diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 474 |
1 files changed, 320 insertions, 154 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 0a6962ebeb..1c408a1520 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2014-2022 Eric Bavier <bavier@posteo.net> ;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch> ;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org> -;;; Copyright © 2015–2021 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2015–2022 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> @@ -19,7 +19,7 @@ ;;; 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, 2019, 2022 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2017–2021 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Dave Love <me@fx@gnu.org> ;;; Copyright © 2018, 2019, 2020, 2021 Jan (janneke) Nieuwenhuizen <janneke@gnu.org> @@ -45,10 +45,11 @@ ;;; 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, 2022 Paul A. Patience <paul@apatience.com> ;;; Copyright © 2021 Ivan Gankevich <i.gankevich@spbu.ru> ;;; Copyright © 2021 Jean-Baptiste Volatier <jbv@pm.me> ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net> +;;; Copyright © 2021 Pierre-Antoine Bouttier <pierre-antoine.bouttier@univ-grenoble-alpes.fr> ;;; ;;; This file is part of GNU Guix. ;;; @@ -151,6 +152,7 @@ #:use-module (gnu packages serialization) #:use-module (gnu packages shells) #:use-module (gnu packages sphinx) + #:use-module (gnu packages swig) #:use-module (gnu packages tcl) #:use-module (gnu packages texinfo) #:use-module (gnu packages tex) @@ -533,6 +535,14 @@ precision floating point numbers.") #:phases (modify-phases %standard-phases ,@(cond + ((and (target-riscv64?) + (%current-target-system)) + '((add-after 'unpack 'force-bootstrap + (lambda _ + ;; gsl ships with an old configure script that does not + ;; support riscv64. Regenerate it. + (delete-file "configure"))))) + ((or (string-prefix? "aarch64" system) (string-prefix? "powerpc" system)) ;; Some sparse matrix tests are failing on AArch64 and PowerPC: @@ -568,6 +578,11 @@ precision floating point numbers.") (string-append "exit (77);\n" all))))))) (else '())))))) + (native-inputs + (if (and (target-riscv64?) + (%current-target-system)) + (list autoconf automake libtool) + '())) (home-page "https://www.gnu.org/software/gsl/") (synopsis "Numerical library for C and C++") (description @@ -730,7 +745,7 @@ computing convex hulls.") (define-public lrslib (package (name "lrslib") - (version "7.1") + (version "7.2") (source (origin (method url-fetch) @@ -739,7 +754,7 @@ computing convex hulls.") (string-delete #\. version) ".tar.gz")) (sha256 (base32 - "05kq3hzam31dlmkccv3v358r478kpvx76mw37ka12c6ypwv5dsnk")))) + "1w1jsnfgny8cihndr5gfm99pvwp48qsvxkqfsi2q87gd3m57aj7w")))) (build-system gnu-build-system) (inputs (list gmp)) @@ -1079,14 +1094,14 @@ in the terminal or with an external viewer.") (define-public gnuplot (package (name "gnuplot") - (version "5.4.2") + (version "5.4.3") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" version "/gnuplot-" version ".tar.gz")) (sha256 - (base32 "1fp7rbhjmz2w63r72kicf8lfszzimz2csfx868fracw167hpaz75")))) + (base32 "112dplskbkdbaqi935m2xlk1xsw8s5l568wm7xad75hgp6x9py2i")))) (build-system gnu-build-system) (inputs (list readline cairo pango gd lua)) (native-inputs @@ -1709,7 +1724,18 @@ HDF5 file is encoded according to the HDF File Format Specification.") (base32 "14ddy2xnb6sgp4hiax9v5sv4pr4l4dd4ps76nfha3nrpr1ikhcqm")))) (build-system cmake-build-system) - (arguments `(#:tests? #f)) ; Tests require googletest *sources* + (arguments `(#:tests? #f ; Tests require googletest *sources* + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'set-man-page-date + (lambda _ + (substitute* "itpp-config.1.cmake.in" + ((".PACKAGE_DATE.") "2012-04-18")))) + (add-before 'build 