diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 512 |
1 files changed, 499 insertions, 13 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 602c696567..7d3ac773b3 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -749,7 +749,7 @@ incompatible with HDF5.") (define-public hdf5 (package (name "hdf5") - (version "1.8.19") + (version "1.8.21") (source (origin (method url-fetch) @@ -759,12 +759,14 @@ incompatible with HDF5.") version ".tar.bz2") (string-append "https://support.hdfgroup.org/ftp/HDF5/" "current" - (apply string-append - (take (string-split version #\.) 2)) + (match (string-split version #\.) + ((major minor _ ...) + (string-append major minor))) "/src/hdf5-" version ".tar.bz2"))) (sha256 - (base32 "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r")) - (patches (list (search-patch "hdf5-config-date.patch"))))) + (base32 "03glk4w4wyb1jyb443g53y3y1ncnf6mj2cqwm6avfr2awkgb3cg5")) + (patches (search-patches "hdf5-config-date.patch" + "hdf5-1.8-mpi-deprecations.patch")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib))) @@ -877,7 +879,8 @@ extremely large and complex data collections.") "/src/hdf5-" version ".tar.bz2"))) (sha256 (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj")) - (patches (list (search-patch "hdf5-config-date.patch"))))))) + (patches (search-patches "hdf5-config-date.patch" + "hdf5-mpi-deprecations.patch")))))) (define-public hdf-java (package @@ -2331,7 +2334,8 @@ void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g, "RowPerm = NOROWPERM;")) #t)) (patches (search-patches "superlu-dist-scotchmetis.patch" - "superlu-dist-awpm-grid.patch")))) + "superlu-dist-awpm-grid.patch" + "superlu-dist-fix-mpi-deprecations.patch")))) (build-system cmake-build-system) (native-inputs `(("tcsh" ,tcsh))) @@ -2691,7 +2695,7 @@ to BMP, JPEG or PNG image formats.") (define-public maxima (package (name "maxima") - (version "5.42.1") + (version "5.42.2") (source (origin (method url-fetch) @@ -2699,7 +2703,7 @@ to BMP, JPEG or PNG image formats.") version "-source/" name "-" version ".tar.gz")) (sha256 (base32 - "1ka0xf70a55ndgmyrq7p5xxbd78pq7bfkqhgxsivaqdw6gn5lmcg")) + "0kdncy6137sg3rradirxzj10mkcvafxd892zlclwhr9sa7b12zhn")) (patches (search-patches "maxima-defsystem-mkdir.patch")))) (build-system gnu-build-system) (inputs @@ -2802,7 +2806,7 @@ point numbers.") (define-public wxmaxima (package (name "wxmaxima") - (version "18.11.4") + (version "19.01.3") (source (origin (method git-fetch) @@ -2812,7 +2816,7 @@ point numbers.") (file-name (git-file-name name version)) (sha256 (base32 - "1sz8n9v23q442l7yjj67pjh0dk78rl4cbcc3j8m1bm88anlfxl9r")))) + "1vwahx3zxkn3qlv4z0fm7v8wh0wspvs026alrh7ff7s0c2dcy95x")))) (build-system cmake-build-system) (native-inputs `(("gettext" ,gettext-minimal))) @@ -2926,7 +2930,7 @@ parts of it.") (define-public openblas (package (name "openblas") - (version "0.3.3") + (version "0.3.4") (source (origin (method url-fetch) @@ -2935,7 +2939,7 @@ parts of it.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0cvlixnpc3cdvvn3f30phfvsgnqljqix6wn72ps9rj7xdhvw06jg")))) + "1s56lgilyyw86dzmj3jkci9zsg24n60wq4d0zri1hrxlxb6ihimj")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -4244,3 +4248,485 @@ linear algebra primitives specifically targeting graph analytics.") license:gpl2+ ;include/psort/(funnel|sort)*.h license:x11 ;usort and psort license:bsd-3)))) ;CombBLAS and MersenneTwister.h + +(define-public dune-common + (package + (name "dune-common") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://dune-project.org/download/" + version "/dune-common-" version ".tar.gz")) + (sha256 + (base32 + "019wcr1qf7jwyxx1y5y290wdlglylskvbb2m01ljkzcza2xnlmhw")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags))) + ;; These tests fail because they require a fully functional MPI + ;; environment. + (add-after 'unpack 'disable-failing-tests + (lambda _ + (setenv "ARGS" + (string-append "--exclude-regex '(" + (string-join + (list + "remoteindicestest" + "remoteindicestest-mpi-2" + "syncertest" + "syncertest-mpi-2" + "variablesizecommunicatortest" + "variablesizecommunicatortest-mpi-2" + "arithmetictestsuitetest" + "assertandreturntest" + "assertandreturntest_ndebug" + "concept" + "debugaligntest" + "mpicollectivecommunication" + "mpicollectivecommunication-mpi-2" + "mpiguardtest" + "mpiguardtest-mpi-2" + "mpihelpertest" + "mpihelpertest-mpi-2" + "mpihelpertest2" + "mpihelpertest2-mpi-2") + "|") + ")'")) + #t))))) + (inputs + `(("gmp" ,gmp) + ("metis" ,metis) + ("openmpi" ,openmpi) + ("openblas" ,openblas) + ("python" ,python) + ("superlu" ,superlu))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "https://dune-project.org/") + (synopsis "Distributed and Unified Numerics Environment") + (description "DUNE, the Distributed and Unified Numerics Environment is a +modular toolbox for solving @dfn{partial differential equations} (PDEs) with +grid-based methods. It supports the easy implementation of methods like +@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite +Differences} (FD).") + ;; GPL version 2 with "runtime exception" to make it behave like LGPLv2. + (license license:gpl2))) + +(define-public dune-geometry + (package + (name "dune-geometry") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://dune-project.org/download/" + version "/dune-geometry-" version ".tar.gz")) + (sha256 + (base32 + "0hlaaxjyv9j05blasvb67sy02hd0w4g9znf68gdh3l731dd1aqbn")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags)))))) + (inputs + `(("dune-common" ,dune-common) + ("openmpi" ,openmpi) + ;; Optional + ("openblas" ,openblas) + ("gmp" ,gmp) + ("python" ,python))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "https://dune-project.org/") + (synopsis "Distributed and Unified Numerics Environment") + (description "DUNE, the Distributed and Unified Numerics Environment is a +modular toolbox for solving @dfn{partial differential equations} (PDEs) with +grid-based methods. It supports the easy implementation of methods like +@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite +Differences} (FD). + +This package contains the basic DUNE geometry classes.") + ;; GPL version 2 with "runtime exception" + (license license:gpl2))) + +(define-public dune-grid + (package + (name "dune-grid") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://dune-project.org/download/" + version "/dune-grid-" version ".tar.gz")) + (sha256 + (base32 + "1jp4vscm9yb9xg0lh7apzccfkhvgbnk652yahigmh3cvzpl4acd0")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags))) + ;; These tests fail because they require a fully functional MPI + ;; environment. + (add-after 'unpack 'disable-failing-tests + (lambda _ + (setenv "ARGS" + (string-append "--exclude-regex '(" + (string-join + (list + "scsgmappertest" + "conformvolumevtktest" + "gnuplottest" + "nonconformboundaryvtktest" + "subsamplingvtktest" + "vtktest" + "vtktest-mpi-2" + "vtksequencetest" + "gmshtest-onedgrid" + "test-dgf-yasp" + "test-dgf-yasp-offset" + "test-dgf-oned" + "test-geogrid-yaspgrid" + "test-gridinfo" + "test-identitygrid" + "testiteratorranges" + "test-hierarchicsearch" + "test-parallel-ug-mpi-2" + "test-yaspgrid-backuprestore-equidistant" + "test-yaspgrid-backuprestore-equidistant-mpi-2" + "test-yaspgrid-backuprestore-equidistantoffset" + "test-yaspgrid-backuprestore-equidistantoffset-mpi-2" + "test-yaspgrid-backuprestore-tensor" + "test-yaspgrid-backuprestore-tensor-mpi-2" + "test-yaspgrid-tensorgridfactory" + "test-yaspgrid-tensorgridfactory-mpi-2" + "test-yaspgrid-yaspfactory-1d" + "test-yaspgrid-yaspfactory-1d-mpi-2" + "test-yaspgrid-yaspfactory-2d" + "test-yaspgrid-yaspfactory-2d-mpi-2" + "test-yaspgrid-yaspfactory-3d" + "test-yaspgrid-yaspfactory-3d-mpi-2" + "globalindexsettest" + "persistentcontainertest" + "structuredgridfactorytest" + "tensorgridfactorytest" + "vertexordertest") + "|") + ")'")) + #t))))) + (inputs + `(("dune-common" ,dune-common) + ("dune-geometry" ,dune-geometry) + ("gmp" ,gmp) + ("metis" ,metis) + ("openblas" ,openblas) + ("openmpi" ,openmpi) + ("python" ,python))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "https://dune-project.org/") + (synopsis "Distributed and Unified Numerics