From debbugs-submit-bounces@debbugs.gnu.org Sun Mar 01 15:06:19 2020 Received: (at submit) by debbugs.gnu.org; 1 Mar 2020 20:06:19 +0000 Received: from localhost ([127.0.0.1]:36979 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8Uqw-0005k4-R5 for submit@debbugs.gnu.org; Sun, 01 Mar 2020 15:06:19 -0500 Received: from lists.gnu.org ([209.51.188.17]:46500) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8Uaz-0005Eo-F8 for submit@debbugs.gnu.org; Sun, 01 Mar 2020 14:49:50 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:46177) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1j8Uay-0004m3-0Q for guix-patches@gnu.org; Sun, 01 Mar 2020 14:49:49 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_05,RCVD_IN_DNSWL_MED, URIBL_BLOCKED autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1j8Uaw-0002Rx-KL for guix-patches@gnu.org; Sun, 01 Mar 2020 14:49:47 -0500 Received: from mout01.posteo.de ([185.67.36.65]:38890) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1j8Uaw-0002Rg-5T for guix-patches@gnu.org; Sun, 01 Mar 2020 14:49:46 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id DC7EB160060 for ; Sun, 1 Mar 2020 20:49:43 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1583092183; bh=Mknqn8aw8MKEnPZGHqNF0+etMDubxHx5+TIpzonLLtc=; h=From:To:Cc:Subject:Date:From; b=Wt0GOLFBWhlR7lXo5hW2XbAehbEEf39T2SHezd7yW8TtweZOd2qz+oP2XXQ+fqPRP 9j37WcsMdN1A7qRHwuQUQhYEFIWvPs7kNKlm74WmEQqwB7f783x+bnD5uz6+jivuaO og8aI9dpXk+zoiBaHnidAj+9K2BQAO0MzX8NDV+SSUdU32ghQt0XSSIPJxhX29Cxi4 bHCGMDBjfWK6h0RLfWwstOINcsQdG7hHep7TlGquW1vQZanc/jz5SQ4EoF22FHQjq8 H0lafFQsoGyoTp2ngLODO29Q3O0RjYmbzHUXhsJDGRGOGg8uGSfRlgf2TaRbNntwUF c1NWuUoGZJViA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48Vv4Q6j98z6tm5; Sun, 1 Mar 2020 20:49:42 +0100 (CET) From: Felix Gruber To: guix-patches@gnu.org Subject: [PATCH 0/4] update Dune finite element packages Date: Sun, 1 Mar 2020 20:49:14 +0100 Message-Id: <20200301194914.899011-1-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 MIME-Version: 1.0 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] [fuzzy] X-Received-From: 185.67.36.65 X-Spam-Score: 0.3 (/) X-Debbugs-Envelope-To: submit X-Mailman-Approved-At: Sun, 01 Mar 2020 15:06:17 -0500 Cc: Felix Gruber 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: -0.7 (/) Hi Guix developers, I've updated the packages of the Dune finite element library to properly set up OpenMPI before running their tests instead of disabling all the tests that failed due to mis-configured OpenMPI. BTW, some other packages exist in variants with and without OpenMPI, e.g. the dealii and dealii-openmpi packages. Do you think that it would be useful to provide similar variants for the dune-* packages, which could also be built without OpenMPI? Additionally, I've added two new packages, dune-uggrid and dune-subgrid that might be useful in combination with the existing Dune packages. Finally, I've added the suitesparse package to dune-istl which as an optional dependency allows to build some additional solvers for sparse linear systems into dune-istl. I've checked that all Dune packages still build after my changes (there don't seem to be any other packages that depend on the dune-* packages). Those builds were done using the updated suitesparse package that I've submitted in bug #39839. Felix Gruber (4): gnu: dune-*: set up MPI for tests gnu: add dune-uggrid 2.6.0 gnu: Add dune-subgrid gnu: dune-istl: Build with suitesparse gnu/packages/maths.scm | 207 +++++++++++++++++++++-------------------- 1 file changed, 106 insertions(+), 101 deletions(-) --=20 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Sun Mar 01 15:24:28 2020 Received: (at 39862) by debbugs.gnu.org; 1 Mar 2020 20:24:29 +0000 Received: from localhost ([127.0.0.1]:36988 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8V8W-0006Fp-HJ for submit@debbugs.gnu.org; Sun, 01 Mar 2020 15:24:28 -0500 Received: from mout02.posteo.de ([185.67.36.66]:40525) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8V8U-0006FZ-4U for 39862@debbugs.gnu.org; Sun, 01 Mar 2020 15:24:27 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id 2BF712400FB for <39862@debbugs.gnu.org>; Sun, 1 Mar 2020 21:24:20 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1583094260; bh=+HK+gAoAGo3lV+N+hjBMvQSYHb66zikufq1YeNk+wzc=; h=From:To:Cc:Subject:Date:From; b=g3rRJOppMPt9MIXBIpaE4G2dC2iKY+JEIcI8S4UdcRdX8fG7JNf+puZtq+7jQzUD9 PUT2dbjjpjm4ZXMqKb0yixVGFMbm9B/QvRfnXdVa3T5S7iKAzNh0m5gnN1xYofwZId 5O+k34tDMugz3yG0n1RTolwi5BlpHiBUFMn65wDNJU+QI/cI+x/EmWG1g6hVXzUEgg Cxg8fUZGeWywtpCJKhMr5jkqu0XPfc6driT+L3JnaEWK2VbJgkHKqgYV2BGVUMVyYF Fv8twFAC4h9vtjf36bUZe0CedC4ZlvI1QJrXC6G3S4BsZhSgmx9+Eop7+J1fOpQDsm uSKVMOhx6XxQQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48VvrM2TZmz9rxG; Sun, 1 Mar 2020 21:24:19 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH 1/4] gnu: dune-*: set up MPI for tests Date: Sun, 1 Mar 2020 21:23:59 +0100 Message-Id: <20200301202402.899669-1-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <20200301194914.899011-1-felgru@posteo.net> References: <20200301194914.899011-1-felgru@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber 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: -3.3 (---) * gnu/packages/maths.scm (dune-common, dune-grid, dune-istl, dune-alugrid): [arguments]: correctly set up MPI instead of disabling tests that require MPI. --- gnu/packages/maths.scm | 110 ++++------------------------------------- 1 file changed, 10 insertions(+), 100 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index cee626f179..effba8956f 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4583,36 +4583,8 @@ linear algebra primitives specifically targeting graph analytics.") (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "build_tests" make-flags))) - ;; These tests fail because they require a fully functional MPI - ;; environment. - (add-after 'unpack 'disable-failing-tests - (lambda _ - (setenv "ARGS" - (string-append "--exclude-regex '(" - (string-join - (list - "remoteindicestest" - "remoteindicestest-mpi-2" - "syncertest" - "syncertest-mpi-2" - "variablesizecommunicatortest" - "variablesizecommunicatortest-mpi-2" - "arithmetictestsuitetest" - "assertandreturntest" - "assertandreturntest_ndebug" - "concept" - "debugaligntest" - "mpicollectivecommunication" - "mpicollectivecommunication-mpi-2" - "mpiguardtest" - "mpiguardtest-mpi-2" - "mpihelpertest" - "mpihelpertest-mpi-2" - "mpihelpertest2" - "mpihelpertest2-mpi-2") - "|") - ")'")) - #t))))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("gmp" ,gmp) ("metis" ,metis) @@ -4693,54 +4665,8 @@ This package contains the basic DUNE geometry classes.") (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "build_tests" make-flags))) - ;; These tests fail because they require a fully functional MPI - ;; environment. - (add-after 'unpack 'disable-failing-tests - (lambda _ - (setenv "ARGS" - (string-append "--exclude-regex '(" - (string-join - (list - "scsgmappertest" - "conformvolumevtktest" - "gnuplottest" - "nonconformboundaryvtktest" - "subsamplingvtktest" - "vtktest" - "vtktest-mpi-2" - "vtksequencetest" - "gmshtest-onedgrid" - "test-dgf-yasp" - "test-dgf-yasp-offset" - "test-dgf-oned" - "test-geogrid-yaspgrid" - "test-gridinfo" - "test-identitygrid" - "testiteratorranges" - "test-hierarchicsearch" - "test-parallel-ug-mpi-2" - "test-yaspgrid-backuprestore-equidistant" - "test-yaspgrid-backuprestore-equidistant-mpi-2" - "test-yaspgrid-backuprestore-equidistantoffset" - "test-yaspgrid-backuprestore-equidistantoffset-mpi-2" - "test-yaspgrid-backuprestore-tensor" - "test-yaspgrid-backuprestore-tensor-mpi-2" - "test-yaspgrid-tensorgridfactory" - "test-yaspgrid-tensorgridfactory-mpi-2" - "test-yaspgrid-yaspfactory-1d" - "test-yaspgrid-yaspfactory-1d-mpi-2" - "test-yaspgrid-yaspfactory-2d" - "test-yaspgrid-yaspfactory-2d-mpi-2" - "test-yaspgrid-yaspfactory-3d" - "test-yaspgrid-yaspfactory-3d-mpi-2" - "globalindexsettest" - "persistentcontainertest" - "structuredgridfactorytest" - "tensorgridfactorytest" - "vertexordertest") - "|") - ")'")) - #t))))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) @@ -4783,24 +4709,8 @@ This package contains the basic DUNE grid classes.") (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "build_tests" make-flags))) - ;; These tests fail because they require a fully functional MPI - ;; environment. - (add-after 'unpack 'disable-failing-tests - (lambda _ - (setenv "ARGS" - (string-append "--exclude-regex '(" - (string-join - (list - "galerkintest" - "hierarchytest" - "pamgtest" - "pamg_comm_repart_test" - "matrixredisttest" - "vectorcommtest" - "matrixmarkettest") - "|") - ")'")) - #t))))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("dune-common" ,dune-common) ("openmpi" ,openmpi) @@ -4886,9 +4796,7 @@ assemble global function spaces on finite-element grids.") "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj")))) (build-system cmake-build-system) (arguments - `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI - ; environment - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'patch-include (lambda _ @@ -4900,7 +4808,9 @@ assemble global function spaces on finite-element grids.") (lambda* (#:key inputs make-flags #:allow-other-keys) (setenv "CPLUS_INCLUDE_PATH" (string-append (assoc-ref inputs "dune-grid") "/share")) - (apply invoke "make" "build_tests" make-flags)))))) + (apply invoke "make" "build_tests" make-flags))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Sun Mar 01 15:25:09 2020 Received: (at 39862) by debbugs.gnu.org; 1 Mar 2020 20:25:09 +0000 Received: from localhost ([127.0.0.1]:36993 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8V9B-0006HS-0C for submit@debbugs.gnu.org; Sun, 01 Mar 2020 15:25:09 -0500 Received: from mout02.posteo.de ([185.67.36.66]:35877) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8V99-0006Gh-5Z for 39862@debbugs.gnu.org; Sun, 01 Mar 2020 15:25:07 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id 2F782240100 for <39862@debbugs.gnu.org>; Sun, 1 Mar 2020 21:25:00 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1583094300; bh=Bh24h/JaCr7msRdhOg+K9kn3vwoqezeM8Eb3VPOLZZ4=; h=From:To:Cc:Subject:Date:From; b=rnjQlAcqiIo437PDR6belE6wCNkeS/zzhfK+cDMyVHpvYagr6iA4Ge9CQ/ygO5Fqe uq2tKsWhUbHgWK01LyHLrE1dDR30ej1bS0R6bS0VyEbWt4zpZ45l6En3wYBdSi0LOw S2J8SH89Jwl6/I2zAkRyHToGN2M74wiQIRT8P2DJvHU3clGnsViHxSV1U0418PXXR9 c1QOcadh0vczlKoanzYtfJ4+WQfYJ+IgEpmioE9TgVxQjUdrPZ1dADAu8kvFYQRV8s fmeiZK4C341XxON5Ob3K1zv9fOVGvJJSQhhgbfkBHOMbjC8Pp3TFiwQRGutHzYXuQ0 btAVSfAoGRoOw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48Vvs75ZcQz9rxT; Sun, 1 Mar 2020 21:24:59 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH 2/4] gnu: add dune-uggrid 2.6.0 Date: Sun, 1 Mar 2020 21:24:50 +0100 Message-Id: <20200301202450.899728-1-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <20200301194914.899011-1-felgru@posteo.net> References: <20200301194914.899011-1-felgru@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber 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: -3.3 (---) * gnu/packages/maths.scm (dune-uggrid): New variable. * gnu/packages/maths.scm (dune-grid): [propagated-inputs]: Add dune-uggrid dependency, so that the UGGrid class in dune-grid can be used by packages that have dune-grid as input. * gnu/packages/maths.scm (dune-functions): [arguments]: enable tests that previously weren't built as they require dune-uggrid. --- gnu/packages/maths.scm | 53 +++++++++++++++++++++++++++++++++++++++++- 1 file changed, 52 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index effba8956f..f78ed51454 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4646,6 +4646,42 @@ This package contains the basic DUNE geometry classes.") ;; GPL version 2 with "runtime exception" (license license:gpl2))) +(define-public dune-uggrid + (package + (name "dune-uggrid") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://dune-project.org/download/" + version "/dune-uggrid-" version ".tar.gz")) + (sha256 + (base32 + "05l7a1gb78mny49anyxk6rjvn66rhgm30y72v5cjg0m5kfgr1a1f")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags)))))) + (inputs + `(("dune-common" ,dune-common) + ("openmpi" ,openmpi))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "https://dune-project.org/") + (synopsis "Distributed and Unified Numerics Environment") + (description "DUNE, the Distributed and Unified Numerics Environment is a +modular toolbox for solving @dfn{partial differential equations} (PDEs) with +grid-based methods. It supports the easy implementation of methods like +@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite +Differences} (FD). + +This package contains the DUNE UG grid classes.") + (license license:lgpl2.1))) + (define-public dune-grid (package (name "dune-grid") @@ -4675,6 +4711,8 @@ This package contains the basic DUNE geometry classes.") ("openblas" ,openblas) ("openmpi" ,openmpi) ("python" ,python))) + (propagated-inputs + `(("dune-uggrid" ,dune-uggrid))) (native-inputs `(("gfortran" ,gfortran) ("pkg-config" ,pkg-config))) @@ -4888,7 +4926,20 @@ operating on statically typed trees of objects.") (base32 "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200")))) (build-system cmake-build-system) - (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-failing-tests + (lambda _ + (setenv "ARGS" + ;; unable to load GMSH file in this test + "--exclude-regex gridviewfunctionspacebasistest") + #t)) + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("dune-common" ,dune-common) ("dune-istl" ,dune-istl) -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Sun Mar 01 15:25:24 2020 Received: (at 39862) by debbugs.gnu.org; 1 Mar 2020 20:25:24 +0000 Received: from localhost ([127.0.0.1]:36997 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8V9Q-0006I4-Aw for submit@debbugs.gnu.org; Sun, 01 Mar 2020 15:25:24 -0500 Received: from mout02.posteo.de ([185.67.36.66]:40481) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8V9O-0006Ho-Qh for 39862@debbugs.gnu.org; Sun, 01 Mar 2020 15:25:23 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id 372E32400FD for <39862@debbugs.gnu.org>; Sun, 1 Mar 2020 21:25:17 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1583094317; bh=kMKsum3QHOltpYYimqRcoeiZ0QyA1tDfdFUBCbY2d/E=; h=From:To:Cc:Subject:Date:From; b=EIyLETsoDJoV0munHVot+GYytgW7rloBhwnErs6FM8e5lXAHNjDYa5LjIyv8EKyU1 28Ue0Oa35zz0W1539igMROf0xa6UCqCELtLLnpCsunSf4yHlMJ70AaNmvGiUc+cE8X DSs4tRpwUp35DLGgtu5OpPP5FJM1bGXEQ12l7q8gTqV7fUtKL2aJHYEH/GHglsZDna sEu00ibVV/f23McFLhAbqfQIuD0/O8czK27fEjUV6+MZwCEEtQZ0qDntzWXMB861p2 lN//7mlCvUJInZRquHMShG2jwLwTfSeS3hFT0FgxN6HzmQRXMrwVtoBT48yqBAWXZs z8xWxxkroRRkA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48VvsS22bbz9rxB; Sun, 1 Mar 2020 21:25:16 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH 3/4] gnu: Add dune-subgrid Date: Sun, 1 Mar 2020 21:25:07 +0100 Message-Id: <20200301202507.899783-1-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <20200301194914.899011-1-felgru@posteo.net> References: <20200301194914.899011-1-felgru@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber 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: -3.3 (---) * gnu/packages/maths.scm (dune-subgrid): New variable. --- gnu/packages/maths.scm | 43 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index f78ed51454..77ff0ede08 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4871,6 +4871,49 @@ implementation of the DUNE grid interface supporting either simplices or cubes.") (license license:gpl2+))) +(define-public dune-subgrid + (package + (name "dune-subgrid") + (version "2.6.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid") + (commit "releases/2.6-1"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1gcv35rx3knqd54r4pp9rzd639db4j8w2r2ibq43w1mgwdcqhs64")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) + (inputs + `(("dune-common" ,dune-common) + ("dune-geometry" ,dune-geometry) + ("dune-grid" ,dune-grid) + ("openmpi" ,openmpi) + ;; Optional + ("metis" ,metis) + ("openblas" ,openblas) + ("gmp" ,gmp))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php") + (synopsis "Distributed and Unified Numerics Environment") + (description "The dune-subgrid module allows to mark elements of +another hierarchical dune grid. The set of marked elements can then be +accessed as a hierarchical dune grid in its own right. Dune-Subgrid +provides the full grid interface including adaptive mesh refinement.") + (license license:gpl2+))) + (define-public dune-typetree (package (name "dune-typetree") -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Sun Mar 01 15:25:40 2020 Received: (at 39862) by debbugs.gnu.org; 1 Mar 2020 20:25:40 +0000 Received: from localhost ([127.0.0.1]:37001 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8V9g-0006In-K8 for submit@debbugs.gnu.org; Sun, 01 Mar 2020 15:25:40 -0500 Received: from mout02.posteo.de ([185.67.36.66]:33167) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8V9e-0006IS-PN for 39862@debbugs.gnu.org; Sun, 01 Mar 2020 15:25:39 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id 2F8902400E6 for <39862@debbugs.gnu.org>; Sun, 1 Mar 2020 21:25:33 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1583094333; bh=oyBBvXpZjjypBYm9sh87zgRgaCBIZWLlf9F9NKwrpsQ=; h=From:To:Cc:Subject:Date:From; b=I36Ewij0HZVvOT+j0DSVSJN2vIQnayRLbaOqvcNftmMUqvvxcsm5EON7YQjzD6AYA bA/040NFjb3tqCzI06J+jBkIGkOhH6kwCS+CkK1KeW//EW61WoH7XzAPaMh/88cM7g OXDwpuh7gd83N/XJJFM021jneOpB5sLhSeiltbLh2LH8mulTGc4jzq9xyRnKKiVQtT 3FgFE2aAjwlRdNIlMF2ZE/uTaLpNBQmSjq3OzNpWq6vqXjFOV1dQdiIkTjqm+g+vyS HvkPKX8ccZIfwjv48Me3d5stGHgpmlxmiU2KjC+6Gnq9feFmwqECaKB6swhZwNrvOV cipgGDzMRh8+Q== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48Vvsm5dmBz9rxG; Sun, 1 Mar 2020 21:25:32 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH 4/4] gnu: dune-istl: Build with suitesparse Date: Sun, 1 Mar 2020 21:25:23 +0100 Message-Id: <20200301202523.899837-1-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <20200301194914.899011-1-felgru@posteo.net> References: <20200301194914.899011-1-felgru@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber 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: -3.3 (---) * gnu/packages/maths.scm (dune-istl)[inputs]: Add suitesparse to build additional solvers in dune-istl. --- gnu/packages/maths.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 77ff0ede08..8b59d8dfaf 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4754,6 +4754,7 @@ This package contains the basic DUNE grid classes.") ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) + ("suitesparse" ,suitesparse) ("superlu" ,superlu) ("openblas" ,openblas) ("gmp" ,gmp) -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Mon Mar 02 09:53:47 2020 Received: (at 39862) by debbugs.gnu.org; 2 Mar 2020 14:53:47 +0000 Received: from localhost ([127.0.0.1]:37513 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8mS3-0007ac-7k for submit@debbugs.gnu.org; Mon, 02 Mar 2020 09:53:47 -0500 Received: from mail-qk1-f193.google.com ([209.85.222.193]:44283) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8mS0-0007aM-KQ for 39862@debbugs.gnu.org; Mon, 02 Mar 2020 09:53:45 -0500 Received: by mail-qk1-f193.google.com with SMTP id f198so2535105qke.11 for <39862@debbugs.gnu.org>; Mon, 02 Mar 2020 06:53:44 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=mime-version:references:in-reply-to:from:date:message-id:subject:to :cc; bh=ogNIDRpUFWQOeXHV87kj6cU8h+3tN55hYQ1oNqGk5OU=; b=meXGJuLAF7nk7pLLmNavIxvCPIzdDEYP+I1U1FfJwk/Hdz07tIHaYsz9TwVr8lK1Bo nxRCrJ5ah80DA1oCrMJTseSvMN+/03gNNIcj4LMKLHaHimDTpOij8hTniQKr3zn0ROCW 0mI9x8o68e0FssdBiWKT9W633ULT5y7ZwGbXoZzyWyVx1osyemXLCIcOUf1r4aZkCYih 1edM0ENfPrUg9U5xBEEOX7r1AMXABRqGEcDPABoKIqR9CCqniwOYuvn631ZtVdt/WApa WIZHLnuZuSmxic2+lWG6SfjQxwAGquRMdIme8D1AmKhFX0eCyPMFBTy/yfjW1mCNW/MN N01g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:mime-version:references:in-reply-to:from:date :message-id:subject:to:cc; bh=ogNIDRpUFWQOeXHV87kj6cU8h+3tN55hYQ1oNqGk5OU=; b=rIX3FcqJrVLhuKUwmrI3XXmEAejsQhGg0Nv0rMCSQiJ/C8Fnnpxqan3oD1puxyJf/O YjkoaIwdutPXvnMiIOsnHzBtwMY60ivh+c1ekCOJZAyhEB/68Imk/fBuXHIe68lSxuAc 9t1kbRbiyDrABjyor9V1H8on+/iV0m13gl9pOWkbJLi5fNW54rOen4/col6SXjWOKHC+ YImA+P02bI3UzTlskkvDYtCH3PGfJV3clq5QRCRp9lWlL/tCwNhFlcm2dFAmM/gRt+H2 +MAu5KD0YpsjuXtt2PWb3GmHCiEVAivY8F+FeMjSRMbKcSwWmCr18Fl0rBp6TqUoTOY3 UPow== X-Gm-Message-State: APjAAAXc+Pv30sn3N5jfBNTAw0zhuhkIv/wQzN6h7DrtSPiiRONHdFSx OlvXnmAa8OwRWcxFbvY8fqiVynytWKeWOVxnLNA= X-Google-Smtp-Source: APXvYqzgG9X81PPh0NRFFPzjPPQB6D7Ql0DT0xJEdviot/Q6NWok63jWiOPJYJ1QvJ1rQneWeExjXqR6nW1ih7IVFYc= X-Received: by 2002:a05:620a:2282:: with SMTP id o2mr14761211qkh.304.1583160819034; Mon, 02 Mar 2020 06:53:39 -0800 (PST) MIME-Version: 1.0 References: <20200301194914.899011-1-felgru@posteo.net> In-Reply-To: <20200301194914.899011-1-felgru@posteo.net> From: zimoun Date: Mon, 2 Mar 2020 15:53:27 +0100 Message-ID: Subject: Re: [bug#39862] [PATCH 0/4] update Dune finite element packages To: Felix Gruber Content-Type: text/plain; charset="UTF-8" X-Spam-Score: -1.5 (-) X-Debbugs-Envelope-To: 39862 Cc: 39862@debbugs.gnu.org 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: -2.5 (--) Hi Felix, Thank for working on that. On Sun, 1 Mar 2020 at 21:07, Felix Gruber wrote: > I've updated the packages of the Dune finite element library to properly > set up OpenMPI before running their tests instead of disabling all the > tests that failed due to mis-configured OpenMPI. > BTW, some other packages exist in variants with and without OpenMPI, > e.g. the dealii and dealii-openmpi packages. Do you think that it would > be useful to provide similar variants for the dune-* packages, which > could also be built without OpenMPI? As an end-user, I prefer regular packages 'dune-*' without the input 'openmpi' and so with the related tests disabled and then their variants; say 'dune-*-openmpi' with the input 'openmpi' correctly setup-ed, as in your patch. > I've checked that all Dune packages still build after my changes (there > don't seem to be any other packages that depend on the dune-* packages). > Those builds were done using the updated suitesparse package that I've > submitted in bug #39839. Usually, 'guix refresh -l' lists the packages that would need to be rebuilt when upgrading a particular one. All the best, simon From debbugs-submit-bounces@debbugs.gnu.org Mon Mar 02 16:56:42 2020 Received: (at 39862) by debbugs.gnu.org; 2 Mar 2020 21:56:42 +0000 Received: from localhost ([127.0.0.1]:38431 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8t3J-00032s-Ob for submit@debbugs.gnu.org; Mon, 02 Mar 2020 16:56:41 -0500 Received: from mout02.posteo.de ([185.67.36.66]:36813) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1j8t3H-00032b-D2 for 39862@debbugs.gnu.org; Mon, 02 Mar 2020 16:56:40 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id BD6102400FB for <39862@debbugs.gnu.org>; Mon, 2 Mar 2020 22:56:32 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1583186192; bh=NW18xNPFB3ZX37ZD3K9XsfngvWjnMXk8qMCuRT/ZGLw=; h=To:Cc:From:Autocrypt:Subject:Date:From; b=EH9dhdn+O1lHI3BI74enf+XinP0m+48+9uNxhnL/mk9r2BMnYII/dFgIFdQVV0zNt LruvOuSUsO3tSMwyF58e9qIthR1g9ZDclMGReAW68eKKHVH8oX/FgG8/KcWuS9KEsY 3aoLT01TOYTr/EI+aGz+64tx70hCsX0ZHDKugUPUod+Ioe2CdOBeyOXvqwXYnIvwCR Sh3HHox3X6uZtTCvMRXeswaxkwKdItr8p+gSVXlQgy2suCi7zwn5tJB8sKPphJRChl DzHDEGd02DSbZLeEU76s7BtF+7+eMH7BbESv7ps9xcN2Oj++SzYajl94eOiGiSwZOB svOD9pIs+3tPg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48WYrH6Rcpz9rxQ; Mon, 2 Mar 2020 22:56:31 +0100 (CET) To: zimoun References: <20200301194914.899011-1-felgru@posteo.net> From: Felix Gruber Autocrypt: addr=felgru@posteo.net; prefer-encrypt=mutual; keydata= mQINBE9iUX0BEAC+0aP2k4eLwP+2vLG6P7au1eSWgHSzbaqZqQvnM/m6RMS7ZMlTZ1R1/gRI THcwtBnweXlcVB8mLLK2B+79y6VlWio8ASDR9xsHAsSwCwuqxwwuXeWr4tZstNQn/W4aIU8S oqEjbmPvJg5vgIPKME8VUiPU/H6RA0pytcqNysZdq4aPYbutmERIkhk7JHyq6Pjw/ZRRnJfq