #o555))))
(replace 'configure
(lambda* (#:key outputs #:allow-other-keys)
- (invoke "./configure"
+ (invoke "sh" "configure"
(string-append "--prefix="
(assoc-ref outputs "out"))))))))
- (inputs `(("scm" ,scm)))
- (native-inputs `(("unzip" ,unzip)
- ("texinfo" ,texinfo)))
+ (inputs (list scm))
+ (native-inputs (list unzip texinfo))
(synopsis "Symbolic mathematics system")
(description "GNU JACAL is an interactive symbolic mathematics program based on
Scheme. It manipulate and simplify a range of mathematical expressions such
theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.")
(license license:expat)))
+(define-public ocaml-z3
+ (package
+ (inherit z3)
+ (name "ocaml-z3")
+ (arguments
+ `(#:imported-modules ((guix build python-build-system)
+ ,@%gnu-build-system-modules)
+ #:modules (((guix build python-build-system) #:select (site-packages))
+ (guix build gnu-build-system)
+ (guix build utils))
+ #:tests? #f; no ml tests
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'bootstrap
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (setenv "OCAMLFIND_LDCONF" "ignore")
+ (setenv "OCAMLFIND_DESTDIR" (string-append out "/lib/ocaml/site-lib"))
+ (mkdir-p (string-append out "/lib/ocaml/site-lib"))
+ (substitute* "scripts/mk_util.py"
+ (("LIBZ3 = LIBZ3")
+ (string-append "LIBZ3 = LIBZ3 + ' -dllpath " out "/lib'"))
+ ;; Do not build z3 again, use the library passed as input
+ ;; instead
+ (("z3linkdep,") "\"\",")
+ (("z3linkdep)") "\"\")"))
+ (invoke "python" "scripts/mk_make.py"))))
+ (replace 'configure
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (invoke "./configure"
+ "--ml"
+ (string-append "--prefix=" (assoc-ref outputs "out")))))
+ (add-after 'configure 'change-directory
+ (lambda _
+ (chdir "build")
+ #t))
+ (replace 'build
+ (lambda _
+ (invoke "make" "ml")))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (invoke "ocamlfind" "install" "-destdir"
+ (string-append (assoc-ref outputs "out") "/lib/ocaml/site-lib")
+ "z3" "api/ml/META" "api/ml/z3enums.mli" "api/ml/z3enums.cmi"
+ "api/ml/z3enums.cmx" "api/ml/z3native.mli"
+ "api/ml/z3native.cmi" "api/ml/z3native.cmx"
+ "../src/api/ml/z3.mli" "api/ml/z3.cmi" "api/ml/z3.cmx"
+ "api/ml/libz3ml.a" "api/ml/z3ml.a" "api/ml/z3ml.cma"
+ "api/ml/z3ml.cmxa" "api/ml/z3ml.cmxs" "api/ml/dllz3ml.so"))))))
+ (native-inputs
+ `(("which" ,which)
+ ("python" ,python-wrapper)
+ ("ocaml" ,ocaml)
+ ("ocaml-findlib" ,ocaml-findlib)))
+ (propagated-inputs
+ (list ocaml-zarith))
+ (inputs
+ (list z3))))
+
(define-public elpa
(package
(name "elpa")
(build-system cmake-build-system)
(home-page "https://github.com/elemental/Elemental")
(native-inputs
- `(("gfortran" ,gfortran)))
+ (list gfortran))
(inputs
`(("blas" ,openblas)
("gfortran:lib" ,gfortran "lib")
version ".tar.gz"))
(sha256
(base32
- "0db9wgy9spwm76mgfisnifrlg69y9cadjgxjr4gdwzfgg6wgqf6d"))))
+ "1xgx3cd57vc7gbjic24j1q2za6j3ybz6nk4afvvpbwsf33xnlf4v"))))
(inputs
- `(("boost" ,boost)
- ("glu" ,glu)
- ("mesa" ,mesa)
- ("qtbase" ,qtbase-5)))
+ (list boost glu mesa qtbase-5))
(build-system cmake-build-system)
(synopsis "Toolset for the mCRL2 formal specification language")
(description
(inherit mcrl2)
(name "mcrl2-minimal")
(inputs
- `(("boost" ,boost)))
+ (list boost))
(arguments
'(#:configure-flags '("-DMCRL2_ENABLE_GUI_TOOLS=OFF")))))
("blas" ,openblas)
("suitesparse" ,suitesparse))) ;TODO: Add hypre
(arguments
- `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON"
+ `(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon"
+ "-DEXAMPLES_ENABLE_C:BOOL=ON"
"-DEXAMPLES_ENABLE_CXX:BOOL=ON"
"-DEXAMPLES_ENABLE_F77:BOOL=ON"
"-DEXAMPLES_ENABLE_F90:BOOL=ON"
(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.")
