diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 1341 |
1 files changed, 1197 insertions, 144 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 758f0a5c32..164924b6af 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -11,24 +11,24 @@ ;;; 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 Kei Kebreau <kkebreau@posteo.net> +;;; Copyright © 2016, 2018, 2020, 2021 Kei Kebreau <kkebreau@posteo.net> ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 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 Paul Garlick <pgarlick@tourbillion-technology.com> +;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com> ;;; Copyright © 2017 Nikita <nikita@n0.is> ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org> ;;; Copyright © 2017, 2019 Arun Isaac <arunisaac@systemreboot.net> -;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Dave Love <me@fx@gnu.org> -;;; Copyright © 2018, 2019, 2020 Jan Nieuwenhuizen <janneke@gnu.org> +;;; Copyright © 2018, 2019, 2020, 2021 Jan (janneke) Nieuwenhuizen <janneke@gnu.org> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com> ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com> ;;; Copyright © 2018, 2020 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2018 Eric Brown <brown@fastmail.com> -;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu> +;;; 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 Steve Sprang <scs@stevesprang.com> @@ -39,12 +39,15 @@ ;;; Copyright © 2020 Vincent Legoll <vincent.legoll@gmail.com> ;;; Copyright © 2020 Nicolò Balzarotti <nicolo@nixo.xyz> ;;; Copyright © 2020 B. Wilson <elaexuotee@wilsonb.com> -;;; Copyright © 2020 Vinicius Monego <monego@posteo.net> +;;; Copyright © 2020, 2021 Vinicius Monego <monego@posteo.net> ;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Martin Becze <mjbecze@riseup.net> ;;; Copyright © 2021 Gerd Heber <gerd.heber@gmail.com> ;;; Copyright © 2021 Franck Pérignon <franck.perignon@univ-grenoble-alpes.fr> ;;; Copyright © 2021 Philip McGrath <philip@philipmcgrath.com> +;;; Copyright © 2021 Paul A. Patience <paul@apatience.com> +;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru> +;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me> ;;; ;;; This file is part of GNU Guix. ;;; @@ -74,6 +77,7 @@ #: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 ocaml) #:use-module (guix build-system python) #:use-module (guix build-system ruby) #:use-module (gnu packages algebra) @@ -85,11 +89,13 @@ #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) + #:use-module (gnu packages coq) #:use-module (gnu packages curl) #:use-module (gnu packages cyrus-sasl) #:use-module (gnu packages dbm) #:use-module (gnu packages documentation) #:use-module (gnu packages elf) + #:use-module (gnu packages emacs) #:use-module (gnu packages file) #:use-module (gnu packages flex) #:use-module (gnu packages fltk) @@ -118,8 +124,11 @@ #: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) @@ -133,6 +142,7 @@ #: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 tcl) #:use-module (gnu packages texinfo) @@ -167,6 +177,39 @@ beginners.") (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 + `(("ncurses" ,ncurses) + ("readline" ,readline))) + (native-inputs + `(("cunit" ,cunit) + ("pkg-config" ,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") @@ -236,16 +279,19 @@ programming languages.") (define-public qhull (package (name "qhull") - (version "2019.1") + (version "2020.2") (source (origin (method url-fetch) (uri (string-append "http://www.qhull.org/download/qhull-" (car (string-split version #\.)) - "-src-7.3.2.tgz")) + "-src-8.0.2.tgz")) (sha256 (base32 - "1ys3vh3qq0v9lh452xb932vp63advds1pxk42lk7cc1niiar0y9b")))) + "0zlbhg0lb6j60188c2xhcrvviskr079552icjldqhy1jhgmxghmm")))) (build-system cmake-build-system) + (arguments + `(#:configure-flags '("-DLINK_APPS_SHARED=ON" + "-DCMAKE_POSITION_INDEPENDENT_CODE=ON"))) (synopsis "Calculate convex hulls and related structures") (description "@code{Qhull} computes the convex hull, Delaunay triangulation, Voronoi @@ -698,6 +744,30 @@ in memory, so even problems with very large output sizes can sometimes be solved.") (license license:gpl2+))) +(define-public libcerf + (package + (name "libcerf") + (version "1.14") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://jugit.fz-juelich.de/mlz/libcerf") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1ic2q7kvxpqmgxlishygvx8d00i4wn51vkq4fyac44ahhf6c3kwd")))) + (build-system cmake-build-system) + (native-inputs + `(("perl" ,perl))) + (home-page "https://jugit.fz-juelich.de/mlz/libcerf") + (synopsis "Library for complex error functions") + (description + "@code{libcerf} is a self-contained numeric library that provides an +efficient and accurate implementation of complex error functions, along with +Dawson, Faddeeva, and Voigt functions.") + (license license:expat))) + (define-public vinci (package (name "vinci") @@ -746,7 +816,7 @@ halfspaces) or by their double description with both representations.") (define-public arpack-ng (package (name "arpack-ng") - (version "3.6.3") + (version "3.8.0") (home-page "https://github.com/opencollab/arpack-ng") (source (origin (method git-fetch) @@ -754,14 +824,16 @@ halfspaces) or by their double description with both representations.") (file-name (git-file-name name version)) (sha256 (base32 - "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y")))) + "0l7as5z6xvbxly8alam9s4kws70952qq35a6vkljzayi4b9gbklx")))) (build-system gnu-build-system) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) - ("libtool" ,libtool))) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) (inputs - `(("lapack" ,lapack) + `(("eigen" ,eigen) + ("lapack" ,lapack) ("fortran" ,gfortran))) (synopsis "Fortran subroutines for solving eigenvalue problems") (description @@ -774,16 +846,15 @@ large scale eigenvalue problems.") (package (inherit arpack-ng) (version "3.3.0") - (name (package-name arpack-ng)) - (home-page (package-home-page arpack-ng)) (source (origin - (method url-fetch) - (uri (string-append home-page "/archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference (url (package-home-page arpack-ng)) + (commit version))) + (file-name (git-file-name (package-name arpack-ng) version)) (sha256 (base32 - "1cz53wqzcf6czmcpfb3vb61xi0rn5bwhinczl65hpmbrglg82ndd")))))) + "00h6bjvxjq7bv0b8pwnc0gw33ns6brlqv00xx2rh3w9b5n205918")))))) (define-public arpack-ng-openmpi (package (inherit arpack-ng) @@ -923,14 +994,14 @@ singular value problems.") (define-public gnuplot (package (name "gnuplot") - (version "5.4.1") + (version "5.4.2") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" version "/gnuplot-" version ".tar.gz")) (sha256 - (base32 "03jrqs5lvxmbbz2c4g17dn2hrxqwd3hfadk9q8wbkbkyas2h8sbb")))) + (base32 "1fp7rbhjmz2w63r72kicf8lfszzimz2csfx868fracw167hpaz75")))) (build-system gnu-build-system) (inputs `(("readline" ,readline) ("cairo" ,cairo) @@ -1145,7 +1216,7 @@ incompatible with HDF5.") ;; libhdf5.so. We truncate the hashes to avoid ;; unnecessary store references to those compilers: (substitute* "src/libhdf5.settings" - (("(/gnu/store/)([a-Z0-9]*)" all prefix hash) + (("(/gnu/store/)([a-zA-Z0-9]*)" all prefix hash) (string-append prefix (string-take hash 10) "...")) ;; Don't record the build-time kernel version to make the ;; settings file reproducible. @@ -1204,7 +1275,8 @@ extremely large and complex data collections.") "https://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) (define-public hdf5-1.10 - (package/inherit hdf5-1.8 + (package + (inherit hdf5-1.8) (version "1.10.7") (source (origin @@ -1223,7 +1295,8 @@ extremely large and complex data collections.") (patches (search-patches "hdf5-config-date.patch")))))) (define-public hdf5-1.12 - (package/inherit hdf5-1.8 + (package + (inherit hdf5-1.8) (version "1.12.0") (source (origin @@ -1721,21 +1794,16 @@ online as well as original implementations of various other algorithms.") (define-public ipopt (package (name "ipopt") - (version "3.12.12") + (version "3.13.4") (source (origin - (method url-fetch) - (uri (string-append - "https://www.coin-or.org/download/source/Ipopt/Ipopt-" - version".tgz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/coin-or/Ipopt") + (commit (string-append "releases/" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "07yn9rzdswjk8n246qq6ci9ssf2bcplkifcpsfz9j6cdxw9vgbkv")) - (modules '((guix build utils))) - (snippet - ;; Make sure we don't use the bundled software. - '(begin - (delete-file-recursively "ThirdParty") - #t)))) + "08gznhwhqv1x4baksz350ih8q16r5rd0k8vals6078m3h94khr4b")))) (build-system gnu-build-system) (arguments '(#:phases (modify-phases %standard-phases @@ -1755,7 +1823,8 @@ online as well as original implementations of various other algorithms.") after "\n"))) #t)))))) (native-inputs - `(("gfortran" ,gfortran))) + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) (inputs ;; TODO: Maybe add dependency on COIN-MUMPS, ASL, and HSL. `(("lapack" ,lapack))) ;for both libblas and liblapack @@ -1765,6 +1834,183 @@ online as well as original implementations of various other algorithms.") "The Interior Point Optimizer (IPOPT) is a software package for large-scale nonlinear optimization. It provides C++, C, and Fortran interfaces.") + (license license:epl2.0))) + +(define-public nomad-optimizer + (package + (name "nomad-optimizer") + (version "4.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bbopt/nomad/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0w386d8r5ldbvnv0c0g7vz95pfpvwdxis26vaalk2amsa5akl775")))) + (build-system cmake-build-system) + (native-inputs + `(("python" ,python-wrapper) + ("python-cython" ,python-cython))) + (arguments + `(#:imported-modules ((guix build python-build-system) + ,@%cmake-build-system-modules) + #:modules (((guix build python-build-system) + #:select (python-version site-packages)) + (guix build cmake-build-system) + (guix build utils)) + #:configure-flags + '("-DBUILD_INTERFACES=ON" + "-DBUILD_TESTS=ON") + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-sources-for-build + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "CMakeLists.txt" + ;; CMAKE_INSTALL_PREFIX is accidentally hardcoded. + (("set\\(CMAKE_INSTALL_PREFIX .* FORCE\\)") "") + ;; Requiring GCC version 8 or later is unwarranted. + (("message\\(FATAL_ERROR \"GCC version < 8") + "message(STATUS \"GCC version < 8")) + + (let ((out (assoc-ref outputs "out"))) + (substitute* "interfaces/PyNomad/CMakeLists.txt" + ;; We don't want to build in-place, and anyway the install + ;; command further below runs build_ext as a prerequisite. + (("COMMAND python setup_PyNomad\\.py .* build_ext --inplace\n") + "") + ;; Don't install locally. + (("COMMAND python (setup_PyNomad\\.py .