From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:35399) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fwmaZ-0000vn-8U for guix-patches@gnu.org; Mon, 03 Sep 2018 07:00:12 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fwmaR-0002br-7K for guix-patches@gnu.org; Mon, 03 Sep 2018 07:00:10 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:38615) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1fwmaQ-0002bE-PL for guix-patches@gnu.org; Mon, 03 Sep 2018 07:00:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1fwmaQ-0005I6-LA for guix-patches@gnu.org; Mon, 03 Sep 2018 07:00:02 -0400 Subject: [bug#32619] [PATCH] gnu: petsc-openmpi: Configure with support for hdf5 data format. Resent-Message-ID: Received: from eggs.gnu.org ([2001:4830:134:3::10]:35241) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fwmZg-0000sc-7d for guix-patches@gnu.org; Mon, 03 Sep 2018 06:59:17 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fwmZd-0002Nv-4U for guix-patches@gnu.org; Mon, 03 Sep 2018 06:59:16 -0400 Received: from smtp.hosts.co.uk ([85.233.160.19]:48912) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1fwmZc-0002NI-Ua for guix-patches@gnu.org; Mon, 03 Sep 2018 06:59:13 -0400 From: Paul Garlick Date: Mon, 3 Sep 2018 11:57:38 +0100 Message-Id: <1535972258-5183-1-git-send-email-pgarlick@tourbillion-technology.com> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 32619@debbugs.gnu.org Cc: Paul Garlick * gnu/packages/maths.scm (petsc-openmpi)[inputs]: Add hdf5-parallel-openmpi. [arguments]: Add '--with-hdf5-include' and '--with-hdf5-lib' flags. Add 'set-test-environment' phase. --- gnu/packages/maths.scm | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 377e47b..465bf92 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -15,7 +15,7 @@ ;;; Copyright © 2016, 2017, 2018 Ludovic Courtès ;;; Copyright © 2016 Leo Famulari ;;; Copyright © 2016, 2017 Thomas Danckaert -;;; Copyright © 2017 Paul Garlick +;;; Copyright © 2017, 2018 Paul Garlick ;;; Copyright © 2017 Nils Gillmann ;;; Copyright © 2017 Ben Woodcroft ;;; Copyright © 2017 Theodoros Foradis @@ -1690,6 +1690,7 @@ scientific applications modeled by partial differential equations.") (name "petsc-openmpi") (inputs `(("openmpi" ,openmpi) + ("hdf5" ,hdf5-parallel-openmpi) ,@(package-inputs petsc))) (arguments (substitute-keyword-arguments (package-arguments petsc) @@ -1697,7 +1698,21 @@ scientific applications modeled by partial differential equations.") ``("--with-mpiexec=mpirun" ,(string-append "--with-mpi-dir=" (assoc-ref %build-inputs "openmpi")) - ,@(delete "--with-mpi=0" ,cf))))) + ,(string-append "--with-hdf5-include=" + (assoc-ref %build-inputs "hdf5") "/include") + ,(string-append "--with-hdf5-lib=" + (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a") + ,@(delete "--with-mpi=0" ,cf))) + ((#:phases phases) + `(modify-phases ,phases + (add-before 'check 'set-test-environment + (lambda _ + ;; By default, running the test suite would fail because 'ssh' + ;; could not be found in $PATH. Define this variable to + ;; placate Open MPI without adding a dependency on OpenSSH (the + ;; agent isn't used anyway.) + (setenv "OMPI_MCA_plm_rsh_agent" (which "cat")) + #t)))))) (synopsis "Library to solve PDEs (with MPI support)"))) (define-public petsc-complex-openmpi -- 1.8.3.1