M6vKLXEU2wU8QHbQlblRnJZum4YP+WGSjCoIJQOVf7tSboBaHQ8ZrOvwxqKps2ZlptBTT+lV SiImTHzdJSWOyc831wLm6wP+2aV+xW/72bhyHgLvGcSSWZyIZPkUy11da9YUok0F1Ud2fR5A CUuVPkbKATM5sL0ykLvrMdOVriwohQGcrdx0m78m/+An3482RJJY3DmpV8zQ+hNoDC1OEkxd S8FTAB+z+uNIvlcAlJ7VsP33bpaEYqPxA51wh54TcIv8vnenaLmiQu0vcXlbJ4Kyw8RKTiHz Nv/avnD0WnZ6P9swdHyeqIoVU722WcINauEimf6AjgBXTYA78PfHowfWIm4qIwerw2QgfcWL wa9UkbGqz3dI43ngQjoj4iNRDJWKYDMv7fhKuCBpkEs+s2iQ4HlFw2Z1z+QixDB+T+jEFubr 6gIv6nixTJpLFozMintsnPCrnMNqrRq1GkI2QVHsDgcOqCy5GQARAQABtCBGZWxpeCBHcnVi ZXIgPGZlbGdydUBwb3N0ZW8ubmV0PokCVAQTAQoAPhYhBHDQ118D0n1En3jkr0UxQWJCvvSc BQJaODuUAhsDBQkQqtq6BQsJCAcDBRUKCQgLBRYCAwEAAh4BAheAAAoJEEUxQWJCvvScplwQ AJtZTwl9ypLfCCvR0sZXJk2c9EHIf6h9iZ04nI0TY3SzAqbJ4lXGqHg2AwbcsaGsWpxFF+nC mZGy5EvL84W19Q274ek5M8cHutVJKamDcY3j9+c/Wjni/8PUVgizQ+iFRWi7Pwn96au+3a43 s9Vlj8cAgjgetP8rL7mS/Z5UoTHADNMfndwU/oQJXuHGeYU2vEVJvboa/oieSlcqxTuHR/Y6 2RcmR+4fVCf9+KER4Oijp2a5K60YHW4hstIUDcDu0ua9/ObnYsRAcWfMS+iIMTn7kL2mil7N OmQq4dWjVWd1P0KznlajvRSCymSBKILcJYyMEAPTO/vV+VWIs8eWyVWR2kG4Ab7+R4UR0Ld8 K2atVjxvWF+12nHx4PDOgph5+N0mad8PREbdrDuxbEcYbXCMUh23b8UfZkMhHec1bHMCNyI7 HFmyg4MWJqkPlRZ+EPUaQfGtFGT1YNZjupn1HTZkirf/xgHfRb2v6TMCBITVLNYcvoWr3ncF enO2iOjIFBXAsHn9R4912MYh2pIi/pOtpzwac1NZz0Naskz6bI3mBPf/wRMb9LhgnvU6gosS 6YDfIxez3CV9XNuprLaTKXPITTguXKfV3KUIUG5NY3tOIr54jlSk1TUPma0IFY/W2dheoVKX KqoAib/2Pj5Omj4hYnjvermPxQgzKhxwqrp+uQINBE9iVK0BEACkVFDYT1vyLCTmxS0Nyn8q NLQp2bXzk5s8afPIjQIQnszNini+HqPxt7F4KrcMJ0o9+KslCcTpyowEK2TZy55NqhdyFP4k ut5LfiFzBvfPiKmQqgw8Sx3hOvQ5YSEfgBq/S2jigJ3HyXQkJlXYLpua5PvRsgX7ijFrMTCU qhn67aoosBAEr2XtzOYiO1rghnTgSOicyKSsKDfc9c4TXAu2i95g8z69JCWVzMkaGUhOyR6S vdFYrhFoBokZQU3bPRQTvOvVycSKQtXZ3hmQkeOtCTdElt07EU7GoGiLAqy1+GyUE/sSY0m7 UwmedRh5og55el08bmvim4tScbsuzLei17O7N34+G8YvYJOICRx4PxujEzby23WFG8t1Ty12 7vwj3dcHhlPc7XoaEi/OLbpbekw6y3KLZxwm4fc/JKiqLsE2mpNWAKVQea9k5T3koQvOsVp4 /Q4VLJTScvSEjF3F9Brj1wtOpgJll1aFw+MJlq38lNYDWVsHWQLesyYu5XRT84qee+JPd6ze RcKmj0f32bqH368XmJeHG9YGJxQpN+yviBT/aJXXlz46BvybzKwryFkZil2vCIEFJvXxNiCL C28J3FzOcRzF2POiKyjWvFLFF6cjFPGxzSc1PQftRmQywfzMTDHf9Iq4r9seNoyinaNcHJff IsLxMAtP+5xv4wARAQABiQIlBBgBCgAPAhsMBQJYiF5BBQkQqteUAAoJEEUxQWJCvvSc548P /31Kt4VaSDznSI6AFgsypRCZLGyClaav5zvyfAj+IkTeXIWvZhu/CvviNtoTr7oAofiOH/S8 zgrHEkpElTW0xUk+/ldkH1vQPbp9GZM0UEbT8KOwxmaVtfcIpSTfocx8F0KlD52AwXXmZpxP 7ZBWIMnO3BprpdHERXG7jtv/alp7Hoz1Fcs2AhWwDE26CM6EX2EewyTtYKOLaHxE2sqnQI6X 2rkzpL+do0vAH4YL/VGDHB2NmqJ9j9vCXWYod9zOfNX89L2QRIyI0Wm0FrwOq1abbUzPbSfO pLXVZGv1J8NhMX0vU3WP3D6pop/zXmrxpWy8Mzn0/pPGnN57fCvQ1O3+HeXwdckVswbcp8WW evG3QhggRTFxAEcATHJGtVoLAZSe3eKaj8HFL0oGeL9U1pc8IqNniI4a0CVkzrWtMSKvKVhU 3W+XRM8blG+aPwxjINlEXydqAPjPgsUHJLYOj9w/i62AOBveDxK+6ZPwtXYpvl5ItnxF3/AF 8u5DqbvzbkOIrza+VKOS6UlChg+9ZIn6hYzRbfELs0fzwdEUVkqnoh9ZmZGCl+P85j6fEtri Bxz7OpLHv47YBwpMruyz2TGSMeHFWHBb7cQslO/CNgR2UfZOvJ3A07t19A4batct1/NwAIcn uN5G9pgdqPYXSd61FIXsZBy6CTES+oX/oueB Subject: Re: [bug#39862] [PATCH 0/4] update Dune finite element packages Message-ID: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> Date: Mon, 2 Mar 2020 22:56:20 +0100 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.5.0 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8 Content-Language: en-US Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: 39862@debbugs.gnu.org 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: -3.3 (---) Hi Simon, Thank you for your feedback. On 3/2/20 3:53 PM, zimoun wrote: > On Sun, 1 Mar 2020 at 21:07, Felix Gruber wrote: > >> BTW, some other packages exist in variants with and without OpenMPI, >> e.g. the dealii and dealii-openmpi packages. Do you think that it would >> be useful to provide similar variants for the dune-* packages, which >> could also be built without OpenMPI? > > As an end-user, I prefer regular packages 'dune-*' without the input > 'openmpi' and so with the related tests disabled and then their > variants; say 'dune-*-openmpi' with the input 'openmpi' correctly > setup-ed, as in your patch. Cool, I'll create an additional patch which splits all the dune packages in those two variants. Still struggling a bit with guile to replace all the dune-* packages with dune-*-openmpi in an inputs list without copy pasting the whole list and changing the packages manually. >> I've checked that all Dune packages still build after my changes (there >> don't seem to be any other packages that depend on the dune-* packages). >> Those builds were done using the updated suitesparse package that I've >> submitted in bug #39839. > > Usually, 'guix refresh -l' lists the packages that would need to be > rebuilt when upgrading a particular one. A `guix refresh -l dune-common` only gives me three other dune-* packages that would result in rebuilding 10 packages overall. Since dune-common is in the input of all the other dune-* packages, I think that tells me that there are no non-dune packages that depend on any dune-* package. Best, Felix From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 10 15:30:09 2020 Received: (at 39862) by debbugs.gnu.org; 10 Mar 2020 19:30:09 +0000 Received: from localhost ([127.0.0.1]:53357 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jBkZt-00028l-1J for submit@debbugs.gnu.org; Tue, 10 Mar 2020 15:30:09 -0400 Received: from mout02.posteo.de ([185.67.36.66]:56415) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jBkZq-00026o-Ii for 39862@debbugs.gnu.org; Tue, 10 Mar 2020 15:30:07 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id EEC22240100 for <39862@debbugs.gnu.org>; Tue, 10 Mar 2020 20:29:59 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1583868600; bh=QyCA56nfcQRtRAjhVma6DYYebJZtPTOtlIgyKHHZQ5o=; h=From:To:Cc:Subject:Date:From; b=hXUNFaYzY466b/3jom53rUmbntc6sMYRtmM1Ikt5hjCFrlQ8a1y+PVx7IntVe4Yh0 2a0zh75hWVZ4zOoBMS7wmtbS83A+pc3pleO0EpKwkv2+sj1Yr/KeszWtGjANT7reQU wHw4PZNdXmi1SNYAcAr2cg4EYIcPzqhDzkabZet94C8bdtDOnG8anxqj1hqdWHR3No GgQIN79JYOZesg6uOe3GEm4cg1cLl+4rfEKrhbCpj/rD3Rc8fw5njNfAsG3UA6IP5O TcrdwkNsuG/pTCGNlwhzBHhQEMu6p+tAZMHlmzh+5qB0i6mNNBfD9rMi1iLSi1DGI/ yrcF4YXURy7Hw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48cQCV5rKHz9ryV; Tue, 10 Mar 2020 20:29:58 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH v2 0/6] Update Dune finite element packages Date: Tue, 10 Mar 2020 20:29:04 +0100 Message-Id: <20200310192910.6251-1-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> References: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber , zimoun 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: -3.3 (---) The first four patches in this patch set are identical to v1. I've added two new patches that remove the openmpi dependency from all dune-* packages and add new dedicated dune-*-openmpi packages instead. To create these openmpi variants of the dune-* packages without a lot of duplication, I've added a helper function add-openmpi-to-dune-package that takes a dune-* package and returns its openmpi variant with the correct dependencies and the setup code necessary to make Dune's tests work with openmpi. Felix Gruber (6): gnu: dune-*: set up MPI for tests gnu: add dune-uggrid 2.6.0 gnu: Add dune-subgrid gnu: dune-istl: Build with suitesparse gnu: dune-*: remove openmpi dependency gnu: define dune-*-openmpi packages gnu/packages/maths.scm | 285 +++++++++++++++++++++++++---------------- 1 file changed, 172 insertions(+), 113 deletions(-) -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 10 15:30:19 2020 Received: (at 39862) by debbugs.gnu.org; 10 Mar 2020 19:30:19 +0000 Received: from localhost ([127.0.0.1]:53360 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jBka2-000298-HA for submit@debbugs.gnu.org; Tue, 10 Mar 2020 15:30:19 -0400 Received: from mout02.posteo.de ([185.67.36.66]:60855) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jBka1-00028x-7H for 39862@debbugs.gnu.org; Tue, 10 Mar 2020 15:30:17 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id 9928B2400FD for <39862@debbugs.gnu.org>; Tue, 10 Mar 2020 20:30:11 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1583868611; bh=lEZVJzoMGbHB6OPD2F5s8Zng9RpXmdjwtzygz/X3FDU=; h=From:To:Cc:Subject:Date:From; b=PNyjPAB54Vv/x98EKBVWia1S7/EWk9lm149nf2HT+BBmz4KcGGWubY94GOs0KQSwe /oMKseY1LTCV/j2eckio3Z6qs6ehNXmRLh7VU+9iKbU0lSPtJxL+D9RBVzejP6X4Rf YFN5M1owPMSMkmbaSrP79nfyPtNjbYwZi8kwjcGj/HXeZ+Ut1M1OkC3Q7yZjJy9ihK SnqtpNDCJFojIMc7FcJm4kU7fMzxfxutdyEZt4z2r12e8vEdQLbrZwg0hv6tBd24qb D+odueW+lE5ZcNzmprI278cxjGDytPRTRPkzJHixxwVvXiGGN9YAwMKvTSiChT0GAs qKrQfKXjsX1dg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48cQCk6TMsz9ryr; Tue, 10 Mar 2020 20:30:10 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH v2 1/6] gnu: dune-*: set up MPI for tests Date: Tue, 10 Mar 2020 20:29:05 +0100 Message-Id: <20200310192910.6251-2-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> References: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber , zimoun 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: -3.3 (---) * gnu/packages/maths.scm (dune-common, dune-grid, dune-istl, dune-alugrid): [arguments]: correctly set up MPI instead of disabling tests that require MPI. --- gnu/packages/maths.scm | 110 ++++------------------------------------- 1 file changed, 10 insertions(+), 100 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index a990ffc45e..bec490ebc3 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4583,36 +4583,8 @@ linear algebra primitives specifically targeting graph analytics.") (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "build_tests" make-flags))) - ;; These tests fail because they require a fully functional MPI - ;; environment. - (add-after 'unpack 'disable-failing-tests - (lambda _ - (setenv "ARGS" - (string-append "--exclude-regex '(" - (string-join - (list - "remoteindicestest" - "remoteindicestest-mpi-2" - "syncertest" - "syncertest-mpi-2" - "variablesizecommunicatortest" - "variablesizecommunicatortest-mpi-2" - "arithmetictestsuitetest" - "assertandreturntest" - "assertandreturntest_ndebug" - "concept" - "debugaligntest" - "mpicollectivecommunication" - "mpicollectivecommunication-mpi-2" - "mpiguardtest" - "mpiguardtest-mpi-2" - "mpihelpertest" - "mpihelpertest-mpi-2" - "mpihelpertest2" - "mpihelpertest2-mpi-2") - "|") - ")'")) - #t))))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("gmp" ,gmp) ("metis" ,metis) @@ -4693,54 +4665,8 @@ This package contains the basic DUNE geometry classes.") (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "build_tests" make-flags))) - ;; These tests fail because they require a fully functional MPI - ;; environment. - (add-after 'unpack 'disable-failing-tests - (lambda _ - (setenv "ARGS" - (string-append "--exclude-regex '(" - (string-join - (list - "scsgmappertest" - "conformvolumevtktest" - "gnuplottest" - "nonconformboundaryvtktest" - "subsamplingvtktest" - "vtktest" - "vtktest-mpi-2" - "vtksequencetest" - "gmshtest-onedgrid" - "test-dgf-yasp" - "test-dgf-yasp-offset" - "test-dgf-oned" - "test-geogrid-yaspgrid" - "test-gridinfo" - "test-identitygrid" - "testiteratorranges" - "test-hierarchicsearch" - "test-parallel-ug-mpi-2" - "test-yaspgrid-backuprestore-equidistant" - "test-yaspgrid-backuprestore-equidistant-mpi-2" - "test-yaspgrid-backuprestore-equidistantoffset" - "test-yaspgrid-backuprestore-equidistantoffset-mpi-2" - "test-yaspgrid-backuprestore-tensor" - "test-yaspgrid-backuprestore-tensor-mpi-2" - "test-yaspgrid-tensorgridfactory" - "test-yaspgrid-tensorgridfactory-mpi-2" - "test-yaspgrid-yaspfactory-1d" - "test-yaspgrid-yaspfactory-1d-mpi-2" - "test-yaspgrid-yaspfactory-2d" - "test-yaspgrid-yaspfactory-2d-mpi-2" - "test-yaspgrid-yaspfactory-3d" - "test-yaspgrid-yaspfactory-3d-mpi-2" - "globalindexsettest" - "persistentcontainertest" - "structuredgridfactorytest" - "tensorgridfactorytest" - "vertexordertest") - "|") - ")'")) - #t))))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) @@ -4783,24 +4709,8 @@ This package contains the basic DUNE grid classes.") (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "build_tests" make-flags))) - ;; These tests fail