diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 344 |
1 files changed, 192 insertions, 152 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index b8ec213d8b..ad7d0e22ee 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org> ;;; Copyright © 2016 Ludovic Courtès <ludo@gnu.org> +;;; Copyright © 2016 Leo Famulari <leo@famulari.name> ;;; ;;; This file is part of GNU Guix. ;;; @@ -35,7 +36,6 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) - #:use-module (guix svn-download) #:use-module (guix utils) #:use-module (guix build utils) #:use-module (guix build-system cmake) @@ -380,35 +380,40 @@ singular value problems.") "See LICENSE in the distribution.")))) (define-public gnuplot - (package - (name "gnuplot") - (version "5.0.2") - (source - (origin - (method url-fetch) - (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" - version "/gnuplot-" version ".tar.gz")) - (sha256 - (base32 - "146qn414z96c7cc42a1kb9a4kpjc2q2hfdwk44kjjvgmfp9k2ass")))) - (build-system gnu-build-system) - (inputs `(("readline" ,readline) - ("cairo" ,cairo) - ("pango" ,pango) - ("gd" ,gd))) - (native-inputs `(("pkg-config" ,pkg-config) - ("texlive" ,texlive-minimal))) - (home-page "http://www.gnuplot.info") - (synopsis "Command-line driven graphing utility") - (description "Gnuplot is a portable command-line driven graphing + ;; Gnuplot version 5.0.4 was updated in-place, resulting in a hash mismatch. + ;; This can be removed at the next version update. + (let ((upstream-version "5.0.4") + (guix-revision "1")) + (package + (name "gnuplot") + (version (string-append upstream-version "-" guix-revision)) + (source + (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/gnuplot/gnuplot/" + upstream-version "/gnuplot-" + upstream-version ".tar.gz")) + (sha256 + (base32 + "07n3w12dkcxjnhsvsliaqnkhajhi818v6q8mkpmpbplbf92vh70m")))) + (build-system gnu-build-system) + (inputs `(("readline" ,readline) + ("cairo" ,cairo) + ("pango" ,pango) + ("gd" ,gd))) + (native-inputs `(("pkg-config" ,pkg-config) + ("texlive" ,texlive-minimal))) + (home-page "http://www.gnuplot.info") + (synopsis "Command-line driven graphing utility") + (description "Gnuplot is a portable command-line driven graphing utility. It was originally created to allow scientists and students to visualize mathematical functions and data interactively, but has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like Octave.") - ;; X11 Style with the additional restriction that derived works may only be - ;; distributed as patches to the original. - (license (license:fsf-free - "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright")))) + ;; X11 Style with the additional restriction that derived works may only be + ;; distributed as patches to the original. + (license (license:fsf-free + "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))) (define-public hdf5 (package @@ -797,7 +802,7 @@ ASCII text files using Gmsh's own scripting language.") (define-public petsc (package (name "petsc") - (version "3.6.2") + (version "3.7.2") (source (origin (method url-fetch) @@ -805,7 +810,7 @@ ASCII text files using Gmsh's own scripting language.") (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" "petsc-lite-" version ".tar.gz")) (sha256 - (base32 "13h0m5f9xsdpps4lsp59iz2m7zkapwavq2zfkfvs3ab6sndla0l9")))) + (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-2) @@ -829,33 +834,34 @@ ASCII text files using Gmsh's own scripting language.") ,(string-append "--with-superlu-lib=" (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a")) #:phases - (alist-replace - 'configure - ;; PETSc's configure script is actually a python script, so we can't - ;; run it with bash. - (lambda* (#:key outputs (configure-flags '()) - #:allow-other-keys) - (let* ((prefix (assoc-ref outputs "out")) - (flags `(,(string-append "--prefix=" prefix) - ,@configure-flags))) - (format #t "build directory: ~s~%" (getcwd)) - (format #t "configure flags: ~s~%" flags) - (zero? (apply system* "./configure" flags)))) - (alist-cons-after - 'configure 'clean-local-references - ;; Try to keep build directory names from leaking into compiled code - (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (substitute* (find-files "." "^petsc(conf|machineinfo).h$") - (((getcwd)) out)))) - (alist-cons-after - 'install 'clean-install + (modify-phases %standard-phases + (replace 'configure + ;; PETSc's configure script is actually a python script, so we can't + ;; run it with bash. + (lambda* (#:key outputs (configure-flags '()) + #:allow-other-keys) + (let* ((prefix (assoc-ref outputs "out")) + (flags `(,(string-append "--prefix=" prefix) + ,@configure-flags))) + (format #t "build directory: ~s~%" (getcwd)) + (format #t "configure flags: ~s~%" flags) + (zero? (apply system* "./configure" flags))))) + (add-after 'configure 'clean-local-references + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (substitute* (find-files "." "^petsc(conf|machineinfo).h$") + ;; Prevent build directory from leaking into compiled code + (((getcwd)) out) + ;; Scrub timestamp for reproducibility + ((".*Libraries compiled on.*") "")) + #t))) + (add-after 'install 'clean-install ;; Try to keep installed files from leaking build directory names. (lambda* (#:key inputs outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) + (let ((out (assoc-ref outputs "out"))) (substitute* (map (lambda (file) (string-append out "/lib/petsc/conf/" file)) - '("petscvariables" "PETScConfig.cmake")) + '("petscvariables")) (((getcwd)) out)) ;; Make compiler references point to the store (substitute* (string-append out "/lib/petsc/conf/petscvariables") @@ -868,9 +874,10 @@ ASCII text files using Gmsh's own scripting language.") (delete-file f)))) '("configure.log" "make.log" "gmake.log" "test.log" "error.log" "RDict.db" + "PETScBuildInternal.cmake" ;; Once installed, should uninstall with Guix - "uninstall.py")))) - %standard-phases))))) + "uninstall.py")) + #t)))))) (home-page "http://www.mcs.anl.gov/petsc") (synopsis "Library to solve PDEs") (description "PETSc, pronounced PET-see (the S is silent), is a suite of @@ -921,7 +928,7 @@ scientific applications modeled by partial differential equations.") (define-public slepc (package (name "slepc") - (version "3.6.2") + (version "3.7.1") (source (origin (method url-fetch) @@ -930,7 +937,7 @@ scientific applications modeled by partial differential equations.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1pv5iqz2kc8sj49zsabyz4arnfpana8mjrhq31vzgk16xldk3d1a")))) + "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) @@ -946,8 +953,7 @@ scientific applications modeled by partial differential equations.") (assoc-ref %build-inputs "arpack") "/lib")) #:phases (modify-phases %standard-phases - (replace - 'configure + (replace 'configure ;; configure is a python script, so we can't run it with bash. (lambda* (#:key inputs outputs (configure-flags '()) #:allow-other-keys) @@ -959,8 +965,7 @@ scientific applications modeled by partial differential equations.") (setenv "SLEPC_DIR" (getcwd)) (setenv "PETSC_DIR" (assoc-ref inputs "petsc")) (zero? (apply system* "./configure" flags))))) - (add-after - 'install 'delete-doc + (add-after 'install 'delete-doc ;; TODO: SLEPc installs HTML documentation alongside headers in ;; $out/include. We'd like to move them to share/doc, but delete ;; them for now, as they are incomplete and installing the complete @@ -968,8 +973,7 @@ scientific applications modeled by partial differential equations.") (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out"))) (for-each delete-file (find-files out "\\.html$"))))) - (add-after - 'install 'clean-install + (add-after 'install 'clean-install ;; Clean up unnecessary build logs from installation. (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) @@ -1208,74 +1212,56 @@ porting.") (define-public superlu (package (name "superlu") - (version "4.3") + (version "5.2.1") (source (origin (method url-fetch) (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" "superlu_" version ".tar.gz")) (sha256 - (base32 "10b785s9s4x0m9q7ihap09275pq4km3k2hk76jiwdfdr5qr2168n")))) - (build-system gnu-build-system) + (base32 "0qzlb7cd608q62kyppd0a8c65l03vrwqql6gsm465rky23b6dyr8")) + (modules '((guix build utils))) + (snippet + ;; Replace the non-free implementation of MC64 with a stub adapted + ;; from Debian + '(begin + (use-modules (ice-9 regex) + (ice-9 rdelim)) + (call-with-output-file "SRC/mc64ad.c" + (lambda (port) + (display " +#include <stdio.h> +#include <stdlib.h> +void mc64id_(int *a) { + fprintf (stderr, \"SuperLU: non-free MC64 not available. Aborting.