diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 559 |
1 files changed, 334 insertions, 225 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 1ddfc6b1ff..2a3fd60510 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -8,7 +8,7 @@ ;;; 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> @@ -52,6 +52,9 @@ ;;; 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. ;;; @@ -73,6 +76,7 @@ #: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) @@ -722,18 +726,31 @@ integer programming problems and computes Markov bases for statistics.") (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 "-" #$version)))) (home-page "https://www.inf.ethz.ch/personal/fukudak/cdd_home/index.html") (synopsis "Library for convex hulls and extreme rays of polyhedra") (description @@ -1121,24 +1138,25 @@ in the terminal or with an external viewer.") (define-public gnuplot (package (name "gnuplot") - (version "5.4.3") + (version "5.4.4") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" version "/gnuplot-" version ".tar.gz")) (sha256 - (base32 "112dplskbkdbaqi935m2xlk1xsw8s5l568wm7xad75hgp6x9py2i")))) + (base32 "00h97y8njhvfjbdvc0njw0znxbrlfynd1iazn8w3anvzhsvh08rp")))) (build-system gnu-build-system) - (inputs (list readline cairo pango gd lua)) (native-inputs - `(("pkg-config" ,pkg-config) - ("texlive" ,texlive-tiny))) - (arguments `(#:configure-flags (list (string-append - "--with-texdir=" %output - "/texmf-local/tex/latex/gnuplot")) - ;; Plot on a dumb terminal during tests. - #:make-flags '("GNUTERM=dumb"))) + (list pkg-config texlive-tiny)) + (inputs + (list cairo gd lua pango readline)) + (arguments + (list #:configure-flags + #~(list (string-append "--with-texdir=" #$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 @@ -1324,7 +1342,7 @@ incompatible with HDF5.") (("/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 =") @@ -1738,6 +1756,58 @@ Blosc-compressed datasets.") 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") @@ -2783,7 +2853,7 @@ script files.") ("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 @@ -3069,14 +3139,14 @@ ASCII text files using Gmsh's own scripting language.") (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/") @@ -3681,19 +3751,18 @@ language understood by many solvers.") (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 @@ -3710,58 +3779,71 @@ language understood by many solvers.") #: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")) @@ -3774,11 +3856,14 @@ IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)" "-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 @@ -4259,7 +4344,7 @@ to BMP, JPEG or PNG image formats.") (define-public maxima (package (name "maxima") - (version "5.45.1") + (version "5.46.0") (source (origin (method url-fetch) @@ -4267,7 +4352,7 @@ to BMP, JPEG or PNG image formats.") version "-source/" name "-" version ".tar.gz")) (sha256 (base32 - "1p77nk5sz1qfkn5zr97szpbi8ib4b22k8i52l4ag5gkhd4kid47y")) + "01wbm8jj43p7gpdj4h55aij0b44bjydn4bwb7q1wjrfs91mz143k")) (patches (search-patches "maxima-defsystem-mkdir.patch")))) (build-system gnu-build-system) (inputs @@ -4350,7 +4435,11 @@ to BMP, JPEG or PNG image formats.") ;; 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 @@ -4367,7 +4456,7 @@ point numbers.") (define-public wxmaxima (package (name "wxmaxima") - (version "21.05.2") + (version "22.05.0") (source (origin (method git-fetch) @@ -4376,7 +4465,7 @@ point numbers.") (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))) @@ -5152,111 +5241,119 @@ revised simplex and the branch-and-bound methods.") (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 @@ -5272,18 +5369,18 @@ A unique design feature of Trilinos is its focus on packages.") (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 @@ -5307,36 +5404,39 @@ A unique design feature of Trilinos is its focus on packages.") (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 @@ -5364,12 +5464,12 @@ in finite element programs.") 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 @@ -5437,11 +5537,19 @@ FLANN is written in C++ and contains bindings for C, Octave and Python.") (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 @@ -5468,7 +5576,7 @@ evaluates expressions using the standard order of operations.") (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. @@ -7147,7 +7255,7 @@ functions.") "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 @@ -7418,6 +7526,7 @@ of C, Java, or Ada programs.") ocaml-graph ocaml-yojson ocaml-zarith + lablgtk3 why3)) (native-search-paths (list (search-path-specification |