because they require a fully functional MPI - ;; environment. - (add-after 'unpack 'disable-failing-tests - (lambda _ - (setenv "ARGS" - (string-append "--exclude-regex '(" - (string-join - (list - "galerkintest" - "hierarchytest" - "pamgtest" - "pamg_comm_repart_test" - "matrixredisttest" - "vectorcommtest" - "matrixmarkettest") - "|") - ")'")) - #t))))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("dune-common" ,dune-common) ("openmpi" ,openmpi) @@ -4886,9 +4796,7 @@ assemble global function spaces on finite-element grids.") "1l9adgyjpra8mvwm445s0lpjshnb63jag85fb2hisbjn6bm320yj")))) (build-system cmake-build-system) (arguments - `(#:tests? #f ; 7 of 8 tests fail because they need a full MPI - ; environment - #:phases + `(#:phases (modify-phases %standard-phases (add-after 'unpack 'patch-include (lambda _ @@ -4900,7 +4808,9 @@ assemble global function spaces on finite-element grids.") (lambda* (#:key inputs make-flags #:allow-other-keys) (setenv "CPLUS_INCLUDE_PATH" (string-append (assoc-ref inputs "dune-grid") "/share")) - (apply invoke "make" "build_tests" make-flags)))))) + (apply invoke "make" "build_tests" make-flags))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 10 15:30:30 2020 Received: (at 39862) by debbugs.gnu.org; 10 Mar 2020 19:30:30 +0000 Received: from localhost ([127.0.0.1]:53363 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jBkaE-00029X-5f for submit@debbugs.gnu.org; Tue, 10 Mar 2020 15:30:30 -0400 Received: from mout02.posteo.de ([185.67.36.66]:49289) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jBkaC-00029K-HD for 39862@debbugs.gnu.org; Tue, 10 Mar 2020 15:30:29 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id 8D9732400E6 for <39862@debbugs.gnu.org>; Tue, 10 Mar 2020 20:30:22 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1583868622; bh=KGuWjYlZMiEPh5TYgwoMeKutnWGkSYo2m50DyTPtKpo=; h=From:To:Cc:Subject:Date:From; b=mElMm3jKzoGOoj1i9AQwxEqCmOfkCD1Qw+S8xYqkrTKqCGcr2qLL4QxKB5fE05VAe c16D4Daiuu4z340AyRuxgcPXhrwXYbqFgg142piD0KRLUbHjXyL2T79bosF+YGFAXT 2BtP3xnykl4vbw08UTjQUW+ASTFLZkYZB+B9JwDXcQ8Qn1Mtn2+GTh19jw2JkFVSYB Vafc11D78IKVVLQhR7f64mHgAtLD/vIkV8lJphDKq1xLzTO6Cx2n2G21ZFuAsnGkKu 1wLQIbQpb4GWWr8yr9uk+NgiRhBsm7h3VSYd4CRIEYkFzzkNjNnX1sW47glA34chVs vAkUrjbw3v81g== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48cQCy0ZS6z9ryl; Tue, 10 Mar 2020 20:30:22 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH v2 2/6] gnu: add dune-uggrid 2.6.0 Date: Tue, 10 Mar 2020 20:29:06 +0100 Message-Id: <20200310192910.6251-3-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> References: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber , zimoun 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: -3.3 (---) * gnu/packages/maths.scm (dune-uggrid): New variable. * gnu/packages/maths.scm (dune-grid): [propagated-inputs]: Add dune-uggrid dependency, so that the UGGrid class in dune-grid can be used by packages that have dune-grid as input. * gnu/packages/maths.scm (dune-functions): [arguments]: enable tests that previously weren't built as they require dune-uggrid. --- gnu/packages/maths.scm | 53 +++++++++++++++++++++++++++++++++++++++++- 1 file changed, 52 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index bec490ebc3..3f89efeff4 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4646,6 +4646,42 @@ This package contains the basic DUNE geometry classes.") ;; GPL version 2 with "runtime exception" (license license:gpl2))) +(define-public dune-uggrid + (package + (name "dune-uggrid") + (version "2.6.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://dune-project.org/download/" + version "/dune-uggrid-" version ".tar.gz")) + (sha256 + (base32 + "05l7a1gb78mny49anyxk6rjvn66rhgm30y72v5cjg0m5kfgr1a1f")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags)))))) + (inputs + `(("dune-common" ,dune-common) + ("openmpi" ,openmpi))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "https://dune-project.org/") + (synopsis "Distributed and Unified Numerics Environment") + (description "DUNE, the Distributed and Unified Numerics Environment is a +modular toolbox for solving @dfn{partial differential equations} (PDEs) with +grid-based methods. It supports the easy implementation of methods like +@dfn{Finite Elements} (FE), @dfn{Finite Volumes} (FV), and also @dfn{Finite +Differences} (FD). + +This package contains the DUNE UG grid classes.") + (license license:lgpl2.1))) + (define-public dune-grid (package (name "dune-grid") @@ -4675,6 +4711,8 @@ This package contains the basic DUNE geometry classes.") ("openblas" ,openblas) ("openmpi" ,openmpi) ("python" ,python))) + (propagated-inputs + `(("dune-uggrid" ,dune-uggrid))) (native-inputs `(("gfortran" ,gfortran) ("pkg-config" ,pkg-config))) @@ -4888,7 +4926,20 @@ operating on statically typed trees of objects.") (base32 "1an8gb477n8j0kzpbrv7nr1snh8pxip0gsxq6w63jc83gg3dj200")))) (build-system cmake-build-system) - (arguments `(#:tests? #f)) ; FIXME: tests require dune-uugrid + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-failing-tests + (lambda _ + (setenv "ARGS" + ;; unable to load GMSH file in this test + "--exclude-regex gridviewfunctionspacebasistest") + #t)) + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) (inputs `(("dune-common" ,dune-common) ("dune-istl" ,dune-istl) -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 10 15:30:44 2020 Received: (at 39862) by debbugs.gnu.org; 10 Mar 2020 19:30:44 +0000 Received: from localhost ([127.0.0.1]:53366 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jBkaS-00029x-IR for submit@debbugs.gnu.org; Tue, 10 Mar 2020 15:30:44 -0400 Received: from mout01.posteo.de ([185.67.36.65]:43563) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jBkaR-00029l-03 for 39862@debbugs.gnu.org; Tue, 10 Mar 2020 15:30:43 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 7DE02160060 for <39862@debbugs.gnu.org>; Tue, 10 Mar 2020 20:30:36 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1583868636; bh=UpD2twPOjpTQkhPrcq4UMu7pjhU7pWUnn54qWM7J8OM=; h=From:To:Cc:Subject:Date:From; b=m8X72WLz+a1Ui5DISq4gyXABGgsF0O8fs36w6Y2z+XE+3Qxrx/ZFz8B2DoB+2FfIx 38YZrtvb8dd3o25t4syX+DNmwypFYA1YXhBkFTgB8jaBKJMHlkpIfpWNf6MMeui60p 0K2Mt1lOAnPzi+ozEyN8Bcs3W8tGYxeAhYhoiFkZmcKE71b0lx43JkSFfSQegVwzas /s5OYMvGXrc8EdA/n4ZS0BMmfJbp4MBZMms/4NIxN3V/d4Fy9yXXARDnmpHd7dYC0+ soIjI/pFwfADzPllPdIAa5/QWO8TjVSbFZMcHPCNphohpb1dEpNBv2cxv1uD68BO0J l9HimBUsc11pw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48cQDC3gX3z6tmf; Tue, 10 Mar 2020 20:30:35 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH v2 3/6] gnu: Add dune-subgrid Date: Tue, 10 Mar 2020 20:29:07 +0100 Message-Id: <20200310192910.6251-4-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> References: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber , zimoun 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: -3.3 (---) * gnu/packages/maths.scm (dune-subgrid): New variable. --- gnu/packages/maths.scm | 43 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 3f89efeff4..9da38aad68 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4871,6 +4871,49 @@ implementation of the DUNE grid interface supporting either simplices or cubes.") (license license:gpl2+))) +(define-public dune-subgrid + (package + (name "dune-subgrid") + (version "2.6.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.imp.fu-berlin.de/agnumpde/dune-subgrid") + (commit "releases/2.6-1"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1gcv35rx3knqd54r4pp9rzd639db4j8w2r2ibq43w1mgwdcqhs64")))) + (build-system cmake-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'build 'build-tests + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "build_tests" make-flags))) + (add-before 'check 'mpi-setup + ,%openmpi-setup)))) + (inputs + `(("dune-common" ,dune-common) + ("dune-geometry" ,dune-geometry) + ("dune-grid" ,dune-grid) + ("openmpi" ,openmpi) + ;; Optional + ("metis" ,metis) + ("openblas" ,openblas) + ("gmp" ,gmp))) + (native-inputs + `(("gfortran" ,gfortran) + ("pkg-config" ,pkg-config))) + (home-page "http://numerik.mi.fu-berlin.de/dune-subgrid/index.php") + (synopsis "Distributed and Unified Numerics Environment") + (description "The dune-subgrid module allows to mark elements of +another hierarchical dune grid. The set of marked elements can then be +accessed as a hierarchical dune grid in its own right. Dune-Subgrid +provides the full grid interface including adaptive mesh refinement.") + (license license:gpl2+))) + (define-public dune-typetree (package (name "dune-typetree") -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 10 15:30:53 2020 Received: (at 39862) by debbugs.gnu.org; 10 Mar 2020 19:30:53 +0000 Received: from localhost ([127.0.0.1]:53369 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jBkaa-0002AJ-SN for submit@debbugs.gnu.org; Tue, 10 Mar 2020 15:30:53 -0400 Received: from mout02.posteo.de ([185.67.36.66]:52873) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jBkaZ-0002A7-9T for 39862@debbugs.gnu.org; Tue, 10 Mar 2020 15:30:51 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id 9A1B12400FE for <39862@debbugs.gnu.org>; Tue, 10 Mar 2020 20:30:45 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1583868645; bh=+wuCeJn+SsWOpm3vuSoEUvjz8Z+C1ypQOQDyDZ6kgb4=; h=From:To:Cc:Subject:Date:From; b=HtyBMtVZPn0P0d8R4ZQOv68hTuOT4vqAxHc3uFg0HqtaGgojvpWcE8pvSi8kj76Ez pvIZmEL6EiQYwGZ0XvkLLLFBRpTW+WaspCniz8iBwIjy9LaDhHWt65GNgONeOtTB3+ JDdfCuJnoKpPMaKWVIsWErlimLlUwQ4OlaHCG7L71fjTxCy6pV8FFt1r3iRe4jEAfK vlIvPhnCRsNCtEgY4OmaSNwQhFRk748oFg2ekVTYGiWj02nhbqVsJ6j6KY11wwXlkf X0Rwua8V83lDVmWFRDEt5LXDzrJ7xWF7HiBFLwADMnMg+QUuNRRcJ6gXmeHh6yFq6c AQVkQo1lmmRvw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48cQDP04c5z9ryd; Tue, 10 Mar 2020 20:30:44 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH v2 4/6] gnu: dune-istl: Build with suitesparse Date: Tue, 10 Mar 2020 20:29:08 +0100 Message-Id: <20200310192910.6251-5-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> References: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber , zimoun 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: -3.3 (---) * gnu/packages/maths.scm (dune-istl)[inputs]: Add suitesparse to build additional solvers in dune-istl. --- gnu/packages/maths.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 9da38aad68..2c03c00366 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4754,6 +4754,7 @@ This package contains the basic DUNE grid classes.") ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) + ("suitesparse" ,suitesparse) ("superlu" ,superlu) ("openblas" ,openblas) ("gmp" ,gmp) -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 10 15:31:04 2020 Received: (at 39862) by debbugs.gnu.org; 10 Mar 2020 19:31:04 +0000 Received: from localhost ([127.0.0.1]:53376 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jBkam-0002BG-2l for submit@debbugs.gnu.org; Tue, 10 Mar 2020 15:31:04 -0400 Received: from mout02.posteo.de ([185.67.36.66]:33337) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jBkak-0002AT-HO for 39862@debbugs.gnu.org; Tue, 10 Mar 2020 15:31:03 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id E60892400FC for <39862@debbugs.gnu.org>; Tue, 10 Mar 2020 20:30:55 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1583868655; bh=3GZPygSugnAL59H8UxmBcWmKxIHJ2dwJSg2tt+w2i9g=; h=From:To:Cc:Subject:Date:From; b=JLtyJJqnbi6oS5nis0svLlqK8YUcJ4tu8zD+n8hEp3F1ORutNHHEPDcEbL2GeiLST tSwVlZyBEdL082AEony3wmvx2X8VTnY/7K4TVpzKF8dPPG3qFSFHi1UYIMe7fl++58 IK1pS3dEesJazz+9IJgBu3rCS0GHym+7FsBAhTOsjuTi1UhKaRA4N2PVdhunnKe65E f5UcQNqYL/InMnfv/mDHrEKrcz5ZdnXv2LV5csf7ATVYpqpOeALyCX99cX1aRJ/m8Y iHwea5uCbNwgkHQWaxASh5BcUx/4yYjShwEDCHCS22QxB+3ctNsg8niqwdMEP63GtY 9Swq2B79udf0w== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48cQDb2ppmz9ryl; Tue, 10 Mar 2020 20:30:55 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH v2 5/6] gnu: dune-*: remove openmpi dependency Date: Tue, 10 Mar 2020 20:29:09 +0100 Message-Id: <20200310192910.6251-6-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> References: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber , zimoun 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: -3.3 (---) * gnu/packages/maths.scm (dune-*)[inputs]: Remove openmpi dependency. [arguments]: remove code to setup openmpi for tests. --- gnu/packages/maths.scm | 37 +++++++------------------------------ 1 file changed, 7 insertions(+), 30 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 2c03c00366..33a5efd2f0 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4582,13 +4582,10 @@ linear algebra primitives specifically targeting graph analytics.