'set-force-source-date + ;; for reproducible dates, texlive needs this to respect respect + ;; SOURCE_DATE_EPOCH + (lambda _ + (setenv "FORCE_SOURCE_DATE" "1")))))) (inputs (list lapack fftw)) ;; FIXME: Even though the fonts are available dvips complains: ;; "Font cmmi10 not found; characters will be left blank." @@ -1839,37 +1865,96 @@ sharing of scientific data.") (home-page (package-home-page netcdf)) (license (package-license netcdf)))) -(define-public nlopt +(define-public n2p2 (package - (name "nlopt") - (version "2.4.2") + (name "n2p2") + (version "2.1.4") (source (origin - (method url-fetch) - (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/CompPhysVienna/n2p2") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0")))) + (base32 + "1lw195ihpxwh08387i4gamk1glhalpq888q6nj8l5vswbgnrv1pq")))) (build-system gnu-build-system) (arguments - `(;; Shared libraries are not built by default. They are required to - ;; build the Guile, Octave, and Python bindings. - #:configure-flags '("--enable-shared") - + `(#:make-flags '("MODE=shared" "-C" "src") #:phases (modify-phases %standard-phases + (add-after 'unpack 'post-unpack + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "src/makefile.gnu" + (("PROJECT_EIGEN=/usr/include/eigen3") + (string-append "PROJECT_EIGEN=" + (assoc-ref inputs "eigen") "/include/eigen3"))) + (substitute* "src/makefile.gnu" + (("-lblas") + (string-append "-L" (assoc-ref inputs "openblas") + "/lib -lopenblas")) + (("-march=native") + "")) + (substitute* "src/application/makefile" + (("LDFLAGS=") + "LDFLAGS=-Wl,-rpath='$$ORIGIN/../lib' ")))) + (delete 'configure) + (delete 'check) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bindir (string-append out "/bin")) + (libdir (string-append out "/lib")) + (incdir (string-append out "/include"))) + (for-each (lambda (f) (install-file f bindir)) + (find-files "bin" "^nnp-")) + (for-each (lambda (f) (install-file f libdir)) + (find-files "lib" "\\.so$")) + (for-each (lambda (f) (install-file f incdir)) + (find-files "include" "\\.h$")))))))) + (inputs + (list openmpi gsl openblas eigen)) + (synopsis "Neural network potentials for chemistry and physics") + (description "This package contains software that will allow you to use +existing neural network potential parameterizations to predict energies and +forces (with standalone tools but also in conjunction with the MD software +LAMMPS). In addition it is possible to train new neural network potentials +with the provided training tools.") + (home-page "https://compphysvienna.github.io/n2p2/") + (properties '((tunable? . #t))) ;to benefit from SIMD code in Eigen + (license license:gpl3+))) + +(define-public nlopt + (package + (name "nlopt") + (version "2.7.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/stevengj/nlopt/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1xpdza28i8w441fwv6a5f3qk4zi7ys6ws9fx6kr5ny27dfdz6rr1")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases (add-before 'configure 'set-libnlopt-file-name (lambda* (#:key outputs #:allow-other-keys) ;; Make sure the Scheme module refers to the library by its - ;; absolute file name (we cannot do that from a snippet - ;; because the expansion of @libdir@ contains - ;; ${exec_prefix}.) + ;; absolute file name. (let ((out (assoc-ref outputs "out"))) - (substitute* "swig/nlopt.scm.in" - (("libnlopt") - (string-append out "/lib/libnlopt"))) - #t)))))) - (inputs (list guile-2.0)) - (native-inputs (list pkg-config)) + (substitute* "src/swig/nlopt-guile.i" + (("\"nlopt_guile\"") + (format #f "~s" + `(format #f "~anlopt_guile" + (if (getenv "NLOPT_UNINSTALLED") + "" + ,(format #f "~a/lib/guile/3.0/extensions/" out)))))) + (setenv "NLOPT_UNINSTALLED" "1"))))))) + (inputs (list guile-3.0 octave python)) + (native-inputs (list pkg-config swig)) (home-page "http://ab-initio.mit.edu/wiki/") (synopsis "Library for nonlinear optimization") (description "NLopt is a library for nonlinear optimization, providing a @@ -1924,21 +2009,20 @@ interfaces.") (define-public nomad-optimizer (package (name "nomad-optimizer") - (version "4.1.0") + (version "4.2.0") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/bbopt/nomad/") - (commit (string-append "v" version)))) + (commit (string-append "v." version)))) (file-name (git-file-name name version)) (sha256 (base32 - "0w386d8r5ldbvnv0c0g7vz95pfpvwdxis26vaalk2amsa5akl775")))) + "1r4ygy3xn83dnppsw1451ynklsxpb238g5gk57inn84ghmdk08mj")))) (build-system cmake-build-system) (native-inputs - `(("python" ,python-wrapper) - ("python-cython" ,python-cython))) + (list python-wrapper python-cython)) (arguments `(#:imported-modules ((guix build python-build-system) ,@%cmake-build-system-modules) @@ -1947,7 +2031,8 @@ interfaces.") (guix build cmake-build-system) (guix build utils)) #:configure-flags - '("-DBUILD_INTERFACES=ON" + '("-DBUILD_INTERFACE_C=ON" + "-DBUILD_INTERFACE_PYTHON=ON" "-DBUILD_TESTS=ON") #:phases (modify-phases %standard-phases @@ -1981,13 +2066,38 @@ interfaces.") (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)) + (("^(installed_lib_dir1 = ).*" _ prefix) + (string-append prefix "\"" out "/lib\"\n")) + (("^installed_lib_dir2 = .*") "") + (("^ +link_args\\.append\\(\"-Wl,-rpath,\" \\+ installed_lib_dir2\\)\n") + ""))))) ;; Fix the tests so they run in out-of-source builds. + ;; + ;; TODO: Add support for examples/basic/batch/single_obj_MPIparallel, + ;; by adding openmpi to native-inputs and adjusting the example's + ;; BB_EXE parameter. (add-after 'fix-sources-for-build 'fix-sources-for-tests (lambda _ + (substitute* "examples/CMakeLists.txt" + ;; This test passes only sometimes. + ;; See https://github.com/bbopt/nomad/issues/72. + (("^ +add_subdirectory\\(\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/advanced/library/PSDMads\\)\n") + "") + ;; examples/basic/batch/example3 is accidentally omitted. + (("^(add_subdirectory\\(\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/basic/batch/example)2(\\)\n)" + _ prefix suffix) + (string-append prefix "2" suffix + prefix "3" suffix)) + + ;; The generated runExampleTest.sh script runs the test as part + ;; of a pipeline and incorrectly (because pipefail is unset) + ;; relies on the value of the exit status immediately after the + ;; pipeline. + ;; (The patch-shebangs phase runs later than this one, so no + ;; need to update the path to bash here.) + (("#!/bin/bash") "#!/bin/bash\nset -o pipefail")) + (substitute* (map (lambda (d) (string-append "examples/" d "/CMakeLists.txt")) (append @@ -1998,58 +2108,74 @@ interfaces.") '("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). + ;; The runExampleTest.sh script is run with WORKING_DIRECTORY + ;; set to CMAKE_CURRENT_SOURCE_DIR. + ;; Other scripts invoked by that script (for example + ;; examples/advanced/batch/SuggestAndObserve/loopSuggestAndObserve.sh) + ;; are in that same directory, but compiled examples are + ;; located in CMAKE_CURRENT_BINARY_DIR. (("(COMMAND \\$\\{CMAKE_BINARY_DIR\\}/examples/runExampleTest\\.sh )\\.(/.*)" _ command test) (string-append command "${CMAKE_CURRENT_BINARY_DIR}" test))) + + ;; The examples/basic/batch/example3 executable is already named + ;; bb3.exe. + (substitute* "examples/basic/batch/single_obj_parallel/CMakeLists.txt" + (("bb3.exe") "bb_parallel.exe")) + ;; (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 "))) + (let ((builddir (string-append (getcwd) "/../build"))) + (let ((dir "examples/advanced/library/FixedVariable")) + (substitute* (string-append dir "/fixedVariable.cpp") + (("^( +std::string sExe = ).