* install) --user\n" + _ args) + (string-append "COMMAND ${CMAKE_COMMAND} -E env" + " CC=" ,(cc-for-target) + " CXX=" ,(cxx-for-target) + " " (which "python") + " " args + " --prefix=" out + "\n"))) + ;; Fix erroneous assumptions about the paths of the include and + ;; library directories. + (substitute* "interfaces/PyNomad/setup_PyNomad.py" + (("^( +os_include_dirs = ).*" _ prefix) + (string-append prefix "[\"../../src\"]\n")) + (("^(installed_lib_dir = ).*" _ prefix) + (string-append prefix "\"" out "/lib\"\n")))) + #t)) + + ;; Fix the tests so they run in out-of-source builds. + (add-after 'fix-sources-for-build 'fix-sources-for-tests + (lambda _ + (substitute* + (map (lambda (d) (string-append "examples/" d "/CMakeLists.txt")) + (append + (map (lambda (d) (string-append "basic/library/" d)) + '("example1" "example2" "example3" + "single_obj_parallel")) + (map (lambda (d) (string-append "advanced/library/" d)) + '("FixedVariable" "NMonly" "PSDMads" "Restart" + "c_api/example1" "c_api/example2" + "exampleSuggestAndObserve")))) + ;; The built examples are assumed to be in the source tree + ;; (which isn't the case here). + (("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)" + _ command test) + (string-append command "${CMAKE_CURRENT_BINARY_DIR}" test))) + ;; (Unrelated to support for out-of-source testing.) + (make-file-writable + "examples/advanced/library/exampleSuggestAndObserve/cache0.txt") + + (let* ((builddir (string-append (getcwd) "/../build")) + ;; The BB_EXE and SURROGATE_EXE paths are interpreted + ;; relative to the configuration file provided to NOMAD. + ;; However, the configuration files are all in the source + ;; tree rather than in the build tree (unlike the compiled + ;; executables). + (fix-exe-path (lambda* (dir #:optional + (file "param.txt") + (exe-opt "BB_EXE")) + (substitute* (string-append dir "/" file) + (((string-append "^" exe-opt " +")) + ;; The $ prevents NOMAD from prefixing + ;; the executable with the path of the + ;; parent directory of the configuration + ;; file NOMAD was provided with as + ;; argument (param.txt or some such). + (string-append exe-opt " $" + builddir "/" dir "/")))))) + (for-each + (lambda (dir) + (let ((dir (string-append "examples/" dir))) + (substitute* (string-append dir "/CMakeLists.txt") + ;; The install phase has not yet run. + (("COMMAND \\$\\{CMAKE_INSTALL_PREFIX\\}/bin/nomad ") + "COMMAND ${CMAKE_BINARY_DIR}/src/nomad ")) + (fix-exe-path dir) + (when (equal? dir "examples/basic/batch/surrogate_sort") + (fix-exe-path dir "param.txt" "SURROGATE_EXE")))) + (append (map (lambda (d) (string-append "basic/batch/" d)) + '("example1" "example2" + "single_obj" "single_obj_parallel" + "surrogate_sort")) + '("advanced/batch/LHonly"))) + + (let ((dir "examples/advanced/batch/FixedVariable")) + (substitute* (string-append dir "/runFixed.sh") + ;; Hardcoded path to NOMAD executable. + (("^\\.\\./\\.\\./\\.\\./\\.\\./bin/nomad ") + (string-append builddir "/src/nomad "))) + (for-each + (lambda (f) (fix-exe-path dir f)) + '("param1.txt" "param2.txt" "param3.txt" "param10.txt")))) + #t)) + + ;; The information in the .egg-info file is not kept up to date. + (add-after 'install 'delete-superfluous-egg-info + (lambda* (#:key inputs outputs #:allow-other-keys) + (delete-file (string-append + (site-packages inputs outputs) + "PyNomad-0.0.0-py" + (python-version (assoc-ref inputs "python")) + ".egg-info")) + #t))))) + (home-page "https://www.gerad.ca/nomad/") + (synopsis "Nonlinear optimization by mesh-adaptive direct search") + (description + "NOMAD is a C++ implementation of the mesh-adaptive direct search (MADS) +algorithm, designed for difficult blackbox optimization problems. These +problems occur when the functions defining the objective and constraints are +the result of costly computer simulations.") + (license license:lgpl3+))) + +(define-public cbc + (package + (name "cbc") + (version "2.10.5") + (source (origin + (method url-fetch) + (uri (string-append "https://www.coin-or.org/download/source/" + "Cbc/Cbc-" version ".tgz")) + (sha256 + (base32 + "0wk9vr6zc62gw71v7gnra5wxqlcljcgbhm5lasx236v791b986ns")) + (modules '((guix build utils))) + (snippet + ;; Make sure we don't use the bundled software. + '(delete-file-recursively "ThirdParty")))) + (build-system gnu-build-system) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (inputs + `(("openblas" ,openblas))) + (home-page "https://www.coin-or.org") + (synopsis "Branch-and-cut solver") + (description + "Cbc (Coin-or branch and cut) is a mixed integer linear programming +solver written in C++. It can be used as a library or as a standalone +executable.") (license license:epl1.0))) (define-public clp @@ -1799,6 +2045,77 @@ linear and quadratic objectives. There are limited facilities for nonlinear 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 + `(("patchelf" ,patchelf) + ("perl" ,perl) + ("sed" ,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") @@ -2013,7 +2330,7 @@ can solve two kinds of problems: "\"" (assoc-ref inputs "texinfo") "/bin/makeinfo\""))) #t))))) (home-page "https://www.gnu.org/software/octave/") - (synopsis "High-level language for numerical computation") + (synopsis "High-level language for numerical computation (no GUI)") (description "GNU Octave is