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-rw-r--r--gnu/packages/maths.scm344
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+)))