+ (properties
+ '((release-monitoring-url
+ . "https://computing.llnl.gov/projects/sundials/sundials-software")))
(license license:bsd-3)))
(define-public sundials-openmpi
,%openmpi-setup)))))
(synopsis "SUNDIALS with OpenMPI support")))
+(define-public sundials-julia
+ (package
+ (inherit sundials)
+ (name "sundials-julia")
+ (version "5.2.0")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/LLNL/sundials")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0nx4sqhmi126m14myzm7syv2053harav9snl0a247wnkcgs5rxrv"))))
+ (inputs
+ (modify-inputs (package-inputs sundials)
+ (prepend lapack)))
+ (arguments
+ (substitute-keyword-arguments (package-arguments sundials)
+ ((#:configure-flags flags '())
+ `(cons* "-DLAPACK_ENABLE:BOOL=ON"
+ ,flags))))
+ (synopsis "SUNDIALS with lapack support as required by julia-sundials-jll")))
+
(define-public combinatorial-blas
(package
(name "combinatorial-blas")
(define-public dune-common
(package
(name "dune-common")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method url-fetch)
version "/dune-common-" version ".tar.gz"))
(sha256
(base32
- "140q1zh44cr5yrjwg4b5ga803rkqv55vk30l2cqm29aklj1wb0rw"))))
+ "0sidwdkyrrqjkqhpvrlc991pzi5xzlvxk91s2n7qk3widwy7fch2"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'build 'build-tests
- (lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags))))))
+ (lambda* (#:key make-flags parallel-build? #:allow-other-keys)
+ (apply invoke "make" "build_tests"
+ `(,@(if parallel-build?
+ `("-j" ,(number->string (parallel-job-count)))
+ '())
+ ,@make-flags)))))))
(inputs
- `(("gmp" ,gmp)
- ("metis" ,metis)
- ("openblas" ,openblas)
- ("python" ,python)
- ("superlu" ,superlu)))
+ (list gmp metis openblas python superlu))
(native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)))
+ (list gfortran pkg-config))
(home-page "https://dune-project.org/")
(synopsis "Distributed and Unified Numerics Environment")
(description "DUNE, the Distributed and Unified Numerics Environment is a
(define-public dune-geometry
(package
(name "dune-geometry")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method url-fetch)
version "/dune-geometry-" version ".tar.gz"))
(sha256
(base32
- "1cicvlwbyyw76npicnblxckyvhbfn3ip8isydiv3hlrlz8zcg5nr"))))
+ "068mh3fd110xl27rwxqlqy4d9cpqw2vqm2pzfrripiaqscb3byfy"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'build 'build-tests
- (lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags))))))
+ (lambda* (#:key make-flags parallel-build? #:allow-other-keys)
+ (apply invoke "make" "build_tests"
+ `(,@(if parallel-build?
+ `("-j" ,(number->string (parallel-job-count)))
+ '())
+ ,@make-flags)))))))
(inputs
- `(("dune-common" ,dune-common)
- ;; Optional
- ("openblas" ,openblas)
- ("gmp" ,gmp)
- ("python" ,python)))
+ (list dune-common
+ ;; Optional
+ openblas gmp python))
(native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)))
+ (list gfortran pkg-config))
(home-page "https://dune-project.org/")
(synopsis "Distributed and Unified Numerics Environment")
(description "DUNE, the Distributed and Unified Numerics Environment is a
(define-public dune-uggrid
(package
(name "dune-uggrid")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "192miqgmfj6jwk969gydzpbv9ki7jg5nky3ydnrwa2nq29b5xkh0"))))
+ "11qz52g9d5k96fqik2lyi80xryw174rnny074pj70ardl6zzz83p"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'build 'build-tests
- (lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags))))))
+ (lambda* (#:key make-flags parallel-build? #:allow-other-keys)
+ (apply invoke "make" "build_tests"
+ `(,@(if parallel-build?
+ `("-j" ,(number->string (parallel-job-count)))
+ '())
+ ,@make-flags)))))))
(inputs
- `(("dune-common" ,dune-common)))
+ (list dune-common))
(native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)))
+ (list gfortran pkg-config))
(home-page "https://dune-project.org/")
(synopsis "Distributed and Unified Numerics Environment")
(description "DUNE, the Distributed and Unified Numerics Environment is a
(define-public dune-grid
(package
(name "dune-grid")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method url-fetch)
version "/dune-grid-" version ".tar.gz"))
(sha256
(base32
- "17fjz30qazjgl11sryyxnw9klai4yz1ji4bs68013xcxc5hdv27s"))))
+ "15iws03hkbmr4a4rqqb0rriz1m8szl96wdr7gw0jmrcnlzbdbbx5"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'build 'build-tests
- (lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags))))))
+ (lambda* (#:key make-flags parallel-build? #:allow-other-keys)
+ (apply invoke "make" "build_tests"
+ `(,@(if parallel-build?
