;;; Copyright © 2015–2022 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 © 2015-2022 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 © 2021 Pierre-Antoine Bouttier <pierre-antoine.bouttier@univ-grenoble-alpes.fr>
;;; Copyright © 2022 Zhu Zihao <all_but_last@163.com>
;;; Copyright © 2022 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2022 Philip McGrath <philip@philipmcgrath.com>
+;;; Copyright © 2022 Marek Felšöci <marek@felsoci.sk>
+;;; Copyright © 2022 vicvbcun <guix@ikherbers.com>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (ice-9 match)
#:use-module (gnu packages)
#:use-module ((guix licenses) #:prefix license:)
+ #:use-module (guix gexp)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix git-download)
(define-public cddlib
(package
(name "cddlib")
- (version "0.94i")
+ (version "0.94m")
(source
(origin
- (method url-fetch)
- (uri (string-append "ftp://ftp.math.ethz.ch/users/fukudak/cdd/cddlib-"
- (string-delete #\. version) ".tar.gz"))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/cddlib/cddlib")
+ (commit version)))
(sha256
(base32
- "00zdgiqb91vx6gd2103h3ijij0llspsxc6zz3iw2bll39fvkl4xq"))))
+ "09s8323h5w9j6mpl1yc6lm770dkskfxd2ayyafkcjllmnncxzfa0"))))
(build-system gnu-build-system)
(inputs
(list gmp))
+ (native-inputs (list autoconf
+ automake
+ libtool
+ texlive-amsfonts
+ texlive-dvips-l3backend
+ texlive-latex-graphics
+ texlive-latex-l3backend
+ texlive-tiny))
+ (arguments
+ (list #:configure-flags
+ #~(list (string-append "--docdir=" #$output
+ "/share/doc/" #$name "-" #$version))))
(home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html")
(synopsis "Library for convex hulls and extreme rays of polyhedra")
(description
(define-public gnuplot
(package
(name "gnuplot")
- (version "5.4.3")
+ (version "5.4.4")
(source (origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
version "/gnuplot-"
version ".tar.gz"))
(sha256
- (base32 "112dplskbkdbaqi935m2xlk1xsw8s5l568wm7xad75hgp6x9py2i"))))
+ (base32 "00h97y8njhvfjbdvc0njw0znxbrlfynd1iazn8w3anvzhsvh08rp"))))
(build-system gnu-build-system)
- (inputs (list readline cairo pango gd lua))
(native-inputs
- `(("pkg-config" ,pkg-config)
- ("texlive" ,texlive-tiny)))
- (arguments `(#:configure-flags (list (string-append
- "--with-texdir=" %output
- "/texmf-local/tex/latex/gnuplot"))
- ;; Plot on a dumb terminal during tests.
- #:make-flags '("GNUTERM=dumb")))
+ (list pkg-config texlive-tiny))
+ (inputs
+ (list cairo gd lua pango readline))
+ (arguments
+ (list #:configure-flags
+ #~(list (string-append "--with-texdir=" #$output
+ "/texmf-local/tex/latex/gnuplot"))
+ ;; Plot on a dumb terminal during tests.
+ #:make-flags #~'("GNUTERM=dumb")))
(home-page "http://www.gnuplot.info")
(synopsis "Command-line driven graphing utility")
(description "Gnuplot is a portable command-line driven graphing
(("/bin/mv") "mv"))
(substitute* "fortran/src/Makefile.in"
(("libhdf5_fortran_la_LDFLAGS =")
- (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath="
+ (string-append "libhdf5_fortran_la_LDFLAGS = -Wl,-rpath="
(assoc-ref outputs "fortran") "/lib")))
(substitute* "hl/fortran/src/Makefile.in"
(("libhdf5hl_fortran_la_LDFLAGS =")
HDF5 file is encoded according to the HDF File Format Specification.")
