diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 533 |
1 files changed, 385 insertions, 148 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 3d571e8cc9..f1b5bb0646 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -15,7 +15,7 @@ ;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2016 Leo Famulari <leo@famulari.name> ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be> -;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com> +;;; Copyright © 2017, 2018 Paul Garlick <pgarlick@tourbillion-technology.com> ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is> ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org> @@ -27,6 +27,8 @@ ;;; Copyright © 2018 Nadya Voronova <voronovank@gmail.com> ;;; Copyright © 2018 Adam Massmann <massmannak@gmail.com> ;;; Copyright © 2018 Marius Bakke <mbakke@fastmail.com> +;;; Copyright © 2018 Eric Brown <brown@fastmail.com> +;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu> ;;; ;;; This file is part of GNU Guix. ;;; @@ -238,16 +240,60 @@ triangulations.") (license (license:non-copyleft "file://COPYING.txt" "See COPYING in the distribution.")))) +(define-public python-cvxopt + (package + (name "python-cvxopt") + (version "1.2.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cvxopt/cvxopt.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "05mnjil9palaa48xafdfh4f5pr4z7aqjr995rwl08qfyxs8y0crf")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'find-libraries + (lambda* (#:key inputs #:allow-other-keys) + (setenv "CVXOPT_BLAS_LIB" "openblas") + (setenv "CVXOPT_BUILD_FFTW" "1") + (setenv "CVXOPT_BUILD_GLPK" "1") + (setenv "CVXOPT_BUILD_GSL" "1") + #t))))) + (inputs + `(("fftw" ,fftw) + ("glpk" ,glpk) + ("gsl" ,gsl) + ("lapack" ,lapack) + ("openblas" ,openblas) + ("suitesparse" ,suitesparse))) + (home-page "https://www.cvxopt.org") + (synopsis "Python library for convex optimization") + (description + "CVXOPT is a package for convex optimization based on the Python +programming language. Its main purpose is to make the development of software +for convex optimization applications straightforward by building on Python’s +extensive standard library and on the strengths of Python as a high-level +programming language.") + (license license:gpl3+))) + +(define-public python2-cvxopt + (package-with-python2 python-cvxopt)) + (define-public units (package (name "units") - (version "2.17") + (version "2.18") (source (origin (method url-fetch) (uri (string-append "mirror://gnu/units/units-" version ".tar.gz")) (sha256 (base32 - "1n2xzpnxfn475zkd8rzs5gg58xszjbr4bdbgvk6hryzimvwwj0qz")))) + "0y26kj349i048y4z3xrk90bvciw2j6ds3rka7r7yn3183hirr5b4")))) (build-system gnu-build-system) (inputs `(("readline" ,readline) @@ -276,15 +322,15 @@ enough to be used effectively as a scientific calculator.") (define-public double-conversion (package (name "double-conversion") - (version "3.0.0") + (version "3.1.0") (home-page "https://github.com/google/double-conversion") (source (origin - (method url-fetch) - (uri (string-append home-page "/archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference (url home-page) (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "059r1czs28ljjd388pn6l3njg1ghbf1cv3q9nkxv3dj2a8siabqm")))) + "123rb2p4snqagrybw66vnapchqdwn2rfpr1wcq0ya9gwbyl7xccx")))) (build-system cmake-build-system) (arguments '(#:test-target "test" @@ -459,22 +505,16 @@ computing convex hulls.") (define-public arpack-ng (package (name "arpack-ng") - (version "3.5.0") + (version "3.6.3") (home-page "https://github.com/opencollab/arpack-ng") - (source - (origin - (method url-fetch) - (uri (string-append home-page "/archive/" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "0f8jx3fifmj9qdp289zr7r651y1q48k1jya859rqxq62mvis7xsh")))) + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1wljl96yqxc9v8r49c37lscwkdp58kaacfb9p6s6nvpm31haax4y")))) (build-system gnu-build-system) - (arguments - '(#:phases (modify-phases %standard-phases - (add-after 'unpack 'autoreconf - (lambda _ - (invoke "autoreconf" "-vfi")))))) (native-inputs `(("autoconf" ,autoconf) ("automake" ,automake) @@ -513,7 +553,11 @@ large scale eigenvalue problems.") (arguments (substitute-keyword-arguments (package-arguments arpack-ng) ((#:configure-flags _ '()) - ''("--enable-mpi")))) + ''("--enable-mpi")) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + (add-before 'check 'mpi-setup + ,%openmpi-setup))))) (synopsis "Fortran subroutines for solving eigenvalue problems with MPI"))) (define-public lapack @@ -574,14 +618,8 @@ problems in numerical linear algebra.") (arguments `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES") #:phases (modify-phases %standard-phases - (add-before 'check 'set-test-environment - (lambda _ - ;; By default, running the test suite would fail because - ;; 'ssh' could not be found in $PATH. Define this - ;; variable to placate Open MPI without adding a - ;; dependency on OpenSSH (the agent isn't used anyway.) - (setenv "OMPI_MCA_plm_rsh_agent" (which "cat")) - #t))))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (home-page "http://www.netlib.org/scalapack/") (synopsis "Library for scalable numerical linear algebra") (description @@ -821,8 +859,11 @@ incompatible with HDF5.") (mkdir-p flib) (mkdir-p finc) (mkdir-p fex) - (rename-file (string-append bin "/h5fc") - (string-append fbin "/h5fc")) + ;; Note: When built with --enable-parallel, the 'h5fc' file + ;; doesn't exist, hence this condition. + (when (file-exists? (string-append bin "/h5fc")) + (rename-file (string-append bin "/h5fc") + (string-append fbin "/h5fc"))) (for-each (lambda (file) (rename-file file (string-append flib "/" (basename file)))) @@ -844,6 +885,25 @@ extremely large and complex data collections.") (license (license:x11-style "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) +(define-public hdf5-1.10 + (package (inherit hdf5) + (version "1.10.4") + (source + (origin + (method url-fetch) + (uri (list (string-append "https://support.hdfgroup.org/ftp/HDF5/releases/" + "hdf5-" (version-major+minor version) + "/hdf5-" version "/src/hdf5-" + version ".tar.bz2") + (string-append "https://support.hdfgroup.org/ftp/HDF5/" + "current" + (apply string-append + (take (string-split version #\.) 2)) + "/src/hdf5-" version ".tar.bz2"))) + (sha256 + (base32 "1pr85fa1sh2ky6ai2hs3f21lp252grl2cq3wbyi4rh7dm83gyrqj")) + (patches (list (search-patch "hdf5-config-date.patch"))))))) + (define-public hdf-java (package (name "hdf-java") @@ -1041,10 +1101,13 @@ Swath).") `(("mpi" ,openmpi) ,@(package-inputs hdf5))) (arguments - (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel") - ,@(package-arguments hdf5)) + (substitute-keyword-arguments (package-arguments hdf5) + ((#:configure-flags flags) + ``("--enable-parallel" ,@(delete "--enable-cxx" ,flags))) ((#:phases phases) `(modify-phases ,phases + (add-after 'build 'mpi-setup + ,%openmpi-setup) (add-before 'check 'patch-tests (lambda _ ;; OpenMPI's mpirun will exit with non-zero status if it @@ -1403,6 +1466,13 @@ can solve two kinds of problems: ("less" ,less) ("ghostscript" ,ghostscript) ("gnuplot" ,gnuplot))) + ;; Octave code uses this variable to detect directories holding multiple CA + ;; certificates to verify peers with. This is required for the networking + ;; functions that