;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015 Sou Bunnbu <iyzsong@gmail.com>
;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
+;;; Copyright © 2015, 2016 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de>
;;;
;;; This file is part of GNU Guix.
;;;
#:use-module (guix download)
#:use-module (guix svn-download)
#:use-module (guix utils)
+ #:use-module (guix build utils)
#:use-module (guix build-system cmake)
#:use-module (guix build-system gnu)
#:use-module (gnu packages algebra)
#:use-module (gnu packages bison)
+ #:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages cmake)
#:use-module (gnu packages compression)
#:use-module (gnu packages ghostscript)
#:use-module (gnu packages glib)
#: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 texlive)
#:use-module (gnu packages wxwidgets)
#:use-module (gnu packages xml)
- #:use-module (gnu packages zip))
+ #:use-module (gnu packages zip)
+ #:use-module (srfi srfi-1))
(define-public units
(package
(name "units")
- (version "2.11")
+ (version "2.12")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/units/units-" version
".tar.gz"))
(sha256 (base32
- "1gjs3wc212aaiq4r76hx9nl1h3fa39n0ljwl9420d6ixl3rdmdjk"))))
+ "1jxvjknz2jhq773jrwx9gc1df3gfy73yqmkjkygqxzpi318yls3q"))))
(build-system gnu-build-system)
(synopsis "Conversion between thousands of scales")
(description
"GNU Units converts numeric quantities between units of measure. It
-can handle scale changes through adaptive usage of standard scale prefixes
-(micro-, kilo-, etc.). It can also handle nonlinear conversions such as
-Fahrenheit to Celsius. Its interpreter is powerful enough to be used
-effectively as a scientific calculator.")
+can handle scale changes through adaptive usage of standard scale
+prefixes (micro-, kilo-, etc.). It can also handle nonlinear
+conversions such as Fahrenheit to Celsius. Its interpreter is powerful
+enough to be used effectively as a scientific calculator.")
(license license:gpl3+)
(home-page "http://www.gnu.org/software/units/")))
(define-public gsl
(package
(name "gsl")
- (version "1.16")
+ (version "2.1")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))
- (patches (map search-patch '("gsl-poly-test-fix-pt1.patch"
- "gsl-poly-test-fix-pt2.patch")))))
+ "0rhcia9jhr3p1f1wybwyllwqfs9bggz99i3mi5lpyqcpff1hdbar"))))
(build-system gnu-build-system)
(arguments
- `(#:parallel-tests? #f
- #:phases
- (alist-replace
- 'configure
- (lambda* (#:key target system outputs #:allow-other-keys #:rest args)
- (let ((configure (assoc-ref %standard-phases 'configure)))
- ;; disable numerically unstable test on i686, see thread at
- ;; http://lists.gnu.org/archive/html/bug-gsl/2011-11/msg00019.html
- (if (string=? (or target system) "i686-linux")
- (substitute* "ode-initval2/Makefile.in"
- (("TESTS = \\$\\(check_PROGRAMS\\)") "TESTS =")))
- (apply configure args)))
- %standard-phases)))
+ `(#:parallel-tests? #f))
(home-page "http://www.gnu.org/software/gsl/")
(synopsis "Numerical library for C and C++")
(description
(define-public glpk
(package
(name "glpk")
- (version "4.55")
+ (version "4.58")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "1rqx5fzj1mhkifilip5mkxybpj2wkniq5qcn8h1w2vkr2rzhs29p"))))
+ "1jmrya04hgwnrxrqqs40i6m9cqka3q601cx3nh9ijyvlg90zlq24"))))
(build-system gnu-build-system)
(inputs
`(("gmp" ,gmp)))
(define-public pspp
(package
(name "pspp")
- (version "0.8.4")
+ (version "0.8.5")
(source
(origin
(method url-fetch)
version ".tar.gz"))
(sha256
(base32
- "0b65q45x05ps95pph6glbg7ymdr638nfb0rk9x5x9qm5k073pk5z"))))
+ "0c8326yykidi94xi7jn27j8iqxc38vc07d4wf5zyk0l8lpzx5vz7"))))
(build-system gnu-build-system)
(inputs
`(("cairo" ,cairo)
("pango" ,pango)
("readline" ,readline)
("gtk" ,gtk+-2)
- ("gtksourceview" ,gtksourceview)
+ ("gtksourceview" ,gtksourceview-2)
("zlib" ,zlib)))
(native-inputs
`(("glib" ,glib "bin") ;for glib-genmarshal
("perl" ,perl)
+ ("texinfo" ,texinfo)
("pkg-config" ,pkg-config)))
(home-page "http://www.gnu.org/software/pspp/")
(synopsis "Statistical analysis")
(license (license:non-copyleft "file://COPYING"
"See COPYING in the distribution."))))