(license (license:x11-style "file://COPYING"))))
+(define-public itex2mml
+ (package
+ (name "itex2mml")
+ (version "1.6.1")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://golem.ph.utexas.edu"
+ "/~distler/blog/files/itexToMML-"
+ version
+ ".tar.gz"))
+ (sha256
+ (base32
+ "0pz51c0hfh2mg8xli0wj7hf92s3b7yf5r4114g8z8722lcm5gwiy"))
+ (snippet
+ #~(begin
+ (use-modules (guix build utils))
+ (delete-file-recursively "itex-binaries")))))
+ (build-system gnu-build-system)
+ (native-inputs
+ (list bison
+ flex))
+ (arguments
+ (list
+ #:make-flags #~(list (string-append "BINDIR=" #$output "/bin/")
+ (string-append "CC=" #$(cc-for-target)))
+ #:tests? #f ;; there are none
+ #:phases
+ #~(modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'build 'chdir
+ (lambda args
+ (chdir "itex-src")))
+ (add-before 'install 'make-bindir
+ (lambda args
+ (mkdir-p (string-append #$output "/bin"))))
+ (add-after 'install 'install-doc
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((doc-prefix (or (assoc-ref outputs "doc")
+ #$output))
+ (itex2mml+version (strip-store-file-name #$output))
+ (doc-dir (string-append doc-prefix
+ "/share/doc/"
+ itex2mml+version)))
+ (install-file "../README" doc-dir)))))))
+ (home-page "https://golem.ph.utexas.edu/~distler/blog/itex2MML.html")
+ (synopsis "LaTeX to XHTML/MathML converter")
+ (description
+ "The @command{itex2MML} utility is a stream filter. It takes text with
+embedded itex equations, converts the itex equations to MathML, and outputs
+the resulting text.")
+ (license (list license:lgpl2.0+ license:gpl2+ license:mpl1.1))))
+
(define-public itpp
(package
(name "itpp")
("qt" ,qtbase-5)
,@(package-inputs octave-cli)))
(native-inputs
- `(("qttools" , qttools) ;for lrelease
+ `(("qttools-5" , qttools-5) ;for lrelease
("texlive" ,(texlive-updmap.cfg (list texlive-epsf))) ; for texi2dvi
,@(package-native-inputs octave-cli)))
(arguments
(define-public gmsh
(package
(name "gmsh")
- (version "4.9.5")
+ (version "4.10.5")
(source
(origin
- (method git-fetch)
- (uri (git-reference
- (url "https://gitlab.onelab.info/gmsh/gmsh.git")
- (commit
- (string-append "gmsh_"
- (string-replace-substring version "." "_")))))
- (file-name (git-file-name name version))
- (sha256
- (base32 "0asd9p64ng5l2zk5glc33x3ynnvdpndlflg3q9mr0jxr7y9x0lrm"))
- (modules '((guix build utils)))
- (snippet
- '(begin
- (delete-file-recursively "contrib/metis")
- #t))))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://gitlab.onelab.info/gmsh/gmsh.git")
+ (commit
+ (string-append "gmsh_"
+ (string-replace-substring version "." "_")))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "08p39yjgf3lbnjg90skpmsq9n1a9pmwppdmy5s94dc6sq2nfr7xl"))
+ (modules '((guix build utils)))
+ (snippet
+ '(delete-file-recursively "contrib/metis"))))
(build-system cmake-build-system)
(propagated-inputs
(list fltk
metis
opencascade-occt))
(inputs
- `(("fontconfig" ,fontconfig)
- ("libxft" ,libxft)
- ("python" ,python)))
+ (list fontconfig
+ libxft
+ python))
(arguments
`(#:configure-flags `("-DENABLE_SYSTEM_CONTRIB:BOOL=ON"
"-DENABLE_BUILD_SHARED:BOOL=ON"
"/lib/libgmsh.so")))
(substitute* "api/gmsh.py"
(("find_library\\(\"gmsh\"\\)")
- (simple-format #f "\"~a\"" libgmsh))))
- #t)))))
+ (simple-format #f "\"~a\"" libgmsh)))))))))
(home-page "http://gmsh.info/")
(synopsis "3D finite element grid generator")
(description "Gmsh is a 3D finite element grid generator with a built-in
(native-inputs
(list pkg-config
;;("python-astropy" ,python-astropy) ;; FIXME: Package this.