*" _ prefix) + (string-append prefix "\"" builddir "/" dir "/ufl.exe" "\";\n")))) + + ;; 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). + (let ((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 " $" + builddir "/" dir "/")))))) (for-each - (lambda (f) (fix-exe-path dir f)) - '("param1.txt" "param2.txt" "param3.txt" "param10.txt")))) - #t)) + (lambda (dir) + (let ((dir (string-append "examples/" dir))) + (substitute* (string-append dir "/CMakeLists.txt") + ;; The install phase has not yet run. + (("COMMAND \\$\\{CMAKE_INSTALL_PREFIX\\}/bin/nomad ") + "COMMAND ${CMAKE_BINARY_DIR}/src/nomad ")) + (fix-exe-path dir) + (when (equal? dir "examples/basic/batch/surrogate_sort") + (fix-exe-path dir "param.txt" "SURROGATE_EXE")))) + (append (map (lambda (d) (string-append "basic/batch/" d)) + '("example1" "example2" "example3" + "single_obj" + "single_obj_parallel" + ;; "single_obj_MPIparallel" + "surrogate_sort")) + '("advanced/batch/LHonly"))) + + (let ((dir "examples/advanced/batch/FixedVariable")) + (substitute* (string-append dir "/runFixed.sh") + ;; Hardcoded path to NOMAD executable. + (("^\\.\\./\\.\\./\\.\\./\\.\\./bin/nomad ") + (string-append builddir "/src/nomad "))) + (for-each + (lambda (f) (fix-exe-path dir f)) + '("param1.txt" "param2.txt" "param3.txt" "param10.txt"))))))) ;; The information in the .egg-info file is not kept up to date. (add-after 'install 'delete-superfluous-egg-info @@ -2058,8 +2184,7 @@ interfaces.") (site-packages inputs outputs) "/PyNomad-0.0.0-py" (python-version (assoc-ref inputs "python")) - ".egg-info")) - #t))))) + ".egg-info"))))))) (home-page "https://www.gerad.ca/nomad/") (synopsis "Nonlinear optimization by mesh-adaptive direct search") (description @@ -2801,7 +2926,7 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") (define-public gmsh (package (name "gmsh") - (version "4.8.4") + (version "4.9.5") (source (origin (method git-fetch) @@ -2812,7 +2937,7 @@ This is the certified version of the Open Cascade Technology (OCCT) library.") (string-replace-substring version "." "_"))))) (file-name (git-file-name name version)) (sha256 - (base32 "07mi6ja3b9libgcdp2b4dwnkap1b9ha2wi2zdn9mhmwvp3g1pxhp")) + (base32 "0asd9p64ng5l2zk5glc33x3ynnvdpndlflg3q9mr0jxr7y9x0lrm")) (modules '((guix build utils))) (snippet '(begin @@ -3121,7 +3246,16 @@ scientific applications modeled by partial differential equations.") (("libptesmumps") "libesmumps") (("libptscotchparmetis") "libptscotchparmetisv3")))) (add-before 'configure 'mpi-setup - #$%openmpi-setup))))) + #$%openmpi-setup) + (add-after 'install 'patch-header-inclusions + ;; TODO: Replace with ‘patch-header-inclusions’ when (some form + ;; of) https://issues.guix.gnu.org/54780#19 is merged. + (lambda _ + (substitute* (string-append #$output "/include/petsclayouthdf5.h") + (("<(H5Ipublic.h)>" _ header) + (format #f "<~a/include/~a>" + #$(this-package-input "hdf5-parallel-openmpi") + header))))))))) (synopsis "Library to solve PDEs (with MUMPS and MPI support)"))) (define-public petsc-complex-openmpi @@ -3213,9 +3347,6 @@ Cassowary solver with typical use cases gaining a 40x improvement. Memory savings are consistently > 5x.") (license license:bsd-3))) -(define-public python2-kiwisolver - (package-with-python2 python-kiwisolver)) - (define-public slepc (package (name "slepc") @@ -3702,14 +3833,14 @@ sparse system of linear equations A x = b using Gaussian elimination.") (define-public ruby-asciimath (package (name "ruby-asciimath") - (version "2.0.1") + (version "2.0.4") (source (origin (method url-fetch) (uri (rubygems-uri "asciimath" version)) (sha256 (base32 - "1aapydwwkydbwgz07n7ma3a5jy9n3v0shy6q6j8mi4wr3crhx45a")))) + "1fy2jrn3gr7cl33qydp3pwyfilcmb4m4z6hfhnvydzg8r3srp36j")))) (build-system ruby-build-system) (native-inputs (list ruby-nokogiri ruby-rspec)) @@ -5117,34 +5248,30 @@ A unique design feature of Trilinos is its focus on packages.") (define-public dealii (package (name "dealii") - (version "9.3.2") + (version "9.3.