+(define-public arpack-ng-openmpi
+ (package (inherit arpack-ng)
+ (name "arpack-ng-openmpi")
+ (inputs
+ `(("mpi" ,openmpi)
+ ,@(package-inputs arpack-ng)))
+ (arguments `(#:configure-flags '("--enable-mpi")))
+ (synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
+
(define-public lapack
(package
(name "lapack")
(define-public gnuplot
(package
(name "gnuplot")
- (version "4.6.3")
+ (version "5.0.2")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://sourceforge/gnuplot/gnuplot/"
- version "/gnuplot-" version ".tar.gz"))
+ version "/gnuplot-" version ".tar.gz"))
(sha256
(base32
- "1xd7gqdhlk7k1p9yyqf9vkk811nadc7m4si0q3nb6cpv4pxglpyz"))))
+ "146qn414z96c7cc42a1kb9a4kpjc2q2hfdwk44kjjvgmfp9k2ass"))))
(build-system gnu-build-system)
(inputs `(("readline" ,readline)
("cairo" ,cairo)
("pango" ,pango)
("gd" ,gd)))
- (native-inputs `(("texlive" ,texlive)
- ("pkg-config" ,pkg-config)))
+ (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
;; 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"))))
+ "http://gnuplot.cvs.sourceforge.net/gnuplot/gnuplot/Copyright"))))
(define-public hdf5
(package
(define-public octave
(package
(name "octave")
- (version "3.8.2")
+ (version "4.0.0")
(source
(origin
(method url-fetch)
(uri (string-append "mirror://gnu/octave/octave-"
- version ".tar.gz"))
+ version ".tar.gz"))
(sha256
(base32
- "05slz8yx8k91fqlnfr1f0vni95iq9qmchz41c7nf4isn3b2fjn7j"))))
+ "101jr9yck798586jz4vkjcgk36zksmxf1pxrzvipgn2xgyay0zjc"))))
(build-system gnu-build-system)
(inputs
`(("lapack" ,lapack)
(define-public gmsh
(package
(name "gmsh")
- (version "2.8.4")
+ (version "2.11.0")
(source
(origin
(method url-fetch)
(uri (string-append "http://www.geuz.org/gmsh/src/gmsh-"
version "-source.tgz"))
(sha256
- (base32 "0jv2yvk28w86rx5mvjkb0w12ff2jxih7axnpvznpd295lg5jg7hr"))
+ (base32 "1ilplibvjgf7a905grpnclrvkmqy9fgrpl7xyp3w4yl1qc682v9b"))
(modules '((guix build utils)))
(snippet
;; Remove non-free METIS code
(arguments
`(#:configure-flags `("-DENABLE_METIS:BOOL=OFF"
"-DENABLE_BUILD_SHARED:BOOL=ON"
- "-DENABLE_BUILD_DYNAMIC:BOOL=ON")))
+ "-DENABLE_BUILD_DYNAMIC:BOOL=ON")
+ #:phases (modify-phases %standard-phases
+ (replace
+ 'check
+ (lambda _
+ (zero? (system* "make" "test"
+ ;; Disable this test. See
+ ;; https://geuz.org/trac/gmsh/ticket/271
+ "ARGS=-E component8_in_a_box")))))))
(home-page "http://www.geuz.org/gmsh/")
(synopsis "3D finite element grid generator")
(description "Gmsh is a 3D finite element grid generator with a built-in
(define-public petsc
(package
(name "petsc")
- (version "3.4.4")
+ (version "3.6.2")
(source
(origin
(method url-fetch)
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
"petsc-lite-" version ".tar.gz"))
(sha256
- (base32 "0v5dg6dhdjpi5ianvd4mm6hsvxzv1bsxwnh9f9myag0a0d9xk9iv"))
- (patches
- (list (search-patch "petsc-fix-threadcomm.patch")))))
+ (base32 "13h0m5f9xsdpps4lsp59iz2m7zkapwavq2zfkfvs3ab6sndla0l9"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)
))
(arguments
`(#:test-target "test"
- #:parallel-build? #f
+ #:parallel-build? #f ;build is parallel by default
#:configure-flags
`("--with-mpi=0"
"--with-openmp=1"
(let ((out (assoc-ref outputs "out"))
(fortran (assoc-ref inputs "gfortran")))
(substitute* (map (lambda (file)
- (string-append out "/" file))
- '("conf/petscvariables"
- "conf/PETScConfig.cmake"))
+ (string-append out "/lib/petsc/conf/" file))
+ '("petscvariables" "PETScConfig.cmake"))
(((getcwd)) out))
;; Make compiler references point to the store
- (substitute* (string-append out "/conf/petscvariables")
+ (substitute* (string-append out "/lib/petsc/conf/petscvariables")
(("= g(cc|\\+\\+|fortran)" _ suffix)
(string-append "= " fortran "/bin/g" suffix)))
;; PETSc installs some build logs, which aren't necessary.