+ `("-j" ,(number->string (parallel-job-count)))
+ '())
+ ,@make-flags)))))))
(inputs
- `(("dune-common" ,dune-common)
- ("dune-geometry" ,dune-geometry)
- ("gmp" ,gmp)
- ("metis" ,metis)
- ("openblas" ,openblas)
- ("python" ,python)))
+ (list dune-common
+ dune-geometry
+ gmp
+ metis
+ openblas
+ python))
(propagated-inputs
- `(("dune-uggrid" ,dune-uggrid)))
+ (list dune-uggrid))
(native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)))
+ (list gfortran pkg-config))
(home-page "https://dune-project.org/")
(synopsis "Distributed and Unified Numerics Environment")
(description "DUNE, the Distributed and Unified Numerics Environment is a
(define-public dune-istl
(package
(name "dune-istl")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method url-fetch)
version "/dune-istl-" version ".tar.gz"))
(sha256
(base32
- "0gl3wgz5rs6sb4m83440ny45sbx7z7lnbi3gx6r9nm3rvy5j33f9"))
- (patches (search-patches "dune-istl-2.7-fix-non-mpi-tests.patch"))))
+ "1cy69s1266hvnh8blznlvvkrf8i2g640rc3mf7kp872wgvdz4nb9"))))
(build-system cmake-build-system)
(arguments
`(#:phases
":"))
#t)))
(add-after 'build 'build-tests
- (lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags))))))
+ (lambda* (#:key make-flags parallel-build? #:allow-other-keys)
+ (apply invoke "make" "build_tests"
+ `(,@(if parallel-build?
+ `("-j" ,(number->string (parallel-job-count)))
+ '())
+ ,@make-flags)))))))
(inputs
- `(("dune-common" ,dune-common)
- ;; Optional
- ("metis" ,metis)
- ("suitesparse" ,suitesparse)
- ("superlu" ,superlu)
- ("openblas" ,openblas)
- ("gmp" ,gmp)
- ("python" ,python)))
+ (list dune-common
+ ;; Optional
+ metis
+ suitesparse
+ superlu
+ openblas
+ gmp
+ python))
(native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)))
+ (list gfortran pkg-config))
(home-page "https://dune-project.org/")
(synopsis "Distributed and Unified Numerics Environment")
(description "DUNE, the Distributed and Unified Numerics Environment is a
(define-public dune-localfunctions
(package
(name "dune-localfunctions")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method url-fetch)
version "/dune-localfunctions-" version ".tar.gz"))
(sha256
(base32
- "1yih59h6vngii696bx1c2vil02lriij4kz0nc583mjn9kiaqxfqd"))))
+ "031i42anrhi0ngpvp42rdjbkic7v3008fwild9xg7flffwvnpshg"))))
(build-system cmake-build-system)
(arguments
`(#:phases
":"))
#t)))
(add-after 'build 'build-tests
- (lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags))))))
+ (lambda* (#:key make-flags parallel-build? #:allow-other-keys)
+ (apply invoke "make" "build_tests"
+ `(,@(if parallel-build?
+ `("-j" ,(number->string (parallel-job-count)))
+ '())
+ ,@make-flags)))))))
(inputs
- `(("dune-common" ,dune-common)
- ("dune-geometry" ,dune-geometry)
- ;; Optional
- ("metis" ,metis)
- ("superlu" ,superlu)
- ("gmp" ,gmp)))
+ (list dune-common
+ dune-geometry
+ ;; Optional
+ metis
+ superlu
+ gmp))
(native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)))
+ (list gfortran pkg-config))
(home-page "https://dune-project.org/")
(synopsis "Distributed and Unified Numerics Environment") ; TODO
(description "This DUNE module provides interface and implementation for
(license license:gpl2)))
(define-public dune-alugrid
- (package
- (name "dune-alugrid")
- (version "2.7.0-git-81d35682")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://gitlab.dune-project.org/extensions/dune-alugrid.git")
- (commit "81d356827c84454b971937db02c02b90bbcd7fe5")))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0z54lwfp53prcrs94k8gwh047l9z642jll3l56xlyfr69z0b2zz1"))))
- (build-system cmake-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'patch-include
- (lambda _
- (substitute* "dune/alugrid/test/test-alugrid.cc"
- (("doc/grids/gridfactory/testgrids")
- "doc/dune-grid/grids/gridfactory/testgrids"))
- #t))
- (add-after 'build 'build-tests
- (lambda* (#:key inputs make-flags #:allow-other-keys)
- (setenv "CPLUS_INCLUDE_PATH"
- (string-append (assoc-ref inputs "dune-grid") "/share"))
- (apply invoke "make" "build_tests" make-flags))))))
- (inputs
- `(("dune-common" ,dune-common)
- ("dune-geometry" ,dune-geometry)
- ("dune-grid" ,dune-grid)
- ;; Optional
- ("metis" ,metis)
- ("openblas" ,openblas)
- ("python" ,python)
- ("superlu" ,superlu)
- ("gmp" ,gmp)
- ("zlib" ,zlib)))
- (native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)))
- (home-page "https://dune-project.org/")
- (synopsis "Distributed and Unified Numerics Environment")
- (description "ALUGrid is an adaptive, loadbalancing, unstructured
+ ;; This was the last commit on the releases/2.7 branch as of 2021-12-17,
+ ;; unfortunately there was no tag for any 2.7 release.