require encryption to work properly. + (native-search-paths + (list (search-path-specification + (variable "CURLOPT_CAPATH") + (files '("etc/ssl/certs"))))) (arguments `(#:configure-flags (list (string-append "--with-shell=" @@ -1585,7 +1655,7 @@ September 2004}") (define-public petsc (package (name "petsc") - (version "3.8.0") + (version "3.10.2") (source (origin (method url-fetch) @@ -1593,7 +1663,9 @@ September 2004}") (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" "petsc-lite-" version ".tar.gz")) (sha256 - (base32 "1lajbk3c29hnh83v6cbmm3a8wv6bdykh0p70kwrr4vrnizalk88s")))) + (base32 "0bl64pydak3rblnjffi482r8bin4xim9sb37ksl2jkcxf0i0irsi")))) + (outputs '("out" ;libraries and headers + "examples")) ;~30MiB of examples (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) @@ -1610,11 +1682,7 @@ September 2004}") #:configure-flags `("--with-mpi=0" "--with-openmp=1" - "--with-superlu=1" - ,(string-append "--with-superlu-include=" - (assoc-ref %build-inputs "superlu") "/include") - ,(string-append "--with-superlu-lib=" - (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a")) + "--with-superlu=1") #:make-flags ;; Honor (parallel-job-count) for build. Do not use --with-make-np, ;; whose value is dumped to $out/lib/petsc/conf/petscvariables. @@ -1667,6 +1735,15 @@ September 2004}") "PETScBuildInternal.cmake" ;; Once installed, should uninstall with Guix "uninstall.py")) + #t))) + (add-after 'install 'move-examples + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (examples (assoc-ref outputs "examples")) + (exdir (string-append out "/share/petsc/examples")) + (exdir' (string-append examples "/share/petsc/examples"))) + (copy-recursively exdir exdir') + (delete-file-recursively exdir) #t)))))) (home-page "http://www.mcs.anl.gov/petsc") (synopsis "Library to solve PDEs") @@ -1689,16 +1766,33 @@ scientific applications modeled by partial differential equations.") (package (inherit petsc) (name "petsc-openmpi") (inputs - `(("openmpi" ,openmpi) + `(("hdf5" ,hdf5-parallel-openmpi) + ("metis" ,metis) + ("mumps" ,mumps-openmpi) + ("openmpi" ,openmpi) + ("scalapack" ,scalapack) + ("scotch" ,pt-scotch) ,@(package-inputs petsc))) (arguments (substitute-keyword-arguments (package-arguments petsc) ((#:configure-flags cf) ``("--with-mpiexec=mpirun" + "--with-metis=1" + "--with-mumps=1" + "--with-scalapack=1" + "--with-ptscotch=1" ,(string-append "--with-mpi-dir=" (assoc-ref %build-inputs "openmpi")) - ,@(delete "--with-mpi=0" ,cf))))) - (synopsis "Library to solve PDEs (with MPI support)"))) + ,(string-append "--with-hdf5-include=" + (assoc-ref %build-inputs "hdf5") "/include") + ,(string-append "--with-hdf5-lib=" + (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a") + ,@(delete "--with-mpi=0" ,cf))) + ((#:phases phases) + `(modify-phases ,phases + (add-before 'configure 'mpi-setup + ,%openmpi-setup))))) + (synopsis "Library to solve PDEs (with MUMPS and MPI support)"))) (define-public petsc-complex-openmpi (package (inherit petsc-complex) @@ -1715,6 +1809,40 @@ scientific applications modeled by partial differential equations.") ,@(delete "--with-mpi=0" ,cf))))) (synopsis "Library to solve PDEs (with complex scalars and MPI support)"))) +(define-public python-petsc4py + (package + (name "python-petsc4py") + (version "3.10.