(for-each (lambda (file)
- (let ((f (string-append out "/" file)))
+ (let ((f (string-append out "/lib/petsc/conf/" file)))
(when (file-exists? f)
(delete-file f))))
- '("conf/configure.log"
- "conf/make.log"
- "conf/test.log"
- "conf/error.log"
- "conf/RDict.db"
+ '("configure.log" "make.log" "gmake.log"
+ "test.log" "error.log" "RDict.db"
;; Once installed, should uninstall with Guix
- "conf/uninstall.py"))))
+ "uninstall.py"))))
%standard-phases)))))
(home-page "http://www.mcs.anl.gov/petsc")
(synopsis "Library to solve PDEs")
,@(delete "--with-mpi=0" ,cf)))))
(synopsis "Library to solve PDEs (with complex scalars and MPI support)")))
+(define-public slepc
+ (package
+ (name "slepc")
+ (version "3.6.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://slepc.upv.es/download/download.php?"
+ "filename=slepc-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1pv5iqz2kc8sj49zsabyz4arnfpana8mjrhq31vzgk16xldk3d1a"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("python" ,python-2)))
+ (inputs
+ `(("arpack" ,arpack-ng)
+ ("gfortran" ,gfortran)))
+ (propagated-inputs
+ `(("petsc" ,petsc)))
+ (arguments
+ `(#:parallel-build? #f ;build is parallel by default
+ #:configure-flags
+ `(,(string-append "--with-arpack-dir="
+ (assoc-ref %build-inputs "arpack") "/lib"))
+ #:phases
+ (modify-phases %standard-phases
+ (replace
+ 'configure
+ ;; configure is a python script, so we can't run it with bash.
+ (lambda* (#:key inputs 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)
+ (setenv "SLEPC_DIR" (getcwd))
+ (setenv "PETSC_DIR" (assoc-ref inputs "petsc"))
+ (zero? (apply system* "./configure" flags)))))
+ (add-after
+ 'install 'delete-doc
+ ;; TODO: SLEPc installs HTML documentation alongside headers in
+ ;; $out/include. We'd like to move them to share/doc, but delete
+ ;; them for now, as they are incomplete and installing the complete
+ ;; documentation is difficult.
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out")))
+ (for-each delete-file (find-files out "\\.html$")))))
+ (add-after
+ 'install 'clean-install
+ ;; Clean up unnecessary build logs from installation.
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (for-each (lambda (file)
+ (let ((f (string-append out "/lib/slepc/conf/" file)))
+ (when (file-exists? f)
+ (delete-file f))))
+ '("configure.log" "make.log" "gmake.log"
+ "test.log" "error.log" "RDict.db"
+ "uninstall.py"))))))))
+ (home-page "http://slepc.upv.es")
+ (synopsis "Scalable library for eigenproblems")
+ (description "SLEPc is a software library for the solution of large sparse
+eigenproblems on parallel computers. It can be used for the solution of
+linear eigenvalue problems formulated in either standard or generalized form,
+as well as other related problems such as the singular value decomposition.