- qttools python-sip-4))
+ qttools-5 python-sip-4))
(inputs
(list ghostscript ;optional, for EPS/PS output
python-dbus
python-h5py ;optional, for HDF5 data
python-pyqt
qtbase-5
- qtsvg))
+ qtsvg-5))
(propagated-inputs
(list python-numpy))
(home-page "https://veusz.github.io/")
(define-public mumps
(package
(name "mumps")
- (version "5.2.1")
+ (version "5.5.1")
(source
(origin
(method url-fetch)
- (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
- version ".tar.gz"))
+ (uri (list (string-append "http://mumps.enseeiht.fr/MUMPS_"
+ version ".tar.gz")
+ (string-append
+ "https://ftp.mcs.anl.gov/pub/petsc/externalpackages"
+ "/MUMPS_" version ".tar.gz")))
(sha256
(base32
- "0jklh54x4y3ik1zkw6db7766kakjm5910diyaghfxxf8vwsgr26r"))
- (patches (search-patches "mumps-build-parallelism.patch"
- "mumps-shared-libseq.patch"
- "mumps-shared-mumps.patch"
- "mumps-shared-pord.patch"))))
+ "05gs2i8b76m9flm1826fxpyfnwibjjawbmfza3ylrvj7zaag5gqs"))))
(build-system gnu-build-system)
(inputs
(list gfortran
#:phases
(modify-phases %standard-phases
(replace 'configure
- (lambda* (#:key inputs #:allow-other-keys)
+ (lambda* (#:key inputs outputs #:allow-other-keys)
(call-with-output-file "Makefile.inc"
(lambda (port)
(format port "
-PLAT =
-LIBEXT = .a
-OUTC = -o
-OUTF = -o
-RM = rm -f~:[
-CC = gcc
-FC = gfortran
-FL = gfortran
-INCSEQ = -I$(topdir)/libseq
-LIBSEQ = $(topdir)/libseq/libmpiseq.a
-LIBSEQNEEDED = libseqneeded~;
-CC = mpicc
-FC = mpifort
-FL = mpifort~]
-AR = ar vr # rules require trailing space, ugh...
-RANLIB = ranlib
-BLASDIR = ~a
-LIBBLAS = -Wl,-rpath=$(BLASDIR) -Wl,-rpath='$$ORIGIN' -L$(BLASDIR) -lopenblas~@[
-SCALAPDIR = ~a
-SCALAP = -Wl,-rpath=$(SCALAPDIR) -Wl,-rpath='$$ORIGIN' -L$(SCALAPDIR) -lscalapack~]
-LIBOTHERS = -pthread
-CDEFS = -DAdd_
-PIC = -fPIC
-OPTF = -O2 -DALLOW_NON_INIT -fallow-argument-mismatch $(PIC)
-OPTL = -O2 $(PIC)
-OPTC = -O2 $(PIC)
-INCS = $(INCSEQ)
-LIBS = $(SCALAP) $(LIBSEQ)
-LPORDDIR = $(topdir)/PORD/lib
-IPORD = -I$(topdir)/PORD/include
-LPORD = $(LPORDDIR)/libpord.a
-ORDERINGSF = -Dpord~@[
-METISDIR = ~a
-IMETIS = -I$(METISDIR)/include
-LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
-ORDERINGSF += -Dmetis~]~@[~:{
-SCOTCHDIR = ~a
-ISCOTCH = -I$(SCOTCHDIR)/include
-LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
-ORDERINGSF += ~a~}~]
-ORDERINGSC = $(ORDERINGSF)
-LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH) $(LIBSEQ)
-IORDERINGSF = $(ISCOTCH)
-IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
- (->bool (which "mpicc")) ;MPI support enabled?