a high-level interpreted language that is specialized for numerical computations. It can be used for both linear and non-linear applications and it provides great support for visualizing results. @@ -2026,7 +2343,7 @@ script files.") (name "octave") (inputs `(("qscintilla" ,qscintilla) - ("qt" ,qtbase) + ("qt" ,qtbase-5) ,@(package-inputs octave-cli))) (native-inputs `(("qttools" , qttools) ;for lrelease @@ -2045,7 +2362,8 @@ script files.") (substitute* "configure" (("qscintilla2-qt5") "qscintilla2_qt5")) - #t)))))))) + #t)))))) + (synopsis "High-level language for numerical computation (with GUI)"))) (define-public opencascade-oce (package @@ -2197,7 +2515,7 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") (define-public gmsh (package (name "gmsh") - (version "4.6.0") + (version "4.8.4") (source (origin (method git-fetch) @@ -2205,11 +2523,10 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") (url "https://gitlab.onelab.info/gmsh/gmsh.git") (commit (string-append "gmsh_" - (string-map (lambda (x) (if (eq? x #\.) #\_ x)) - version))))) + (string-replace-substring version "." "_"))))) (file-name (git-file-name name version)) (sha256 - (base32 "0m0pjxcy1bnr7a20i11lh0ih159pphq9wsvfjr3sfx4y3lginz5y")) + (base32 "07mi6ja3b9libgcdp2b4dwnkap1b9ha2wi2zdn9mhmwvp3g1pxhp")) (modules '((guix build utils))) (snippet '(begin @@ -2219,22 +2536,48 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") (propagated-inputs `(("fltk" ,fltk) ("gfortran" ,gfortran) + ("glu" ,glu) ("gmp" ,gmp) ("hdf5" ,hdf5) ("lapack" ,lapack) + ("libx11" ,libx11) + ("libxext" ,libxext) ("mesa" ,mesa) - ("glu" ,glu) ("metis" ,metis) - ("opencascade-occt" ,opencascade-occt) - ("libx11" ,libx11) - ("libxext" ,libxext))) + ("opencascade-occt" ,opencascade-occt))) (inputs `(("fontconfig" ,fontconfig) - ("libxft" ,libxft))) + ("libxft" ,libxft) + ("python" ,python))) (arguments `(#:configure-flags `("-DENABLE_SYSTEM_CONTRIB:BOOL=ON" "-DENABLE_BUILD_SHARED:BOOL=ON" - "-DENABLE_BUILD_DYNAMIC:BOOL=ON"))) + "-DENABLE_BUILD_DYNAMIC:BOOL=ON") + #:imported-modules (,@%cmake-build-system-modules + (guix build python-build-system)) + #:modules (((guix build python-build-system) #:select (site-packages)) + (guix build cmake-build-system) + (guix build utils)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-paths + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Use the standard Guix site-package path for + ;; installation of the Python API. + (substitute* "CMakeLists.txt" + (("include\\(GNUInstallDirs\\)\n") + (string-append "include(GNUInstallDirs)\n" + " set(GMSH_PY_LIB " + (site-packages inputs outputs) ")\n")) + (("\\$\\{GMSH\\_PY\\} DESTINATION \\$\\{GMSH\\_LIB\\}") + "${GMSH_PY} DESTINATION ${GMSH_PY_LIB}")) + ;; Find the shared library. + (let ((libgmsh (string-append (assoc-ref outputs "out") + "/lib/libgmsh.so"))) + (substitute* "api/gmsh.py" + (("find_library\\(\"gmsh\"\\)") + (simple-format #f "\"~a\"" libgmsh)))) + #t))))) (home-page "http://gmsh.info/") (synopsis "3D finite element grid generator") (description "Gmsh is a 3D finite element grid generator with a built-in @@ -2298,7 +2641,7 @@ ASCII text files using Gmsh's own scripting language.") ("python-dbus" ,python-dbus) ("python-h5py" ,python-h5py) ;optional, for HDF5 data ("python-pyqt" ,python-pyqt) - ("qtbase" ,qtbase) + ("qtbase" ,qtbase-5) ("qtsvg" ,qtsvg))) (propagated-inputs `(("python-numpy" ,python-numpy))) @@ -2356,7 +2699,7 @@ September 2004}") `(("python" ,python-2))) (inputs `(("gfortran" ,gfortran) - ("lapack" ,lapack) + ("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 @@ -2367,6 +2710,7 @@ September 2004}") #: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, @@ -2750,6 +3094,136 @@ the Cauchy-Schwarz inequality, Stirling's formula, etc. See the Metamath 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 + `(("bison" ,bison) + ("flex" ,flex))) + (inputs + `(("cbc" ,cbc) + ("gecode" ,gecode) + ("zlib" ,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") @@ -3106,14 +3580,14 @@ implemented in ANSI C, and MPI for communications.") (define-public scotch (package (name "scotch") - (version "6.1.0") + (version "6.1.1") (source (origin (method url-fetch) (uri (string-append "https://gforge.inria.fr/frs/download.php/" "latestfile/298/scotch_" version ".tar.gz")) (sha256 - (base32 "1184fcv4wa2df8szb5lan6pjh0raarr45pk8ilpvbz23naikzg53")) + (base32 "04dkz24a2g20wq703fnyi4440ac4mwycy9gwrrllljj7zxcjy19r")) (patches (search-patches "scotch-build-parallelism.patch" "scotch-integer-declarations.patch")))) (build-system gnu-build-system) @@ -3121,7 +3595,8 @@ implemented in ANSI C, and MPI for communications.") `(("zlib" ,zlib))) (native-inputs `(("flex" ,flex) - ("bison" ,bison))) + ("bison" ,bison) + ("gfortran" ,gfortran))) (outputs '("out" "metis")) (arguments `(#:make-flags (list (string-append "prefix=" %output)) @@ -3146,6 +3621,7 @@ CAT = cat CCS = gcc CCP = mpicc CCD = gcc +FC = gfortran CPPFLAGS =~{ -D~a~} CFLAGS = -O2 -g -fPIC $(CPPFLAGS) LDFLAGS = -lz -lm -lrt -lpthread @@ -3189,6 +3665,8 @@ YACC = bison -pscotchyy -y -b y (find-files "../lib/" ".*metis\\..