Environment") + (description "DUNE, the Distributed and Unified Numerics Environment is a +modular toolbox for solving @dfn{partial differential equations} (PDEs) with +grid-based methods. It supports the easy implementation of methods like +@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite +Differences} (FD). + +This package contains the basic DUNE grid classes.") + ;; GPL version 2 with "runtime exception" + (license license:gpl2))) + +(define-public dune-istl + (package + (name "dune-istl") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://dune-project.org/download/" + version "/dune-istl-" version ".tar.gz")) + (sha256 + (base32 + "0l2gyrvys5w6wsmk0ckbb7295s80b7yk7qrl7x66akv2jv1nzq2w")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags))) + ;; These tests fail because they require a fully functional MPI + ;; environment. + (add-after 'unpack 'disable-failing-tests + (lambda _ + (setenv "ARGS" + (string-append "--exclude-regex '(" + (string-join + (list + "galerkintest" + "hierarchytest" + "pamgtest" + "pamg_comm_repart_test" + "matrixredisttest" + "vectorcommtest" + "matrixmarkettest") + "|") + ")'")) + #t))))) + (inputs + `(("dune-common" ,dune-common) + ("openmpi" ,openmpi) + ;; Optional + ("metis" ,metis) + ("superlu" ,superlu) + ("openblas" ,openblas) + ("gmp" ,gmp) + ("python" ,python))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "https://dune-project.org/") + (synopsis "Distributed and Unified Numerics Environment") + (description "DUNE, the Distributed and Unified Numerics Environment is a +modular toolbox for solving @dfn{partial differential equations} (PDEs) with +grid-based methods. + +This is the iterative solver template library which provides generic sparse +matrix/vector classes and a variety of solvers based on these classes. A +special feature is the use of templates to exploit the recursive block +structure of finite element matrices at compile time. Available solvers +include Krylov methods, (block-) incomplete decompositions and +aggregation-based algebraic multigrid.") + ;; GPL version 2 with "runtime exception" + (license license:gpl2))) + +(define-public dune-localfunctions + (package + (name "dune-localfunctions") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://dune-project.org/download/" + version "/dune-localfunctions-" version ".tar.gz")) + (sha256 + (base32 + "19c6zjinwwpy8jh4v4prhphyd438rapd4x80fj93apmwgw04nrhl")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags)))))) + (inputs + `(("dune-common" ,dune-common) + ("dune-geometry" ,dune-geometry) + ("openmpi" ,openmpi) + ;; Optional + ("metis" ,metis) + ("superlu" ,superlu) + ("gmp" ,gmp))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "https://dune-project.org/") + (synopsis "Distributed and Unified Numerics Environment") ; TODO + (description "This DUNE module provides interface and implementation for +shape functions defined on the DUNE reference elements. In addition to the +shape function, interpolation operators and special keys are provided which +can be used to assemble global function spaces on finite-element grids. + +This package provides an interface and implementation for shape functions +defined on the DUNE reference elements. In addition to the shape function, +interpolation operators and special keys are provided which can be used to +assemble global function spaces on finite-element grids.") + ;; GPL version 2 with "runtime exception" + (license license:gpl2))) + +(define-public dune-alugrid + (package + (name "dune-alugrid") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://dune-project.org/download/" + version "/dune-alugrid-" version ".tar.gz")) + (sha256 + (base32 + "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj")))) + (build-system cmake-build-system) + (arguments + `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI + ; environment + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-include + (lambda _ + (substitute* "dune/alugrid/test/test-alugrid.cc" + (("doc/grids/gridfactory/testgrids") + "doc/dune-grid/grids/gridfactory/testgrids")) + #t)) + (add-after 