- (dirname
- (dirname (search-input-file inputs "/include/cblas.h")))
+PLAT =
+LIBEXT = .a
+LIBEXT_SHARED = .so
+OUTC = -o
+OUTF = -o
+BLASDIR = ~a
+LIBBLAS = -Wl,-rpath=$(BLASDIR)/lib -Wl,-rpath='$$ORIGIN'
+LIBBLAS += -L$(BLASDIR)/lib
+LIBBLAS += -lopenblas~@[
+SCALAPDIR = ~a
+SCALAP = -Wl,-rpath=$(SCALAPDIR)/lib -Wl,-rpath='$$ORIGIN'
+SCALAP += -L$(SCALAPDIR)/lib -lscalapack~]
+RM = rm -f~:[
+CC = gcc
+FC = gfortran
+FL = gfortran
+INCSEQ = -I$(topdir)/libseq
+LIBSEQ = $(LAPACK) -L$(topdir)/libseq -lmpiseq
+LIBSEQNEEDED = libseqneeded
+INCS = $(INCSEQ)
+LIBS = $(LIBSEQ)~;
+CC = mpicc
+FC = mpifort
+FL = mpifort
+INCPAR =
+LIBPAR = $(SCALAP) $(LAPACK)
+LIBSEQNEEDED =
+INCS = $(INCPAR)
+LIBS = $(LIBPAR)~]
+AR = ar vr # rules require trailing space, ugh...
+RANLIB = ranlib
+LIBOTHERS = -pthread
+CDEFS = -DAdd_
+PIC = -fPIC
+FPIC_OPT = $(PIC)
+RPATH_OPT = -Wl,-rpath,~a/lib
+OPTF = -O2 -fopenmp -DALLOW_NON_INIT -DBLR_MT
+OPTF += -fallow-argument-mismatch $(PIC)
+OPTL = -O2 -fopenmp $(PIC)
+OPTC = -O2 -fopenmp $(PIC)
+LPORDDIR = $(topdir)/PORD/lib
+IPORD = -I$(topdir)/PORD/include
+LPORD = $(LPORDDIR)/libpord.a
+ORDERINGSF = -Dpord~@[
+METISDIR = ~a
+IMETIS = -I$(METISDIR)/include
+LMETIS = -Wl,-rpath $(METISDIR)/lib -L$(METISDIR)/lib -lmetis
+ORDERINGSF += -Dmetis~]~@[~:{
+SCOTCHDIR = ~a
+ISCOTCH = -I$(SCOTCHDIR)/include
+LSCOTCH = -Wl,-rpath $(SCOTCHDIR)/lib -L$(SCOTCHDIR)/lib ~a -lesmumps
+LSCOTCH += -lscotch -lscotcherr
+ORDERINGSF += ~a~}~]
+ORDERINGSC = $(ORDERINGSF)
+LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
+IORDERINGSF = $(ISCOTCH)
+IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
+ (assoc-ref inputs "openblas")
(assoc-ref inputs "scalapack")
+ (->bool (which "mpicc")) ;; MPI support enabled?
+ (assoc-ref outputs "out")
(assoc-ref inputs "metis")
(match (list (assoc-ref inputs "pt-scotch")
(assoc-ref inputs "scotch"))
"-lesmumps -lptscotch -lptscotcherr "
"-Dptscotch")))))))))
(replace 'build
- ;; By default only the d-precision library is built. Make with "all"
- ;; target so that all precision libraries and examples are built.
- (lambda _
- (invoke "make" "all"
- (format #f "-j~a" (parallel-job-count)))))
+ ;; By default only the d-precision library is built. Make with "all"
+ ;; target so that all precision libraries and examples are built.
+ ;; Then, "make allshared" builts equivalent shared libraries as well.
+ (lambda _
+ (invoke "make" "all"
+ (format #f "-j~a" (parallel-job-count)))
+ (invoke "make" "allshared"
+ (format #f "-j~a" (parallel-job-count)))))
(replace 'check
;; Run the simple test drivers, which read test input from stdin:
;; from the "real" input for the single- and double-precision
(define-public maxima
(package
(name "maxima")
- (version "5.45.1")
+ (version "5.46.0")
(source
(origin
(method url-fetch)
version "-source/" name "-" version ".tar.gz"))
(sha256
(base32
- "1p77nk5sz1qfkn5zr97szpbi8ib4b22k8i52l4ag5gkhd4kid47y"))
+ "01wbm8jj43p7gpdj4h55aij0b44bjydn4bwb7q1wjrfs91mz143k"))
(patches (search-patches "maxima-defsystem-mkdir.patch"))))
(build-system gnu-build-system)
(inputs
;; components at runtime.