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "petsc4py" version)) + (sha256 + (base32 + "0ch3g6dsvxl7qi984fcssv7cxfbif4bw04gkvxl2l1b8wrmvrm25")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'pre-build + (lambda _ + ;; Define path to PETSc installation. + (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) + #t)) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) + (inputs + `(("petsc" ,petsc-openmpi) + ("python-numpy" ,python-numpy))) + (home-page "https://bitbucket.org/petsc/petsc4py/") + (synopsis "Python bindings for PETSc") + (description "PETSc, the Portable, Extensible Toolkit for +Scientific Computation, is a suite of data structures and routines for +the scalable (parallel) solution of scientific applications modeled by +partial differential equations. It employs the MPI standard for all +message-passing communication. @code{petsc4py} provides Python +bindings to almost all functions of PETSc.") + (license license:bsd-3))) (define-public python-kiwisolver (package @@ -1743,7 +1871,7 @@ savings are consistently > 5x.") (define-public slepc (package (name "slepc") - (version "3.8.2") + (version "3.10.1") (source (origin (method url-fetch) @@ -1751,7 +1879,7 @@ savings are consistently > 5x.") version ".tar.gz")) (sha256 (base32 - "04zd48p43rnvg68p6cp28zll0px5whglc5v0sc3s6vdj1v920z8y")))) + "188j1a133q91h8pivpnzwcf78kz8dvz2nzf6ndnjygdbqb48fizn")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) @@ -1828,14 +1956,8 @@ arising after the discretization of partial differential equations.") (substitute-keyword-arguments (package-arguments slepc) ((#:phases phases '%standard-phases) `(modify-phases ,phases - (add-before 'check 'set-test-environment - (lambda _ - ;; By default, running the test suite would fail because 'ssh' - ;; could not be found in $PATH. Define this variable to - ;; placate Open MPI without adding a dependency on OpenSSH (the - ;; agent isn't used anyway.) - (setenv "OMPI_MCA_plm_rsh_agent" (which "cat")) - #t)))))) + (add-before 'check 'mpi-setup + ,%openmpi-setup))))) (inputs `(("mpi" ,openmpi) ("arpack" ,arpack-ng-openmpi) @@ -1853,6 +1975,43 @@ arising after the discretization of partial differential equations.") ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi)))) (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)"))) +(define-public python-slepc4py + (package + (name "python-slepc4py") + (version "3.10.0") + (source + (origin + (method url-fetch) + (uri (pypi-uri "slepc4py" version)) + (sha256 + (base32 + "0x049dyc8frgh79fvvavf4vlbqp4mgm61nsaivzdav4316vvlv1j")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-before 'build 'pre-build + (lambda _ + ;; Define path to PETSc installation. + (setenv "PETSC_DIR" (assoc-ref %build-inputs "petsc")) + ;; Define path to SLEPc installation. + (setenv "SLEPC_DIR" (assoc-ref %build-inputs "slepc")) + #t)) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) + (inputs + `(("python-numpy" ,python-numpy) + ("python-petsc4py" ,python-petsc4py) + ("slepc" ,slepc-openmpi))) + (home-page "https://bitbucket.org/slepc/slepc4py/") + (synopsis "Python bindings for SLEPc") + (description "SLEPc, the Scalable Library for Eigenvalue Problem +Computations, is based on PETSc, the Portable, Extensible Toolkit for +Scientific Computation. It employs the MPI standard for all +message-passing communication. @code{slepc4py} provides Python +bindings to almost all functions of SLEPc.") + (license license:bsd-3))) + (define-public mumps (package (name "mumps") @@ -2005,14 +2164,8 @@ sparse system of linear equations A x = b using Guassian elimination.") (substitute-keyword-arguments (package-arguments mumps) ((#:phases phases) `(modify-phases ,phases - (add-before 'check 'set-test-environment - (lambda _ - ;; By default, running the test suite would fail because 'ssh' - ;; could not be found in $PATH. Define this variable to - ;; placate Open MPI without adding a dependency on OpenSSH (the - ;; agent isn't used anyway.) - (setenv "OMPI_MCA_plm_rsh_agent" (which "cat")) - #t)) + (add-before 'check 'mpi-setup + ,%openmpi-setup) (replace 'check (lambda _ ((assoc-ref ,phases 'check) @@ -2049,16 +2202,14 @@ programming problems.") (define-public r-pracma (package (name "r-pracma") - (version "2.1.4") + (version "2.1.8") (source (origin (method url-fetch) (uri (cran-uri "pracma" version)) (sha256 - (base32 "1ygm81i7mqvh229dp9935djjyb120p3bqvaf4k572sa4q63fzjhc")))) + (base32 "0m8ladhrfyxwybblkcdgg4xv1mk5kibmwarpj2k0c2y34zzcix4z")))) (build-system r-build-system) - (propagated-inputs - `(("r-quadprog" ,r-quadprog))) - (home-page "https://cran.r-project.org/web/packages/pracma") + (home-page "https://cran.r-project.org/web/packages/pracma/") (synopsis "Practical numerical math functions") (description "This package provides functions for numerical analysis and linear algebra, numerical optimization, differential equations, plus some @@ -2087,7 +2238,8 @@ porting.") (lambda _ (substitute* "spec/parser_spec.rb" (("\\\\\"") - "\""))))))) + "\"")) + #t))))) (native-inputs `(("bundler" ,bundler) ("ruby-rspec" ,ruby-rspec))) @@ -2258,13 +2410,10 @@ CDEFS = -DAdd_" "/" dir))) '("lib" "include")) #t)) + (add-before 'check 'mpi-setup + ,%openmpi-setup) (replace 'check (lambda _ - ;; By default, running the test suite would fail because 'ssh' - ;; could not be found in $PATH. Define this variable to placate - ;; Open MPI without adding a dependency on OpenSSH (the agent - ;; isn't used anyway.) - (setenv "OMPI_MCA_plm_rsh_agent" (which "cat")) (with-directory-excursion "EXAMPLE" (invoke "mpirun" "-n" "2" "./pddrive" "-r" "1" "-c" "2" "g20.rua") @@ -2357,15 +2506,8 @@ YACC = bison -pscotchyy -y -b y ;; "SCOTCH_PTHREAD_NUMBER=2" "restrict=__restrict")))) #t)) - (add-after - 'build 'build-esmumps + (add-after 'build 'build-esmumps (lambda _ - ;; By default, running the test suite would fail because 'ssh' - ;; could not be found in $PATH. Define this variable to placate - ;; Open MPI without adding a dependency on OpenSSH (the agent - ;; isn't used anyway.) - (setenv "OMPI_MCA_plm_rsh_agent" (which "cat")) - (invoke "make" (format #f "-j~a" (parallel-job-count)) "esmumps"))) @@ -2458,15 +2600,16 @@ YACC = bison -pscotchyy -y -b y (replace 'build (lambda _ - (and - (zero? (system* "make" - (format #f "-j~a" (parallel-job-count)) - "ptscotch" "ptesmumps")) - ;; Install the serial metis compatibility library - (zero? (system* "make" "-C" "libscotchmetis" "install"))))) - (replace - 'check - (lambda _ (zero? (system* "make" "ptcheck")))))))) + (invoke "make" (format #f "-j~a" (parallel-job-count)) + "ptscotch" "ptesmumps") + + ;; Install the serial metis compatibility library + (invoke "make" "-C" "libscotchmetis" "install"))) + (add-before 'check 'mpi-setup + ,%openmpi-setup) + (replace 'check + (lambda _ + (invoke "make" "ptcheck"))))))) (synopsis "Programs and libraries for graph algorithms (with MPI)"))) (define-public pt-scotch32 @@ -2480,15 +2623,15 @@ YACC = bison -pscotchyy -y -b y `(modify-phases ,scotch32-phases (replace 'build (lambda _ - (and - (zero? (system* "make" - (format #f "-j~a" (parallel-job-count)) - "ptscotch" "ptesmumps")) - ;; Install the serial metis compatibility library - (zero? (system* "make" "-C" "libscotchmetis" "install"))))) + (invoke "make" (format #f "-j~a" (parallel-job-count)) + "ptscotch" "ptesmumps") + ;; Install the serial metis compatibility library + (invoke "make" "-C" "libscotchmetis" "install"))) + (add-before 'check 'mpi-setup + ,%openmpi-setup) (replace 'check (lambda _ - (zero? (system* "make" "ptcheck")))))))) + (invoke "make" "ptcheck"))))))) (synopsis "Programs and libraries for graph