From patchwork Fri Oct 13 12:35:45 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Patchwork-Submitter: "Paul A. Patience" X-Patchwork-Id: 54797 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 C3C5027BBEA; Fri, 13 Oct 2023 13:37:12 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-2.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 2AC1827BBE2 for ; Fri, 13 Oct 2023 13:37:09 +0100 (BST) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1qrHPI-00056C-Mv; Fri, 13 Oct 2023 08:36:44 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1qrHPE-00054S-VE for guix-patches@gnu.org; Fri, 13 Oct 2023 08:36:41 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1qrHPE-0006Jo-My for guix-patches@gnu.org; Fri, 13 Oct 2023 08:36:40 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1qrHPb-0003Yq-LW for guix-patches@gnu.org; Fri, 13 Oct 2023 08:37:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#66516] [PATCH 2/2] gnu: dealii: Update to 9.5.1. 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Patience" Message-ID: <68f367b14a8e01145318a9cd2525a36e436d9963.1697199836.git.paul@apatience.com> In-Reply-To: References: Feedback-ID: 19227857:user:proton MIME-Version: 1.0 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: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/maths.scm (dealii): Update to 9.5.1. [propagated-inputs]: Add kokkos. [arguments]<#:phases>: Add 'unset-cpath' phase. (dealii-openmpi)[propagated-inputs]: Remove kokkos. [arguments]<#:phases>: Delete 'unset-cpath' phase. --- gnu/packages/maths.scm | 28 +++++++++++++++++++++++----- 1 file changed, 23 insertions(+), 5 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 2762e13a4f..e8d3cfed99 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -6613,17 +6613,17 @@ (define trilinos-for-dealii-openmpi (define-public dealii (package (name "dealii") - (version "9.4.0") + (version "9.5.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/dealii/dealii/releases/" "download/v" version "/dealii-" version ".tar.gz")) (sha256 - (base32 "0v73q6f35f2yrjihaq6vh9lma07qc4cdv75nwmc3c5yrdh07g1i3")) + (base32 "0phgcfnil4rb41xipsdbm4lxrymlqxbiccakg3pkm3a8wqsva658")) (modules '((guix build utils))) (snippet - ;; Remove bundled boost, muparser, TBB and UMFPACK. + ;; Remove bundled boost, Kokkos, muparser, TBB and UMFPACK. #~(delete-file-recursively "bundled")))) (build-system cmake-build-system) (outputs '("out" "doc")) @@ -6647,6 +6647,7 @@ (define-public dealii ;; the requisite interpreter to its native inputs. (list boost hdf5 + kokkos suitesparse ; For UMFPACK. sundials tbb)) @@ -6671,6 +6672,18 @@ (define-public dealii "/examples"))) #:phases #~(modify-phases %standard-phases + ;; Without unsetting CPATH, the build fails with the following + ;; error (similar to ): + ;; + ;; /gnu/store/…-gcc-11.3.0/include/c++/math.h:30:16: fatal error: math.h: No such file or directory + ;; 30 | # include_next + ;; | ^~~~~~~~ + ;; + ;; Why does unsetting CPATH magically fix the error? + ;; TODO: Properly fix this issue. + (add-after 'set-paths 'unset-cpath + (lambda _ + (unsetenv "CPATH"))) (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 @@ -6702,7 +6715,7 @@ (define-public dealii-openmpi scalapack))) (propagated-inputs (modify-inputs (package-propagated-inputs dealii) - (delete "hdf5" "sundials") + (delete "hdf5" "kokkos" "sundials") (prepend hdf5-parallel-openmpi openmpi p4est-openmpi @@ -6713,7 +6726,12 @@ (define-public dealii-openmpi (arguments (substitute-keyword-arguments (package-arguments dealii) ((#:configure-flags flags) - #~(cons "-DDEAL_II_WITH_MPI=ON" #$flags)))) + #~(cons "-DDEAL_II_WITH_MPI=ON" #$flags)) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + ;; The build failure fixed by this phase does not manifest when + ;; Kokkos is included via Trilinos. + (delete 'unset-cpath))))) (synopsis "Finite element library (with MPI support)"))) (define-public flann