\\n\"); + abort (); +} +void mc64ad_ (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: non-free MC64 not available. Aborting.\\n\"); + abort (); +}\n" port))) + ;; Remove the corresponding license verbiage. MC64 license follows + ;; a "------" line separator. + (with-atomic-file-replacement "License.txt" + (let ((rx (make-regexp "-{8}"))) + (lambda (in out) + (let loop () + (let ((line (read-line in 'concat))) + (unless (regexp-exec rx line) + (display line out) + (loop))))))))))) + (build-system cmake-build-system) (native-inputs `(("tcsh" ,tcsh))) (inputs - `(("lapack" ,lapack) + `(("blas" ,openblas) ("gfortran" ,gfortran))) (arguments - `(#:parallel-build? #f - #:tests? #f ;tests are run as part of `make all` - #:phases - (alist-replace - 'configure - (lambda* (#:key inputs outputs #:allow-other-keys) - (call-with-output-file "make.inc" - (lambda (port) - (format port " -PLAT = -SuperLUroot = ~a -SUPERLULIB = ~a/lib/libsuperlu.a -TMGLIB = libtmglib.a -BLASDEF = -DUSE_VENDOR_BLAS -BLASLIB = -L~a/lib -lblas -LIBS = $(SUPERLULIB) $(BLASLIB) -ARCH = ar -ARCHFLAGS = cr -RANLIB = ranlib -CC = gcc -PIC = -fPIC -CFLAGS = -O3 -DPRNTlevel=0 $(PIC) -NOOPTS = -O0 $(PIC) -FORTRAN = gfortran -FFLAGS = -O2 $(PIC) -LOADER = $(CC) -CDEFS = -DAdd_" - (getcwd) - (assoc-ref outputs "out") - (assoc-ref inputs "lapack"))))) - (alist-cons-before - 'build 'create-install-directories - (lambda* (#:key outputs #:allow-other-keys) - (for-each - (lambda (dir) - (mkdir-p (string-append (assoc-ref outputs "out") - "/" dir))) - '("lib" "include"))) - (alist-replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - ;; Library is placed in lib during the build phase. Copy over - ;; headers to include. - (let* ((out (assoc-ref outputs "out")) - (incdir (string-append out "/include"))) - (for-each (lambda (file) - (let ((base (basename file))) - (format #t "installing `~a' to `~a'~%" - base incdir) - (copy-file file - (string-append incdir "/" base)))) - (find-files "SRC" ".*\\.h$")))) - %standard-phases))))) + `(#:configure-flags '("-Denable_blaslib:BOOL=NO" ;do not use internal cblas + "-DTPL_BLAS_LIBRARIES=openblas" + "-DBUILD_SHARED_LIBS:BOOL=YES" + "-DCMAKE_INSTALL_LIBDIR=lib"))) (home-page "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/") (synopsis "Supernodal direct solver for sparse linear systems") (description @@ -1285,7 +1271,9 @@ The library is written in C and is callable from either C or Fortran. The library routines perform an LU decomposition with partial pivoting and triangular system solves through forward and back substitution. The library also provides threshold-based ILU factorization preconditioners.") - (license license:bsd-3))) + (license (list license:bsd-3 + license:gpl2+ ;EXAMPLE/*fgmr.c + (license:fsf-free "file://SRC/colamd.h"))))) (define-public superlu-dist (package @@ -1298,6 +1286,30 @@ also provides threshold-based ILU factorization preconditioners.") "superlu_dist_" version ".tar.gz")) (sha256 (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj")) + (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" + (lambda (port) + (display " +#include <stdio.h> +#include <stdlib.h> +void mc64id_(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, + 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")))) (patches (search-patches "superlu-dist-scotchmetis.patch")))) (build-system gnu-build-system) (native-inputs @@ -1791,29 +1803,36 @@ associated functions (eg. contiguous and non-contiguous submatrix views).") "1cdpjxb0fz5f28y5qrqgpw53s7qi8s2v3al9lfdldqxngb21vpx8")))))) (define-public muparser - (package - (name "muparser") - (version "2.2.5") - (source - (origin - (method svn-fetch) - (uri (svn-reference - (url "http://muparser.googlecode.com/svn/trunk/") - (revision 34))) - (sha256 - (base32 - "1d6bdbhx9zj3srwj3m7c9hvr18gnx1fx43h6d25my7q85gicpcwn")))) - (build-system gnu-build-system) - (arguments - `(#:configure-flags '("--enable-samples=no") - #:tests? #f)) ;no "check" target - (home-page "http://muparser.beltoforion.de/") - (synopsis "Fast parser library for