+The emphasis of the software is on methods and techniques appropriate for
+problems in which the associated matrices are sparse, for example, those
+arising after the discretization of partial differential equations.")
+ (license license:lgpl3)))
+
+(define-public slepc-complex
+ (package (inherit slepc)
+ (name "slepc-complex")
+ (propagated-inputs
+ `(("petsc" ,petsc-complex)
+ ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
+ (synopsis "Scalable library for eigenproblems (with complex scalars)")))
+
+(define-public slepc-openmpi
+ (package (inherit slepc)
+ (name "slepc-openmpi")
+ (inputs
+ `(("mpi" ,openmpi)
+ ("arpack" ,arpack-ng-openmpi)
+ ,@(alist-delete "arpack" (package-inputs slepc))))
+ (propagated-inputs
+ `(("petsc" ,petsc-openmpi)
+ ,@(alist-delete "petsc" (package-propagated-inputs slepc))))
+ (synopsis "Scalable library for eigenproblems (with MPI support)")))
+
+(define-public slepc-complex-openmpi
+ (package (inherit slepc-openmpi)
+ (name "slepc-complex-openmpi")
+ (propagated-inputs
+ `(("petsc" ,petsc-complex-openmpi)
+ ,@(alist-delete "petsc" (package-propagated-inputs slepc-openmpi))))
+ (synopsis "Scalable library for eigenproblems (with complex scalars and MPI support)")))
+
+(define-public mumps
+ (package
+ (name "mumps")
+ (version "5.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://mumps.enseeiht.fr/MUMPS_"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1820jfp3mbl7n85765v5mp6p0gzqpgr4d2lrnhwj4gl7cwp5ndah"))
+ (patches (list (search-patch "mumps-build-parallelism.patch")))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("fortran" ,gfortran)
+ ;; These are required for linking against mumps, but we let the user
+ ;; declare the dependency.
+ ("blas" ,openblas)
+ ("metis" ,metis)
+ ("scotch" ,scotch)))
+ (arguments
+ `(#:modules ((ice-9 match)
+ (ice-9 popen)
+ (srfi srfi-1)
+ ,@%gnu-build-system-modules)
+ #:phases
+ (modify-phases %standard-phases
+ (replace
+ 'configure
+ (lambda* (#:key inputs #:allow-other-keys)
+ (call-with-output-file "Makefile.inc"
+ (lambda (port)
+ (format port "
+PLAT =
+LIBEXT = .a
+OUTC = -o
+OUTF = -o
+RM = rm -f~:[
+CC = gcc
+FC = gfortran
+FL = gfortran
+INCSEQ = -I$(topdir)/libseq
+LIBSEQ = -L$(topdir)/libseq -lmpiseq
+LIBSEQNEEDED = libseqneeded~;
+CC = mpicc
+FC = mpifort
+FL = mpifort~]
+AR = ar vr # rules require trailing space, ugh...
+RANLIB = ranlib
+LIBBLAS = -L~a -lopenblas~@[
+SCALAP = -L~a -lscalapack~]
+LIBOTHERS = -pthread
+CDEFS = -DAdd_
+PIC = -fPIC
+OPTF = -O2 -DALLOW_NON_INIT $(PIC)
+OPTL = -O2 $(PIC)
+OPTC = -O2 $(PIC)
+INCS = $(INCSEQ)
+LIBS = $(SCALAP) $(LIBSEQ)
+LPORDDIR = $(topdir)/PORD/lib
+IPORD = -I$(topdir)/PORD/include
+LPORD = -L$(LPORDDIR) -lpord
+ORDERINGSF = -Dpord~@[
+METISDIR = ~a
+IMETIS = -I$(METISDIR)/include
+LMETIS = -L$(METISDIR)/lib -lmetis
+ORDERINGSF += -Dmetis~]~@[~:{
+SCOTCHDIR = ~a
+ISCOTCH = -I$(SCOTCHDIR)/include
+LSCOTCH = -L$(SCOTCHDIR)/lib ~a-lesmumps -lscotch -lscotcherr
+ORDERINGSF += ~a~}~]
+ORDERINGSC = $(ORDERINGSF)
+LORDERINGS = $(LPORD) $(LMETIS) $(LSCOTCH)
+IORDERINGSF = $(ISCOTCH)
+IORDERINGSC = $(IPORD) $(IMETIS) $(ISCOTCH)"
+ (assoc-ref inputs "mpi")
+ (assoc-ref inputs "blas")
+ (assoc-ref inputs "scalapack")
+ (assoc-ref inputs "metis")
+ (match (list (assoc-ref inputs "pt-scotch")
+ (assoc-ref inputs "scotch"))
+ ((#f #f)
+ #f)
+ ((#f scotch)
+ `((,scotch "" "-Dscotch")))
+ ((ptscotch _)
+ `((,ptscotch
+ "-lptesmumps -lptscotch -lptscotcherr "
+ "-Dptscotch")))))))))
+ (replace
+ 'build
+ ;; By default only the d-precision library is built. Make with "all"
+ ;; target so that all precision libraries and examples are built.
