From patchwork Wed Jul 14 01:32:41 2021 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: "Paul A. Patience" X-Patchwork-Id: 31391 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 9C6F127BC82; Wed, 14 Jul 2021 02:33:10 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.8 required=5.0 tests=BAYES_00,DKIM_SIGNED, MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H4,RCVD_IN_MSPIKE_WL,SPF_HELO_PASS, T_DKIM_INVALID,URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.2 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 001B027BC6B for ; Wed, 14 Jul 2021 02:33:10 +0100 (BST) Received: from localhost ([::1]:52806 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1m3Tls-00072Q-Tw for patchwork@mira.cbaines.net; Tue, 13 Jul 2021 21:33:08 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:60326) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1m3Tlm-00071h-H2 for guix-patches@gnu.org; Tue, 13 Jul 2021 21:33:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:59154) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1m3Tlm-0002I7-9S for guix-patches@gnu.org; Tue, 13 Jul 2021 21:33:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1m3Tlm-0005N8-05 for guix-patches@gnu.org; Tue, 13 Jul 2021 21:33:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#49500] [PATCH] gnu: dealii: Update to 9.3.0 and clean up. 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Patience" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 14 Jul 2021 01:33:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 49500 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 49500@debbugs.gnu.org X-Debbugs-Original-To: "guix-patches@gnu.org" Received: via spool by submit@debbugs.gnu.org id=B.162622637520632 (code B ref -1); Wed, 14 Jul 2021 01:33:01 +0000 Received: (at submit) by debbugs.gnu.org; 14 Jul 2021 01:32:55 +0000 Received: from localhost ([127.0.0.1]:42467 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m3Tle-0005Mi-Fr for submit@debbugs.gnu.org; Tue, 13 Jul 2021 21:32:54 -0400 Received: from lists.gnu.org ([209.51.188.17]:40306) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m3Tla-0005MY-Fx for submit@debbugs.gnu.org; Tue, 13 Jul 2021 21:32:52 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:60232) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1m3TlZ-00071L-Gu for guix-patches@gnu.org; Tue, 13 Jul 2021 21:32:50 -0400 Received: from mail-4317.protonmail.ch ([185.70.43.17]:11594) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1m3TlV-00025U-79 for guix-patches@gnu.org; Tue, 13 Jul 2021 21:32:49 -0400 Date: Wed, 14 Jul 2021 01:32:41 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=apatience.com; s=protonmail3; t=1626226362; bh=xgSeBiWDdgCg7g2fG/6DQZxs5jg8+IZr4uUaP856jGA=; h=Date:To:From:Reply-To:Subject:In-Reply-To:References:From; b=rC8t2KU3JMBnU94Iuime+6s/pf4yZyGd7y1f44gU4sMauUIK6GwWXpTniDws1JBDG lkayYm+Gw0mLne7cro28TDcn/bd8kRkjK5JWZmm+ZT/FY4GVwKnQrxu2IMiMB4YIXo XbB5UXTRrnZVePcP8Kb12ywIBJJ3xmmUz6KA51SvJlX75Z3+APmjMsg2EVgito1gTo pLjUPU3CPtlh4Fqz0ziIG4MGofsqAr0/HOci3MR+DB2TQZSF/BK1EQYZ+npjVgY0sf HRGBnrrM810+QThorH3CGHBv9PAR7ri211GdlpgpWCvq1fVAdxS/qK3+njsXq2P8oU 9ttlXjrafV6hA== From: "Paul A. Patience" Message-ID: In-Reply-To: References: MIME-Version: 1.0 Received-SPF: pass client-ip=185.70.43.17; envelope-from=paul@apatience.com; helo=mail-4317.protonmail.ch X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_MSPIKE_H4=0.001, RCVD_IN_MSPIKE_WL=0.001, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-To: "Paul A. Patience" Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches deal.II 9.3.1 has been released in the meantime, so update to that. Best regards, Paul From 3e4b62a5af1e71eb37474ab9f719e0b9a9cc66a0 Mon Sep 17 00:00:00 2001 From: "Paul A. Patience" Date: Tue, 13 Jul 2021 21:29:51 -0400 Subject: [PATCH] gnu: dealii: Update to 9.3.1 and clean up. The cleanup notably: * Builds and installs the documentation into a separate doc output (in the process moving around some files erroneously installed into the root directory); and * Removes unnecessary inputs and moves some inputs into propagated-inputs (the candidates of which were determined with a search for "include.*LIBNAME" in include/deal.II). * gnu/packages/maths.scm (dealii): Reword comments. [version]: Update to 9.3.1. [outputs]: New field including doc output. [native-inputs]: New field. [inputs]: Sort them. Remove p4est (deal.II interfaces with it only when MPI is enabled). Move boost, suitesparse and tbb to... [propagated-inputs]: ...here. New field including hdf5, which is actually supported in deal.II without MPI. [arguments]<#:tests?>: New argument. The tests were not being run before anyway. <#:configure-flags>[-DDEAL_II_COMPONENT_DOCUMENTATION]: New flag. [-DDEAL_II_DOCREADME_RELDIR]: New flag. Prevents the LICENSE.md, README.md, detailed.log and summary.log files from being installed in the root directory (though note that the logs are removed in the new remove-build-logs phase). [-DDEAL_II_DOCHTML_RELDIR]: New flag. [-DDEAL_II_COMPILE_EXAMPLES]: New flag. [-DDEAL_II_EXAMPLES_RELDIR]: New flag. Prevents the examples directory from being installed in the root directory. [-DCMAKE_POSITION_INDEPENDENT_CODE]: Remove flag. The issue has been resolved. <#:phases>{remove-build-logs}: New phase. [home-page]: Add trailing slash. (dealii-openmpi): Use package/inherit. [inputs]: Sort them. Remove mumps-metis-openmpi (deal.II no longer interfaces with MUMPS). Move hdf5-parallel-openmpi, openmpi, p4est-openmpi, petsc-openmpi and slepc-openmpi to... [propagated-inputs]: ...here. New field. [arguments]<#:configure-flags>: Rename cf variable to flags. <#:phases>{mpi-setup}: Remove phase which is unused because the tests are disabled. --- gnu/packages/maths.scm | 95 +++++++++++++++++++++++++++--------------- 1 file changed, 62 insertions(+), 33 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index b8e9a31be7..3242e47834 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -4436,40 +4436,75 @@ revised simplex and the branch-and-bound methods.") (define-public dealii (package (name "dealii") - (version "9.2.0") + (version "9.3.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/dealii/dealii/releases/" "download/v" version "/dealii-" version ".tar.gz")) (sha256 - (base32 - "0fm4xzrnb7dfn4415j24d8v3jkh0lssi86250x2f5wgi83xq4nnh")) + (base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6")) (modules '((guix build utils))) (snippet - ;; Remove bundled sources: UMFPACK, TBB, muParser, and boost '(begin + ;; Remove bundled boost, muparser, TBB and UMFPACK. (delete-file-recursively "bundled") #t)))) (build-system cmake-build-system) + (outputs '("out" "doc")) + (native-inputs + ;; Required to build the documentation. + `(("dot" ,graphviz) + ("doxygen" ,doxygen) + ("perl" ,perl))) (inputs - `(("tbb" ,tbb) - ("zlib" ,zlib) - ("boost" ,boost) - ("p4est" ,p4est) + `(("arpack" ,arpack-ng) ("blas" ,openblas) + ("gfortran" ,gfortran) ("lapack" ,lapack) - ("arpack" ,arpack-ng) ("muparser" ,muparser) - ("gfortran" ,gfortran) - ("suitesparse" ,suitesparse))) ;for UMFPACK + ("zlib" ,zlib))) + (propagated-inputs + ;; Some scripts are