*")) #t)))))) (home-page "https://www.labri.fr/perso/pelegrin/scotch/") + (properties + `((release-monitoring-url . "https://gforge.inria.fr/frs/?group_id=248"))) (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 @@ -3225,6 +3703,7 @@ CAT = cat CCS = gcc CCP = mpicc CCD = gcc +FC = gfortran CPPFLAGS =~{ -D~a~} CFLAGS = -O2 -g -fPIC $(CPPFLAGS) LDFLAGS = -lz -lm -lrt -lpthread @@ -3279,6 +3758,7 @@ CAT = cat CCS = gcc CCP = mpicc CCD = gcc +FC = gfortran CPPFLAGS =~{ -D~a~} CFLAGS = -O2 -g -fPIC $(CPPFLAGS) $(RPATHFLAGS) CLIBFLAGS = -shared -fPIC @@ -3458,31 +3938,32 @@ processor cores.") (synopsis "Parallel adaptive mesh refinement on forests of octrees"))) (define-public gsegrafix + ;; This is an old and equally dead "experimental fork" of the longer-dead + ;; original. At least it no longer requires the even-deader libgnomeprint{,ui} + ;; libraries, instead rendering plots with Pango. (package (name "gsegrafix") - (version "1.0.6") + (version "1.0.7.2") (source (origin - (method url-fetch) - (uri (string-append "mirror://gnu/" name "/" name "-" - version ".tar.gz")) - (sha256 - (base32 - "1b13hvx063zv970y750bx41wpx6hwd5ngjhbdrna8w8yy5kmxcda")))) + (method url-fetch) + (uri (string-append "mirror://savannah/gsegrafix-experimental/" + "gsegrafix-experimental-" version ".tar.gz")) + (sha256 + (base32 "0fwh6719xy2zasmqlp0vdx6kzm45hn37ga88xmw5cz0yx7xw4j6f")))) (build-system gnu-build-system) (arguments - `(#:configure-flags '("LDFLAGS=-lm"))) + `(#:configure-flags + (list "--disable-static"))) (inputs - `(("libgnomecanvas" ,libgnomecanvas) - ("libbonoboui" ,libbonoboui) - ("libgnomeui" ,libgnomeui) - ("libgnomeprintui" ,libgnomeprintui) - ("popt" ,popt))) + `(("glib" ,glib) + ("gtk+" ,gtk+))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "https://www.gnu.org/software/gsegrafix/") (synopsis "GNOME application to create scientific and engineering plots") - (description "GSEGrafix is an application which produces high-quality graphical + (description + "GSEGrafix is an application which produces high-quality graphical plots for science and engineering. Plots are specified via simple ASCII parameter files and data files and are presented in an anti-aliased GNOME canvas. The program supports rectangular two-dimensional plots, histograms, @@ -3493,7 +3974,7 @@ to BMP, JPEG or PNG image formats.") (define-public maxima (package (name "maxima") - (version "5.44.0") + (version "5.45.1") (source (origin (method url-fetch) @@ -3501,7 +3982,7 @@ to BMP, JPEG or PNG image formats.") version "-source/" name "-" version ".tar.gz")) (sha256 (base32 - "1v6jr5s6hhj6r18gfk6hgxk2qd6z1dxkrjq9ss2z1y6sqi45wgyr")) + "1p77nk5sz1qfkn5zr97szpbi8ib4b22k8i52l4ag5gkhd4kid47y")) (patches (search-patches "maxima-defsystem-mkdir.patch")))) (build-system gnu-build-system) (inputs @@ -3592,7 +4073,7 @@ to BMP, JPEG or PNG image formats.") (wrap-program (string-append out "/bin/maxima") `("PATH" prefix (,binutils)))) #t))))) - (home-page "http://maxima.sourceforge.net") + (home-page "https://maxima.sourceforge.io") (synopsis "Numeric and symbolic expression manipulation") (description "Maxima is a system for the manipulation of symbolic and numerical expressions. It yields high precision numeric results by using @@ -3608,7 +4089,7 @@ point numbers.") (define-public wxmaxima (package (name "wxmaxima") - (version "21.02.0") + (version "21.05.2") (source (origin (method git-fetch) @@ -3617,7 +4098,7 @@ point numbers.") (commit (string-append "Version-" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "19sab596ydwz65151bwymnfilyfmr8qcxb0k8cxlnj1gmdldlyz6")))) + (base32 "0h7ryykh2dapcyvpp4f1j1b3vrrz80x9k8nkci2yxifgdb29vyhw")))) (build-system cmake-build-system) (native-inputs `(("gettext" ,gettext-minimal))) @@ -3775,13 +4256,17 @@ parts of it.") ;; Build the library for all supported CPUs. This allows ;; switching CPU targets at runtime with the environment variable ;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type. - ;; Unfortunately, this is not supported on non-x86 architectures, + ;; Unfortunately, this is not supported on all architectures, ;; where it leads to failed builds. ,@(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. + ((string-prefix? "powerpc64le" system) + '("DYNAMIC_ARCH=1" + "TARGET=GENERIC")) ;; On MIPS we force the "SICORTEX" TARGET, as for the other ;; two available MIPS targets special extended instructions ;; for Loongson cores are used. @@ -3790,6 +4275,9 @@ parts of it.") ;; On aarch64 force the generic 'armv8-a' target ((string-prefix? "aarch64" system) '("TARGET=ARMV8")) + ;; Failed to detect CPU. + ((string-prefix? "armhf" system) + '("TARGET=ARMV7")) (else '())))) ;; no configure script #:phases @@ -3934,7 +4422,7 @@ access to BLIS implementations via traditional BLAS routine calls.") (define-public openlibm (package (name "openlibm") - (version "0.6.0") + (version "0.7.4") (source (origin (method git-fetch) @@ -3943,11 +4431,12 @@ access to BLIS implementations via traditional BLAS routine calls.