'build 'build-tests + (lambda* (#:key inputs make-flags #:allow-other-keys) + (setenv "CPLUS_INCLUDE_PATH" + (string-append (assoc-ref inputs "dune-grid") "/share:" + (getenv "CPLUS_INCLUDE_PATH"))) + (apply invoke "make" "build_tests" make-flags)))))) + (inputs + `(("dune-common" ,dune-common) + ("dune-geometry" ,dune-geometry) + ("dune-grid" ,dune-grid) + ("openmpi" ,openmpi) + ;; Optional + ("metis" ,metis) + ("openblas" ,openblas) + ("python" ,python) + ("superlu" ,superlu) + ("gmp" ,gmp) + ("zlib" ,zlib))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "https://dune-project.org/") + (synopsis "Distributed and Unified Numerics Environment") + (description "ALUGrid is an adaptive, loadbalancing, unstructured +implementation of the DUNE grid interface supporting either simplices or +cubes.") + (license license:gpl2+))) + +(define-public dune-typetree + (package + (name "dune-typetree") + (version "2.6.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.dune-project.org/staging/dune-typetree.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0mnv6w2f22lz3j4bdpdjq55vjm8xxfx9v4vvhg9bd36xpsbjpjp9")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags)))))) + (inputs + `(("dune-common" ,dune-common) + ("openmpi" ,openmpi) + ;; Optional + ("openblas" ,openblas) + ("python" ,python) + ("metis" ,metis) + ("superlu" ,superlu) + ("gmp" ,gmp))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "https://dune-project.org/") + (synopsis "Distributed and Unified Numerics Environment") + (description "TypeTree is a template library for constructing and +operating on statically typed trees of objects.") + ;; Either GPL version 2 with "runtime exception" or LGPLv3+. + (license (list license:lgpl3+ license:gpl2)))) + +(define-public dune-functions + (package + (name "dune-functions") + (version "2.6.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.dune-project.org/staging/dune-functions.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200")))) + (build-system cmake-build-system) + (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid + (inputs + `(("dune-common" ,dune-common) + ("dune-istl" ,dune-istl) + ("dune-localfunctions" ,dune-localfunctions) + ("dune-grid" ,dune-grid) + ("dune-geometry" ,dune-geometry) + ("dune-typetree" ,dune-typetree) + ("openmpi" ,openmpi) + ("openblas" ,openblas) + ("metis" ,metis) + ("python" ,python) + ("superlu" ,superlu) + ("gmp" ,gmp))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "https://dune-project.org/") + (synopsis "Distributed and Unified Numerics Environment") + (description "The dune-functions module provides an abstraction layer for +global finite element functions. Its two main concepts are functions +implemented as callable objects, and bases of finite element spaces.") + ;; Either GPL version 2 with "runtime exception" or LGPLv3+. + (license (list license:lgpl3+ license:gpl2)))) + +(define-public dune-pdelab + (package + (name "dune-pdelab") + (version "2.6.0-rc1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.dune-project.org/pdelab/dune-pdelab") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "07g0s9448z65vjrq88g5rv3340iifil85k170n8kbqchsvi4ny5v")))) + (build-system cmake-build-system) + (arguments '(#:tests? #f)) ; XXX: the tests cannot be compiled + (inputs + `(("dune-common" ,dune-common) + ("dune-istl" ,dune-istl) + ("dune-localfunctions" ,dune-localfunctions) + ("dune-geometry" ,dune-geometry) + ("dune-grid" ,dune-grid) + ("dune-typetree" ,dune-typetree) + ("dune-functions" ,dune-functions) + ("openmpi" ,openmpi) + ;; Optional + ("openblas" ,openblas) + ("eigen" ,eigen) + ("metis" ,metis) + ("python" ,python) + ("superlu" ,superlu) + ("gmp" ,gmp))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "https://dune-project.org/") + (synopsis "Differential equations solver toolbox") + (description "PDELab is a partial differential equations solver toolbox +built on top of DUNE, the Distributed and Unified Numerics Environment.") + ;; Either GPL version 2 with "runtime exception" or LGPLv3+. + (license (list license:lgpl3+ license:gpl2)))) |