From unknown Sat Sep 13 05:10:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#32619] [PATCH] gnu: petsc-openmpi: Configure with support for hdf5 data format. Resent-From: Paul Garlick Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 03 Sep 2018 11:00:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 32619 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 32619@debbugs.gnu.org Cc: Paul Garlick X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.153597236920258 (code B ref -1); Mon, 03 Sep 2018 11:00:02 +0000 Received: (at submit) by debbugs.gnu.org; 3 Sep 2018 10:59:29 +0000 Received: from localhost ([127.0.0.1]:43633 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fwmZp-0005Gc-5I for submit@debbugs.gnu.org; Mon, 03 Sep 2018 06:59:29 -0400 Received: from eggs.gnu.org ([208.118.235.92]:42498) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fwmZn-0005GO-DA for submit@debbugs.gnu.org; Mon, 03 Sep 2018 06:59:23 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fwmZh-0002On-9D for submit@debbugs.gnu.org; Mon, 03 Sep 2018 06:59:18 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-0.0 required=5.0 tests=BAYES_40 autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:40662) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1fwmZh-0002Oj-68 for submit@debbugs.gnu.org; Mon, 03 Sep 2018 06:59:17 -0400 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 Received: from [79.123.23.187] (helo=parkin.tourbillion-technology.com.com) by smtp.hosts.co.uk with esmtpsa (TLSv1.2:ECDHE-RSA-AES128-GCM-SHA256:128) (Exim) (envelope-from ) id 1fwmZX-00012W-7S; Mon, 03 Sep 2018 11:59:08 +0100 From: Paul Garlick Date: Mon, 3 Sep 2018 11:57:38 +0100 Message-Id: <1535972258-5183-1-git-send-email-pgarlick@tourbillion-technology.com> X-Mailer: git-send-email 1.8.3.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x (no timestamps) [generic] [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) * 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 From unknown Sat Sep 13 05:10:28 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#32619] [PATCH] gnu: petsc-openmpi: Configure with support for hdf5 data format. Resent-From: ludovic.courtes@inria.fr (Ludovic =?UTF-8?Q?Court=C3=A8s?=) Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 04 Sep 2018 13:35:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 32619 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Paul Garlick Cc: 32619@debbugs.gnu.org Received: via spool by 32619-submit@debbugs.gnu.org id=B32619.153606804326831 (code B ref 32619); Tue, 04 Sep 2018 13:35:02 +0000 Received: (at 32619) by debbugs.gnu.org; 4 Sep 2018 13:34:03 +0000 Received: from localhost ([127.0.0.1]:45180 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fxBT0-0006yg-QT for submit@debbugs.gnu.org; Tue, 04 Sep 2018 09:34:02 -0400 Received: from mail3-relais-sop.national.inria.fr ([192.134.164.104]:29403) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fxBSy-0006y9-KW for 32619@debbugs.gnu.org; Tue, 04 Sep 2018 09:34:01 -0400 X-IronPort-AV: E=Sophos;i="5.53,329,1531778400"; d="scan'208";a="277676155" Received: from unknown (HELO ribbon) ([193.50.110.186]) by mail3-relais-sop.national.inria.fr with ESMTP/TLS/AES256-GCM-SHA384; 04 Sep 2018 15:33:54 +0200 From: ludovic.courtes@inria.fr (Ludovic =?UTF-8?Q?Court=C3=A8s?=) References: <1535972258-5183-1-git-send-email-pgarlick@tourbillion-technology.com> Date: Tue, 04 Sep 2018 15:33:54 +0200 In-Reply-To: <1535972258-5183-1-git-send-email-pgarlick@tourbillion-technology.com> (Paul Garlick's message of "Mon, 3 Sep 2018 11:57:38 +0100") Message-ID: <878t4hbd4t.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -5.0 (-----) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) Hi Paul, Paul Garlick skribis: > * 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. Applied, thanks! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Wed Sep 05 05:52:27 2018 Received: (at control) by debbugs.gnu.org; 5 Sep 2018 09:52:27 +0000 Received: from localhost ([127.0.0.1]:46395 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fxUU6-0002xY-Rr for submit@debbugs.gnu.org; Wed, 05 Sep 2018 05:52:27 -0400 Received: from eggs.gnu.org ([208.118.235.92]:33858) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1fxUU5-0002xK-6W for control@debbugs.gnu.org; Wed, 05 Sep 2018 05:52:25 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1fxUTz-0007P8-Ee for control@debbugs.gnu.org; Wed, 05 Sep 2018 05:52:20 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00 autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:39263) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1fxUTz-0007P4-Aa for control@debbugs.gnu.org; Wed, 05 Sep 2018 05:52:19 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=32804 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1fxUTz-0003St-1o for control@debbugs.gnu.org; Wed, 05 Sep 2018 05:52:19 -0400 Date: Wed, 05 Sep 2018 11:52:18 +0200 Message-Id: <878t4g8e5p.fsf@gnu.org> To: control@debbugs.gnu.org From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) Subject: control message for bug #32619 MIME-version: 1.0 Content-type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: control X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -6.0 (------) tags 32619 fixed close 32619