+ (lambda _
+ (zero? (system* "make" "all"
+ (format #f "-j~a" (parallel-job-count))))))
+ (replace
+ 'check
+ ;; Run the simple test drivers, which read test input from stdin:
+ ;; from the "real" input for the single- and double-precision
+ ;; testers, and from the "cmplx" input for complex-precision
+ ;; testers. The EXEC-PREFIX key is used by the mumps-openmpi
+ ;; package to prefix execution with "mpirun".
+ (lambda* (#:key (exec-prefix '()) #:allow-other-keys)
+ (with-directory-excursion "examples"
+ (every
+ (lambda (prec type)
+ (let ((tester (apply open-pipe*
+ `(,OPEN_WRITE
+ ,@exec-prefix
+ ,(string-append "./" prec
+ "simpletest"))))
+ (input (open-input-file
+ (string-append "input_simpletest_" type))))
+ (begin
+ (dump-port input tester)
+ (close-port input)
+ (zero? (close-pipe tester)))))
+ '("s" "d" "c" "z")
+ '("real" "real" "cmplx" "cmplx")))))
+ (replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (copy-recursively "lib" (string-append out "/lib"))
+ (copy-recursively "include" (string-append out "/include"))
+ (when (file-exists? "libseq/libmpiseq.a")
+ (copy-file "libseq/libmpiseq.a"
+ (string-append out "/lib/libmpiseq.a")))))))))
+ (home-page "http://mumps.enseeiht.fr")
+ (synopsis "Multifrontal sparse direct solver")
+ (description
+ "MUMPS (MUltifrontal Massively Parallel sparse direct Solver) solves a
+sparse system of linear equations A x = b using Guassian elimination.")
+ (license license:cecill-c)))
+
+(define-public mumps-metis
+ (package (inherit mumps)
+ (name "mumps-metis")
+ (inputs
+ (alist-delete "scotch" (package-inputs mumps)))))
+
+(define-public mumps-openmpi
+ (package (inherit mumps)
+ (name "mumps-openmpi")
+ (inputs
+ `(("mpi" ,openmpi)
+ ("scalapack" ,scalapack)
+ ("pt-scotch" ,pt-scotch)
+ ,@(alist-delete "scotch" (package-inputs mumps))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments mumps)
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (replace
+ 'check
+ (lambda _
+ ((assoc-ref ,phases 'check)
+ #:exec-prefix '("mpirun" "-n" "2"))))))))
+ (synopsis "Multifrontal sparse direct solver (with MPI)")))
+
+(define-public mumps-metis-openmpi
+ (package (inherit mumps-openmpi)
+ (name "mumps-metis-openmpi")
+ (inputs
+ (alist-delete "pt-scotch" (package-inputs mumps-openmpi)))))
+
(define-public superlu
(package
(name "superlu")
(lambda _ (zero? (system* "make" "ptcheck"))))))))
(synopsis "Programs and libraries for graph algorithms (with MPI)")))
+(define-public metis
+ (package
+ (name "metis")
+ (version "5.1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/"
+ "metis-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1cjxgh41r8k6j029yxs8msp3z6lcnpm16g5pvckk35kc7zhfpykn"))))
+ (build-system cmake-build-system)
+ (inputs
+ `(("blas" ,openblas)))
+ (arguments
+ `(#:tests? #f ;no tests
+ #:configure-flags `("-DSHARED=ON"
+ ,(string-append "-DGKLIB_PATH=" (getcwd)
+ "/metis-" ,version "/GKlib"))))
+ (home-page "http://glaros.dtc.umn.edu/gkhome/metis/metis/overview")
+ (synopsis "Graph partitioning and fill-reducing matrix ordering library")
+ (description
+ "METIS is a set of serial programs for partitioning graphs, partitioning
+finite element meshes, and producing fill-reducing orderings for sparse
+matrices. The algorithms implemented in METIS are based on the multilevel
+recursive-bisection, multilevel k-way, and multi-constraint partitioning
+schemes.")