algorithms (with MPI and 32-bit integers)"))) @@ -2548,14 +2691,8 @@ schemes.") (assoc-ref %build-inputs "lapack") " -llapack")) #:phases (modify-phases %standard-phases - (add-before 'check 'set-test-environment - (lambda _ - ;; By default, running the test suite would fail because - ;; 'ssh' could not be found in $PATH. Define this - ;; variable to placate Open MPI without adding a - ;; dependency on OpenSSH (the agent isn't used anyway.) - (setenv "OMPI_MCA_plm_rsh_agent" (which "cat")) - #t))))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (home-page "http://www.p4est.org") (synopsis "Adaptive mesh refinement on forests of octrees") (description @@ -2613,7 +2750,7 @@ to BMP, JPEG or PNG image formats.") (define-public maxima (package (name "maxima") - (version "5.41.0") + (version "5.42.1") (source (origin (method url-fetch) @@ -2621,7 +2758,7 @@ to BMP, JPEG or PNG image formats.") version "-source/" name "-" version ".tar.gz")) (sha256 (base32 - "0x0n81z0s4pl8nwpf7ivlsbvsdphm9w42250g7qdkizl0132by6s")) + "1ka0xf70a55ndgmyrq7p5xxbd78pq7bfkqhgxsivaqdw6gn5lmcg")) (patches (search-patches "maxima-defsystem-mkdir.patch")))) (build-system gnu-build-system) (inputs @@ -2653,6 +2790,18 @@ to BMP, JPEG or PNG image formats.") (lambda _ (chmod "src/maxima" #o555) #t)) + (replace 'check + (lambda _ + ;; This is derived from the testing code in the "debian/rules" file + ;; of Debian's Maxima package. + ;; If Maxima can successfully run this, the binary to be installed + ;; should be fine. + (zero? + (system + (string-append "./maxima-local " + "--lisp=gcl " + "--batch-string=\"run_testsuite();\" " + "| grep -q \"No unexpected errors found\""))))) ;; Make sure the doc and emacs files are found in the ;; standard location. Also configure maxima to find gnuplot ;; without having it on the PATH. @@ -2700,18 +2849,17 @@ point numbers.") (define-public wxmaxima (package (name "wxmaxima") - (version "18.02.0") + (version "18.11.4") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/andrejv/" name "/archive" - "/Version-" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/wxMaxima-developers/wxmaxima.git") + (commit (string-append "Version-" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "03kr2rgfp4hcf3is8m8d8f9hj660c3xgrc50vrrfpixx4syh6wvj")) - (patches - (search-patches "wxmaxima-do-not-use-old-gnuplot-parameters.patch")))) + "1sz8n9v23q442l7yjj67pjh0dk78rl4cbcc3j8m1bm88anlfxl9r")))) (build-system cmake-build-system) (native-inputs `(("gettext" ,gettext-minimal))) @@ -2825,16 +2973,16 @@ parts of it.") (define-public openblas (package (name "openblas") - (version "0.3.2") + (version "0.3.3") (source (origin (method url-fetch) - (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v" - version)) + (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20" + version "%20version.tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0b20km2jv7m6qiylrlvhq2vnmkmilb633mr8rhqmgbn1wqrp58jq")))) + "0cvlixnpc3cdvvn3f30phfvsgnqljqix6wn72ps9rj7xdhvw06jg")))) (build-system gnu-build-system) (arguments `(#:test-target "test" @@ -2892,6 +3040,18 @@ parts of it.") "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.") (license license:bsd-3))) +(define-public openblas-ilp64 + (package (inherit openblas) + (name "openblas-ilp64") + (supported-systems '("x86_64-linux" "aarch64-linux" "mips64el-linux")) + (arguments + (substitute-keyword-arguments (package-arguments openblas) + ((#:make-flags flags '()) + `(append (list "INTERFACE64=1" "LIBNAMESUFFIX=ilp64") + ,flags)))) + (synopsis "Optimized BLAS library based on GotoBLAS (ILP64 version)") + (license license:bsd-3))) + (define* (make-blis