;;; 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.
;;;
#: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)
#:use-module (gnu packages image)
#:use-module (gnu packages less)
#:use-module (gnu packages lisp)
+ #:use-module (gnu packages logging)
#:use-module (gnu packages gnome)
#:use-module (gnu packages guile)
#:use-module (gnu packages xorg)
(inputs `(("fortran" ,gfortran)
("python" ,python-2)))
(arguments
- `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES")
+ `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
+ "-DLAPACKE=ON")
#:phases (alist-cons-before
'check 'patch-python
(lambda* (#:key inputs #:allow-other-keys)
"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
(build-system cmake-build-system)
(arguments
;; TODO: Build HTML user documentation and install separately.
- ;; XXX: Use the embedded "miniglog" as a replacement for
- ;; <https://github.com/google/glog>. TODO: Use Glog when it's available.
- '(#:configure-flags '("-DMINIGLOG=ON"
- "-DBUILD_EXAMPLES=OFF"
+ '(#:configure-flags '("-DBUILD_EXAMPLES=OFF"
"-DBUILD_SHARED_LIBS=ON")
#:phases (modify-phases %standard-phases
#t)))))
(native-inputs
`(("pkg-config" ,pkg-config)))
+ (propagated-inputs
+ `(("glog" ,glog))) ;for #include <glog/glog.h>
(inputs
`(("eigen" ,eigen)
("blas" ,openblas)
(define-public petsc
(package
(name "petsc")
- (version "3.6.2")
+ (version "3.7.2")
(source
(origin
(method url-fetch)
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
"petsc-lite-" version ".tar.gz"))
(sha256
- (base32 "13h0m5f9xsdpps4lsp59iz2m7zkapwavq2zfkfvs3ab6sndla0l9"))))
+ (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)
,(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")
(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
(define-public slepc
(package
(name "slepc")
- (version "3.6.2")
+ (version "3.7.1")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "1pv5iqz2kc8sj49zsabyz4arnfpana8mjrhq31vzgk16xldk3d1a"))))
+ "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)))
(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)
(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
;; $out/include. We'd like to move them to share/doc, but delete
;; them for now, as they are incomplete and installing the complete
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out")))
(for-each delete-file (find-files out "\\.html$")))))
- (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")))
(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
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
"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
"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
(define-public openlibm
(package
(name "openlibm")
- (version "0.4.1")
+ (version "0.5.1")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0cwqqqlblj3kzp9aq1wnpfs1fl0qd1wp1xzm5shb09w06i4rh9nn"))))
+ "11czx2z7nh6dfpz45s3xl7v38hw36jxzxfvny454bk3if14pfakq"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
(define-public openspecfun
(package
(name "openspecfun")
- (version "0.4")
+ (version "0.5.2")
(source
(origin
(method url-fetch)
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
- "0nsa3jjmlhcqkw5ba5ypbn3n0c8b6lc22zzlxnmxkxi9shhdx65z"))))
+ "1y5b2h6f2k72536kym3vzy3li3bhpd23x463g7hdmjdi3cncavz1"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f ;no "check" target
(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"))))
the machine where it is installed, without resorting to pre-built substitutes.
Before building the library, CPU throttling should be disabled. This can be
-done in the BIOS, or, on GNU/Linux, with the following commands:
+done in the BIOS, or, on GNU/Linux, with the following command:
-cpufreq-selector -g performance -c 0
-...
-cpufreq-selector -g performance -c N-1
+@example
+# cpupower --governor performance
+@end example
-where N is the number of cores of your CPU. Failure to do so will result in a
-library with poor performance.")
+Failure to do so will result in a library with poor performance.")
(license license:bsd-3)))
(define-public glm
(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"))))
;; 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=.*$") "PLATFORM=ux64\n")))))
+ (("^PLATFORM=.*$") "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.)")))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no check target
(delete 'configure)
(replace 'build
(lambda _
- (with-directory-excursion "lpsolve55"
- (system* "bash" "ccc"))
- (with-directory-excursion "lp_solve"
- (system* "bash" "ccc"))
- #t))
+ (and (with-directory-excursion "lpsolve55"
+ (zero? (system* "bash" "ccc")))
+ (with-directory-excursion "lp_solve"
+ (zero? (system* "bash" "ccc"))))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let* ((out (assoc-ref outputs "out"))
(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"))))
(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"))))
(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
(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+)))
HCoop / jackhill / guix / guix.git / blobdiff