+ (license license:asl2.0))) ;As of version 5.0.3
+
(define-public p4est
(package
(name "p4est")
(description "Maxima is a system for the manipulation of symbolic and
numerical expressions. It yields high precision numeric results by using
exact fractions, arbitrary precision integers, and variable precision floating
-point numbers")
+point numbers.")
;; Some files are lgpl2.1+. Some are gpl2+. Some explicitly state gpl1+.
;; Others simply say "GNU General Public License" without stating a
;; version (which implicitly means gpl1+).
full text searching.")
(license license:gpl2+)))
+(define-public armadillo
+ (package
+ (name "armadillo")
+ (version "6.400.3")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/arma/armadillo-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "0bsgrmldlx77w5x26n3axj1hg6iw6csyw0dwl1flrbdwl51f9701"))))
+ (build-system cmake-build-system)
+ (arguments `(#:tests? #f)) ;no test target
+ (inputs
+ `(("openblas" ,openblas)
+ ("lapack" ,lapack)
+ ("arpack" ,arpack-ng)))
+ (home-page "http://arma.sourceforge.net/")
+ (synopsis "C++ linear algebra library")
+ (description
+ "Armadillo is a C++ linear algebra library, aiming towards a good balance
+between speed and ease of use. It is useful for algorithm development
+directly in C++, or quick conversion of research code into production
+environments. It can be used for machine learning, pattern recognition,
+signal processing, bioinformatics, statistics, econometrics, etc. The library
+provides efficient classes for vectors, matrices and cubes, as well as 150+
+associated functions (eg. contiguous and non-contiguous submatrix views).")
+ (license license:mpl2.0)))
+
+(define-public armadillo-for-rcpparmadillo
+ (package (inherit armadillo)
+ (version "6.200.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/arma/armadillo-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1f69rlqhnf2wv8khyn2a8vi6gx1i72qgfy8b9b760ssk85dcl763"))))))
+
(define-public muparser
(package
(name "muparser")
(define-public openblas
(package
(name "openblas")
- (version "0.2.14")
+ (version "0.2.15")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0av3pd96j8rx5i65f652xv9wqfkaqn0w4ma1gvbyz73i6j2hi9db"))))
+ "1k5f6vjlk54qlplk5m7xkbaw6g2y7dl50lwwdv6xsbcsgsbxfcpy"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ;no "check" target
- ;; DYNAMIC_ARCH is not supported on MIPS. When it is disabled,
- ;; OpenBLAS will tune itself to the build host, so we need to disable
- ;; substitutions.
- #:substitutable? ,(not (string-prefix? "mips" (%current-system)))
+ ;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
+ ;; TARGET is specified, OpenBLAS will tune itself to the build host, so
+ ;; we need to disable substitutions.
+ #:substitutable?
+ ,(let ((system (or (%current-target-system) (%current-system))))
+ (or (string-prefix? "x86_64" system)
+ (string-prefix? "i686" system)
+ (string-prefix? "mips" system)))
#:make-flags
(list (string-append "PREFIX=" (assoc-ref %outputs "out"))
"SHELL=bash"
;; Build the library for all supported CPUs. This allows
;; switching CPU targets at runtime with the environment variable
;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
- ;; Unfortunately, this is not supported on MIPS.
- ,@(if (string-prefix? "mips" (%current-system))
- '()
- '("DYNAMIC_ARCH=1")))
+ ;; Unfortunately, this is not supported on non-x86 architectures,
+ ;; where it leads to failed builds.
+ ,@(let ((system (or (%current-target-system) (%current-system))))
+ (cond
+ ((or (string-prefix? "x86_64" system)
+ (string-prefix? "i686" system))
+ '("DYNAMIC_ARCH=1"))
+ ;; On MIPS we force the "SICORTEX" TARGET, as for the other
+ ;; two available MIPS targets special extended instructions
+ ;; for Loongson cores are used.