+ (let ((commit "51bde29a2dfa7cfac4fb73d40ffd42b9c1eb1d3d"))
+ (package
+ (name "dune-alugrid")
+ (version (git-version "2.7.1" "0" commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.dune-project.org/extensions/dune-alugrid.git")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0z16wg6llzxs7vjg2yilg31vwnkz8k050j6bspg3blbym0razy15"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-include
+ (lambda _
+ (substitute* "dune/alugrid/test/test-alugrid.cc"
+ (("doc/grids/gridfactory/testgrids")
+ "doc/dune-grid/grids/gridfactory/testgrids"))
+ #t))
+ (add-after 'build 'build-tests
+ (lambda* (#:key make-flags parallel-build? #:allow-other-keys)
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-append (assoc-ref inputs "dune-grid") "/share"))
+ (apply invoke "make" "build_tests"
+ `(,@(if parallel-build?
+ `("-j" ,(number->string (parallel-job-count)))
+ '())
+ ,@make-flags)))))))
+ (inputs
+ (list dune-common
+ dune-geometry
+ dune-grid
+ ;; Optional
+ metis
+ openblas
+ python
+ superlu
+ gmp
+ zlib))
+ (native-inputs
+ (list gfortran pkg-config))
+ (home-page "https://dune-project.org/")
+ (synopsis "Distributed and Unified Numerics Environment")
+ (description "ALUGrid is an adaptive, loadbalancing, unstructured
implementation of the DUNE grid interface supporting either simplices or
cubes.")
- (license license:gpl2+)))
+ (license license:gpl2+))))
(define-public dune-subgrid
- (package
- (name "dune-subgrid")
- (version "2.7.0-git-2103a363")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid")
- (commit "2103a363f32e8d7b60e66eee7ddecf969f6cf762")))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "1wsjlypd3835c3arqjkw836cxx5q67zy447wa65q634lf6f6v9ia"))))
- (build-system cmake-build-system)
- (arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'build 'build-tests
- (lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags))))))
- (inputs
- `(("dune-common" ,dune-common)
- ("dune-geometry" ,dune-geometry)
- ("dune-grid" ,dune-grid)
- ;; Optional
- ("metis" ,metis)
- ("openblas" ,openblas)
- ("gmp" ,gmp)))
- (native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)))
- (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php")
- (synopsis "Distributed and Unified Numerics Environment")
- (description "The dune-subgrid module marks elements of
+ ;; This was the last commit on the releases/2.7 branch as of 2021-12-17.
+ ;; Unfortunately the dune-subgrid repository contains no release tags.
+ (let ((commit "45d1ee9f3f711e209695deee97912f4954f7f280"))
+ (package
+ (name "dune-subgrid")
+ (version (git-version "2.7.1" "0" commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0xjf7865wil7kzym608kv3nc3ff3m3nlqich4k9wjyvy3lz6panh"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-after 'build 'build-tests
+ (lambda* (#:key make-flags parallel-build? #:allow-other-keys)
+ (apply invoke "make" "build_tests"
+ `(,@(if parallel-build?
+ `("-j" ,(number->string (parallel-job-count)))
+ '())
+ ,@make-flags)))))))
+ (inputs
+ (list dune-common
+ dune-geometry
+ dune-grid
+ ;; Optional
+ metis
+ openblas
+ gmp))
+ (native-inputs
+ (list gfortran pkg-config))
+ (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php")
+ (synopsis "Distributed and Unified Numerics Environment")
+ (description "The dune-subgrid module marks elements of
another hierarchical dune grid. The set of marked elements can then be
accessed as a hierarchical dune grid in its own right. Dune-Subgrid
provides the full grid interface including adaptive mesh refinement.")
- (license license:gpl2+)))
+ (license license:gpl2+))))
(define-public dune-typetree
(package
(name "dune-typetree")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "1rhv25yg0q1hw50c8wlfqhgwrjl4mh62zq9v14ilwgzbfgxmpiy7"))))
+ "1kx9k8i7pdw6l6ny6nq85v5p1nd6yxldzaj8k3nizaz3q1j407pv"))))
(build-system cmake-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'build 'build-tests
- (lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags))))))
+ (lambda* (#:key make-flags parallel-build? #:allow-other-keys)
+ (apply invoke "make" "build_tests"
+ `(,@(if parallel-build?