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "08wfchmmr5200fvmn1kwq9byc1fhsq46hn0y5k8scdl74771c7gh")))) + (base32 "1azms0lpxb7vxb3bln5lyz0wpwx6jnzbffkclclpq2v5aiw8d14i")))) (build-system gnu-build-system) (arguments `(#:make-flags - (list (string-append "prefix=" (assoc-ref %outputs "out"))) + (list (string-append "prefix=" (assoc-ref %outputs "out")) + ,(string-append "CC=" (cc-for-target))) #:phases ;; no configure script (modify-phases %standard-phases (delete 'configure)) @@ -4011,7 +4500,7 @@ Fresnel integrals, and similar related functions as well.") (define-public suitesparse (package (name "suitesparse") - (version "5.9.0") + (version "5.10.1") (source (origin (method git-fetch) @@ -4021,7 +4510,7 @@ Fresnel integrals, and similar related functions as well.") (file-name (git-file-name name version)) (sha256 (base32 - "1zhkix58afw92s7p291prljdm3yi0pjg1kbi3lczdb8rb14jkz5n")) + "19gx5wlgqnqpgz6mvam9lalyzpbfwgqhppps8z3np9sh0mgaiyw9")) (patches (search-patches "suitesparse-mongoose-cmake.patch")) (modules '((guix build utils))) (snippet @@ -4036,6 +4525,11 @@ Fresnel integrals, and similar related functions as well.") (list (string-append "CC=" ,(cc-for-target)) "TBB=-ltbb" "MY_METIS_LIB=-lmetis" + + ;; The default is to link against netlib lapack. Use OpenBLAS + ;; instead. + "BLAS=-lopenblas" "LAPACK=-lopenblas" + ;; Flags for cmake (required to build GraphBLAS and Mongoose) (string-append "CMAKE_OPTIONS=-DCMAKE_INSTALL_PREFIX=" (assoc-ref %outputs "out") @@ -4055,7 +4549,7 @@ Fresnel integrals, and similar related functions as well.") (delete 'configure)))) ;no configure script (inputs `(("tbb" ,tbb) - ("lapack" ,lapack) + ("openblas" ,openblas) ("gmp" ,gmp) ("mpfr" ,mpfr) ("metis" ,metis))) @@ -4200,8 +4694,39 @@ done in the BIOS, or, on GNU/Linux, with the following command: @end example Failure to do so will result in a library with poor performance.") + ;; The test suite is notoriously lengthy and routinely exceeds the default + ;; timeout of 21600 seconds on the not unbeefy berlin build nodes. + (properties '((timeout . 86400))) ; 1 day (license license:bsd-3))) +(define-public cglm + (package + (name "cglm") + (version "0.8.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/recp/cglm") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1lcfl9ph4bnl3hckpx4hzwh8r4llnw94ik75igc5qy38wk468gmk")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DCGLM_USE_TEST=ON"))) + (home-page "https://github.com/recp/cglm") + (synopsis "Mathematics C library for graphics programming") + (description + "@acronym{CGLM, C OpenGL Mathematics} is an optimised 3D maths library +for graphics software based on the @acronym{GLSL, OpenGL Shading Language} +specifications. + +It's similar to the original C++ GLM library but written in C99 and compatible +with C89.") + (license license:expat))) + (define-public glm (package (name "glm") @@ -4322,43 +4847,226 @@ specifications.") 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 "9.2.0") + (version "9.3.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/dealii/dealii/releases/" "download/v" version "/dealii-" version ".tar.gz")) (sha256 - (base32 - "0fm4xzrnb7dfn4415j24d8v3jkh0lssi86250x2f5wgi83xq4nnh")) + (base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6")) (modules '((guix build utils))) (snippet - ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost '(begin + ;; Remove bundled boost, muparser, TBB and UMFPACK. (delete-file-recursively "bundled") #t)))) (build-system cmake-build-system) + (outputs '("out" "doc")) + (native-inputs + ;; Required to build the documentation. + `(("dot" ,graphviz) + ("doxygen" ,doxygen) + ("perl" ,perl))) (inputs - `(("tbb" ,tbb) - ("zlib" ,zlib) - ("boost" ,boost) - ("p4est" ,p4est) + `(("arpack" ,arpack-ng) ("blas" ,openblas) + ("gfortran" ,gfortran) ("lapack" ,lapack) - ("arpack" ,arpack-ng) ("muparser" ,muparser) - ("gfortran" ,gfortran) - ("suitesparse" ,suitesparse))) ;for UMFPACK + ("zlib" ,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 + ;; shebang line) and therefore must be explicitly passed to the + ;; interpreter. + ;; 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))) (arguments - `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease + `(#: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 - ;; Work around a bug in libsuitesparseconfig linking - ;; see https://github.com/dealii/dealii/issues/4745 - '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON"))) - (home-page "https://www.dealii.org") + (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")))) + #t))))) + (home-page "https://www.dealii.org/") (synopsis "Finite element library") (description "Deal.II is a C++ program library targeted at the computational solution @@ -4369,30 +5077,25 @@ in finite element programs.") (license license:lgpl2.1+))) (define-public dealii-openmpi - (package (inherit dealii) + (package/inherit dealii (name "dealii-openmpi") (inputs - `(("mpi" ,openmpi) - ;;Supported only with MPI: - ("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate? + `(("arpack" ,arpack-ng-openmpi) + ("metis" ,metis) + ("scalapack" ,scalapack) + ,@(alist-delete "arpack" (package-inputs dealii)))) + (propagated-inputs + `(("hdf5" ,hdf5-parallel-openmpi) + ("mpi" ,openmpi) ("p4est" ,p4est-openmpi) ("petsc" ,petsc-openmpi) ("slepc" ,slepc-openmpi) - ("metis" ,metis) ;for MUMPS - ("scalapack" ,scalapack) ;for MUMPS - ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings - ("arpack" ,arpack-ng-openmpi) - ,@(fold alist-delete (package-inputs dealii) - '("p4est" "arpack")))) + ("trilinos" ,trilinos-for-dealii-openmpi) + ,@(alist-delete "hdf5" (package-propagated-inputs dealii)))) (arguments (substitute-keyword-arguments (package-arguments dealii) - ((#:configure-flags cf) - `(cons "-DDEAL_II_WITH_MPI:BOOL=ON" - ,cf)) - ((#:phases phases '%standard-phases) - `(modify-phases ,phases - (add-before 'check 'mpi-setup - ,%openmpi-setup))))) + ((#:configure-flags flags) + `(cons "-DDEAL_II_WITH_MPI=ON" ,flags)))) (synopsis "Finite element library (with MPI support)"))) (define-public flann @@ -4480,7 +5183,7 @@ evaluates expressions using the standard order of operations.") (define-public xaos (package (name "xaos") - (version "4.0") + (version "4.2.1") (source (origin (method git-fetch) (uri (git-reference @@ -4489,10 +5192,10 @@ evaluates expressions using the standard order of operations.") (file-name (git-file-name name version)) (sha256 (base32 - "00110p5xscjsmn7avfqgydn656zbmdj3l3y2fpv9b4ihzpid8n7a")))) + "0maw5am6rrkyjrprfg113zjq37mqj0iaznkg4h2927ff7wrprc94")))) (build-system gnu-build-system) (native-inputs `(("gettext" ,gettext-minimal) - ("qtbase" ,qtbase) + ("qtbase" ,qtbase-5) ("qttools" ,qttools))) (inputs `(("libx11" ,libx11) ("zlib" ,zlib) @@ -4512,12 +5215,14 @@ evaluates expressions using the standard order of operations.") (replace 'configure (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) - ;; The DESTDIR is originally set to install the xaos binary to - ;; the "bin" folder inside the build directory. Setting make - ;; flags doesn't seem to change this. (substitute* "XaoS.pro" + ;; The DESTDIR is originally set to install the xaos binary to + ;; the "bin" folder inside the build directory. Setting make + ;; flags doesn't seem to change this. (("DESTDIR.*$") - (string-append "DESTDIR=" out "/bin"))) + (string-append "DESTDIR=" out "/bin")) + ;; Set the correct path to the lrelease binary. + (("lrelease-qt5") "lrelease")) (substitute* "src/include/config.h" (("/usr/share/XaoS") (string-append out "/share/XaoS"))) @@ -4554,7 +5259,7 @@ set.") (origin (method git-fetch) (uri (git-reference - (url "https://github.com/LLNL/hypre") + (url "https://github.com/hypre-space/hypre") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 @@ -4640,7 +5345,8 @@ set.") '("HYPRE_usr_manual" "HYPRE_ref_manual"))) #t)))))) - (home-page "http://www.llnl.gov/casc/hypre/") + (home-page "https://computing.llnl.gov/projects\ +/hypre-scalable-linear-solvers-multigrid-methods") (synopsis "Library of solvers and preconditioners for linear equations") (description "HYPRE is a software library of high performance preconditioners and @@ -4696,14 +5402,14 @@ supports compressed MAT files, as well as newer (version 7.3) MAT files.") (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 @@ -5062,7 +5768,7 @@ reduction.") (define-public mcrl2 (package (name "mcrl2") - (version "202006.0") + (version "202106.0") (source (origin (method url-fetch) (uri (string-append @@ -5070,12 +5776,12 @@ reduction.") version ".tar.gz")) (sha256 (base32 - "167ryrzk1a2j53c2j198jlxa98amcaym070gkcj730619gymv5zl")))) + "0db9wgy9spwm76mgfisnifrlg69y9cadjgxjr4gdwzfgg6wgqf6d")))) (inputs `(("boost" ,boost) ("glu" ,glu) ("mesa" ,mesa) - ("qtbase" ,qtbase))) + ("qtbase" ,qtbase-5))) (build-system cmake-build-system) (synopsis "Toolset for the mCRL2 formal specification language") (description @@ -5885,7 +6591,7 @@ management via the GIMPS project's Primenet server.") (define-public nauty (package (name "nauty") - (version "2.7r1") + (version "2.7r3") (source (origin (method url-fetch) @@ -5893,7 +6599,7 @@ management via the GIMPS project's Primenet server.") "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 @@ -6006,7 +6712,7 @@ functions.") (base32 "0vh7cd1915bjqzkdp3sk25ngy8cq624mkh8c53c5bnzk357kb0fk")))) (build-system cmake-build-system) - (inputs `(("qtbase" ,qtbase))) + (inputs `(("qtbase" ,qtbase-5))) (native-inputs `(("qttools" ,qttools))) (arguments `(#:phases @@ -6066,7 +6772,7 @@ researchers and developers alike to get started on SAT.") (define-public libqalculate (package (name "libqalculate") - (version "3.8.0") + (version "3.19.0") (source (origin (method git-fetch) @@ -6075,7 +6781,7 @@ researchers and developers alike to get started on SAT.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1vbaza9c7159xf2ym90l0xkyj2mp6c3hbghhsqn29yvz08fda9df")) + (base32 "1w44407wb552q21dz4m2nwwdi8b9hzjb2w1l3ffsikzqckc7wbyj")) (patches (search-patches "libqalculate-3.8.0-libcurl-ssl-fix.patch")))) (build-system gnu-build-system) @@ -6120,7 +6826,7 @@ cli.") (define-public qalculate-gtk (package (name "qalculate-gtk") - (version "3.8.0") + (version "3.19.0") (source (origin (method git-fetch) @@ -6129,7 +6835,7 @@ cli.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0nsg6dzg5r7rzqr671nvrf1c50rjwpz7bxv5f20i4s7agizgv840")))) + (base32 "1nrx7gp6f1yalbdda1gb97azhbr4xclq2xf08vvbvsk8jfd6fd2v")))) (build-system glib-or-gtk-build-system) (native-inputs `(("pkg-config" ,pkg-config) @@ -6153,15 +6859,6 @@ cli.") ;; script, which has not yet been patched to replace /bin/sh. (lambda _ (setenv "NOCONFIGURE" "TRUE") - #t)) - (add-before 'check 'add-pot-file - ;; the file contains translations and are currently not in use - ;; left out on purpose so add it to POTFILES.skip - (lambda _ - (with-output-to-file "po/POTFILES.skip" - (lambda _ - (format #t "data/shortcuts.ui~%") - #t)) #t))))) (home-page "https://qalculate.github.io/") (synopsis "Multi-purpose graphical desktop calculator") @@ -6173,3 +6870,359 @@ and conversions, physical constants, symbolic calculations (including integrals and equations), arbitrary precision, uncertainty propagation, interval