(wrap-program (string-append out "/bin/maxima")
`("PATH" prefix (,binutils))))
- #t)))))
+ #t))
+ ;; The Maxima command ‘describe’ allows to pick the relevant portions
+ ;; from Maxima’s Texinfo docs. However it does not support reading
+ ;; gzipped info files.
+ (delete 'compress-documentation))))
(home-page "https://maxima.sourceforge.io")
(synopsis "Numeric and symbolic expression manipulation")
(description "Maxima is a system for the manipulation of symbolic and
(define-public wxmaxima
(package
(name "wxmaxima")
- (version "21.05.2")
+ (version "22.05.0")
(source
(origin
(method git-fetch)
(commit (string-append "Version-" version))))
(file-name (git-file-name name version))
(sha256
- (base32 "0h7ryykh2dapcyvpp4f1j1b3vrrz80x9k8nkci2yxifgdb29vyhw"))))
+ (base32 "1va56v9dys97yln4m1z3fz3k90lpy8i3kvcq0v1cbg36689aghm5"))))
(build-system cmake-build-system)
(native-inputs
`(("gettext" ,gettext-minimal)))
(define-public suitesparse
(package
(name "suitesparse")
- (version "5.10.1")
+ (version "5.12.0")
(source
(origin
(method git-fetch)
(file-name (git-file-name name version))
(sha256
(base32
- "19gx5wlgqnqpgz6mvam9lalyzpbfwgqhppps8z3np9sh0mgaiyw9"))
+ "0zpl51pfpv7ap7z97jlryba2la1qdmzm11bhzkn55wlb03xzi6k6"))
(patches (search-patches "suitesparse-mongoose-cmake.patch"))
(modules '((guix build utils)))
(snippet
(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)))
+ (list
+ ;; The build fails with the current gcc.
+ ;; Use the version from when Trilinos was added.
+ gcc-7
+ 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
+ python-2))
(inputs
- `(("blas" ,openblas)
- ("lapack" ,lapack)
- ("mumps" ,mumps-openmpi)
- ("scalapack" ,scalapack)))
+ (list openblas
+ lapack
+ mumps-openmpi
+ scalapack))
(propagated-inputs
- `(("mpi" ,openmpi)))
+ (list 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))))
+ (list #:build-type "Release"
+ #:configure-flags
+ #~(list "-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"
+ (("\\\\#") "#"))))
+ (add-before 'check 'mpi-setup
+ #$%openmpi-setup))))
(home-page "https://trilinos.github.io/")
(synopsis "Algorithms for engineering and scientific problems")
(description
(define-public dealii
(package
(name "dealii")
- (version "9.3.3")
+ (version "9.4.0")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/dealii/dealii/releases/"
"download/v" version "/dealii-" version ".tar.gz"))
(sha256
- (base32 "0a8s4yxcbvzmfgv5qcg27h2ss4fcnyhrhhs35glqj59l9cbmkysx"))
+ (base32 "0v73q6f35f2yrjihaq6vh9lma07qc4cdv75nwmc3c5yrdh07g1i3"))
(modules '((guix build utils)))
(snippet
;; Remove bundled boost, muparser, TBB and UMFPACK.
- '(delete-file-recursively "bundled"))))
+ #~(delete-file-recursively "bundled"))))
(build-system cmake-build-system)
(outputs '("out" "doc"))
(native-inputs
(list boost
hdf5
suitesparse ; For UMFPACK.
- ;; SUNDIALS 6.0.0 and later will be supported in deal.II 9.4.0.
- sundials-5
+ sundials
tbb))
(arguments
- `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease.
- ;; The tests take too long and must be explicitly enabled with "make
- ;; setup_tests".
- ;; See https://www.dealii.org/developer/developers/testsuite.html.
- ;; (They can also be run for an already installed deal.II.)