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/dealii/dealii/releases/" "download/v" version "/dealii-" version ".tar.gz")) (sha256 - (base32 "1s0kawnljg24jj6nibwrif5gxdgg2daqfylhqqpl1lvmzmmxfhak")) - (patches (search-patches "dealii-fix-compiliation-with-boost-1.78.patch" - "dealii-fix-sundials.patch")) + (base32 "0a8s4yxcbvzmfgv5qcg27h2ss4fcnyhrhhs35glqj59l9cbmkysx")) (modules '((guix build utils))) (snippet - '(begin - ;; Remove bundled boost, muparser, TBB and UMFPACK. - (delete-file-recursively "bundled") - #t)))) + ;; Remove bundled boost, muparser, TBB and UMFPACK. + '(delete-file-recursively "bundled")))) (build-system cmake-build-system) (outputs '("out" "doc")) (native-inputs ;; Required to build the documentation. - (list graphviz doxygen perl)) + (list graphviz doxygen perl)) (inputs - (list arpack-ng - openblas - gfortran - lapack - muparser - zlib)) + (list arpack-ng + openblas + gfortran + lapack + muparser + zlib)) (propagated-inputs ;; Some scripts are installed into share/deal.II/scripts that require ;; perl and python, but they are not executable (and some are missing the @@ -5153,7 +5280,11 @@ A unique design feature of Trilinos is its focus on packages.") ;; 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. - (list boost hdf5 suitesparse ; For UMFPACK. + (list boost + hdf5 + suitesparse ; For UMFPACK. + ;; SUNDIALS 6.0.0 and later will be supported in deal.II 9.4.0. + sundials-5 tbb)) (arguments `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease. @@ -5181,8 +5312,7 @@ A unique design feature of Trilinos is its focus on packages.") (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))))) + '("detailed.log" "summary.log"))))))))) (home-page "https://www.dealii.org/") (synopsis "Finite element library") (description @@ -5197,18 +5327,21 @@ in finite element programs.") (package/inherit dealii (name "dealii-openmpi") (inputs - `(("arpack" ,arpack-ng-openmpi) - ("metis" ,metis) - ("scalapack" ,scalapack) - ,@(alist-delete "arpack" (package-inputs dealii)))) + (modify-inputs (package-inputs dealii) + (delete "arpack") + (prepend arpack-ng-openmpi + metis + scalapack))) (propagated-inputs - `(("hdf5" ,hdf5-parallel-openmpi) - ("mpi" ,openmpi) - ("p4est" ,p4est-openmpi) - ("petsc" ,petsc-openmpi) - ("slepc" ,slepc-openmpi) - ("trilinos" ,trilinos-for-dealii-openmpi) - ,@(alist-delete "hdf5" (package-propagated-inputs dealii)))) + (modify-inputs (package-propagated-inputs dealii) + (delete "hdf5" "sundials") + (prepend hdf5-parallel-openmpi + openmpi + p4est-openmpi + petsc-openmpi + slepc-openmpi + sundials-openmpi-5 + trilinos-for-dealii-openmpi))) (arguments (substitute-keyword-arguments (package-arguments dealii) ((#:configure-flags flags) @@ -5241,7 +5374,6 @@ in finite element programs.") ;; Disable it for now. ;;("octave" ,octave-cli) ("python" ,python-2) ; print syntax - ;; ("python2-numpy" ,python2-numpy) ; only required for the tests ("zlib" ,zlib))) (arguments `(;; The 'share/flann/octave' contains a .mex file, which is an ELF file @@ -6064,33 +6196,34 @@ and comparisons are supported.") (define-public sundials (package (name "sundials") - (version "3.1.1") + (version "6.2.0") (source (origin (method url-fetch) - (uri (string-append "https://computation.llnl.gov/projects/sundials/download/" - "sundials-" version ".tar.gz")) + (uri (string-append "https://github.com/LLNL/sundials/releases/download/v" + version "/sundials-" version ".tar.gz")) (sha256 (base32 - "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2")))) + "07gk9060xk3bzfqf8v4fqlp0rcxswiwlsy887zv87i1gfy9map8r")))) (build-system cmake-build-system) (native-inputs - `(("python" ,python-2))) ;for tests; syntax incompatible with python 3 + (list python-2)) ; For tests; syntax incompatible with Python 3. (inputs - `(("fortran" ,gfortran) ;for fcmix - ("blas" ,openblas) - ("suitesparse" ,suitesparse))) ;TODO: Add hypre + (list openblas suitesparse)) (arguments - `(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon" + '(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon" + + "-DSUNDIALS_INDEX_SIZE=32" + ;; Incompatible with 32-bit indices. + ;;"-DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON" + "-DEXAMPLES_ENABLE_C:BOOL=ON" "-DEXAMPLES_ENABLE_CXX:BOOL=ON" - "-DEXAMPLES_ENABLE_F77:BOOL=ON" - "-DEXAMPLES_ENABLE_F90:BOOL=ON" + ;; Requires -DBUILD_FORTRAN_MODULE_INTERFACE:BOOL=ON. + ;;"-DEXAMPLES_ENABLE_F2003:BOOL=ON" "-DEXAMPLES_INSTALL:BOOL=OFF" - "-DFCMIX_ENABLE:BOOL=ON" - - "-DKLU_ENABLE:BOOL=ON" + "-DENABLE_KLU:BOOL=ON" ,(string-append "-DKLU_INCLUDE_DIR=" (assoc-ref %build-inputs "suitesparse") "/include") @@ -6108,29 +6241,56 @@ easily be incorporated into existing simulation codes.") (license license:bsd-3))) (define-public sundials-openmpi - (package (inherit sundials) + (package/inherit sundials (name "sundials-openmpi") - (inputs - `(("mpi" ,openmpi) - ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI - ,@(package-inputs sundials))) + (propagated-inputs + (list openmpi + ;; Support for the below requires MPI. + hypre-openmpi + petsc-openmpi)) (arguments (substitute-keyword-arguments (package-arguments sundials) ((#:configure-flags flags '()) - `(cons* "-DMPI_ENABLE:BOOL=ON" - "-DPETSC_ENABLE:BOOL=ON" - (string-append "-DPETSC_INCLUDE_DIR=" - (assoc-ref %build-inputs "petsc") + `(cons* "-DENABLE_MPI:BOOL=ON" + "-DENABLE_HYPRE:BOOL=ON" + (string-append "-DHYPRE_INCLUDE_DIR=" + (assoc-ref %build-inputs "hypre-openmpi") "/include") - (string-append "-DPETSC_LIBRARY_DIR=" - (assoc-ref %build-inputs "petsc") + (string-append "-DHYPRE_LIBRARY_DIR=" + (assoc-ref %build-inputs "hypre-openmpi") "/lib") + "-DENABLE_PETSC:BOOL=ON" + (string-append "-DPETSC_DIR=" + (assoc-ref %build-inputs "petsc-openmpi")) ,flags)) ((#:phases phases '%standard-phases) `(modify-phases ,phases (add-before 'check 'mpi-setup - ,%openmpi-setup))))) - (synopsis "SUNDIALS with OpenMPI support"))) + ,%openmpi-setup))))) + (synopsis "SUNDIALS with MPI support"))) + +(define-public sundials-5 + (package + (inherit sundials) + (name "sundials") + (version "5.8.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/LLNL/sundials/releases/download/v" + version "/sundials-" version ".tar.gz")) + (sha256 + (base32 + "04x2x0jchf9kbcw2a1c6f4h4as8sr6k2snfz8z9k897pa4rl1vfl")))))) + +(define-public sundials-openmpi-5 + (package/inherit sundials-5 + (name "sundials-openmpi") + (propagated-inputs + (package-propagated-inputs sundials-openmpi)) + (arguments + (package-arguments sundials-openmpi)) + (synopsis (package-synopsis sundials-openmpi)))) (define-public sundials-julia (package @@ -6149,13 +6309,19 @@ easily be incorporated into existing simulation codes.") "0nx4sqhmi126m14myzm7syv2053harav9snl0a247wnkcgs5rxrv")))) (inputs (modify-inputs (package-inputs sundials) - (prepend lapack))) + (prepend gfortran lapack))) (arguments - (substitute-keyword-arguments (package-arguments sundials) - ((#:configure-flags flags '()) - `(cons* "-DLAPACK_ENABLE:BOOL=ON" - ,flags)))) - (synopsis "SUNDIALS with lapack support as required by julia-sundials-jll"))) + '(#:configure-flags `("-DCMAKE_C_FLAGS=-O2 -g -fcommon" + "-DSUNDIALS_INDEX_SIZE=32" + "-DKLU_ENABLE:BOOL=ON" + ,(string-append "-DKLU_INCLUDE_DIR=" + (assoc-ref %build-inputs "suitesparse") + "/include") + ,(string-append "-DKLU_LIBRARY_DIR=" + (assoc-ref %build-inputs "suitesparse") + "/lib") + "-DLAPACK_ENABLE:BOOL=ON"))) + (synopsis "SUNDIALS with LAPACK support as required by julia-sundials-jll"))) (define-public combinatorial-blas (package |