diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 298 |
1 files changed, 290 insertions, 8 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index d37897da20..10b1e9be45 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -46,6 +46,7 @@ #:use-module (gnu packages cmake) #:use-module (gnu packages compression) #:use-module (gnu packages curl) + #:use-module (gnu packages documentation) #:use-module (gnu packages elf) #:use-module (gnu packages flex) #:use-module (gnu packages fltk) @@ -54,16 +55,19 @@ #:use-module (gnu packages gcc) #:use-module (gnu packages gd) #:use-module (gnu packages ghostscript) + #:use-module (gnu packages graphviz) #:use-module (gnu packages gtk) #:use-module (gnu packages image) #:use-module (gnu packages less) #:use-module (gnu packages lisp) #:use-module (gnu packages gnome) + #:use-module (gnu packages guile) #:use-module (gnu packages xorg) #:use-module (gnu packages gl) #:use-module (gnu packages m4) #:use-module (gnu packages mpi) #:use-module (gnu packages multiprecision) + #:use-module (gnu packages netpbm) #:use-module (gnu packages pcre) #:use-module (gnu packages popt) #:use-module (gnu packages perl) @@ -403,7 +407,7 @@ plotting engine by third-party applications like Octave.") (define-public hdf5 (package (name "hdf5") - (version "1.8.12") + (version "1.8.17") (source (origin (method url-fetch) @@ -411,18 +415,27 @@ plotting engine by third-party applications like Octave.") version "/src/hdf5-" version ".tar.bz2")) (sha256 - (base32 "0f9n0v3p3lwc7564791a39c6cn1d3dbrn7d1j3ikqsi27a8hy23d")))) + (base32 "0sj8x0gfs5fb28gipnynb9wpkz113h8wq9sva9mxx66kv27xsdgw")) + (patches (list (search-patch "hdf5-config-date.patch"))))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib))) (arguments `(#:phases - (alist-cons-before - 'configure 'patch-configure - (lambda _ - (substitute* "configure" - (("/bin/mv") "mv"))) - %standard-phases))) + (modify-phases %standard-phases + (add-before 'configure 'patch-configure + (lambda _ + (substitute* "configure" + (("/bin/mv") "mv")) + #t)) + (add-after 'install 'patch-references + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin")) + (zlib (assoc-ref inputs "zlib"))) + (substitute* (find-files bin "h5p?cc") + (("-lz" lib) + (string-append "-L" zlib "/lib " lib))) + #t)))))) (home-page "http://www.hdfgroup.org") (synopsis "Management suite for extremely large and complex data") (description "HDF5 is a suite that makes possible the management of @@ -430,6 +443,140 @@ extremely large and complex data collections.") (license (license:x11-style "http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING")))) +(define-public hdf5-parallel-openmpi + (package (inherit hdf5) + (name "hdf5-parallel-openmpi") + (inputs + `(("mpi" ,openmpi) + ,@(package-inputs hdf5))) + (arguments + (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel") + ,@(package-arguments hdf5)) + ((#:phases phases) + `(modify-phases ,phases + (add-before 'check 'patch-tests + (lambda _ + ;; OpenMPI's mpirun will exit with non-zero status if it + ;; detects an "abnormal termination", i.e. any process not + ;; calling MPI_Finalize(). Since the test is explicitely + ;; avoiding MPI_Finalize so as not to have at_exit and thus + ;; H5C_flush_cache from being called, mpirun will always + ;; complain, so turn this test off. + (substitute* "testpar/Makefile" + (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back) + (string-append front back "\n"))) + (substitute* "tools/h5diff/testph5diff.sh" + (("/bin/sh") (which "sh"))) + #t)))))) + (synopsis "Management suite for data with parallel IO support"))) + +(define-public h5check + (package + (name "h5check") + (version "2.0.1") + (source + (origin + (method url-fetch) + (uri (string-append "http://www.hdfgroup.org/ftp/HDF5/tools/" + "h5check/src/h5check-" version ".tar.gz")) + (sha256 + (base32 + "1gm76jbwhz9adbxgn14zx8cj33dmjdr2g5xcy0m9c2gakp8w59kj")))) + (build-system gnu-build-system) + (inputs `(("hdf5" ,hdf5))) ;h5cc for tests + (home-page "https://www.hdfgroup.org/products/hdf5_tools/h5check.html") + (synopsis "HDF5 format checker") + (description "@code{h5check} is a validation tool for verifying that an +HDF5 file is encoded according to the HDF File Format Specification.") + (license (license:x11-style "file://COPYING")))) + +(define-public netcdf + (package + (name "netcdf") + (version "4.4.0") + (source + (origin + (method url-fetch) + (uri (string-append "ftp://ftp.unidata.ucar.edu/pub/netcdf/" + "netcdf-" version ".tar.gz")) + (sha256 + (base32 + "0y6gdcplarwqqnrav2xg1xd6ih732rzzbmdw78v3rl5b8mwcnh0d")) + (patches (list (search-patch "netcdf-config-date.patch"))))) + (build-system gnu-build-system) + (native-inputs + `(("m4" ,m4) + ("doxygen" ,doxygen) + ("graphviz" ,graphviz))) + (inputs + `(("hdf5" ,hdf5) + ("zlib" ,zlib))) + (arguments + `(#:configure-flags '("--enable-doxygen" "--enable-dot") + #:parallel-tests? #f)) ;various race conditions + (home-page "http://www.unidata.ucar.edu/software/netcdf/") + (synopsis "Library for scientific data") + (description "NetCDF is an interface for scientific data access and a +software library that provides an implementation of the interface. The netCDF +library defines a machine-independent format for representing scientific data. +Together, the interface, library, and format support the creation, access, and +sharing of scientific data.") + (license (license:x11-style "file://COPYRIGHT")))) + +(define-public netcdf-parallel-openmpi + (package (inherit netcdf) + (name "netcdf-parallel-openmpi") + (inputs + `(("mpi" ,openmpi) + ,@(alist-replace "hdf5" (list hdf5-parallel-openmpi) + (package-inputs netcdf)))) + ;; TODO: Replace pkg-config references in nc-config with absolute references + (arguments + (substitute-keyword-arguments (package-arguments netcdf) + ((#:configure-flags flags) + `(cons* "CC=mpicc" "CXX=mpicxx" + "--enable-parallel-tests" + ;; Shared libraries not supported with parallel IO. + "--disable-shared" "--with-pic" + ,flags)))))) + +(define-public nlopt + (package + (name "nlopt") + (version "2.4.2") + (source (origin + (method url-fetch) + (uri (string-append "http://ab-initio.mit.edu/nlopt/nlopt-" + version ".tar.gz")) + (sha256 + (base32 "12cfkkhcdf4zmb6h7y6qvvdvqjs2xf9sjpa3rl3bq76px4yn76c0")))) + (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") + + #: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 + ;; ${exec_prefix}.) + (let ((out (assoc-ref outputs "out"))) + (substitute* "swig/nlopt.scm.in" + (("libnlopt") + (string-append out "/lib/libnlopt"))) + #t)))))) + (inputs `(("guile" ,guile-2.0))) + (native-inputs `(("pkg-config" ,pkg-config))) + (home-page "http://ab-initio.mit.edu/wiki/") + (synopsis "Library for nonlinear optimization") + (description "NLopt is a library for nonlinear optimization, providing a +common interface for a number of different free optimization routines available +online as well as original implementations of various other algorithms.") + (license license:lgpl2.1+))) ;; For a fully featured Octave, users are strongly recommended also to install ;; the following packages: texinfo, less, ghostscript, gnuplot. @@ -2119,3 +2266,138 @@ are built. It can generate many different fractal types such as the Mandelbrot set.") (home-page "http://www.gnu.org/software/xaos/") (license license:gpl2+))) + +(define-public hypre + (package + (name "hypre") + (version "2.11.0") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/LLNL/hypre/archive/" + "v" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0q69ia0jivzcr8p049dn3mg8yjpn6nwq4sw9iqac8vr63vi54l6m")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Remove use of __DATE__ and __TIME__ for reproducibility; + ;; substitute the tarball creation time. + (substitute* "src/utilities/HYPRE_utilities.h" + (("Date Compiled: .