- #:tests? #f
- #:configure-flags
- (let ((doc (string-append (assoc-ref %outputs "doc")
- "/share/doc/" ,name "-" ,version)))
- `("-DDEAL_II_COMPONENT_DOCUMENTATION=ON"
- ,(string-append "-DDEAL_II_DOCREADME_RELDIR=" doc)
- ,(string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html")
- ;; Don't compile the examples because the source and CMakeLists.txt
- ;; are installed anyway, allowing users to do so for themselves.
- "-DDEAL_II_COMPILE_EXAMPLES=OFF"
- ,(string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc "/examples")))
- #:phases
- (modify-phases %standard-phases
- (add-after 'install 'remove-build-logs
- ;; These build logs leak the name of the build directory by storing
- ;; the values of CMAKE_SOURCE_DIR and CMAKE_BINARY_DIR.
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((doc (string-append (assoc-ref outputs "doc")
- "/share/doc/" ,name "-" ,version)))
- (for-each delete-file (map (lambda (f) (string-append doc "/" f))
- '("detailed.log" "summary.log")))))))))
+ (list #:build-type "DebugRelease" ; Only Debug, Release or DebugRelease.
+ ;; The tests take too long and must be explicitly enabled with
+ ;; "make setup_tests".
+ ;; See https://www.dealii.org/developer/developers/testsuite.html.
+ ;; (They can also be run for an already installed deal.II.)
+ #:tests? #f
+ #:configure-flags
+ #~(let ((doc (string-append #$output:doc "/share/doc/"
+ #$name "-" #$version)))
+ (list "-DDEAL_II_COMPONENT_DOCUMENTATION=ON"
+ (string-append "-DDEAL_II_DOCREADME_RELDIR=" doc)
+ (string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html")
+ ;; Don't compile the examples because the source and
+ ;; CMakeLists.txt are installed anyway, allowing users to
+ ;; do so for themselves.
+ "-DDEAL_II_COMPILE_EXAMPLES=OFF"
+ (string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc
+ "/examples")))
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'install 'remove-build-logs
+ ;; These build logs leak the name of the build directory by
+ ;; storing the values of CMAKE_SOURCE_DIR and
+ ;; CMAKE_BINARY_DIR.
+ (lambda _
+ (let ((doc (string-append #$output:doc "/share/doc/"
+ #$name "-" #$version)))
+ (for-each delete-file
+ (map (lambda (f) (string-append doc "/" f))
+ '("detailed.log" "summary.log")))))))))
(home-page "https://www.dealii.org/")
(synopsis "Finite element library")
(description
p4est-openmpi
petsc-openmpi
slepc-openmpi
- sundials-openmpi-5
+ sundials-openmpi
trilinos-for-dealii-openmpi)))
(arguments
(substitute-keyword-arguments (package-arguments dealii)
((#:configure-flags flags)
- `(cons "-DDEAL_II_WITH_MPI=ON" ,flags))))
+ #~(cons "-DDEAL_II_WITH_MPI=ON" #$flags))))
(synopsis "Finite element library (with MPI support)")))
(define-public flann
(uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/"
"wcalc-" version ".tar.bz2"))
(sha256
- (base32
- "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
+ (base32
+ "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))
+ (snippet
+ #~(begin
+ (for-each delete-file
+ (list "src/common/scanner.c"
+ "src/common/parser.c"
+ "src/common/parser.h"))))))
(build-system gnu-build-system)
(inputs
(list mpfr readline))
+ (native-inputs
+ (list bison flex))
(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
(build-system gnu-build-system)
(native-inputs `(("gettext" ,gettext-minimal)
("qtbase" ,qtbase-5)
- ("qttools" ,qttools)))
+ ("qttools-5" ,qttools-5)))
(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.
"0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk"))))
(build-system cmake-build-system)
(inputs (list qtbase-5))
- (native-inputs (list qttools))
+ (native-inputs (list qttools-5))
(arguments
`(#:phases
(modify-phases %standard-phases
ocaml-graph
ocaml-yojson
ocaml-zarith
+ lablgtk3
why3))
(native-search-paths
(list (search-path-specification
HCoop / jackhill / guix / guix.git / blobdiff