+ `("-j" ,(number->string (parallel-job-count)))
+ '())
+ ,@make-flags)))))))
(inputs
- `(("dune-common" ,dune-common)
- ;; Optional
- ("openblas" ,openblas)
- ("python" ,python)
- ("metis" ,metis)
- ("superlu" ,superlu)
- ("gmp" ,gmp)))
+ (list dune-common
+ ;; Optional
+ openblas
+ python
+ metis
+ superlu
+ gmp))
(native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)))
+ (list gfortran pkg-config))
(home-page "https://dune-project.org/")
(synopsis "Distributed and Unified Numerics Environment")
(description "TypeTree is a template library for constructing and
(define-public dune-functions
(package
(name "dune-functions")
- (version "2.7.0")
+ (version "2.7.1")
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "1na4gcih0kin37ksj2xj07ds04v7zx53pjdhm1hzy55jjfqdjk8h"))))
+ "04dhr4asnl38bf1gp8hrk31maav33m7q71lhl2n5yk1q1x6i77nw"))))
(build-system cmake-build-system)
(arguments
`(#:phases
"--exclude-regex gridviewfunctionspacebasistest")
#t))
(add-after 'build 'build-tests
- (lambda* (#:key make-flags #:allow-other-keys)
- (apply invoke "make" "build_tests" make-flags))))))
+ (lambda* (#:key make-flags parallel-build? #:allow-other-keys)
+ (apply invoke "make" "build_tests"
+ `(,@(if parallel-build?
+ `("-j" ,(number->string (parallel-job-count)))
+ '())
+ ,@make-flags)))))))
(inputs
- `(("dune-common" ,dune-common)
- ("dune-istl" ,dune-istl)
- ("dune-localfunctions" ,dune-localfunctions)
- ("dune-grid" ,dune-grid)
- ("dune-geometry" ,dune-geometry)
- ("dune-typetree" ,dune-typetree)
- ("openblas" ,openblas)
- ("metis" ,metis)
- ("python" ,python)
- ("superlu" ,superlu)
- ("gmp" ,gmp)))
+ (list dune-common
+ dune-istl
+ dune-localfunctions
+ dune-grid
+ dune-geometry
+ dune-typetree
+ openblas
+ metis
+ python
+ superlu
+ gmp))
(native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)))
+ (list gfortran pkg-config))
(home-page "https://dune-project.org/")
(synopsis "Distributed and Unified Numerics Environment")
(description "The dune-functions module provides an abstraction layer for
(license (list license:lgpl3+ license:gpl2))))
(define-public dune-pdelab
- (package
- (name "dune-pdelab")
- (version "2.7.0-git-476fe437")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
- (commit "476fe43763fa6f459c5e4658e2a2b4b5582db834")))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0cs36piqzn6rq0j2ih3ab3q3q9yg199wk72k5qi86pkzh7i7fdn1"))))
- (build-system cmake-build-system)
- (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
- (inputs
- `(("dune-common" ,dune-common)
- ("dune-istl" ,dune-istl)
- ("dune-localfunctions" ,dune-localfunctions)
- ("dune-geometry" ,dune-geometry)
- ("dune-grid" ,dune-grid)
- ("dune-typetree" ,dune-typetree)
- ("dune-functions" ,dune-functions)
- ;; Optional
- ("openblas" ,openblas)
- ("eigen" ,eigen)
- ("metis" ,metis)
- ("python" ,python)
- ("superlu" ,superlu)
- ("gmp" ,gmp)))
- (native-inputs
- `(("gfortran" ,gfortran)
- ("pkg-config" ,pkg-config)))
- (home-page "https://dune-project.org/")
- (synopsis "Differential equations solver toolbox")
- (description "PDELab is a partial differential equations solver toolbox
+ ;; This was the last commit on the releases/2.7 branch as of 2021-12-17,
+ ;; unfortunately there was no tag for any 2.7 release.
+ (let ((commit "09aef74d95661d18a7789d2f517ae77797eec738"))
+ (package
+ (name "dune-pdelab")
+ (version (git-version "2.7.1" "0" commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.dune-project.org/pdelab/dune-pdelab")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0nv69ayr4gln9m1s94z9zkrxqi8nzar3z6awnvgqz595nmjf82ac"))))
+ (build-system cmake-build-system)
+ (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled
+ (inputs
+ (list dune-common
+ dune-istl
+ dune-localfunctions
+ dune-geometry
+ dune-grid
+ dune-typetree
+ dune-functions
+ ;; Optional
+ openblas
+ eigen
+ metis
+ python
+ superlu
+ gmp))
+ (native-inputs
+ (list gfortran pkg-config))
+ (home-page "https://dune-project.org/")
+ (synopsis "Differential equations solver toolbox")
+ (description "PDELab is a partial differential equations solver toolbox
built on top of DUNE, the Distributed and Unified Numerics Environment.")
- ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
- (license (list license:lgpl3+ license:gpl2))))
+ ;; Either GPL version 2 with "runtime exception" or LGPLv3+.
+ (license (list license:lgpl3+ license:gpl2)))))
(define add-openmpi-to-dune-package
(let ((dune-package?