arithmetic, plotting.") (license license:gpl2+))) + +(define-public numdiff + (package + (name "numdiff") + (version "5.9.0") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://savannah/numdiff/numdiff-" + version ".tar.gz")) + (sha256 + (base32 + "1vzmjh8mhwwysn4x4m2vif7q2k8i19x8azq7pzmkwwj4g48lla47")))) + (build-system gnu-build-system) + (arguments + '(#:tests? #f ; There are no tests. + #:phases + (modify-phases %standard-phases + (add-before 'compress-documentation 'delete-precompressed-info-file + (lambda _ + (delete-file (string-append (assoc-ref %outputs "out") + "/share/info/numdiff.info.gz")) + #t))))) + (home-page "https://nongnu.org/numdiff/") + (synopsis "Compare files with numeric fields") + (description + "Numdiff compares files line by line and field by field, ignoring small +numeric differences and differences in numeric formats.") + (license license:gpl3+))) + +(define-public why3 + (package + (name "why3") + (version "1.3.3") + (source (origin + (method url-fetch) + (uri (string-append "https://gforge.inria.fr/frs/download.php/file" + "/38367/why3-" version ".tar.gz")) + (sha256 + (base32 + "1n0a2nn1gnk0zg339lh698g4wpk7m8m1vyi2yvifd5adqvk4milw")))) + (build-system ocaml-build-system) + (native-inputs + `(("coq" ,coq) + ("ocaml" ,ocaml) + ("which" ,which))) + (propagated-inputs + `(("camlzip" ,camlzip) + ("ocaml-graph" ,ocaml-graph) + ("ocaml-menhir" ,ocaml-menhir) + ("ocaml-num" ,ocaml-num) + ("ocaml-zarith" ,ocaml-zarith))) + (inputs + `(("coq-flocq" ,coq-flocq) + ("emacs-minimal" ,emacs-minimal) + ("zlib" ,zlib))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'configure 'fix-configure + (lambda _ + (setenv "CONFIG_SHELL" (which "sh")) + (substitute* "configure" + ;; find ocaml-num in the correct directory + (("\\$DIR/nums.cma") "$DIR/num.cma") + (("\\$DIR/num.cmi") "$DIR/core/num.cmi")) + #t)) + (add-after 'configure 'fix-makefile + (lambda _ + (substitute* "Makefile" + ;; find ocaml-num in the correct directory + (("site-lib/num") "site-lib")) + #t)) + (add-after 'install 'install-lib + (lambda _ + (invoke "make" "byte") + (invoke "make" "install-lib") + #t))))) + (home-page "http://why3.lri.fr") + (synopsis "Deductive program verification") + (description "Why3 provides a language for specification and programming, +called WhyML, and relies on external theorem provers, both automated and +interactive, to discharge verification conditions. Why3 comes with a standard +library of logical theories (integer and real arithmetic, Boolean operations, +sets and maps, etc.) and basic programming data structures (arrays, queues, +hash tables, etc.). A user can write WhyML programs directly and get +correct-by-construction OCaml programs through an automated extraction +mechanism. WhyML is also used as an intermediate language for the verification +of C, Java, or Ada programs.") + (license license:lgpl2.1))) + +(define-public frama-c + (package + (name "frama-c") + (version "22.0") + (source (origin + (method url-fetch) + (uri (string-append "http://frama-c.com/download/frama-c-" + version "-Titanium.tar.gz")) + (sha256 + (base32 + "1mq1fijka95ydrla486yr4w6wdl9l7vmp512s1q00b0p6lmfwmkh")))) + (build-system ocaml-build-system) + (arguments + `(#:tests? #f; no test target in Makefile + #:phases + (modify-phases %standard-phases + (add-before 'configure 'export-shell + (lambda* (#:key inputs #:allow-other-keys) + (setenv "CONFIG_SHELL" (string-append (assoc-ref inputs "bash") + "/bin/sh")) + #t))))) + (inputs + `(("gmp" ,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))) + (native-search-paths + (list (search-path-specification + (variable "FRAMAC_SHARE") + (files '("share/frama-c")) + (separator #f)) + (search-path-specification + (variable "FRAMAC_LIB") + (files '("lib/frama-c")) + (separator #f)))) + (home-page "http://frama-c.com") + (synopsis "C source code analysis platform") + (description "Frama-C is an extensible and collaborative platform dedicated +to source-code analysis of C software. The Frama-C analyzers assist you in +various source-code-related activities, from the navigation through unfamiliar +projects up to the certification of critical software.") + (license license:lgpl2.1+))) + +(define-public blitz + (package + (name "blitz") + (version "1.0.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/blitzpp/blitz") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0c88gc72j3zggyk4yrrip6i0v7xkx97l140vpy3xhxs2i7xy1461")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags '("-DBUILD_DOC=ON" + "-DBUILD_TESTING=ON") + ;; The default "check" target also includes examples and benchmarks. + #:test-target "check-testsuite" + #:phases + (modify-phases %standard-phases + (add-after 'build 'build-doc + (lambda _ + (invoke "make" "-j" (number->string (parallel-job-count)) + "blitz-doc")))))) + (native-inputs + `(("python" ,python) + ("texinfo" ,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.") + (home-page "https://github.com/blitzpp/blitz") + (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 + `(("googletest" ,googletest) + ("googlebenchmark" ,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 + `(("python-wrapper" ,python-wrapper))) + (inputs + `(("psimd" ,psimd) + ("googletest" ,googletest) + ("googlebenchmark" ,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)))) |