From mboxrd@z Thu Jan 1 00:00:00 1970 From: ericbavier@openmailbox.org Subject: [PATCH 11/14] gnu: petsc: Upgrade to 3.6.0. Date: Sat, 27 Jun 2015 22:45:48 -0500 Message-ID: <1435463151-32099-12-git-send-email-ericbavier@openmailbox.org> References: <1435463151-32099-1-git-send-email-ericbavier@openmailbox.org> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:45097) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z93Wj-0001FW-9w for guix-devel@gnu.org; Sat, 27 Jun 2015 23:45:08 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z93We-0003jr-SE for guix-devel@gnu.org; Sat, 27 Jun 2015 23:45:05 -0400 Received: from smtp20.openmailbox.org ([62.4.1.54]:59077) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z93We-0003in-KO for guix-devel@gnu.org; Sat, 27 Jun 2015 23:45:00 -0400 In-Reply-To: <1435463151-32099-1-git-send-email-ericbavier@openmailbox.org> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel@gnu.org Cc: Eric Bavier From: Eric Bavier * gnu/packages/maths.scm (petsc): Upgrade to 3.6.0. * gnu/packages/patches/petsc-fix-threadcomm.patch: Delete patch. * gnu-system.am (dist_patch_DATA): Remove it. --- gnu-system.am | 1 - gnu/packages/maths.scm | 26 ++++++++++--------------- gnu/packages/patches/petsc-fix-threadcomm.patch | 15 -------------- 3 files changed, 10 insertions(+), 32 deletions(-) delete mode 100644 gnu/packages/patches/petsc-fix-threadcomm.patch diff --git a/gnu-system.am b/gnu-system.am index af2c0eb..16b71e9 100644 --- a/gnu-system.am +++ b/gnu-system.am @@ -544,7 +544,6 @@ dist_patch_DATA = \ gnu/packages/patches/perl-net-ssleay-disable-ede-test.patch \ gnu/packages/patches/perl-no-sys-dirs.patch \ gnu/packages/patches/perl-tk-x11-discover.patch \ - gnu/packages/patches/petsc-fix-threadcomm.patch \ gnu/packages/patches/pingus-sdl-libs-config.patch \ gnu/packages/patches/plotutils-libpng-jmpbuf.patch \ gnu/packages/patches/polkit-drop-test.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 369457d..a6c4bba 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -501,7 +501,7 @@ ASCII text files using Gmsh's own scripting language.") (define-public petsc (package (name "petsc") - (version "3.4.4") + (version "3.6.0") (source (origin (method url-fetch) @@ -509,9 +509,7 @@ 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 "0v5dg6dhdjpi5ianvd4mm6hsvxzv1bsxwnh9f9myag0a0d9xk9iv")) - (patches - (list (search-patch "petsc-fix-threadcomm.patch"))))) + (base32 "0lzhk1flgszks1wlhz2b92rnlx5np7bgad8vqy9fcqziz5b4pr26")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-2) @@ -525,7 +523,7 @@ ASCII text files using Gmsh's own scripting language.") )) (arguments `(#:test-target "test" - #:parallel-build? #f + #:parallel-build? #f ;build is parallel by default #:configure-flags `("--with-mpi=0" "--with-openmp=1" @@ -561,26 +559,22 @@ ASCII text files using Gmsh's own scripting language.") (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") diff --git a/gnu/packages/patches/petsc-fix-threadcomm.patch b/gnu/packages/patches/petsc-fix-threadcomm.patch deleted file mode 100644 index 3ef4f2d..0000000 --- a/gnu/packages/patches/petsc-fix-threadcomm.patch +++ /dev/null @@ -1,15 +0,0 @@ -Fix "error: unknown type name 'cpu_set_t'". Patch submitted upstream -http://lists.mcs.anl.gov/pipermail/petsc-dev/2014-May/015345.html - ---- a/src/sys/threadcomm/impls/openmp/tcopenmp.c 2014-03-13 21:47:22.000000000 -0500 -+++ b/src/sys/threadcomm/impls/openmp/tcopenmp.c 2014-04-02 14:44:57.185170151 -0500 -@@ -1,6 +1,9 @@ - #define PETSC_DESIRE_FEATURE_TEST_MACROS - #include <../src/sys/threadcomm/impls/openmp/tcopenmpimpl.h> - #include -+#if defined(PETSC_HAVE_SCHED_CPU_SET_T) -+#include -+#endif - - PetscErrorCode PetscThreadCommGetRank_OpenMP(PetscInt *trank) - { -- 2.2.1