diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 210 |
1 files changed, 152 insertions, 58 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 00f35659eb..ee5be3ed5d 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -25,6 +25,8 @@ ;;; Copyright © 2018 Jan 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 Marius Bakke <mbakke@fastmail.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -53,6 +55,7 @@ #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) #:use-module (guix build-system ocaml) + #:use-module (guix build-system python) #:use-module (guix build-system r) #:use-module (guix build-system ruby) #:use-module (gnu packages algebra) @@ -176,9 +179,11 @@ interactive dialogs to guide them.") (modules '((guix build utils))) (snippet ;; Make sure we don't use the bundled software. - '(for-each (lambda (d) - (delete-file-recursively (string-append "libcoda/" d))) - '("zlib" "pcre" "expat"))))) + '(begin + (for-each (lambda (d) + (delete-file-recursively (string-append "libcoda/" d))) + '("zlib" "pcre" "expat")) + #t)))) (native-inputs `(("fortran" ,gfortran) ("python" ,python) @@ -476,7 +481,10 @@ large scale eigenvalue problems.") (inputs `(("mpi" ,openmpi) ,@(package-inputs arpack-ng))) - (arguments `(#:configure-flags '("--enable-mpi"))) + (arguments + (substitute-keyword-arguments (package-arguments arpack-ng) + ((#:configure-flags _ '()) + ''("--enable-mpi")))) (synopsis "Fortran subroutines for solving eigenvalue problems with MPI"))) (define-public lapack @@ -517,19 +525,6 @@ problems in numerical linear algebra.") (license (license:non-copyleft "file://LICENSE" "See LICENSE in the distribution.")))) -(define-public lapack-3.5 - (package - (inherit lapack) - (version "3.5.0") - (source - (origin - (method url-fetch) - (uri (string-append "http://www.netlib.org/lapack/lapack-" - version ".tgz")) - (sha256 - (base32 - "0lk3f97i9imqascnlf6wr5mjpyxqcdj73pgj97dj2mgvyg9z1n4s")))))) - (define-public scalapack (package (name "scalapack") @@ -548,7 +543,16 @@ problems in numerical linear algebra.") ("fortran" ,gfortran) ("lapack" ,lapack))) ;for testing only (arguments - `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES"))) + `(#: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))))) (home-page "http://www.netlib.org/scalapack/") (synopsis "Library for scalable numerical linear algebra") (description @@ -562,7 +566,7 @@ singular value problems.") (define-public gnuplot (package (name "gnuplot") - (version "5.0.6") + (version "5.2.2") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" @@ -570,7 +574,7 @@ singular value problems.") version ".tar.gz")) (sha256 (base32 - "0q5lr6nala3ln6f3yp6g17ziymb9r9gx9zylnw1y3hjmwl9lggjv")))) + "18diyy7aib9mn098x07g25c7jij1x7wbfpicz0z8gwxx08px45m4")))) (build-system gnu-build-system) (inputs `(("readline" ,readline) ("cairo" ,cairo) @@ -580,6 +584,9 @@ singular value problems.") (native-inputs `(("pkg-config" ,pkg-config) ("texlive" ,texlive-tiny))) + (arguments `(#:configure-flags (list (string-append + "--with-texdir=" %output + "/texmf-local/tex/latex/gnuplot")))) (home-page "http://www.gnuplot.info") (synopsis "Command-line driven graphing utility") (description "Gnuplot is a portable command-line driven graphing @@ -826,7 +833,8 @@ extremely large and complex data collections.") (for-each delete-file (list "SZip.tar.gz" "ZLib.tar.gz" "JPEG8d.tar.gz" "HDF4.tar.gz" "HDF5.tar.gz")) - (delete-file-recursively ,(string-append "hdfjava-" version "/lib")))))) + (delete-file-recursively ,(string-append "hdfjava-" version "/lib")) + #t)))) (build-system gnu-build-system) (native-inputs `(("jdk" ,icedtea "jdk") @@ -1229,7 +1237,9 @@ online as well as original implementations of various other algorithms.") (modules '((guix build utils))) (snippet ;; Make sure we don't use the bundled software. - '(delete-file-recursively "ThirdParty")))) + '(begin + (delete-file-recursively "ThirdParty") + #t)))) (build-system gnu-build-system) (arguments '(#:phases (modify-phases %standard-phases @@ -1314,7 +1324,7 @@ can solve two kinds of problems: (define-public octave (package (name "octave") - (version "4.2.2") + (version "4.4.0") (source (origin (method url-fetch) @@ -1322,7 +1332,7 @@ can solve two kinds of problems: version ".tar.lz")) (sha256 (base32 - "0pkkz1vazsh7ipffb09q0nc2jgx6q27pkkngygjij6jrpcly5zsp")))) + "0nm766737gbkq9wqry54a026k3dg7rb1065kngfpwgjz8b544xbp")))) (build-system gnu-build-system) (inputs `(("lapack" ,lapack) @@ -1482,7 +1492,9 @@ Open CASCADE library.") (modules '((guix build utils))) (snippet ;; Remove non-free METIS code - '(delete-file-recursively "contrib/Metis")))) + '(begin + (delete-file-recursively "contrib/Metis") + #t)))) (build-system cmake-build-system) (propagated-inputs `(("fltk" ,fltk) @@ -1670,6 +1682,31 @@ 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-kiwisolver + (package + (name "python-kiwisolver") + (version "1.0.1") + (source (origin + (method url-fetch) + (uri (pypi-uri "kiwisolver" version)) + (sha256 + (base32 + "0y22ci86znwwwfhbmvbgdfnbi6lv5gv2xkdlxvjw7lml43ayafyf")))) + (build-system python-build-system) + (home-page "https://github.com/nucleic/kiwi") + (synopsis "Fast implementation of the Cassowary constraint solver") + (description + "Kiwi is an efficient C++ implementation of the Cassowary constraint +solving algorithm. Kiwi has been designed from the ground up to be +lightweight and fast. Kiwi ranges from 10x to 500x faster than the original +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") @@ -1752,6 +1789,18 @@ arising after the discretization of partial differential equations.") (define-public slepc-openmpi (package (inherit slepc) (name "slepc-openmpi") + (arguments + (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)))))) (inputs `(("mpi" ,openmpi) ("arpack" ,arpack-ng-openmpi) @@ -1921,11 +1970,18 @@ sparse system of linear equations A x = b using Guassian elimination.") (substitute-keyword-arguments (package-arguments mumps) ((#:phases phases) `(modify-phases ,phases - (replace - 'check - (lambda _ - ((assoc-ref ,phases 'check) - #:exec-prefix '("mpirun" "-n" "2")))))))) + (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)) + (replace 'check + (lambda _ + ((assoc-ref ,phases 'check) + #:exec-prefix '("mpirun" "-n" "2")))))))) (synopsis "Multifrontal sparse direct solver (with MPI)"))) (define-public mumps-metis-openmpi @@ -2048,7 +2104,8 @@ void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g, (let ((line (read-line in 'concat))) (unless (regexp-exec rx line) (display line out) - (loop))))))))))) + (loop)))) + #t))))))) (build-system cmake-build-system) (native-inputs `(("tcsh" ,tcsh))) @@ -2075,38 +2132,38 @@ also provides threshold-based ILU factorization preconditioners.") (define-public superlu-dist (package (name "superlu-dist") - (version "3.3") + (version "5.3.0") (source (origin (method url-fetch) (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" "superlu_dist_" version ".tar.gz")) (sha256 - (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj")) - (modules '((guix build utils))) + (base32 "0ja5ihqivkda1wd58y4lmzvmwssm9g91f70c5q0fzwhng6580h6y")) + (modules '((guix build utils))) (snippet ;; Replace the non-free implementation of MC64 with a stub '(begin (use-modules (ice-9 regex) (ice-9 rdelim)) - (call-with-output-file "SRC/mc64ad.c" + (call-with-output-file "SRC/mc64ad_dist.c" (lambda (port) (display " #include <stdio.h> #include <stdlib.h> -void mc64id_(int *a) { +void mc64id_dist(int *a) { fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\"); abort (); } -void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g, +void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g, int *h, int *i, int *j, int *k, double *l, int *m, int *n) { fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\"); abort (); }\n" port))) - (delete-file "SRC/mc64ad.f.bak") (substitute* "SRC/util.c" ;adjust default algorithm (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag") - "RowPerm = NOROWPERM")))) + "RowPerm = NOROWPERM")) + #t)) (patches (search-patches "superlu-dist-scotchmetis.patch")))) (build-system gnu-build-system) (native-inputs @@ -2168,6 +2225,11 @@ CDEFS = -DAdd_" #t)) (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" (and (zero? (system* "mpirun" "-n" "2" @@ -2262,6 +2324,12 @@ YACC = bison -pscotchyy -y -b y (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")) + (zero? (system* "make" (format #f "-j~a" (parallel-job-count)) "esmumps")))) @@ -2441,7 +2509,16 @@ schemes.") " -lopenblas") ,(string-append "LAPACK_LIBS=-L" (assoc-ref %build-inputs "lapack") - " -llapack")))) + " -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 $PATH. Define this + ;; variable to placate Open MPI without adding a + ;; dependency on OpenSSH (the agent isn't used anyway.) + (setenv "OMPI_MCA_plm_rsh_agent" (which "cat")) + #t))))) (home-page "http://www.p4est.org") (synopsis "Adaptive mesh refinement on forests of octrees") (description @@ -2957,7 +3034,9 @@ Fresnel integrals, and similar related functions as well.") (modules '((guix build utils))) (snippet ;; Remove bundled metis source - '(delete-file-recursively "metis-5.1.0")))) + '(begin + (delete-file-recursively "metis-5.1.0") + #t)))) (build-system gnu-build-system) (arguments '(#:tests? #f ;no "check" target @@ -3153,19 +3232,21 @@ specifications.") "12pj1idjz31r7c2mb5w03vy1cmvycvbkx9z29s40qdmkp1i7q6i0")) (modules '((guix build utils))) (snippet - '(substitute* (list "lp_solve/ccc" "lpsolve55/ccc") - (("^c=cc") "c=gcc") - ;; Pretend to be on a 64 bit platform to obtain a common directory - ;; name for the build results on all architectures; nothing else - ;; seems to depend on it. - (("^PLATFORM=.*$") "PLATFORM=ux64\n") - - ;; The check for 'isnan' as it is written fails with - ;; "non-floating-point argument in call to function - ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro - ;; definition, which in turn leads to bad things. Fix the feature - ;; test. - (("isnan\\(0\\)") "isnan(0.)"))))) + '(begin + (substitute* (list "lp_solve/ccc" "lpsolve55/ccc") + (("^c=cc") "c=gcc") + ;; Pretend to be on a 64 bit platform to obtain a common directory + ;; name for the build results on all architectures; nothing else + ;; seems to depend on it. + (("^PLATFORM=.*$") "PLATFORM=ux64\n") + + ;; The check for 'isnan' as it is written fails with + ;; "non-floating-point argument in call to function + ;; ‘__builtin_isnan’", which leads to the 'NOISNAN' cpp macro + ;; definition, which in turn leads to bad things. Fix the feature + ;; test. + (("isnan\\(0\\)") "isnan(0.)")) + #t)))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no check target @@ -3223,7 +3304,9 @@ revised simplex and the branch-and-bound methods.") (modules '((guix build utils))) (snippet ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost - '(delete-file-recursively "bundled")))) + '(begin + (delete-file-recursively "bundled") + #t)))) (build-system cmake-build-system) (inputs `(("tbb" ,tbb) @@ -3420,6 +3503,7 @@ set.") (native-inputs `(("doc++" ,doc++) ("netpbm" ,netpbm) + ("perl" ,perl) ;needed to run 'ppmquant' during tests ("texlive" ,texlive) ;full package required for fonts ("ghostscript" ,ghostscript))) (inputs @@ -3497,7 +3581,17 @@ problems.") (substitute-keyword-arguments (package-arguments hypre) ((#:configure-flags flags) ``("--with-MPI" - ,@(delete "--without-MPI" ,flags))))) + ,@(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)))))) (synopsis "Parallel solvers and preconditioners for linear equations") (description "HYPRE is a software library of high performance preconditioners and @@ -3854,14 +3948,14 @@ are noisy or are discontinuous at the solution.") (define-public r-desolve (package (name "r-desolve") - (version "1.20") + (version "1.21") (source (origin (method url-fetch) (uri (cran-uri "deSolve" version)) (sha256 (base32 - "18nx3maww979a8p8ly4hv63y65mnjx8vbj2fpipd6rhcbf1lbsan")))) + "0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5")))) (properties `((upstream-name . "deSolve"))) (build-system r-build-system) (native-inputs |