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("gmp" ,gmp) ("metis" ,metis) - ("openmpi" ,openmpi) ("openblas" ,openblas) ("python" ,python) ("superlu" ,superlu))) @@ -4626,7 +4623,6 @@ Differences} (FD).") (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) - ("openmpi" ,openmpi) ;; Optional ("openblas" ,openblas) ("gmp" ,gmp) @@ -4666,8 +4662,7 @@ This package contains the basic DUNE geometry classes.") (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "build_tests" make-flags)))))) (inputs - `(("dune-common" ,dune-common) - ("openmpi" ,openmpi))) + `(("dune-common" ,dune-common))) (native-inputs `(("gfortran" ,gfortran) ("pkg-config" ,pkg-config))) @@ -4700,16 +4695,13 @@ This package contains the DUNE UG grid classes.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) ("gmp" ,gmp) ("metis" ,metis) ("openblas" ,openblas) - ("openmpi" ,openmpi) ("python" ,python))) (propagated-inputs `(("dune-uggrid" ,dune-uggrid))) @@ -4746,12 +4738,9 @@ This package contains the basic DUNE grid classes.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("suitesparse" ,suitesparse) @@ -4799,7 +4788,6 @@ aggregation-based algebraic multigrid.") (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("superlu" ,superlu) @@ -4847,14 +4835,11 @@ assemble global function spaces on finite-element grids.") (lambda* (#:key inputs make-flags #:allow-other-keys) (setenv "CPLUS_INCLUDE_PATH" (string-append (assoc-ref inputs "dune-grid") "/share")) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) ("dune-grid" ,dune-grid) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("openblas" ,openblas) @@ -4892,14 +4877,11 @@ cubes.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) ("dune-grid" ,dune-grid) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("openblas" ,openblas) @@ -4938,7 +4920,6 @@ provides the full grid interface including adaptive mesh refinement.") (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) - ("openmpi" ,openmpi) ;; Optional ("openblas" ,openblas) ("python" ,python) @@ -4981,9 +4962,7 @@ operating on statically typed trees of objects.") #t)) (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-istl" ,dune-istl) @@ -4991,7 +4970,6 @@ operating on statically typed trees of objects.") ("dune-grid" ,dune-grid) ("dune-geometry" ,dune-geometry) ("dune-typetree" ,dune-typetree) - ("openmpi" ,openmpi) ("openblas" ,openblas) ("metis" ,metis) ("python" ,python) @@ -5032,7 +5010,6 @@ implemented as callable objects, and bases of finite element spaces.") ("dune-grid" ,dune-grid) ("dune-typetree" ,dune-typetree) ("dune-functions" ,dune-functions) - ("openmpi" ,openmpi) ;; Optional ("openblas" ,openblas) ("eigen" ,eigen) -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Tue Mar 10 15:31:19 2020 Received: (at 39862) by debbugs.gnu.org; 10 Mar 2020 19:31:20 +0000 Received: from localhost ([127.0.0.1]:53380 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jBkb1-0002Bz-Iv for submit@debbugs.gnu.org; Tue, 10 Mar 2020 15:31:19 -0400 Received: from mout02.posteo.de ([185.67.36.66]:51609) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jBkaz-0002Bm-6I for 39862@debbugs.gnu.org; Tue, 10 Mar 2020 15:31:17 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id 8DDB62400FE for <39862@debbugs.gnu.org>; Tue, 10 Mar 2020 20:31:11 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1583868671; bh=Ed+qNDa3Qvub2ohKgPuQYcgVumLet4qM95oAhr4yKuc=; h=From:To:Cc:Subject:Date:From; b=a+3zuGMshQSdgU7kPzA23VE2vWnc2uj+hhMS292TS1Uwk8F2Pst93ZLz1Oag055NK z00QMm9wc4yZ9tbvdoXBQ4fV0k5NFSJ07AYNVnWjAyA7M3Z3VCp5t8bWywWntbY+JN J9+4XVZ6L3Rgu5eaZ1xnFDX/LgtIYCBIKStv8mMZd1tV9lb5VpMg6/ea0r0WidogkQ z7oICM9+gGko0xgGjNeLlQu+07+VptkA3iL3iLDhurwy0NRiWUacbJXfpNaZ8pFSem HmGFME087rM2SjhsFK2CaISQXRC1S5XWr4LFvsa6WYQmI9pIQcBJHQyg7l1uw8Z7se /ZyEGWZGnPEmQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48cQDt0mYgz9ryd; Tue, 10 Mar 2020 20:31:10 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH v2 6/6] gnu: define dune-*-openmpi packages Date: Tue, 10 Mar 2020 20:29:10 +0100 Message-Id: <20200310192910.6251-7-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> References: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber , zimoun 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: -3.3 (---) * gnu/packages/maths.scm (dune-*-openmpi): New variables. * gnu/packages/maths.scm (add-openmpi-to-dune-package): New function to add openmpi to the inputs of a dune-* package and replace all dune-* packages in its input with the corresponding dune-*-openmpi package. --- gnu/packages/maths.scm | 79 +++++++++++++++++++++++++++++++++++++++++- 1 file changed, 78 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 33a5efd2f0..e904ca1bd8 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -126,7 +126,9 @@ #:use-module (gnu packages version-control) #:use-module (gnu packages wxwidgets) #:use-module (gnu packages xml) - #:use-module (srfi srfi-1)) + #:use-module (srfi srfi-1) + #:use-module (srfi srfi-34) + #:use-module (srfi srfi-35)) (define-public aris (package @@ -5027,6 +5029,81 @@ built on top of DUNE, the Distributed and Unified Numerics Environment.") ;; Either GPL version 2 with "runtime exception" or LGPLv3+. (license (list license:lgpl3+ license:gpl2)))) +(define add-openmpi-to-dune-package + (let ((transformed-packages '())) + (lambda (p) + (let* ((p-name (package-name p)) + (replace-package + (lambda (mapping) + (let* ((name (car mapping)) + (p (cadr mapping)) + (new-p + (match (assoc-ref transformed-packages name) + (#f + (if (string-prefix? "dune-" name) + (raise (condition + (&message + (message + (format #f "Need to call \ +add-openmpi-to-dune-package on '~a' before '~a'." + name p-name))))) + p)) + (transformed-p transformed-p)))) + `(,name ,new-p)))) + (substitute-mpi-packages (lambda (inputs) + (map replace-package inputs))) + (mpi-p + (package (inherit p) + (name (string-append p-name "-openmpi")) + (inputs `(,@(substitute-mpi-packages (package-inputs p)) + ("openmpi" ,openmpi))) + (propagated-inputs + (substitute-mpi-packages (package-propagated-inputs p))) + (arguments + (substitute-keyword-arguments (package-arguments p) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + (add-before 'check 'mpi-setup + ,%openmpi-setup))))) + (synopsis (string-append (package-synopsis p) " (with MPI support)"))))) + (begin + (set! transformed-packages + (acons p-name mpi-p transformed-packages)) + mpi-p))))) + +(define-public dune-common-openmpi + (add-openmpi-to-dune-package dune-common)) + +(define-public dune-geometry-openmpi + (add-openmpi-to-dune-package dune-geometry)) + +(define-public dune-istl-openmpi + (add-openmpi-to-dune-package dune-istl)) + +(define-public dune-typetree-openmpi + (add-openmpi-to-dune-package dune-typetree)) + +(define-public dune-uggrid-openmpi + (add-openmpi-to-dune-package dune-uggrid)) + +(define-public dune-grid-openmpi + (add-openmpi-to-dune-package dune-grid)) + +(define-public dune-alugrid-openmpi + (add-openmpi-to-dune-package dune-alugrid)) + +(define-public dune-subgrid-openmpi + (add-openmpi-to-dune-package dune-subgrid)) + +(define-public dune-localfunctions-openmpi + (add-openmpi-to-dune-package dune-localfunctions)) + +(define-public dune-functions-openmpi + (add-openmpi-to-dune-package dune-functions)) + +(define-public dune-pdelab-openmpi + (add-openmpi-to-dune-package dune-pdelab)) + (define-public mlucas (package (name "mlucas") -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 12 06:46:19 2020 Received: (at 39862) by debbugs.gnu.org; 12 Mar 2020 10:46:19 +0000 Received: from localhost ([127.0.0.1]:56019 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCLM2-0004H5-N9 for submit@debbugs.gnu.org; Thu, 12 Mar 2020 06:46:19 -0400 Received: from eggs.gnu.org ([209.51.188.92]:55674) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCLM0-0004Gk-Mz for 39862@debbugs.gnu.org; Thu, 12 Mar 2020 06:46:17 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:53187) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1jCLLv-0002CT-Gj; Thu, 12 Mar 2020 06:46:11 -0400 Received: from [2001:660:6102:320:e120:2c8f:8909:cdfe] (port=49060 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jCLLv-0008JD-0o; Thu, 12 Mar 2020 06:46:11 -0400 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Felix Gruber Subject: Re: [bug#39862] [PATCH v2 0/6] Update Dune finite element packages References: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> <20200310192910.6251-1-felgru@posteo.net> Date: Thu, 12 Mar 2020 11:46:08 +0100 In-Reply-To: <20200310192910.6251-1-felgru@posteo.net> (Felix Gruber's message of "Tue, 10 Mar 2020 20:29:04 +0100") Message-ID: <87v9n9vojz.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 39862 Cc: zimoun , 39862@debbugs.gnu.org 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: -1.7 (-) Hi Felix, Felix Gruber skribis: > The first four patches in this patch set are identical to v1. I've added > two new patches that remove the openmpi dependency from all dune-* > packages and add new dedicated dune-*-openmpi packages instead. > To create these openmpi variants of the dune-* packages without a lot of > duplication, I've added a helper function add-openmpi-to-dune-package > that takes a dune-* package and returns its openmpi variant with the > correct dependencies and the setup code necessary to make Dune's tests > work with openmpi. > > Felix Gruber (6): > gnu: dune-*: set up MPI for tests > gnu: add dune-uggrid 2.6.0 > gnu: Add dune-subgrid > gnu: dune-istl: Build with suitesparse I applied all these. > gnu: dune-*: remove openmpi dependency > gnu: define dune-*-openmpi packages I=E2=80=99ll comment on these separately. Thank you! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 12 08:42:47 2020 Received: (at 39862) by debbugs.gnu.org; 12 Mar 2020 12:42:48 +0000 Received: from localhost ([127.0.0.1]:56138 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCNAl-0001E7-IP for submit@debbugs.gnu.org; Thu, 12 Mar 2020 08:42:47 -0400 Received: from eggs.gnu.org ([209.51.188.92]:57235) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCNAj-0001Dr-UW for 39862@debbugs.gnu.org; Thu, 12 Mar 2020 08:42:46 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:55171) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1jCNAe-0007fy-Oi; Thu, 12 Mar 2020 08:42:40 -0400 Received: from [2001:660:6102:320:e120:2c8f:8909:cdfe] (port=49168 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jCNAe-0001QX-9u; Thu, 12 Mar 2020 08:42:40 -0400 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Felix Gruber Subject: Re: [bug#39862] [PATCH v2 6/6] gnu: define dune-*-openmpi packages References: <5e890189-d5f7-a646-fe37-1f93115d17f9@posteo.net> <20200310192910.6251-7-felgru@posteo.net> Date: Thu, 12 Mar 2020 13:42:37 +0100 In-Reply-To: <20200310192910.6251-7-felgru@posteo.net> (Felix Gruber's message of "Tue, 10 Mar 2020 20:29:10 +0100") Message-ID: <87k13pvj5u.