mathematical expressions") - (description - "muParser is an extensible high performance math parser library. It is -based on transforming an expression into a bytecode and precalculating -constant parts of it.") - (license license:expat))) + ;; When switching download sites, muparser re-issued a 2.2.5 release with a + ;; different hash. In order to make `guix package --upgrade` work correctly, + ;; we set a Guix packaging revision. + ;; When the next version of muparser is released, we can remove + ;; UPSTREAM-VERSION and REVISION and use the plain VERSION. + (let ((upstream-version "2.2.5") + (revision "2")) + (package + (name "muparser") + (version (string-append upstream-version "-" revision)) + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/beltoforion/muparser/archive/v" + upstream-version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0277qsi5l23jsck1vhn383bmvc2n9l4a1dl5r9bf7hvjv9ayyrh6")))) + (build-system gnu-build-system) + (arguments + `(#:configure-flags '("--enable-samples=no") + #:tests? #f)) ;no "check" target + (home-page "http://muparser.beltoforion.de/") + (synopsis "Fast parser library for mathematical expressions") + (description + "muParser is an extensible high performance math parser library. It is +based on transforming an expression into a bytecode and precalculating constant +parts of it.") + (license license:expat)))) (define-public openblas (package @@ -2006,8 +2025,8 @@ packages.") (version "3.10.2") (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/math-atlas/atlas" - version ".tar.bz2")) + (uri (string-append "mirror://sourceforge/math-atlas/Stable/" + version "/atlas" version ".tar.bz2")) (sha256 (base32 "0bqh4bdnjdyww4mcpg6kn0x7338mfqbdgysn97dzrwwb26di7ars")))) @@ -2136,8 +2155,8 @@ Failure to do so will result in a library with poor performance.") (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/ogl-math/glm-" - version ".zip")) + (uri (string-append "mirror://sourceforge/ogl-math/glm-" version + "/glm-" version ".zip")) (sha256 (base32 "1cnjmi033a16a95v6xfkr1bvfmkd26hzdjka8j1819hgn5b1nr8l")))) @@ -2355,9 +2374,8 @@ FLANN is written in C++ and contains bindings for C, Octave and Python.") (source (origin (method url-fetch) - (uri - (string-append - "mirror://sourceforge/w-calc/wcalc-" version ".tar.bz2")) + (uri (string-append "mirror://sourceforge/w-calc/Wcalc/" version "/" + "wcalc-" version ".tar.bz2")) (sha256 (base32 "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f")))) @@ -2381,8 +2399,8 @@ evaluates expressions using the standard order of operations.") (version "3.6") (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/xaos/xaos-" - version ".tar.gz")) + (uri (string-append "mirror://sourceforge/xaos/XaoS/" version + "/xaos-" version ".tar.gz")) (sha256 (base32 "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq")))) @@ -2524,7 +2542,7 @@ structured and unstructured grid problems."))) (source (origin (method url-fetch) - (uri (string-append "mirror://sourceforge/matio/" version "/" + (uri (string-append "mirror://sourceforge/matio/matio/" version "/" "matio-" version ".tar.gz")) (sha256 (base32 @@ -2538,3 +2556,25 @@ structured and unstructured grid problems."))) (description "Matio is a library for reading and writing MAT files. It supports compressed MAT files, as well as newer (version 7.3) MAT files.") (license license:bsd-2))) + +(define-public libhilbert + (package + (name "libhilbert") + (version "0.2-1") + (source + (origin + (method url-fetch) + (uri (string-append "http://web.cs.dal.ca/~chamilto/hilbert/" + "libhilbert-" version ".tar.gz")) + (sha256 + (base32 + "0v48x8405dj95gjn2saja4bzhw86d6zl6d3dg8h7dzac2qr97s34")))) + (build-system gnu-build-system) + (home-page "http://web.cs.dal.ca/~chamilto/hilbert") + (synopsis "Hilbert indices for multidimensional data") + (description "The libhilbert library can efficiently calculate Hilbert +curves and order-preserving representations of Hilbert curve indices that use +the same amount of space as the original point representation. This is useful +when using the Gilbert curve as a space filling curve through a +high-dimensional space where not all demensions have the same cardinality.") + (license license:lgpl2.1+))) |