(if (dune-package? p)
(package (inherit p)
(name (string-append (package-name p) "-openmpi"))
- (inputs `(,@(package-inputs p)
- ("openmpi" ,openmpi)))
+ (inputs (modify-inputs (package-inputs p)
+ (append openmpi)))
(arguments
(substitute-keyword-arguments (package-arguments p)
((#:phases phases '%standard-phases)
(base32 "0h4xj6pyyac79ka5ibqjilfa3s9j3yxnzgpwc57b54kfh2bj3447"))))
(build-system gnu-build-system)
(inputs
- `(("python2" ,python-2)))
+ (list python-2))
(arguments
`(#:tests? #f ; no tests
#:phases
(define-public nauty
(package
(name "nauty")
- (version "2.7r1")
+ (version "2.7r3")
(source
(origin
(method url-fetch)
"https://pallini.di.uniroma1.it/"
"nauty" (string-join (string-split version #\.) "") ".tar.gz"))
(sha256
- (base32 "0xsfqfcknbd6g6wzpa5l7crmmk3bf3zjh37rhylq6b20dqcmvjkn"))))
+ (base32 "1hl81gpf3xjf809w04jczvilq1ixy9ch1qrax8a7lgx52svna1jg"))))
(build-system gnu-build-system)
(outputs '("out" "lib"))
(arguments
(append '("formats.txt" "README" "schreier.txt")
(find-files "." "\\.pdf$")))))))))
(inputs
- `(("gmp" ,gmp))) ;for sumlines
+ (list gmp)) ;for sumlines
(home-page "https://pallini.di.uniroma1.it/")
(synopsis "Library for graph automorphisms")
(description "@code{nauty} (No AUTomorphisms, Yes?) is a set of
"1j5aji1g2vmdvc0gqz45n2ll2l2f6czca04wiyfl5g3sm3a6vhvb"))))
(build-system gnu-build-system)
(native-inputs
- `(("m4" ,m4)))
+ (list m4))
(inputs
- `(("glpk" ,glpk)
- ("gmp" ,gmp)))
+ (list glpk gmp))
(home-page "https://www.bugseng.com/parma-polyhedra-library")
(synopsis
"Parma Polyhedra Library for computations with polyhedra")
(base32
"0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
(build-system cmake-build-system)
- (inputs `(("qtbase" ,qtbase-5)))
- (native-inputs `(("qttools" ,qttools)))
+ (inputs (list qtbase-5))
+ (native-inputs (list qttools))
(arguments
`(#:phases
(modify-phases %standard-phases
("doxygen" ,doxygen)
("file" ,file)))
(inputs
- `(("gmp" ,gmp)
- ("mpfr" ,mpfr)
- ("libxml2" ,libxml2)
- ("curl" ,curl)
- ("icu4c" ,icu4c)
- ("gnuplot" ,gnuplot)
- ("readline" ,readline)
- ("libiconv" ,libiconv)))
+ (list gmp
+ mpfr
+ libxml2
+ curl
+ icu4c
+ gnuplot
+ readline))
(arguments
`(#:phases
(modify-phases %standard-phases
(base32 "1nrx7gp6f1yalbdda1gb97azhbr4xclq2xf08vvbvsk8jfd6fd2v"))))
(build-system glib-or-gtk-build-system)
(native-inputs
- `(("pkg-config" ,pkg-config)
- ("intltool" ,intltool)
- ("automake" ,automake)
- ("autoconf" ,autoconf)
- ("libtool" ,libtool)
- ("file" ,file)))
+ (list pkg-config
+ intltool
+ automake
+ autoconf
+ libtool
+ file))
(inputs
- `(("gmp" ,gmp)
- ("mpfr" ,mpfr)
- ("libqalculate" ,libqalculate)
- ("libxml2" ,libxml2)
- ("glib" ,glib)
- ("gtk+" ,gtk+)))
+ (list gmp
+ mpfr
+ libqalculate
+ libxml2
+ glib
+ gtk+))
(arguments
`(#:phases
(modify-phases %standard-phases
(define-public why3
(package
(name "why3")
- (version "1.3.3")
+ (version "1.4.0")
(source (origin
- (method url-fetch)
- (uri (string-append "https://gforge.inria.fr/frs/download.php/file"
- "/38367/why3-" version ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.inria.fr/why3/why3")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "1n0a2nn1gnk0zg339lh698g4wpk7m8m1vyi2yvifd5adqvk4milw"))))
+ "0pfsiddnk26f384wbazfpgzh1n1ibf3xq101q74mxvczi7z0a791"))))
(build-system ocaml-build-system)
(native-inputs
- `(("coq" ,coq)
- ("ocaml" ,ocaml)
- ("which" ,which)))
+ (list autoconf automake coq ocaml which))
(propagated-inputs
- `(("camlzip" ,camlzip)
- ("ocaml-graph" ,ocaml-graph)
- ("ocaml-menhir" ,ocaml-menhir)
- ("ocaml-num" ,ocaml-num)
- ("ocaml-zarith" ,ocaml-zarith)))
+ (list camlzip ocaml-graph ocaml-menhir ocaml-num ocaml-zarith))
(inputs
- `(("coq-flocq" ,coq-flocq)
- ("emacs-minimal" ,emacs-minimal)
- ("zlib" ,zlib)))
+ (list coq-flocq emacs-minimal zlib))
(arguments
`(#:phases
(modify-phases %standard-phases
- (add-before 'configure 'fix-configure
+ (add-before 'configure 'bootstrap
(lambda _
+ (invoke "./autogen.sh")
(setenv "CONFIG_SHELL" (which "sh"))
(substitute* "configure"
+ (("#! /bin/sh") (string-append "#!" (which "sh")))
;; find ocaml-num in the correct directory
(("\\$DIR/nums.cma") "$DIR/num.cma")
(("\\$DIR/num.cmi") "$DIR/core/num.cmi"))
(define-public frama-c
(package
(name "frama-c")
- (version "22.0")
+ (version "24.0")
(source (origin
(method url-fetch)
(uri (string-append "http://frama-c.com/download/frama-c-"
- version "-Titanium.tar.gz"))
+ version "-Chromium.tar.gz"))
(sha256
(base32
- "1mq1fijka95ydrla486yr4w6wdl9l7vmp512s1q00b0p6lmfwmkh"))))
+ "0x1xgip50jdz1phsb9rzwf2ra8lshn1hmd9g967xia402wrg3sjf"))))
(build-system ocaml-build-system)
(arguments
`(#:tests? #f; no test target in Makefile
(setenv "CONFIG_SHELL"
(search-input-file inputs "/bin/sh")))))))
(inputs
- `(("gmp" ,gmp)))
+ (list gmp))
(propagated-inputs
- `(("ocaml-biniou" ,ocaml-biniou)
- ("ocaml-easy-format" ,ocaml-easy-format)
- ("ocaml-graph" ,ocaml-graph)
- ("ocaml-yojson" ,ocaml-yojson)
- ("ocaml-zarith" ,ocaml-zarith)
- ("why3" ,why3)))
+ (list ocaml-biniou
+ ocaml-easy-format
+ ocaml-graph
+ ocaml-yojson
+ ocaml-zarith
+ why3))
(native-search-paths
(list (search-path-specification
(variable "FRAMAC_SHARE")
(invoke "make" "-j" (number->string (parallel-job-count))
"blitz-doc"))))))
(native-inputs
- `(("python" ,python)
- ("texinfo" ,texinfo)))
+ (list python texinfo))
(synopsis "C++ template class library for multidimensional arrays")
(description "Blitz++ is a C++ template class library that provides
high-performance multidimensional array containers for scientific computing.")
(license (list license:artistic2.0
license:bsd-3
license:lgpl3+))))
+
+(define-public fxdiv
+ ;; There is currently no tag in this repo.
+ (let ((commit "63058eff77e11aa15bf531df5dd34395ec3017c8")
+ (version "0.0")
+ (revision "1"))
+ (package
+ (name "fxdiv")
+ (version (git-version version revision commit))
+ (home-page "https://github.com/Maratyszcza/FXdiv")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference (url home-page) (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0zwzh8gmbx4m6b18s5nf13b0dk5yjkd1fs8f421bl7fz5f9gjd9f"))
+ (patches (search-patches "fxdiv-system-libraries.patch"))))
+ (build-system cmake-build-system)
+ (inputs
+ (list googletest googlebenchmark))
+ (synopsis
+ "C++ library for division via fixed-point multiplication by inverse")
+ (description
+ "On modern CPUs and GPUs, integer division is several times slower than
+multiplication. FXdiv implements an algorithm to replace an integer division
+with a multiplication and two shifts. This algorithm improves performance
+when an application performs repeated divisions by the same divisor.")
+ (license license:expat))))
+
+(define-public fp16
+ ;; There is currently no tag in this repo.
+ (let ((commit "0a92994d729ff76a58f692d3028ca1b64b145d91")
+ (version "0.0")
+ (revision "1"))
+ (package
+ (name "fp16")
+ (version (git-version version revision commit))
+ (home-page "https://github.com/Maratyszcza/FP16")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference (url home-page) (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "05mm4vrxsac35hjf5djif9r6rdxj9ippg97ia3p6q6b8lrp7srwv"))
+ (patches (search-patches "fp16-system-libraries.patch"))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:imported-modules ((guix build python-build-system)
+ ,@%cmake-build-system-modules)
+ #:modules (((guix build python-build-system)
+ #:select (site-packages))
+ (guix build cmake-build-system)
+ (guix build utils))
+ #:phases (modify-phases %standard-phases
+ (add-after 'install 'move-python-files
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; Python files get installed to $includedir (!).
+ ;; Move them to the usual Python site directory.
