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authorMark H Weaver <mhw@netris.org>2017-08-09 17:25:31 -0400
committerMark H Weaver <mhw@netris.org>2017-08-09 17:25:31 -0400
commitcc294bcee6bfaa4524ac43450e41f083539f9cb1 (patch)
tree1248811a6fd39e9169fd4b3c58f456bd21d1c7d5 /gnu/packages/maths.scm
parent32b7506c987d8b7281382da4831958a64c048fc1 (diff)
parentae7f246cf1c7e20ebf4025024bb10361938abaa2 (diff)
downloadguix-cc294bcee6bfaa4524ac43450e41f083539f9cb1.tar
guix-cc294bcee6bfaa4524ac43450e41f083539f9cb1.tar.gz
Merge branch 'master' into core-updates
Diffstat (limited to 'gnu/packages/maths.scm')
-rw-r--r--gnu/packages/maths.scm80
1 files changed, 38 insertions, 42 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index e29a3864df..9096838d6f 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -2,7 +2,7 @@
;;; Copyright © 2013, 2014, 2015, 2016 Andreas Enge <andreas@enge.fr>
;;; Copyright © 2013 Nikita Karetnikov <nikita@karetnikov.org>
;;; Copyright © 2014, 2016, 2017 John Darrington <jmd@gnu.org>
-;;; Copyright © 2014, 2015, 2016 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014, 2015, 2016, 2017 Eric Bavier <bavier@member.fsf.org>
;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
;;; Copyright © 2014 Mathieu Lirzin <mathieu.lirzin@openmailbox.org>
;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
@@ -1216,7 +1216,7 @@ September 2004}")
(define-public petsc
(package
(name "petsc")
- (version "3.7.2")
+ (version "3.7.6")
(source
(origin
(method url-fetch)
@@ -1224,7 +1224,7 @@ September 2004}")
(uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/"
"petsc-lite-" version ".tar.gz"))
(sha256
- (base32 "0jfrq6rd4zagw1iimz05m2w91k0jvz3qbik1lk8pqcxw3rvdqk5d"))))
+ (base32 "1y3f5jjq0v5b62i3sabp4kp5mgfyp3vnk0dxhwkrhpypax77nzxh"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)
@@ -1247,6 +1247,10 @@ September 2004}")
(assoc-ref %build-inputs "superlu") "/include")
,(string-append "--with-superlu-lib="
(assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a"))
+ #:make-flags
+ ;; Honor (parallel-job-count) for build. Do not use --with-make-np,
+ ;; whose value is dumped to $out/lib/petsc/conf/petscvariables.
+ (list (format #f "MAKE_NP=~a" (parallel-job-count)))
#:phases
(modify-phases %standard-phases
(replace 'configure
@@ -1261,13 +1265,17 @@ September 2004}")
(format #t "configure flags: ~s~%" flags)
(zero? (apply system* "./configure" flags)))))
(add-after 'configure 'clean-local-references
- (lambda* (#:key inputs outputs #:allow-other-keys)
+ (lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(substitute* (find-files "." "^petsc(conf|machineinfo).h$")
;; Prevent build directory from leaking into compiled code
(((getcwd)) out)
;; Scrub timestamp for reproducibility
((".*Libraries compiled on.*") ""))
+ (substitute* (find-files "." "petscvariables")
+ ;; Do not expose build machine characteristics, set to defaults.
+ (("MAKE_NP = [:digit:]+") "MAKE_NP = 2")
+ (("NPMAX = [:digit:]+") "NPMAX = 2"))
#t)))
(add-after 'install 'clean-install
;; Try to keep installed files from leaking build directory names.
@@ -1342,16 +1350,15 @@ scientific applications modeled by partial differential equations.")
(define-public slepc
(package
(name "slepc")
- (version "3.7.1")
+ (version "3.7.4")
(source
(origin
(method url-fetch)
- (uri (string-append "http://slepc.upv.es/download/download.php?"