+ ((string-prefix? "mips" system)
+ '("TARGET=SICORTEX"))
+ (else '()))))
;; no configure script
#:phases (alist-delete 'configure %standard-phases)))
(inputs
"OpenLibm is an effort to have a high quality, portable, standalone C
mathematical library (libm). It can be used standalone in applications and
programming language implementations. The project was born out of a need to
-have a good libm for the Julia programming langage that worked consistently
+have a good libm for the Julia programming language that worked consistently
across compilers and operating systems, and in 32-bit and 64-bit
environments.")
;; See LICENSE.md for details.
(string-append lib "/liblpsolve55.a"))
(copy-file "lpsolve55/bin/ux64/liblpsolve55.so"
(string-append lib "/liblpsolve55.so"))
- (mkdir-p bin)
- (copy-file "lp_solve/bin/ux64/lp_solve"
- (string-append bin "/lp_solve"))
- (mkdir-p include)
+ (install-file "lp_solve/bin/ux64/lp_solve" bin)
+
;; Install a subset of the header files as on Debian
;; (plus lp_bit.h, which matches the regular expression).
- (for-each
- (lambda (name)
- (copy-file name (string-append include "/" name)))
- (find-files "." "lp_[HMSa-z].*\\.h$"))
+ (for-each (lambda (name)
+ (install-file name include))
+ (find-files "." "lp_[HMSa-z].*\\.h$"))
(with-directory-excursion "shared"
- (for-each
- (lambda (name)
- (copy-file name (string-append include "/" name)))
- (find-files "." "\\.h$")))
+ (for-each (lambda (name)
+ (install-file name include))
+ (find-files "." "\\.h$")))
#t))))))
(home-page "http://lpsolve.sourceforge.net/")
(synopsis "Mixed integer linear programming (MILP) solver")
"lp_solve is a mixed integer linear programming solver based on the
revised simplex and the branch-and-bound methods.")
(license license:lgpl2.1+)))
+
+(define-public dealii
+ (package
+ (name "dealii")
+ (version "8.2.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/dealii/dealii/releases/"
+ "download/v" version "/dealii-" version ".tar.gz"))
+ (sha256
+ (base32
+ "185jych0gdnpkjwxni7pd0dda149492zwq2457xdjg76bzj78mnp"))
+ (patches (list (search-patch "dealii-p4est-interface.patch")))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
+ '(delete-file-recursively "bundled"))))
+ (build-system cmake-build-system)
+ (inputs
+ `(("tbb" ,tbb)
+ ("zlib" ,zlib)
+ ("boost" ,boost)
+ ("p4est" ,p4est)
+ ("blas" ,openblas)
+ ("lapack" ,lapack)
+ ("arpack" ,arpack-ng)
+ ("muparser" ,muparser)
+ ("gfortran" ,gfortran)
+ ("suitesparse" ,suitesparse))) ;for UMFPACK
+ (arguments
+ `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease
+ #:configure-flags '("-DCOMPAT_FILES=OFF") ;Follow new directory structure
+ #:phases (modify-phases %standard-phases
+ (add-after
+ 'install 'hint-example-prefix
+ ;; Set Cmake hints in examples so that they can find this
+ ;; deal.II when configuring.
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref %outputs "out"))
+ (exmpl (string-append out "/share/doc"
+ "/dealii/examples")))
+ (substitute* (find-files exmpl "CMakeLists.txt")
+ (("([[:space:]]*HINTS.*)\n" _ line)
+ (string-append line " $ENV{HOME}/.guix-profile "
+ out "\n")))
+ #t))))))
+ (home-page "https://www.dealii.org")
+ (synopsis "Finite element library")
+ (description
+ "Deal.II is a C++ program library targeted at the computational solution
+of partial differential equations using adaptive finite elements. The main
+aim of deal.II is to enable rapid development of modern finite element codes,
+using among other aspects adaptive meshes and a wide array of tools often used
+in finite element programs.")