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 39862 Cc: zimoun , 39862@debbugs.gnu.org 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: -1.7 (-) Hi again, Felix Gruber skribis: > +(define add-openmpi-to-dune-package > + (let ((transformed-packages '())) > + (lambda (p) > + (let* ((p-name (package-name p)) > + (replace-package > + (lambda (mapping) > + (let* ((name (car mapping)) > + (p (cadr mapping)) > + (new-p > + (match (assoc-ref transformed-packages name) > + (#f > + (if (string-prefix? "dune-" name) > + (raise (condition > + (&message > + (message > + (format #f "Need to call \ > +add-openmpi-to-dune-package on '~a' before '~a'." > + name p-name))))) > + p)) > + (transformed-p transformed-p)))) > + `(,name ,new-p)))) > + (substitute-mpi-packages (lambda (inputs) > + (map replace-package inputs))) > + (mpi-p > + (package (inherit p) > + (name (string-append p-name "-openmpi")) > + (inputs `(,@(substitute-mpi-packages (package-inputs p)) > + ("openmpi" ,openmpi))) > + (propagated-inputs > + (substitute-mpi-packages (package-propagated-inputs p))) > + (arguments > + (substitute-keyword-arguments (package-arguments p) > + ((#:phases phases '%standard-phases) > + `(modify-phases ,phases > + (add-before 'check 'mpi-setup > + ,%openmpi-setup))))) > + (synopsis (string-append (package-synopsis p) " (with MPI= support)"))))) > + (begin > + (set! transformed-packages > + (acons p-name mpi-p transformed-packages)) > + mpi-p))))) I think it=E2=80=99s a good idea to add those =E2=80=9C-openmpi=E2=80=9D pa= ckages. However, I have suggestions regarding the code above. :-) A general note: set!, car, cdr, etc. are frowned upon in Guix: https://guix.gnu.org/manual/en/html_node/Coding-Style.html It seems to me that =E2=80=98replace-package=E2=80=99 above is overly gener= ic: since it=E2=80=99s an internal procedure, we don=E2=80=99t need to add error case= s, messages, etc. Last, could it be written in terms of =E2=80=98package-mapping=E2=80=99? T= hat takes care of graph traversal and memoization. Thanks, Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 12 17:05:49 2020 Received: (at 39862) by debbugs.gnu.org; 12 Mar 2020 21:05:49 +0000 Received: from localhost ([127.0.0.1]:57875 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCV1Z-0002Zc-35 for submit@debbugs.gnu.org; Thu, 12 Mar 2020 17:05:49 -0400 Received: from mout02.posteo.de ([185.67.36.66]:59933) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCV1X-0002ZP-Ao for 39862@debbugs.gnu.org; Thu, 12 Mar 2020 17:05:48 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id 736572400FE for <39862@debbugs.gnu.org>; Thu, 12 Mar 2020 22:05:41 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1584047141; bh=8iROR+7sMKKRQOc5Fkq6uHnN8rio6LlK3hwSQGKI814=; h=From:To:Cc:Subject:Date:From; b=KtzK1ZelOoYAg0pG+ybUKD6Ln/mMt2N1PXI+rjIgqkdSepWFkJgFzeqiEPoZZ66CZ T9WgK3yVlAUyzkJMQ5hpWFyU0drq1j7nsCV3UvKVcXaeabgTGjGfvWX1V7rmMF3xM8 ZciNl4f45e2wu9iifVLX4uK96KV6oBwg72oNdvFTyc0AAnlRm/4+pBjWO6iWLySBdT BXBtG1HxBQkdqBIj7tRt5Mbkt0lWt0EfLcNvPws0kvTnt76wjXOuhTzKeNbhItGOKR C4CkJk50bISxIO31Snc/bGhYHLUe9TLfoSjNz2hGQRYg6OvzbIZrDumYXCyeQVHNQt iExWH/GPjChiw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48dhF04vvjz9rxY; Thu, 12 Mar 2020 22:05:40 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH v3 0/2] Add dune-*-openmpi packages Date: Thu, 12 Mar 2020 22:05:11 +0100 Message-Id: <20200312210513.107891-1-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <87k13pvj5u.fsf@gnu.org> References: <87k13pvj5u.fsf@gnu.org> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber , =?UTF-8?q?Ludovic=20Court=C3=A8s?= 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: -3.3 (---) Hi Ludo’, thanks for your suggestions regarding the creation of the dune-*-openmpi packages. I've rewritten the add-openmpi-to-dune-package in terms of package-mapping as you suggested. You'll find the modified version of my last two patches in the following two emails. Many thanks, Felix Felix Gruber (2): gnu: dune-*: remove openmpi dependency gnu: define dune-*-openmpi packages gnu/packages/maths.scm | 90 ++++++++++++++++++++++++++++-------------- 1 file changed, 60 insertions(+), 30 deletions(-) -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 12 17:05:54 2020 Received: (at 39862) by debbugs.gnu.org; 12 Mar 2020 21:05:54 +0000 Received: from localhost ([127.0.0.1]:57878 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCV1e-0002Zu-9L for submit@debbugs.gnu.org; Thu, 12 Mar 2020 17:05:54 -0400 Received: from mout02.posteo.de ([185.67.36.66]:52567) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCV1c-0002ZV-Os for 39862@debbugs.gnu.org; Thu, 12 Mar 2020 17:05:53 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id 33E4D240100 for <39862@debbugs.gnu.org>; Thu, 12 Mar 2020 22:05:47 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1584047147; bh=3GZPygSugnAL59H8UxmBcWmKxIHJ2dwJSg2tt+w2i9g=; h=From:To:Cc:Subject:Date:From; b=k5AYZsGaVvrVg4rRmTLmS1g3HUeJVDJKoS/GQufaPf9AG87Jchah/AQNCLJyzIwar RYfAkEZxx95YwpwKZw8sPnuUJnw+lCnYamEc12l1ksdTeCzzKHcx4fqqn5C2g2McnP FJoItioxnWq9moXE0T27zk9tkebQWgqP6I2YMqkk0LR83qRQkwS3liRGNreqss9goT xpoD1Ouph4bRLrzIABHSwGuLvvWKyKR+ex1dzlnU5uWN5RrAYwemuSgMB4vTmo+p/9 sYluVCd75+E/17SHVcXAq4Hg2dbRT4wwvOOUDry9H6VcRuqlA7oVkUa/FscqUVVbE/ cvTl1Gxvro8NQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48dhF64zgNz9rxM; Thu, 12 Mar 2020 22:05:46 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH v3 1/2] gnu: dune-*: remove openmpi dependency Date: Thu, 12 Mar 2020 22:05:12 +0100 Message-Id: <20200312210513.107891-2-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <87k13pvj5u.fsf@gnu.org> References: <87k13pvj5u.fsf@gnu.org> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber , =?UTF-8?q?Ludovic=20Court=C3=A8s?= 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: -3.3 (---) * gnu/packages/maths.scm (dune-*)[inputs]: Remove openmpi dependency. [arguments]: remove code to setup openmpi for tests. --- gnu/packages/maths.scm | 37 +++++++------------------------------ 1 file changed, 7 insertions(+), 30 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 2c03c00366..33a5efd2f0 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4582,13 +4582,10 @@ linear algebra primitives specifically targeting graph analytics.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("gmp" ,gmp) ("metis" ,metis) - ("openmpi" ,openmpi) ("openblas" ,openblas) ("python" ,python) ("superlu" ,superlu))) @@ -4626,7 +4623,6 @@ Differences} (FD).") (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) - ("openmpi" ,openmpi) ;; Optional ("openblas" ,openblas) ("gmp" ,gmp) @@ -4666,8 +4662,7 @@ This package contains the basic DUNE geometry classes.") (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "build_tests" make-flags)))))) (inputs - `(("dune-common" ,dune-common) - ("openmpi" ,openmpi))) + `(("dune-common" ,dune-common))) (native-inputs `(("gfortran" ,gfortran) ("pkg-config" ,pkg-config))) @@ -4700,16 +4695,13 @@ This package contains the DUNE UG grid classes.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) ("gmp" ,gmp) ("metis" ,metis) ("openblas" ,openblas) - ("openmpi" ,openmpi) ("python" ,python))) (propagated-inputs `(("dune-uggrid" ,dune-uggrid))) @@ -4746,12 +4738,9 @@ This package contains the basic DUNE grid classes.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("suitesparse" ,suitesparse) @@ -4799,7 +4788,6 @@ aggregation-based algebraic multigrid.") (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("superlu" ,superlu) @@ -4847,14 +4835,11 @@ assemble global function spaces on finite-element grids.") (lambda* (#:key inputs make-flags #:allow-other-keys) (setenv "CPLUS_INCLUDE_PATH" (string-append (assoc-ref inputs "dune-grid") "/share")) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) ("dune-grid" ,dune-grid) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("openblas" ,openblas) @@ -4892,14 +4877,11 @@ cubes.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) ("dune-grid" ,dune-grid) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("openblas" ,openblas) @@ -4938,7 +4920,6 @@ provides the full grid interface including adaptive mesh refinement.") (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) - ("openmpi" ,openmpi) ;; Optional ("openblas" ,openblas) ("python" ,python) @@ -4981,9 +4962,7 @@ operating on statically typed trees of objects.") #t)) (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-istl" ,dune-istl) @@ -4991,7 +4970,6 @@ operating on statically typed trees of objects.") ("dune-grid" ,dune-grid) ("dune-geometry" ,dune-geometry) ("dune-typetree" ,dune-typetree) - ("openmpi" ,openmpi) ("openblas" ,openblas) ("metis" ,metis) ("python" ,python) @@ -5032,7 +5010,6 @@ implemented as callable objects, and bases of finite element spaces.") ("dune-grid" ,dune-grid) ("dune-typetree" ,dune-typetree) ("dune-functions" ,dune-functions) - ("openmpi" ,openmpi) ;; Optional ("openblas" ,openblas) ("eigen" ,eigen) -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 12 17:06:02 2020 Received: (at 39862) by debbugs.gnu.org; 12 Mar 2020 21:06:03 +0000 Received: from localhost ([127.0.0.1]:57883 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCV1m-0002ab-MU for submit@debbugs.gnu.org; Thu, 12 Mar 2020 17:06:02 -0400 Received: from mout01.posteo.de ([185.67.36.65]:35719) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCV1k-0002a2-V4 for 39862@debbugs.gnu.org; Thu, 12 Mar 2020 17:06:01 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 01D3C160063 for <39862@debbugs.gnu.org>; Thu, 12 Mar 2020 22:05:54 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1584047155; bh=QKawdtAdkg9XbD9QjHX7Pm+NyHVKdg1hYeufDuxDm+o=; h=From:To:Cc:Subject:Date:From; b=EMpJ8IBmppjFSPv5G/SjYV7yvEIgOpBEUf22aXmVY4nU2M23lsVkzPtOmZOdX5Sv/ +OvqZWnEmU6gyloD3OEQze4U6kaFCr/ig2gfGuegCrXHkg5/HJ1V5XEZeKBBiBX4KP BN2ohq7sfMbYkLp93Q0br/czw5HohrDi6a/OxnHj/v3i7ylRLGecTXTku5MOWXfpmO oMAEPeRouVSm4I/MBJ+gb7OFnSm20cUyx2LSpGzu5ez8mg0bnFm0Gn6WP5k49J+3Eo bMcykUaGSKW+gC4QNz8pe1PWST5kgb1Jl0YduSJn04YmwTUFXb0XXv6VTVuK6a5FZc Gzwm+7HrWewOQ== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48dhFD6n4Nz6tmQ; Thu, 12 Mar 2020 22:05:52 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH v3 2/2] gnu: define dune-*-openmpi packages Date: Thu, 12 Mar 2020 22:05:13 +0100 Message-Id: <20200312210513.107891-3-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <87k13pvj5u.fsf@gnu.org> References: <87k13pvj5u.fsf@gnu.org> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber , =?UTF-8?q?Ludovic=20Court=C3=A8s?= 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: -3.3 (---) * gnu/packages/maths.scm (dune-*-openmpi): New variables. * gnu/packages/maths.scm (add-openmpi-to-dune-package): New function to add openmpi to the inputs of a dune-* package and replace all dune-* packages in its input with the corresponding dune-*-openmpi package. --- gnu/packages/maths.scm | 53 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 33a5efd2f0..ac89064a7f 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5027,6 +5027,59 @@ built on top of DUNE, the Distributed and Unified Numerics Environment.") ;; Either GPL version 2 with "runtime exception" or LGPLv3+. (license (list license:lgpl3+ license:gpl2)))) +(define add-openmpi-to-dune-package + (let ((dune-package? + (lambda (p) (string-prefix? "dune-" (package-name p))))) + (package-mapping + (lambda (p) + (if (dune-package? p) + (package (inherit p) + (name (string-append (package-name p) "-openmpi")) + (inputs `(,@(package-inputs p) + ("openmpi" ,openmpi))) + (arguments + (substitute-keyword-arguments (package-arguments p) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + (add-before 'check 'mpi-setup + ,%openmpi-setup))))) + (synopsis (string-append (package-synopsis p) " (with MPI support)"))) + p)) + (lambda (p) (not (dune-package? p)))))) + +(define-public dune-common-openmpi + (add-openmpi-to-dune-package dune-common)) + +(define-public dune-geometry-openmpi + (add-openmpi-to-dune-package dune-geometry)) + +(define-public dune-istl-openmpi + (add-openmpi-to-dune-package dune-istl)) + +(define-public dune-typetree-openmpi + (add-openmpi-to-dune-package dune-typetree)) + +(define-public dune-uggrid-openmpi + (add-openmpi-to-dune-package dune-uggrid)) + +(define-public dune-grid-openmpi + (add-openmpi-to-dune-package dune-grid)) + +(define-public dune-alugrid-openmpi + (add-openmpi-to-dune-package dune-alugrid)) + +(define-public dune-subgrid-openmpi + (add-openmpi-to-dune-package dune-subgrid)) + +(define-public dune-localfunctions-openmpi + (add-openmpi-to-dune-package dune-localfunctions)) + +(define-public dune-functions-openmpi + (add-openmpi-to-dune-package dune-functions)) + +(define-public dune-pdelab-openmpi + (add-openmpi-to-dune-package dune-pdelab)) + (define-public mlucas (package (name "mlucas") -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 13 05:42:51 2020 Received: (at 39862) by debbugs.gnu.org; 13 Mar 2020 09:42:51 +0000 Received: from localhost ([127.0.0.1]:58168 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCgqB-0003Nl-Aw for submit@debbugs.gnu.org; Fri, 13 Mar 2020 05:42:51 -0400 Received: from eggs.gnu.org ([209.51.188.92]:44377) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCgqA-0003Na-0w for 39862@debbugs.gnu.org; Fri, 13 Mar 2020 05:42:50 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:49878) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1jCgq4-0000kC-R8; Fri, 13 Mar 2020 05:42:44 -0400 Received: from [2001:660:6102:320:e120:2c8f:8909:cdfe] (port=53438 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jCgq4-00024b-9r; Fri, 13 Mar 2020 05:42:44 -0400 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Felix Gruber Subject: Re: [PATCH v3 2/2] gnu: define dune-*-openmpi packages References: <87k13pvj5u.fsf@gnu.org> <20200312210513.107891-3-felgru@posteo.net> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 24 =?utf-8?Q?Vent=C3=B4se?