*$") + "Date Compiled: Mar 28 2016 20:19:59 +0000\"\n")) + #t)))) + (build-system gnu-build-system) + (outputs '("out" ;6.1 MiB of headers and libraries + "doc")) ;4.8 MiB of documentation + (native-inputs + `(("doc++" ,doc++) + ("netpbm" ,netpbm) + ("texlive" ,texlive) ;full package required for fonts + ("ghostscript" ,ghostscript))) + (inputs + `(("blas" ,openblas) + ("lapack" ,lapack))) + (arguments + `(#:modules ((srfi srfi-1) + ,@%gnu-build-system-modules) + #:configure-flags '("--enable-shared" + "--disable-fortran" + "--without-MPI" + "--with-openmp" + "--with-fei" + "--with-lapack" + "--with-blas") + #:phases + (modify-phases %standard-phases + (add-before 'configure 'chdir-src + (lambda _ (chdir "src"))) + (replace 'configure + (lambda* (#:key build target configure-flags + #:allow-other-keys #:rest args) + (let* ((configure (assoc-ref %standard-phases 'configure))) + (apply configure + (append args + (list #:configure-flags + (cons (string-append + "--host=" (or target build)) + configure-flags))))))) + (add-after 'build 'build-docs + (lambda _ + (zero? (system* "make" "-Cdocs" "pdf" "html")))) + (replace 'check + (lambda _ + (setenv "LD_LIBRARY_PATH" (string-append (getcwd) "/hypre/lib")) + (setenv "PATH" (string-append "." ":" (getenv "PATH"))) + (and (system* "make" "check" "CHECKRUN=") + (fold (lambda (filename result) + (and result + (let ((size (stat:size (stat filename)))) + (when (not (zero? size)) + (format #t "~a size ~d; error indication~%" + filename size)) + (zero? size)))) + #t + (find-files "test" ".*\\.err$"))))) + (add-after 'install 'install-docs + (lambda* (#:key outputs #:allow-other-keys) + ;; Custom install because docs/Makefile doesn't honor ${docdir}. + (let* ((doc (assoc-ref outputs "doc")) + (docdir (string-append doc "/share/doc/hypre-" ,version))) + (mkdir-p docdir) + (with-directory-excursion "docs" + (for-each (lambda (base) + (install-file (string-append base ".pdf") docdir) + (copy-recursively base docdir)) ;html docs + '("HYPRE_usr_manual" + "HYPRE_ref_manual"))) + #t)))))) + (home-page "http://www.llnl.gov/casc/hypre/") + (synopsis "Library of solvers and preconditioners for linear equations") + (description + "HYPRE is a software library of high performance preconditioners and +solvers for the solution of large, sparse linear systems of equations. It +features multigrid solvers for both structured and unstructured grid +problems.") + (license license:lgpl2.1))) + +(define-public hypre-openmpi + (package (inherit hypre) + (name "hypre-openmpi") + (inputs + `(("mpi" ,openmpi) + ,@(package-inputs hypre))) + (arguments + (substitute-keyword-arguments (package-arguments hypre) + ((#:configure-flags flags) + ``("--with-MPI" + ,@(delete "--without-MPI" ,flags))))) + (synopsis "Parallel solvers and preconditioners for linear equations") + (description + "HYPRE is a software library of high performance preconditioners and +solvers for the solution of large, sparse linear systems of equations on +parallel computers. It features parallel multigrid solvers for both +structured and unstructured grid problems."))) + +(define-public matio + (package + (name "matio") + (version "1.5.6") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://sourceforge/matio/" version "/" + "matio-" version ".tar.gz")) + (sha256 + (base32 + "0y2qymgxank8wdiwc68ap8bxdzrhvyw86i29yh3xgn4z1njfd9ir")))) + (build-system gnu-build-system) + (inputs + `(("zlib" ,zlib) + ("hdf5" ,hdf5))) + (home-page "http://matio.sourceforge.net/") + (synopsis "Library for reading and writing MAT files") + (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))) |