implementation #:optional substitutable?) "Return a BLIS package with the given IMPLEMENTATION (see config/ in the source tree for a list of implementations.) @@ -3236,7 +3396,7 @@ Failure to do so will result in a library with poor performance.") (define-public glm (package (name "glm") - (version "0.9.9.0") + (version "0.9.9.3") (source (origin (method url-fetch) @@ -3244,7 +3404,7 @@ Failure to do so will result in a library with poor performance.") version "/glm-" version ".zip")) (sha256 (base32 - "0ihjadp2sb8w312a276skfjsljm3y41bjscbxf79wn23gi00giz1")))) + "0yqk5r3qh60d4r2iab5q7wq0fryn8p3pz6s28y1i7amqj1aqavj9")))) (build-system cmake-build-system) (native-inputs `(("unzip" ,unzip))) @@ -3517,7 +3677,7 @@ set.") (define-public hypre (package (name "hypre") - (version "2.11.0") + (version "2.14.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/LLNL/hypre/archive/" @@ -3525,7 +3685,7 @@ set.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m")) + "0v515i73bvaz378h5465b1dy9v2gf924zy2q94cpq4qqarawvkqh")) (modules '((guix build utils))) (snippet '(begin @@ -3533,7 +3693,7 @@ set.") ;; substitute the tarball creation time. (substitute* "src/utilities/HYPRE_utilities.h" (("Date Compiled: .*$") - "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n")) + "Date Compiled: Apr 11 2018 16:24:59 +0000\"\n")) #t)))) (build-system gnu-build-system) (outputs '("out" ;6.1 MiB of headers and libraries @@ -3622,14 +3782,8 @@ problems.") ,@(delete "--without-MPI" ,flags))) ((#:phases phases) `(modify-phases ,phases - (add-before 'check 'set-test-environment - (lambda _ - ;; By default, running the test suite would fail because 'ssh' - ;; could not be found in $PATH. Define this variable to - ;; placate Open MPI without adding a dependency on OpenSSH (the - ;; agent isn't used anyway.) - (setenv "OMPI_MCA_plm_rsh_agent" (which "cat")) - #t)))))) + (add-before 'check 'mpi-setup + ,%openmpi-setup))))) (synopsis "Parallel solvers and preconditioners for linear equations") (description "HYPRE is a software library of high performance preconditioners and @@ -3794,15 +3948,15 @@ as equations, scalars, vectors, and matrices.") (define-public z3 (package (name "z3") - (version "4.5.0") + (version "4.8.1") + (home-page "https://github.com/Z3Prover/z3") (source (origin - (method url-fetch) - (uri (string-append - "https://github.com/Z3Prover/z3/archive/z3-" - version ".tar.gz")) + (method git-fetch) + (uri (git-reference (url home-page) + (commit (string-append "z3-" version)))) (sha256 (base32 - "032a5lvji2liwmc25jv52bdrhimqflvqbpg77ccaq1jykhiivbmf")))) + "1vr57bwx40sd5riijyrhy70i2wnv9xrdihf6y5zdz56yq88rl48f")))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -3831,43 +3985,57 @@ as equations, scalars, vectors, and matrices.") (synopsis "Theorem prover") (description "Z3 is a theorem prover and @dfn{satisfiability modulo theories} (SMT) solver. It provides a C/C++ API, as well as Python bindings.") - (home-page "https://github.com/Z3Prover/z3") (license license:expat))) (define-public cubicle (package (name "cubicle") - (version "1.1.1") + (version "1.1.2") (source (origin (method url-fetch) (uri (string-append "http://cubicle.lri.fr/cubicle-" version ".tar.gz")) (sha256 (base32 - "1sny9c4fm14k014pk62ibpwbrjjirkx8xmhs9jg7q1hk7y7x3q2h")))) + "10kk80jdmpdvql88sdjsh7vqzlpaphd8vip2lp47aarxjkwjlz1q")))) (build-system gnu-build-system) (native-inputs - `(("ocaml" ,ocaml) + `(("automake" ,automake) + ("ocaml" ,ocaml) ("which" ,(@@ (gnu packages base) which)))) (propagated-inputs - `(("z3" ,z3))) + `(("ocaml-num" ,ocaml-num) + ("z3" ,z3))) (arguments `(#:configure-flags (list "--with-z3") + #:make-flags (list "QUIET=") #:tests? #f #:phases (modify-phases %standard-phases (add-before 'configure 'configure-for-release (lambda _ (substitute* "Makefile.in" - (("SVNREV=") "#SVNREV=")))) + (("SVNREV=") "#SVNREV=")) + #t)) (add-before 'configure 'fix-/bin/sh (lambda _ (substitute* "configure" - (("/bin/sh") (which "sh"))))) + (("-/bin/sh") (string-append "-" (which "sh")))) + #t)) (add-before 'configure 'fix-smt-z3wrapper.ml (lambda _ (substitute* "Makefile.in" - (("\\\\n") ""))))))) + (("\\\\n") "")) + #t)) + (add-before 'configure 'fix-ocaml-num + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "Makefile.in" + (("= \\$\\(FUNCTORYLIB\\)") + (string-append "= -I " + (assoc-ref inputs "ocaml-num") + "/lib/ocaml/site-lib" + " $(FUNCTORYLIB)"))) + #t))))) (home-page "http://cubicle.lri.fr/") (synopsis "Model checker for array-based systems") (description "Cubicle is a model checker for verifying safety properties @@ -3912,6 +4080,8 @@ exclusion algorithms are typical examples of such systems.") "-DCMAKE_INSTALL_LIBDIR=lib" "-DGFORTRAN_LIB=gfortran") #:phases (modify-phases %standard-phases + (add-before 'check 'mpi-setup + ,%openmpi-setup) (add-before 'check 'setup-tests (lambda _ ;; Parallelism is done at the MPI layer. @@ -3958,7 +4128,7 @@ toolset supports analysis and automatic verification, linearisation, simulation, state-space exploration and generation, and tools to optimise and analyse specifications. Also, state spaces can be manipulated, visualised and analysed.") - (home-page "http://mcrl2.org") + (home-page "https://mcrl2.org") (license license:boost1.0))) (define-public r-subplex @@ -4032,3 +4202,70 @@ terminal do calculations simply and quickly. The formula to be calculated can be fed to @command{tcalc} through the command line.") (home-page "https://sites.google.com/site/mohammedisam2000/tcalc") (license license:gpl3+))) + +(define-public sundials + (package + (name "sundials") + (version "3.1.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://computation.llnl.gov/projects/sundials/download/" + "sundials-" version ".tar.gz")) + (sha256 + (base32 + "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2")))) + (build-system cmake-build-system) + (native-inputs + `(("python" ,python-2))) ;for tests; syntax incompatible with python 3 + (inputs + `(("fortran" ,gfortran) ;for fcmix + ("blas" ,openblas) + ("suitesparse" ,suitesparse))) ;TODO: Add hypre + (arguments + `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON" + "-DEXAMPLES_ENABLE_CXX:BOOL=ON" + "-DEXAMPLES_ENABLE_F77:BOOL=ON" + "-DEXAMPLES_ENABLE_F90:BOOL=ON" + "-DEXAMPLES_INSTALL:BOOL=OFF" + + "-DFCMIX_ENABLE:BOOL=ON" + + "-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")))) + (home-page "https://computation.llnl.gov/projects/sundials") + (synopsis "Suite of nonlinear and differential/algebraic equation solvers") + (description "SUNDIALS is a family of software packages implemented with +the goal of providing robust time integrators and nonlinear solvers that can +easily be incorporated into existing simulation codes.") + (license license:bsd-3))) + +(define-public sundials-openmpi + (package (inherit sundials) + (name "sundials-openmpi") + (inputs + `(("mpi" ,openmpi) + ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI + ,@(package-inputs sundials))) + (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") + "/include") + (string-append "-DPETSC_LIBRARY_DIR=" + (assoc-ref %build-inputs "petsc") + "/lib") + ,flags)) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + (add-before 'check 'mpi-setup + ,%openmpi-setup))))) + (synopsis "SUNDIALS with OpenMPI support"))) |