= an 228 de la =?utf-8?Q?R?= =?utf-8?Q?=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Fri, 13 Mar 2020 10:42:42 +0100 In-Reply-To: <20200312210513.107891-3-felgru@posteo.net> (Felix Gruber's message of "Thu, 12 Mar 2020 22:05:13 +0100") Message-ID: <87blp0pp4d.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 39862 Cc: 39862@debbugs.gnu.org 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: -1.7 (-) Hi Felix, Felix Gruber skribis: > * gnu/packages/maths.scm (dune-*-openmpi): New variables. > * gnu/packages/maths.scm (add-openmpi-to-dune-package): New function to > add openmpi to the inputs of a dune-* package and replace all dune-* > packages in its input with the corresponding dune-*-openmpi package. Nitpick: no need to repeat the file name above. It would also be great if you could list all the new variables. > + (lambda (p) (not (dune-package? p)))))) You can replace the lambda with: (negate dune-package?) One last thing: could you look at the output of, say, =E2=80=98guix graph dune-geometry-openmpi=E2=80=99 and ensure we=E2=80=99re not duplicating mor= e nodes than needed in the graph? For example, you can compare node counts with: guix graph dune-geometry | grep 'label =3D' | wc -l guix graph dune-geometry-openmpi | grep 'label =3D' | wc -l The difference should be less than: guix graph openmpi | grep 'label =3D' | wc -l If that works well, please send an updated patch and we should be ready to go! Thanks, Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 13 13:26:30 2020 Received: (at 39862) by debbugs.gnu.org; 13 Mar 2020 17:26:30 +0000 Received: from localhost ([127.0.0.1]:60193 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCo4r-0001GC-VQ for submit@debbugs.gnu.org; Fri, 13 Mar 2020 13:26:30 -0400 Received: from mout02.posteo.de ([185.67.36.66]:36591) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCo4o-0001Fy-PZ for 39862@debbugs.gnu.org; Fri, 13 Mar 2020 13:26:27 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id DD14F2400FC for <39862@debbugs.gnu.org>; Fri, 13 Mar 2020 18:26:20 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1584120380; bh=4Ccjx8LaTOa1McklYX7N2up/lsi07eLMBh1QvrpZHi4=; h=To:Cc:From:Autocrypt:Subject:Date:From; b=S3n+c1m64HRINl+LP7IokDmG7bNYftvC5lRdwmGwVwKLQedVLHTbnFrILylP3i3C3 H69bP4jc5NOVQd+gv/jstVtsOvE3ssZnReWHln2o39H4URGJBRjbNyT9JVkgmrvvKP ap9yaJUjL67tpxR7Cj83traL2NmtbeGfwYn2tXDlo6zfwzxQDRCduYfQ8bbFG6CEiR yDHD/P68necpUONeI8P99KRfNpojxMj0ng5TMnHtgVBCK9h6udHu4zFuw0bzysz9g5 5YTsZAW3okOwOCQxGm7VQy7DKeoKb/QrgHFIx951iI5xmL2B2pPRYVQz5ARoL2yY0S 9UgBzk9maRznA== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48fCKR663gz9rxQ; Fri, 13 Mar 2020 18:26:19 +0100 (CET) To: =?UTF-8?Q?Ludovic_Court=c3=a8s?= References: <87k13pvj5u.fsf@gnu.org> <20200312210513.107891-3-felgru@posteo.net> <87blp0pp4d.fsf@gnu.org> From: Felix Gruber Autocrypt: addr=felgru@posteo.net; prefer-encrypt=mutual; keydata= mQINBE9iUX0BEAC+0aP2k4eLwP+2vLG6P7au1eSWgHSzbaqZqQvnM/m6RMS7ZMlTZ1R1/gRI THcwtBnweXlcVB8mLLK2B+79y6VlWio8ASDR9xsHAsSwCwuqxwwuXeWr4tZstNQn/W4aIU8S oqEjbmPvJg5vgIPKME8VUiPU/H6RA0pytcqNysZdq4aPYbutmERIkhk7JHyq6Pjw/ZRRnJfq M6vKLXEU2wU8QHbQlblRnJZum4YP+WGSjCoIJQOVf7tSboBaHQ8ZrOvwxqKps2ZlptBTT+lV SiImTHzdJSWOyc831wLm6wP+2aV+xW/72bhyHgLvGcSSWZyIZPkUy11da9YUok0F1Ud2fR5A CUuVPkbKATM5sL0ykLvrMdOVriwohQGcrdx0m78m/+An3482RJJY3DmpV8zQ+hNoDC1OEkxd S8FTAB+z+uNIvlcAlJ7VsP33bpaEYqPxA51wh54TcIv8vnenaLmiQu0vcXlbJ4Kyw8RKTiHz Nv/avnD0WnZ6P9swdHyeqIoVU722WcINauEimf6AjgBXTYA78PfHowfWIm4qIwerw2QgfcWL wa9UkbGqz3dI43ngQjoj4iNRDJWKYDMv7fhKuCBpkEs+s2iQ4HlFw2Z1z+QixDB+T+jEFubr 6gIv6nixTJpLFozMintsnPCrnMNqrRq1GkI2QVHsDgcOqCy5GQARAQABtCBGZWxpeCBHcnVi ZXIgPGZlbGdydUBwb3N0ZW8ubmV0PokCVAQTAQoAPhYhBHDQ118D0n1En3jkr0UxQWJCvvSc BQJaODuUAhsDBQkQqtq6BQsJCAcDBRUKCQgLBRYCAwEAAh4BAheAAAoJEEUxQWJCvvScplwQ AJtZTwl9ypLfCCvR0sZXJk2c9EHIf6h9iZ04nI0TY3SzAqbJ4lXGqHg2AwbcsaGsWpxFF+nC mZGy5EvL84W19Q274ek5M8cHutVJKamDcY3j9+c/Wjni/8PUVgizQ+iFRWi7Pwn96au+3a43 s9Vlj8cAgjgetP8rL7mS/Z5UoTHADNMfndwU/oQJXuHGeYU2vEVJvboa/oieSlcqxTuHR/Y6 2RcmR+4fVCf9+KER4Oijp2a5K60YHW4hstIUDcDu0ua9/ObnYsRAcWfMS+iIMTn7kL2mil7N OmQq4dWjVWd1P0KznlajvRSCymSBKILcJYyMEAPTO/vV+VWIs8eWyVWR2kG4Ab7+R4UR0Ld8 K2atVjxvWF+12nHx4PDOgph5+N0mad8PREbdrDuxbEcYbXCMUh23b8UfZkMhHec1bHMCNyI7 HFmyg4MWJqkPlRZ+EPUaQfGtFGT1YNZjupn1HTZkirf/xgHfRb2v6TMCBITVLNYcvoWr3ncF enO2iOjIFBXAsHn9R4912MYh2pIi/pOtpzwac1NZz0Naskz6bI3mBPf/wRMb9LhgnvU6gosS 6YDfIxez3CV9XNuprLaTKXPITTguXKfV3KUIUG5NY3tOIr54jlSk1TUPma0IFY/W2dheoVKX KqoAib/2Pj5Omj4hYnjvermPxQgzKhxwqrp+uQINBE9iVK0BEACkVFDYT1vyLCTmxS0Nyn8q NLQp2bXzk5s8afPIjQIQnszNini+HqPxt7F4KrcMJ0o9+KslCcTpyowEK2TZy55NqhdyFP4k ut5LfiFzBvfPiKmQqgw8Sx3hOvQ5YSEfgBq/S2jigJ3HyXQkJlXYLpua5PvRsgX7ijFrMTCU qhn67aoosBAEr2XtzOYiO1rghnTgSOicyKSsKDfc9c4TXAu2i95g8z69JCWVzMkaGUhOyR6S vdFYrhFoBokZQU3bPRQTvOvVycSKQtXZ3hmQkeOtCTdElt07EU7GoGiLAqy1+GyUE/sSY0m7 UwmedRh5og55el08bmvim4tScbsuzLei17O7N34+G8YvYJOICRx4PxujEzby23WFG8t1Ty12 7vwj3dcHhlPc7XoaEi/OLbpbekw6y3KLZxwm4fc/JKiqLsE2mpNWAKVQea9k5T3koQvOsVp4 /Q4VLJTScvSEjF3F9Brj1wtOpgJll1aFw+MJlq38lNYDWVsHWQLesyYu5XRT84qee+JPd6ze RcKmj0f32bqH368XmJeHG9YGJxQpN+yviBT/aJXXlz46BvybzKwryFkZil2vCIEFJvXxNiCL C28J3FzOcRzF2POiKyjWvFLFF6cjFPGxzSc1PQftRmQywfzMTDHf9Iq4r9seNoyinaNcHJff IsLxMAtP+5xv4wARAQABiQIlBBgBCgAPAhsMBQJYiF5BBQkQqteUAAoJEEUxQWJCvvSc548P /31Kt4VaSDznSI6AFgsypRCZLGyClaav5zvyfAj+IkTeXIWvZhu/CvviNtoTr7oAofiOH/S8 zgrHEkpElTW0xUk+/ldkH1vQPbp9GZM0UEbT8KOwxmaVtfcIpSTfocx8F0KlD52AwXXmZpxP 7ZBWIMnO3BprpdHERXG7jtv/alp7Hoz1Fcs2AhWwDE26CM6EX2EewyTtYKOLaHxE2sqnQI6X 2rkzpL+do0vAH4YL/VGDHB2NmqJ9j9vCXWYod9zOfNX89L2QRIyI0Wm0FrwOq1abbUzPbSfO pLXVZGv1J8NhMX0vU3WP3D6pop/zXmrxpWy8Mzn0/pPGnN57fCvQ1O3+HeXwdckVswbcp8WW evG3QhggRTFxAEcATHJGtVoLAZSe3eKaj8HFL0oGeL9U1pc8IqNniI4a0CVkzrWtMSKvKVhU 3W+XRM8blG+aPwxjINlEXydqAPjPgsUHJLYOj9w/i62AOBveDxK+6ZPwtXYpvl5ItnxF3/AF 8u5DqbvzbkOIrza+VKOS6UlChg+9ZIn6hYzRbfELs0fzwdEUVkqnoh9ZmZGCl+P85j6fEtri Bxz7OpLHv47YBwpMruyz2TGSMeHFWHBb7cQslO/CNgR2UfZOvJ3A07t19A4batct1/NwAIcn uN5G9pgdqPYXSd61FIXsZBy6CTES+oX/oueB Subject: Re: [PATCH v3 2/2] gnu: define dune-*-openmpi packages Message-ID: Date: Fri, 13 Mar 2020 18:26:11 +0100 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.5.0 MIME-Version: 1.0 In-Reply-To: <87blp0pp4d.fsf@gnu.org> Content-Type: text/plain; charset=utf-8 Content-Language: en-US Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: 39862@debbugs.gnu.org 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: -3.3 (---) Hi Ludo’, On 3/13/20 10:42 AM, Ludovic Courtès wrote: > Felix Gruber skribis: > >> * gnu/packages/maths.scm (dune-*-openmpi): New variables. >> * gnu/packages/maths.scm (add-openmpi-to-dune-package): New function to >> add openmpi to the inputs of a dune-* package and replace all dune-* >> packages in its input with the corresponding dune-*-openmpi package. > > Nitpick: no need to repeat the file name above. It would also be great > if you could list all the new variables. Sure, no problem. >> + (lambda (p) (not (dune-package? p)))))) > > You can replace the lambda with: > > (negate dune-package?) Thanks for this hint, as I'm new to Scheme, my knowledge of its standard library is still pretty limited. The negate function is quite useful. > One last thing: could you look at the output of, say, ‘guix graph > dune-geometry-openmpi’ and ensure we’re not duplicating more nodes than > needed in the graph? > > For example, you can compare node counts with: > > guix graph dune-geometry | grep 'label =' | wc -l > guix graph dune-geometry-openmpi | grep 'label =' | wc -l > > The difference should be less than: > > guix graph openmpi | grep 'label =' | wc -l > > If that works well, please send an updated patch and we should be ready > to go! I get the following numbers: graph dune-geometry | grep 'label =' | wc -l 70 guix graph dune-geometry-openmpi | grep 'label =' | wc -l 143 guix graph openmpi | grep 'label =' | wc -l 137 The difference seems to be OK: 143 - 70 = 73 < 137. I'll send the updated patch ASAP. Best Regards, Felix From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 13 13:31:10 2020 Received: (at 39862) by debbugs.gnu.org; 13 Mar 2020 17:31:10 +0000 Received: from localhost ([127.0.0.1]:60199 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCo9N-0001PS-Jm for submit@debbugs.gnu.org; Fri, 13 Mar 2020 13:31:09 -0400 Received: from mout02.posteo.de ([185.67.36.66]:60547) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCo9L-0001PC-Uv for 39862@debbugs.gnu.org; Fri, 13 Mar 2020 13:31:08 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id E359A2400FD for <39862@debbugs.gnu.org>; Fri, 13 Mar 2020 18:31:01 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1584120661; bh=3GZPygSugnAL59H8UxmBcWmKxIHJ2dwJSg2tt+w2i9g=; h=From:To:Cc:Subject:Date:From; b=DjHsbAWxRlaO73pgO35t9+DL63Qy5bZ9ecSvDY5KAZlflpVxH+uFzqmmQr0e76Vlz QCgwhOrXfMIwtsk1Vh09hjRSubeaKwDuhvCiIuS1kTX4Ob2ZrgUzayaGbOuTrPyHJM Sk9bglQYuWBQC6X/1/jiD86mVp9X+ZzsWILjWyx9UjZIx1RfiicKaPbSsdHuY3oSBv tRkaQlrv1Hl4WtjrdXqC6HmuKC1JVqxm2PhDGEDtHsMyxKnCJlQROknPJk/HDW2GqG Nxg5fJx5obDuahMpbE9tN9UGLsn/IUV0TI5ZhfpbJI3g27doQJ+cO0DZCGf4ZlH8to mEr/4Q7ycAzfg== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48fCQs18nlz9rxD; Fri, 13 Mar 2020 18:31:01 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH v4 1/2] gnu: dune-*: remove openmpi dependency Date: Fri, 13 Mar 2020 18:30:37 +0100 Message-Id: <20200313173038.4175-1-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <87blp0pp4d.fsf@gnu.org> References: <87blp0pp4d.fsf@gnu.org> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber , =?UTF-8?q?Ludovic=20Court=C3=A8s?= 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: -3.3 (---) * gnu/packages/maths.scm (dune-*)[inputs]: Remove openmpi dependency. [arguments]: remove code to setup openmpi for tests. --- gnu/packages/maths.scm | 37 +++++++------------------------------ 1 file changed, 7 insertions(+), 30 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 2c03c00366..33a5efd2f0 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4582,13 +4582,10 @@ linear algebra primitives specifically targeting graph analytics.