- "filename=slepc-" version ".tar.gz"))
- (file-name (string-append name "-" version ".tar.gz"))
+ (uri (string-append "http://slepc.upv.es/download/distrib/slepc-"
+ version ".tar.gz"))
(sha256
(base32
- "1hijlmrvxvfqslnx8yydzw5xqbsn1yy02g32w0hln1z3cgr1c0k7"))))
+ "12pbl8yd6r8k9xjlr1qw25rs0k1acgic7hw1s6l6bhiv9s285drg"))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)))
@@ -1365,6 +1372,8 @@ scientific applications modeled by partial differential equations.")
#:configure-flags
`(,(string-append "--with-arpack-dir="
(assoc-ref %build-inputs "arpack") "/lib"))
+ #:make-flags ;honor (parallel-job-count)
+ `(,(format #f "MAKE_NP=~a" (parallel-job-count)))
#:phases
(modify-phases %standard-phases
(replace 'configure
@@ -2415,7 +2424,7 @@ Fresnel integrals, and similar related functions as well.")
(define-public suitesparse
(package
(name "suitesparse")
- (version "4.4.3")
+ (version "4.5.5")
(source
(origin
(method url-fetch)
@@ -2424,33 +2433,31 @@ Fresnel integrals, and similar related functions as well.")
version ".tar.gz"))
(sha256
(base32
- "100hdzr0mf4mzlwnqpmwpfw4pymgsf9n3g0ywb1yps2nk1zbkdy5"))))
+ "1dnr6pmjzc2qmbkmb4shigx1l74ilf6abn7svyd6brxgvph8vadr"))
+ (modules '((guix build utils)))
+ (snippet
+ ;; Remove bundled metis source
+ '(delete-file-recursively "metis-5.1.0"))))
(build-system gnu-build-system)
(arguments
- '(#:parallel-build? #f ;cholmod build fails otherwise
- #:tests? #f ;no "check" target
+ '(#:tests? #f ;no "check" target
#:make-flags
(list "CC=gcc"
"BLAS=-lblas"
"TBB=-ltbb"
- "CHOLMOD_CONFIG=-DNPARTITION" ;required when METIS is not used
+ "MY_METIS_LIB=-lmetis"
(string-append "INSTALL_LIB="
(assoc-ref %outputs "out") "/lib")
(string-append "INSTALL_INCLUDE="
- (assoc-ref %outputs "out") "/include"))
+ (assoc-ref %outputs "out") "/include")
+ "library")
#:phases
- (alist-cons-before
- 'install 'prepare-out
- ;; README.txt states that the target directories must exist prior to
- ;; running "make install".
- (lambda _
- (mkdir-p (string-append (assoc-ref %outputs "out") "/lib"))
- (mkdir-p (string-append (assoc-ref %outputs "out") "/include")))
- ;; no configure script
- (alist-delete 'configure %standard-phases))))
+ (modify-phases %standard-phases
+ (delete 'configure)))) ;no configure script
(inputs
`(("tbb" ,tbb)
- ("lapack" ,lapack)))
+ ("lapack" ,lapack)
+ ("metis" ,metis)))
(home-page "http://faculty.cse.tamu.edu/davis/suitesparse.html")
(synopsis "Suite of sparse matrix software")
(description
@@ -2686,7 +2693,7 @@ revised simplex and the branch-and-bound methods.")
(define-public dealii
(package
(name "dealii")
- (version "8.4.1")
+ (version "8.5.0")
(source
(origin
(method url-fetch)
@@ -2694,7 +2701,7 @@ revised simplex and the branch-and-bound methods.")
"download/v" version "/dealii-" version ".tar.gz"))
(sha256
(base32
- "1bdksvvyp1rj37df1ndh8j3x9nzpc3sazw8nd0hzvnlw0qnyk800"))
+ "0yfpy4zh8j7hmqakw17zdlmvfdcmhwgs66wcb716plc4y7v3z4g6"))
(modules '((guix build utils)))
(snippet
;; Remove bundled sources: UMFPACK, TBB, muParser, and boost
@@ -2713,21 +2720,10 @@ revised simplex and the branch-and-bound methods.")
("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))))))
+ #:configure-flags
+ ;; Work around a bug in libsuitesparseconfig linking
+ ;; see https://github.com/dealii/dealii/issues/4745
+ '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON")))
(home-page "https://www.dealii.org")
(synopsis "Finite element library")
(description