+ (license license:lgpl2.1+)))
+
+(define-public dealii-openmpi
+ (package (inherit dealii)
+ (name "dealii-openmpi")
+ (inputs
+ `(("mpi" ,openmpi)
+ ;;Supported only with MPI:
+ ("p4est" ,p4est-openmpi)
+ ("petsc" ,petsc-openmpi)
+ ("slepc" ,slepc-openmpi)
+ ("metis" ,metis) ;for MUMPS
+ ("scalapack" ,scalapack) ;for MUMPS
+ ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings
+ ("arpack" ,arpack-ng-openmpi)
+ ,@(fold alist-delete (package-inputs dealii)
+ '("p4est" "arpack"))))
+ (arguments
+ (substitute-keyword-arguments (package-arguments dealii)
+ ((#:configure-flags cf)
+ ``("-DMPI_C_COMPILER=mpicc"
+ "-DMPI_CXX_COMPILER=mpicxx"
+ "-DMPI_Fortran_COMPILER=mpifort"
+ ,@,cf))))
+ (synopsis "Finite element library (with MPI support)")))
+
+(define-public flann
+ (package
+ (name "flann")
+ (version "1.8.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append
+ "http://www.cs.ubc.ca/research/flann/uploads/FLANN/flann-"
+ version "-src.zip"))
+ (sha256
+ (base32
+ "022w8hph7bli5zbpnk3z1qh1c2sl5hm8fw2ccim651ynn0hr7fyz"))))
+ (build-system cmake-build-system)
+ (native-inputs
+ `(("unzip" ,unzip)))
+ (inputs
+ `(("hdf5" ,hdf5)
+ ("octave" ,octave)
+ ("python" ,python-2) ; print syntax
+ ;; ("python2-numpy" ,python2-numpy) ; only required for the tests
+ ("zlib" ,zlib)))
+ (arguments
+ `(#:tests? #f)) ; The test data are downloaded from the Internet.
+ (home-page "http://www.cs.ubc.ca/research/flann/")
+ (synopsis "Library for approximate nearest neighbors computation")
+ (description "FLANN is a library for performing fast approximate
+nearest neighbor searches in high dimensional spaces. It implements a
+collection of algorithms and a system for automatically choosing the best
+algorithm and optimum parameters depending on the dataset.
+
+FLANN is written in C++ and contains bindings for C, Octave and Python.")
+ (license (license:non-copyleft "file://COPYING"
+ "See COPYING in the distribution."))))
+
+(define-public wcalc
+ (package
+ (name "wcalc")
+ (version "2.5")
+ (source
+ (origin
+ (method url-fetch)
+ (uri
+ (string-append
+ "mirror://sourceforge/w-calc/wcalc-" version ".tar.bz2"))
+ (sha256
+ (base32
+ "1vi8dl6rccqiq1apmpwawyg2ywx6a1ic1d3cvkf2hlwk1z11fb0f"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("mpfr" ,mpfr)
+ ("readline" ,readline)))
+ (home-page "http://w-calc.sourceforge.net/index.php")
+ (synopsis "Flexible command-line scientific calculator")
+ (description "Wcalc is a very capable calculator. It has standard functions
+(sin, asin, and sinh for example, in either radians or degrees), many
+pre-defined constants (pi, e, c, etc.), support for using variables, \"active\"
+variables, a command history, hex/octal/binary input and output, unit
+conversions, embedded comments, and an expandable expression entry field. It
+evaluates expressions using the standard order of operations.")
+ (license license:gpl2+)))
+
+(define-public xaos
+ (package
+ (name "xaos")
+ (version "3.6")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "mirror://sourceforge/xaos/xaos-"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "15cd1cx1dyygw6g2nhjqq3bsfdj8sj8m4va9n75i0f3ryww3x7wq"))))
+ (build-system gnu-build-system)
+ (native-inputs `(("gettext" ,gnu-gettext)))
+ (inputs `(("libx11" ,libx11)
+ ("zlib" ,zlib)
+ ("libpng" ,libpng)
+ ("gsl" ,gsl)))
+ (arguments
+ `(#:tests? #f ;no "check" target
+ #:make-flags '("LOCALEDIR=$DATAROOTDIR/locale")))
+ (synopsis "Real-time fractal zoomer")
+ (description "GNU XaoS is a graphical program that generates fractal
+patterns and allows you to zoom in and out of them infinitely in a fluid,
+continuous manner. It also includes tutorials that help to explain how fractals
+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+)))
HCoop / jackhill / guix / guix.git / blobdiff