installed into share/deal.II/scripts that require + ;; perl and python, but they are not executable (and some are missing the + ;; shebang line) and therefore must be explicitly passed to the + ;; interpreter. + ;; Anyway, they are meant to be used at build time, so rather than adding + ;; the interpreters here, any package depending on them should just add + ;; the requisite interpreter to its native inputs. + `(("boost" ,boost) + ("hdf5" ,hdf5) + ("suitesparse" ,suitesparse) ; For UMFPACK. + ("tbb" ,tbb))) (arguments - `(#:build-type "DebugRelease" ;only supports Release, Debug, or DebugRelease + `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease. + ;; The tests take too long and must be explicitly enabled with "make + ;; setup_tests". + ;; See https://www.dealii.org/developer/developers/testsuite.html. + ;; (They can also be run for an already installed deal.II.) + #:tests? #f #:configure-flags - ;; Work around a bug in libsuitesparseconfig linking - ;; see https://github.com/dealii/dealii/issues/4745 - '("-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON"))) - (home-page "https://www.dealii.org") + (let ((doc (string-append (assoc-ref %outputs "doc") + "/share/doc/" ,name "-" ,version))) + `("-DDEAL_II_COMPONENT_DOCUMENTATION=ON" + ,(string-append "-DDEAL_II_DOCREADME_RELDIR=" doc) + ,(string-append "-DDEAL_II_DOCHTML_RELDIR=" doc "/html") + ;; Don't compile the examples because the source and CMakeLists.txt + ;; are installed anyway, allowing users to do so for themselves. + "-DDEAL_II_COMPILE_EXAMPLES=OFF" + ,(string-append "-DDEAL_II_EXAMPLES_RELDIR=" doc "/examples"))) + #:phases + (modify-phases %standard-phases + (add-after 'install 'remove-build-logs + ;; These build logs leak the name of the build directory by storing + ;; the values of CMAKE_SOURCE_DIR and CMAKE_BINARY_DIR. + (lambda* (#:key outputs #:allow-other-keys) + (let ((doc (string-append (assoc-ref outputs "doc") + "/share/doc/" ,name "-" ,version))) + (for-each delete-file (map (lambda (f) (string-append doc "/" f)) + '("detailed.log" "summary.log")))) + #t))))) + (home-page "https://www.dealii.org/") (synopsis "Finite element library") (description "Deal.II is a C++ program library targeted at the computational solution @@ -4480,30 +4515,24 @@ in finite element programs.") (license license:lgpl2.1+))) (define-public dealii-openmpi - (package (inherit dealii) + (package/inherit dealii (name "dealii-openmpi") (inputs - `(("mpi" ,openmpi) - ;;Supported only with MPI: - ("hdf5" ,hdf5-parallel-openmpi) ;TODO: have petsc-openmpi propagate? + `(("arpack" ,arpack-ng-openmpi) + ("metis" ,metis) + ("scalapack" ,scalapack) + ,@(alist-delete "arpack" (package-inputs dealii)))) + (propagated-inputs + `(("hdf5" ,hdf5-parallel-openmpi) + ("mpi" ,openmpi) ("p4est" ,p4est-openmpi) ("petsc" ,petsc-openmpi) ("slepc" ,slepc-openmpi) - ("metis" ,metis) ;for MUMPS - ("scalapack" ,scalapack) ;for MUMPS - ("mumps" ,mumps-metis-openmpi) ;configure supports only metis orderings - ("arpack" ,arpack-ng-openmpi) - ,@(fold alist-delete (package-inputs dealii) - '("p4est" "arpack")))) + ,@(alist-delete "hdf5" (package-propagated-inputs dealii)))) (arguments (substitute-keyword-arguments (package-arguments dealii) - ((#:configure-flags cf) - `(cons "-DDEAL_II_WITH_MPI:BOOL=ON" - ,cf)) - ((#:phases phases '%standard-phases) - `(modify-phases ,phases - (add-before 'check 'mpi-setup - ,%openmpi-setup))))) + ((#:configure-flags flags) + `(cons "-DDEAL_II_WITH_MPI=ON" ,flags)))) (synopsis "Finite element library (with MPI support)"))) (define-public flann -- 2.32.0