+ (let* ((out (assoc-ref outputs "out"))
+ (include (string-append out "/include"))
+ (site (site-packages inputs outputs))
+ (target (string-append site "/fp16")))
+ (mkdir-p target)
+ (for-each (lambda (file)
+ (rename-file file
+ (string-append target "/"
+ (basename
+ file))))
+ (find-files include "\\.py$"))))))))
+ (native-inputs
+ (list python-wrapper))
+ (inputs
+ (list psimd googletest googlebenchmark))
+ (synopsis "C++ library for half-precision floating point formats")
+ (description
+ "This header-only C++ library implements conversion to and from
+half-precision floating point formats.")
+ (license license:expat))))
+
+(define-public optizelle
+ (let ((commit "ed4160b5287518448caeb34789d92dc6a0b7e2cc"))
+ (package
+ (name "optizelle")
+ (version (git-version "1.3.0" "0" commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/OptimoJoe/Optizelle")
+ (commit commit)))
+ (file-name (git-file-name "optizelle" commit))
+ (sha256
+ (base32
+ "0rjrs5sdmd33a9f4xm8an7p0953aa0bxsmr4hs3ss1aad9k181vq"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Reduce the stopping tolerance in one test so that the
+ ;; convergence check returns the correct stopping
+ ;; condition.
+ (substitute*
+ "src/unit/linear_algebra/tcg_loss_of_orthogonality.cpp"
+ (("1e-13") "5e-14"))
+ ;; Skip one set of python tests. See
+ ;; https://github.com/OptimoJoe/Optizelle/issues/2.
+ (substitute*
+ "src/examples/inequality_scaling/CMakeLists.txt"
+ (("add_unit(.*)\\$\\{interfaces\\}(.*)$" all middle end)
+ (string-append "add_unit" middle "\"cpp\"" end)))
+ ;; Install the licence for Optizelle, without also
+ ;; including the licences for the dependencies.
+ (substitute* "licenses/CMakeLists.txt"
+ (("file.*package.*$" all)
+ (string-append "# " all))
+ ((".*[^l].[.]txt\\)\n") "")
+ (("add_license.*\"\n") ""))
+ #t))))
+ (build-system cmake-build-system)
+ (arguments
+ `(#:imported-modules ((guix build python-build-system)
+ ,@%cmake-build-system-modules)
+ #:modules (((guix build python-build-system) #:select
+ (python-version))
+ (guix build cmake-build-system)
+ (guix build utils))
+ #:configure-flags `("-DCMAKE_CXX_FLAGS:STRING=-pthread"
+ "-DENABLE_CPP_UNIT:BOOL=ON"
+ "-DENABLE_CPP_EXAMPLES:BOOL=ON"
+ "-DENABLE_PYTHON:BOOL=ON"
+ "-DENABLE_PYTHON_UNIT:BOOL=ON"
+ "-DENABLE_PYTHON_EXAMPLES:BOOL=ON"
+ ,(string-append "-DBLAS_LIBRARY:FILEPATH="
+ (assoc-ref %build-inputs
+ "blas/lapack")
+ "/lib/libopenblas.so")
+ ,(string-append "-DLAPACK_LIBRARY:FILEPATH="
+ (assoc-ref %build-inputs
+ "fortran:lib")
+ "/lib/libgfortran.so;"
+ (assoc-ref %build-inputs
+ "fortran:lib")
+ "/lib/libquadmath.so"))
+ #:phases
+ (modify-phases %standard-phases
+ (add-after 'unpack 'set-numpy-path ; Needed for the unit tests.
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let* ((pyver (python-version (assoc-ref inputs "python")))
+ (npdir (string-append (assoc-ref inputs "numpy")
+ "/lib/python" pyver
+ "/site-packages")))
+ (substitute* "src/cmake/Modules/Optizelle.cmake"
+ (("PYTHONPATH=")
+ (string-append "LD_LIBRARY_PATH=$ENV{LIBRARY_PATH};"
+ "PYTHONPATH=" npdir ":"))))))
+ (delete 'install-license-files)))) ; LICENSE.txt is installed.
+ (inputs
+ `(("blas/lapack" ,openblas)
+ ("fortran:lib" ,gfortran "lib")
+ ("jsoncpp" ,jsoncpp)
+ ("numpy" ,python-numpy)
+ ("python" ,python)))
+ (native-inputs
+ `(("fortran" ,gfortran)
+ ("pkg-config" ,pkg-config)))
+ (home-page "https://www.optimojoe.com/products/optizelle/")
+ (synopsis "Mathematical optimization library")
+ (description "@code{optizelle} is a software library designed to
+solve nonlinear optimization problems. Four types of problem are
+considered: unconstrained, equality constrained, inequality
+constrained and constrained. Constraints may be applied as values of
+functions or sets of partial differential equations (PDEs).
+
+Solution algorithms such as the preconditioned nonlinear conjugate
+gradient method, sequential quadratic programming (SQP) and the
+primal-dual interior-point method are made available. Interfaces are
+provided for applications written in C++ and Python. Parallel
+computation is supported via MPI.")
+ (license license:bsd-2))))
HCoop / jackhill / guix / guix.git / blobdiff