;;; 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 © 2015–2021 Ricardo Wurmus <rekado@elephly.net>
;;; 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>
(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
programming language.")
(license license:gpl3+)))
-(define-public python2-cvxopt
- (package-with-python2 python-cvxopt))
-
(define-public units
(package
(name "units")
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 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.
(propagated-inputs
(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.
(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
(list doxygen
;("freeimage" ,freeimage)
"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)
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
(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
(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
(list zlib))
(native-inputs
(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
- (list gcc flex 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
- (list 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
(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
- (list 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
;; Failed to detect CPU.
((string-prefix? "armhf" system)
'("TARGET=ARMV7"))
+ ((string-prefix? "riscv64" system)
+ '("TARGET=RISCV64_GENERIC"))
(else '()))))
;; no configure script
#:phases
(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
("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-tocloft
texlive-latex-upquote
texlive-latex-varwidth
+ texlive-ulem
texlive-wasysym
texlive-latex-wrapfig)))))
(inputs
(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 (list scm))
(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
(list gmp metis openblas python superlu))
(native-inputs
(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
(list dune-common
;; Optional
(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
(list dune-common))
(native-inputs
(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
(list dune-common
dune-geometry
(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
(list dune-common
;; Optional
(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
(list dune-common
dune-geometry
(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
- (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
+ ;; 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
- (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
+ ;; 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
(list dune-common
;; Optional
(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
(list dune-common
dune-istl
(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
- (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
+ ;; 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)
curl
icu4c
gnuplot
- readline
- libiconv))
+ readline))
(arguments
`(#:phases
(modify-phases %standard-phases
HCoop / jackhill / guix / guix.git / blobdiff