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("gmp" ,gmp) ("metis" ,metis) - ("openmpi" ,openmpi) ("openblas" ,openblas) ("python" ,python) ("superlu" ,superlu))) @@ -4626,7 +4623,6 @@ Differences} (FD).") (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) - ("openmpi" ,openmpi) ;; Optional ("openblas" ,openblas) ("gmp" ,gmp) @@ -4666,8 +4662,7 @@ This package contains the basic DUNE geometry classes.") (lambda* (#:key make-flags #:allow-other-keys) (apply invoke "make" "build_tests" make-flags)))))) (inputs - `(("dune-common" ,dune-common) - ("openmpi" ,openmpi))) + `(("dune-common" ,dune-common))) (native-inputs `(("gfortran" ,gfortran) ("pkg-config" ,pkg-config))) @@ -4700,16 +4695,13 @@ This package contains the DUNE UG grid classes.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) ("gmp" ,gmp) ("metis" ,metis) ("openblas" ,openblas) - ("openmpi" ,openmpi) ("python" ,python))) (propagated-inputs `(("dune-uggrid" ,dune-uggrid))) @@ -4746,12 +4738,9 @@ This package contains the basic DUNE grid classes.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("suitesparse" ,suitesparse) @@ -4799,7 +4788,6 @@ aggregation-based algebraic multigrid.") (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("superlu" ,superlu) @@ -4847,14 +4835,11 @@ assemble global function spaces on finite-element grids.") (lambda* (#:key inputs make-flags #:allow-other-keys) (setenv "CPLUS_INCLUDE_PATH" (string-append (assoc-ref inputs "dune-grid") "/share")) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) ("dune-grid" ,dune-grid) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("openblas" ,openblas) @@ -4892,14 +4877,11 @@ cubes.") (modify-phases %standard-phases (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-geometry" ,dune-geometry) ("dune-grid" ,dune-grid) - ("openmpi" ,openmpi) ;; Optional ("metis" ,metis) ("openblas" ,openblas) @@ -4938,7 +4920,6 @@ provides the full grid interface including adaptive mesh refinement.") (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) - ("openmpi" ,openmpi) ;; Optional ("openblas" ,openblas) ("python" ,python) @@ -4981,9 +4962,7 @@ operating on statically typed trees of objects.") #t)) (add-after 'build 'build-tests (lambda* (#:key make-flags #:allow-other-keys) - (apply invoke "make" "build_tests" make-flags))) - (add-before 'check 'mpi-setup - ,%openmpi-setup)))) + (apply invoke "make" "build_tests" make-flags)))))) (inputs `(("dune-common" ,dune-common) ("dune-istl" ,dune-istl) @@ -4991,7 +4970,6 @@ operating on statically typed trees of objects.") ("dune-grid" ,dune-grid) ("dune-geometry" ,dune-geometry) ("dune-typetree" ,dune-typetree) - ("openmpi" ,openmpi) ("openblas" ,openblas) ("metis" ,metis) ("python" ,python) @@ -5032,7 +5010,6 @@ implemented as callable objects, and bases of finite element spaces.") ("dune-grid" ,dune-grid) ("dune-typetree" ,dune-typetree) ("dune-functions" ,dune-functions) - ("openmpi" ,openmpi) ;; Optional ("openblas" ,openblas) ("eigen" ,eigen) -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 13 13:31:17 2020 Received: (at 39862) by debbugs.gnu.org; 13 Mar 2020 17:31:17 +0000 Received: from localhost ([127.0.0.1]:60203 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCo9V-0001Pr-0Z for submit@debbugs.gnu.org; Fri, 13 Mar 2020 13:31:17 -0400 Received: from mout02.posteo.de ([185.67.36.66]:52675) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCo9T-0001Pa-Ae for 39862@debbugs.gnu.org; Fri, 13 Mar 2020 13:31:15 -0400 Received: from submission (posteo.de [89.146.220.130]) by mout02.posteo.de (Postfix) with ESMTPS id AE8D02400FE for <39862@debbugs.gnu.org>; Fri, 13 Mar 2020 18:31:09 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1584120669; bh=0eLwr/8/2yOTO57WBJoBIy/1F/H74Xeig80JvBYk14Q=; h=From:To:Cc:Subject:Date:From; b=OuRhdcfuO9CCc8FzrVE1q/0FM4IQDZrIENNqMuUCG+SSeZexBu1nKpLMv8LfN9Dze gur2qT1W3ZfJyvuHRkWNmDTp0qAjJmFErK+WHsXhQkf0tEV6uwMYoTWcxbjWVs3xOq 9Qzppdw1KJglsH6jhVs5dwpaQixh9HZsxYmoJtuWEFjLDV2Enh74oM1ugXcm7whtU6 PsLlTDp3dowsh85RpWcoDfOhV2EJtl2nz3QoytsB9kN+RKUj+Q/ejZFgFobHmpTO8j x2ED0U15EIo0gvQjUHUk3wq4BNIDKA7wWuUavIqlbOw3quXzuQZJzXfpuuUx+StJOs FX0iw4TTlse0g== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 48fCR05MQXz9rxG; Fri, 13 Mar 2020 18:31:08 +0100 (CET) From: Felix Gruber To: 39862@debbugs.gnu.org Subject: [PATCH v4 2/2] gnu: define dune-*-openmpi packages Date: Fri, 13 Mar 2020 18:30:38 +0100 Message-Id: <20200313173038.4175-2-felgru@posteo.net> X-Mailer: git-send-email 2.25.1 In-Reply-To: <87blp0pp4d.fsf@gnu.org> References: <87blp0pp4d.fsf@gnu.org> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 39862 Cc: Felix Gruber , =?UTF-8?q?Ludovic=20Court=C3=A8s?= 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: -3.3 (---) * gnu/packages/maths.scm (dune-common-openmpi, dune-geometry-openmpi, dune-istl-openmpi, dune-typetree-openmpi, dune-uggrid-openmpi, dune-grid-openmpi, dune-alugrid-openmpi, dune-subgrid-openmpi, dune-localfunctions-openmpi, dune-functions-openmpi, dune-pdelab-openmpi): New variables. (add-openmpi-to-dune-package): New function to add openmpi to the inputs of a dune-* package and replace all dune-* packages in its input with the corresponding dune-*-openmpi package. --- gnu/packages/maths.scm | 53 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 33a5efd2f0..6c2813f100 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5027,6 +5027,59 @@ built on top of DUNE, the Distributed and Unified Numerics Environment.") ;; Either GPL version 2 with "runtime exception" or LGPLv3+. (license (list license:lgpl3+ license:gpl2)))) +(define add-openmpi-to-dune-package + (let ((dune-package? + (lambda (p) (string-prefix? "dune-" (package-name p))))) + (package-mapping + (lambda (p) + (if (dune-package? p) + (package (inherit p) + (name (string-append (package-name p) "-openmpi")) + (inputs `(,@(package-inputs p) + ("openmpi" ,openmpi))) + (arguments + (substitute-keyword-arguments (package-arguments p) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + (add-before 'check 'mpi-setup + ,%openmpi-setup))))) + (synopsis (string-append (package-synopsis p) " (with MPI support)"))) + p)) + (negate dune-package?)))) + +(define-public dune-common-openmpi + (add-openmpi-to-dune-package dune-common)) + +(define-public dune-geometry-openmpi + (add-openmpi-to-dune-package dune-geometry)) + +(define-public dune-istl-openmpi + (add-openmpi-to-dune-package dune-istl)) + +(define-public dune-typetree-openmpi + (add-openmpi-to-dune-package dune-typetree)) + +(define-public dune-uggrid-openmpi + (add-openmpi-to-dune-package dune-uggrid)) + +(define-public dune-grid-openmpi + (add-openmpi-to-dune-package dune-grid)) + +(define-public dune-alugrid-openmpi + (add-openmpi-to-dune-package dune-alugrid)) + +(define-public dune-subgrid-openmpi + (add-openmpi-to-dune-package dune-subgrid)) + +(define-public dune-localfunctions-openmpi + (add-openmpi-to-dune-package dune-localfunctions)) + +(define-public dune-functions-openmpi + (add-openmpi-to-dune-package dune-functions)) + +(define-public dune-pdelab-openmpi + (add-openmpi-to-dune-package dune-pdelab)) + (define-public mlucas (package (name "mlucas") -- 2.25.1 From debbugs-submit-bounces@debbugs.gnu.org Fri Mar 13 17:28:28 2020 Received: (at 39862) by debbugs.gnu.org; 13 Mar 2020 21:28:28 +0000 Received: from localhost ([127.0.0.1]:60299 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCrr1-0007Sg-Ow for submit@debbugs.gnu.org; Fri, 13 Mar 2020 17:28:28 -0400 Received: from eggs.gnu.org ([209.51.188.92]:37440) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jCrqz-0007ST-Ne for 39862@debbugs.gnu.org; Fri, 13 Mar 2020 17:28:26 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:55585) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1jCrqt-0007aY-NG; Fri, 13 Mar 2020 17:28:20 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=38628 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jCrqn-0008H5-AF; Fri, 13 Mar 2020 17:28:19 -0400 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Felix Gruber Subject: Re: [PATCH v3 2/2] gnu: define dune-*-openmpi packages References: <87k13pvj5u.fsf@gnu.org> <20200312210513.107891-3-felgru@posteo.net> <87blp0pp4d.fsf@gnu.org> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 24 =?utf-8?Q?Vent=C3=B4se?= an 228 de la =?utf-8?Q?R?= =?utf-8?Q?=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Fri, 13 Mar 2020 22:28:11 +0100 In-Reply-To: (Felix Gruber's message of "Fri, 13 Mar 2020 18:26:11 +0100") Message-ID: <87d09gndw4.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 39862 Cc: 39862@debbugs.gnu.org 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: -1.7 (-) Hi, Felix Gruber skribis: >>> + (lambda (p) (not (dune-package? p)))))) >>=20 >> You can replace the lambda with: >>=20 >> (negate dune-package?) > > Thanks for this hint, as I'm new to Scheme, my knowledge of its standard > library is still pretty limited. Sure, I think sharing knowledge is one of the goals of review. >> One last thing: could you look at the output of, say, =E2=80=98guix graph >> dune-geometry-openmpi=E2=80=99 and ensure we=E2=80=99re not duplicating = more nodes than >> needed in the graph? >>=20 >> For example, you can compare node counts with: >>=20 >> guix graph dune-geometry | grep 'label =3D' | wc -l >> guix graph dune-geometry-openmpi | grep 'label =3D' | wc -l >>=20 >> The difference should be less than: >>=20 >> guix graph openmpi | grep 'label =3D' | wc -l >>=20 >> If that works well, please send an updated patch and we should be ready >> to go! > > I get the following numbers: > > graph dune-geometry | grep 'label =3D' | wc -l > 70 > > guix graph dune-geometry-openmpi | grep 'label =3D' | wc -l > 143 > > guix graph openmpi | grep 'label =3D' | wc -l > 137 > > The difference seems to be OK: 143 - 70 =3D 73 < 137. Looks good, thanks! Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Sat Mar 14 12:55:46 2020 Received: (at 39862-done) by debbugs.gnu.org; 14 Mar 2020 16:55:46 +0000 Received: from localhost ([127.0.0.1]:33882 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jDA4g-0006t7-6K for submit@debbugs.gnu.org; Sat, 14 Mar 2020 12:55:46 -0400 Received: from eggs.gnu.org ([209.51.188.92]:39705) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jDA4e-0006sv-LP for 39862-done@debbugs.gnu.org; Sat, 14 Mar 2020 12:55:44 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:41416) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1jDA4Y-0006Nl-SW; Sat, 14 Mar 2020 12:55:38 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=40380 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jDA4X-0007Jt-Gj; Sat, 14 Mar 2020 12:55:38 -0400 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Felix Gruber Subject: Re: [PATCH v4 1/2] gnu: dune-*: remove openmpi dependency References: <87blp0pp4d.fsf@gnu.org> <20200313173038.4175-1-felgru@posteo.net> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 25 =?utf-8?Q?Vent=C3=B4se?= an 228 de la =?utf-8?Q?R?= =?utf-8?Q?=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Sat, 14 Mar 2020 17:55:34 +0100 In-Reply-To: <20200313173038.4175-1-felgru@posteo.net> (Felix Gruber's message of "Fri, 13 Mar 2020 18:30:37 +0100") Message-ID: <877dzmkha1.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 39862-done Cc: 39862-done@debbugs.gnu.org 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: -1.7 (-) Hi, Felix Gruber skribis: > * gnu/packages/maths.scm (dune-*)[inputs]: Remove openmpi dependency. > [arguments]: remove code to setup openmpi for tests. [...] > * gnu/packages/maths.scm (dune-common-openmpi, dune-geometry-openmpi, > dune-istl-openmpi, dune-typetree-openmpi, dune-uggrid-openmpi, > dune-grid-openmpi, dune-alugrid-openmpi, dune-subgrid-openmpi, > dune-localfunctions-openmpi, dune-functions-openmpi, > dune-pdelab-openmpi): New variables. > (add-openmpi-to-dune-package): New function to add openmpi to the > inputs of a dune-* package and replace all dune-* packages in its > input with the corresponding dune-*-openmpi package. Pushed, thanks! Ludo=E2=80=99. From unknown Fri Jun 20 20:11:49 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Sun, 12 Apr 2020 11:24:06 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator