From patchwork Thu Apr 28 18:19:22 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: "Paul A. Patience" X-Patchwork-Id: 38992 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 A34A327BBEA; Thu, 28 Apr 2022 19:21:01 +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=unavailable 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 6A55D27BBE9 for ; Thu, 28 Apr 2022 19:21:01 +0100 (BST) Received: from localhost ([::1]:39536 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nk8lA-0000fs-Je for patchwork@mira.cbaines.net; Thu, 28 Apr 2022 14:21:00 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:38548) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nk8kE-0007hx-VY for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:56022) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nk8kE-0004k8-Lv for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nk8kE-00038E-DZ for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55170] [PATCH 1/5] gnu: sundials: Add 5.8.0. References: <20220428181532.281677-1-paul@apatience.com> In-Reply-To: <20220428181532.281677-1-paul@apatience.com> Resent-From: "Paul A. Patience" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 28 Apr 2022 18:20:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 55170 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 55170@debbugs.gnu.org Cc: ludovic.courtes@inria.fr, paul@apatience.com Received: via spool by 55170-submit@debbugs.gnu.org id=B55170.165116997311938 (code B ref 55170); Thu, 28 Apr 2022 18:20:02 +0000 Received: (at 55170) by debbugs.gnu.org; 28 Apr 2022 18:19:33 +0000 Received: from localhost ([127.0.0.1]:49903 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nk8jl-00036T-9p for submit@debbugs.gnu.org; Thu, 28 Apr 2022 14:19:33 -0400 Received: from mail-40136.proton.ch ([185.70.40.136]:14920) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nk8jj-00036D-5O for 55170@debbugs.gnu.org; Thu, 28 Apr 2022 14:19:31 -0400 Date: Thu, 28 Apr 2022 18:19:22 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=apatience.com; s=protonmail2; t=1651169964; bh=L8NkkCMPvPLQu2Bl/SyRzJ7vhTJIIzjXFGEU2MLrQpM=; h=Date:To:From:Cc:Reply-To:Subject:Message-ID:Feedback-ID:From:To: Cc:Date:Subject:Reply-To:Feedback-ID:Message-ID; b=EoAk4RzRAd4fhk19T2LQaNOfqKqqsDn/m4r1S/4BlHpRzUTUgSF+EV8HAuQDykJD4 1ukDX/FCnku665sbxJn2NOH9Ycnr18yGpAQBuD5nl5Z65i6u/8JBgWOS+my4aE+gxC WIbe0oiMEy8eXicFlFBG3Y/7sfAXJmwXw+nRNfPofkcrXoX6f8iOhc0jmOPyKRfp97 6k/cu2OMS6fRp6zCnPw1qbn2w/6GdCrs7Ejg+sez7hvMTLyDKRD+/Nua9e9zdwOIQO QNoXRJlnc4CHHzp10rZHZW7FrHvfNvL7S8LAu6KOyQGm2mDqnhvlg5CeLNmtnppOJ4 CYKI0AO5/At1w== From: "Paul A. Patience" Message-ID: <20220428181919.281837-1-paul@apatience.com> 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: , 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 * gnu/packages/maths.scm (sundials-5, sundials-openmpi-5): New variables. --- gnu/packages/maths.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) -- 2.36.0 diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e97f732def..dbb9bf1cf3 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -6190,6 +6190,29 @@ (define-public sundials-openmpi ,%openmpi-setup))))) (synopsis "SUNDIALS with MPI support"))) +(define-public sundials-5 + (package + (inherit sundials) + (name "sundials") + (version "5.8.0") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/LLNL/sundials/releases/download/v" + version "/sundials-" version ".tar.gz")) + (sha256 + (base32 + "04x2x0jchf9kbcw2a1c6f4h4as8sr6k2snfz8z9k897pa4rl1vfl")))))) + +(define-public sundials-openmpi-5 + (package/inherit sundials-5 + (name "sundials-openmpi") + (propagated-inputs + (package-propagated-inputs sundials-openmpi)) + (arguments + (package-arguments sundials-openmpi)) + (synopsis (package-synopsis sundials-openmpi)))) + (define-public sundials-julia (package (inherit sundials) From patchwork Thu Apr 28 18:19:25 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: "Paul A. Patience" X-Patchwork-Id: 38989 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 4BFA127BBEA; Thu, 28 Apr 2022 19:20:29 +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=unavailable 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 0A2A027BBE9 for ; Thu, 28 Apr 2022 19:20:29 +0100 (BST) Received: from localhost ([::1]:37626 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nk8ke-0007mj-4k for patchwork@mira.cbaines.net; Thu, 28 Apr 2022 14:20:28 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:38552) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nk8kF-0007is-Aj for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:56023) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nk8kF-0004kq-19 for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nk8kE-00038L-T4 for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55170] [PATCH 2/5] gnu: dealii: Remove trailing booleans. Resent-From: "Paul A. Patience" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 28 Apr 2022 18:20:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 55170 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 55170@debbugs.gnu.org Cc: ludovic.courtes@inria.fr, paul@apatience.com Received: via spool by 55170-submit@debbugs.gnu.org id=B55170.165116998111966 (code B ref 55170); Thu, 28 Apr 2022 18:20:02 +0000 Received: (at 55170) by debbugs.gnu.org; 28 Apr 2022 18:19:41 +0000 Received: from localhost ([127.0.0.1]:49909 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nk8jt-00036w-HF for submit@debbugs.gnu.org; Thu, 28 Apr 2022 14:19:41 -0400 Received: from mail-4317.proton.ch ([185.70.43.17]:20056) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nk8js-00036c-8j for 55170@debbugs.gnu.org; Thu, 28 Apr 2022 14:19:40 -0400 Date: Thu, 28 Apr 2022 18:19:25 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=apatience.com; s=protonmail2; t=1651169973; bh=uOUmP7P4KrWPsdLvrHVZaFFjtEsD1nCIJn8rooYtV+8=; h=Date:To:From:Cc:Reply-To:Subject:Message-ID:In-Reply-To: References:Feedback-ID:From:To:Cc:Date:Subject:Reply-To: Feedback-ID:Message-ID; b=UWT2YvqV8kYY1fKWUdK1oTARUqVzaD/NuhLVVq6neyoV26v1BZg2RwzumXPVpFB7t TGw8jZ4XM/TCaOqSNMcMM7cC9qgtmR1CzKmIylbfFmMRCT+dCGUJIVCYvY+A8s85f0 1Cs3BwXnc4iysHpOyYuEd5aT4wjnVwIkShjusCPhn8eRz9rZluGgTTfiTnL1GLOb4R Uuf+ns8bOyDgDu/0QrWXH5lZB0/Vw1jFFdVtRvhFTWEr3vC8BFNJrdNExIkUkqxz47 9Qdw+WW8XWxJEwz1qHOyqg3wkIMmIhxmj3jvFE65lURuho42F3QYtXps6YWtyz53ow fRP/KstVE5SRQ== From: "Paul A. Patience" Message-ID: <20220428181919.281837-2-paul@apatience.com> In-Reply-To: <20220428181919.281837-1-paul@apatience.com> References: <20220428181919.281837-1-paul@apatience.com> 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: , 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 * gnu/packages/maths.scm (dealii)[snippet]: Remove trailing boolean (and therefore the 'begin'). [native-inputs, inputs]: Reindent. [arguments]<#:phases>: Remove trailing boolean. --- gnu/packages/maths.scm | 23 ++++++++++------------- 1 file changed, 10 insertions(+), 13 deletions(-) -- 2.36.0 diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index dbb9bf1cf3..3c96378a4e 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5183,22 +5183,20 @@ (define-public dealii "dealii-fix-sundials.patch")) (modules '((guix build utils))) (snippet - '(begin - ;; Remove bundled boost, muparser, TBB and UMFPACK. - (delete-file-recursively "bundled") - #t)))) + ;; Remove bundled boost, muparser, TBB and UMFPACK. + '(delete-file-recursively "bundled")))) (build-system cmake-build-system) (outputs '("out" "doc")) (native-inputs ;; Required to build the documentation. - (list graphviz doxygen perl)) + (list graphviz doxygen perl)) (inputs - (list arpack-ng - openblas - gfortran - lapack - muparser - zlib)) + (list arpack-ng + openblas + gfortran + lapack + muparser + 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 @@ -5235,8 +5233,7 @@ (define-public dealii (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))))) + '("detailed.log" "summary.log"))))))))) (home-page "https://www.dealii.org/") (synopsis "Finite element library") (description From patchwork Thu Apr 28 18:19:29 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: "Paul A. Patience" X-Patchwork-Id: 38993 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 99D5527BBEA; Thu, 28 Apr 2022 19:21:10 +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=unavailable 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 62A7027BBE9 for ; Thu, 28 Apr 2022 19:21:10 +0100 (BST) Received: from localhost ([::1]:40030 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nk8lJ-00014D-Gj for patchwork@mira.cbaines.net; Thu, 28 Apr 2022 14:21:09 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:38562) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nk8kF-0007iz-Sh for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:56024) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nk8kF-0004pP-Ht for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nk8kF-00038T-CX for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55170] [PATCH 3/5] gnu: dealii-openmpi: Remove input labels. Resent-From: "Paul A. Patience" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 28 Apr 2022 18:20:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 55170 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 55170@debbugs.gnu.org Cc: ludovic.courtes@inria.fr, paul@apatience.com Received: via spool by 55170-submit@debbugs.gnu.org id=B55170.165116998511977 (code B ref 55170); Thu, 28 Apr 2022 18:20:03 +0000 Received: (at 55170) by debbugs.gnu.org; 28 Apr 2022 18:19:45 +0000 Received: from localhost ([127.0.0.1]:49911 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nk8jw-000377-P2 for submit@debbugs.gnu.org; Thu, 28 Apr 2022 14:19:44 -0400 Received: from mail-40136.proton.ch ([185.70.40.136]:62641) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nk8js-00036e-UI for 55170@debbugs.gnu.org; Thu, 28 Apr 2022 14:19:41 -0400 Date: Thu, 28 Apr 2022 18:19:29 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=apatience.com; s=protonmail2; t=1651169974; bh=L/yl2X3MhvbNdbaFOypnzAbF6PEMwL2FMYOudExAltk=; h=Date:To:From:Cc:Reply-To:Subject:Message-ID:In-Reply-To: References:Feedback-ID:From:To:Cc:Date:Subject:Reply-To: Feedback-ID:Message-ID; b=eacUK7b/g1s0ZIQX15O5sBSAie046KrigItTI9yMzcEqDrb5Ix009dYZLUhoQVhsz ULBEyUmj++VzKy03q2UbJsnIpCSxyHOIf9ToWibXGIboTSiNULauAASxAszYYYuCEX k0SJYccjfAU6rAa0B0PsAZYFAO6TMDSIq0rEiRZYsuJch/4O/1nJC+vpLoHOTcK6ZV XDyy+KKpBuFGa/3YFQ21NfRVvs+637t3ufpmM7J9vumUnCtBjHA5f2/RMfqFcLgm2P jQ5KqJWocPXZUjXoRGnLLvIqk6AKag8mlWXtMMmKXtUK24HF3KaiHP6ysEW0FI4eft 1fscw8WjsFXBw== From: "Paul A. Patience" Message-ID: <20220428181919.281837-3-paul@apatience.com> In-Reply-To: <20220428181919.281837-1-paul@apatience.com> References: <20220428181919.281837-1-paul@apatience.com> 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: , 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 * gnu/packages/maths.scm (dealii-openmpi)[inputs]: Remove labels. [propagated-inputs]: Same. --- gnu/packages/maths.scm | 24 +++++++++++++----------- 1 file changed, 13 insertions(+), 11 deletions(-) -- 2.36.0 diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 3c96378a4e..e6ebada82b 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5248,18 +5248,20 @@ (define-public dealii-openmpi (package/inherit dealii (name "dealii-openmpi") (inputs - `(("arpack" ,arpack-ng-openmpi) - ("metis" ,metis) - ("scalapack" ,scalapack) - ,@(alist-delete "arpack" (package-inputs dealii)))) + (modify-inputs (package-inputs dealii) + (delete "arpack") + (prepend arpack-ng-openmpi + metis + scalapack))) (propagated-inputs - `(("hdf5" ,hdf5-parallel-openmpi) - ("mpi" ,openmpi) - ("p4est" ,p4est-openmpi) - ("petsc" ,petsc-openmpi) - ("slepc" ,slepc-openmpi) - ("trilinos" ,trilinos-for-dealii-openmpi) - ,@(alist-delete "hdf5" (package-propagated-inputs dealii)))) + (modify-inputs (package-propagated-inputs dealii) + (delete "hdf5") + (prepend hdf5-parallel-openmpi + openmpi + p4est-openmpi + petsc-openmpi + slepc-openmpi + trilinos-for-dealii-openmpi))) (arguments (substitute-keyword-arguments (package-arguments dealii) ((#:configure-flags flags) From patchwork Thu Apr 28 18:19:32 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: "Paul A. Patience" X-Patchwork-Id: 38990 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 476A027BBEA; Thu, 28 Apr 2022 19:20:45 +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=unavailable 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 174F527BBE9 for ; Thu, 28 Apr 2022 19:20:45 +0100 (BST) Received: from localhost ([::1]:38314 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nk8ku-0008GN-8p for patchwork@mira.cbaines.net; Thu, 28 Apr 2022 14:20:44 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:38566) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nk8kG-0007jw-Fw for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:56025) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nk8kG-0004ua-6R for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nk8kG-00038c-1m for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55170] [PATCH 4/5] gnu: dealii: Add SUNDIALS dependency. Resent-From: "Paul A. Patience" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 28 Apr 2022 18:20:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 55170 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 55170@debbugs.gnu.org Cc: ludovic.courtes@inria.fr, paul@apatience.com Received: via spool by 55170-submit@debbugs.gnu.org id=B55170.165116998911998 (code B ref 55170); Thu, 28 Apr 2022 18:20:03 +0000 Received: (at 55170) by debbugs.gnu.org; 28 Apr 2022 18:19:49 +0000 Received: from localhost ([127.0.0.1]:49917 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nk8k0-00037S-VZ for submit@debbugs.gnu.org; Thu, 28 Apr 2022 14:19:49 -0400 Received: from mail-4018.proton.ch ([185.70.40.18]:15129) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nk8jy-00036k-8j for 55170@debbugs.gnu.org; Thu, 28 Apr 2022 14:19:46 -0400 Date: Thu, 28 Apr 2022 18:19:32 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=apatience.com; s=protonmail2; t=1651169980; bh=GfughrNWlPrfAe1MnjjEkxq8bxS1CYnNu9BsK/6X24M=; h=Date:To:From:Cc:Reply-To:Subject:Message-ID:In-Reply-To: References:Feedback-ID:From:To:Cc:Date:Subject:Reply-To: Feedback-ID:Message-ID; b=gldHwZIFxwSAIxVHlhg6Fc8MhfOG7WaHt6R4OzOnacA2p2oTsCM+aDMUPp/uHXtBi wuNDg9GkYocmCD3aYQE6Qr84tp8yVDY26P6GPaC/UFdXkziA84bP/P+25yWuGQCjsJ be7CdwPB88uXlOdCY+5ATmjAsvA+QQg7B/3Axg6JC3P4oD8G5N/YCjGuJFHFD4Pjnq D4sMtm8KrBlAJfqIa8DtSRVin4tmetw2fAGOxH1Q/mmH8UvZWygsPUO0s8iQv5suRI /bYRDZ8Be36gMdCtKNjASCv6Py0sQ3LKFE30uoxduI2cWnQYjClXz9gjBaEkZCMx6H fOXFlc+IrBGIw== From: "Paul A. Patience" Message-ID: <20220428181919.281837-4-paul@apatience.com> In-Reply-To: <20220428181919.281837-1-paul@apatience.com> References: <20220428181919.281837-1-paul@apatience.com> 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: , 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 * gnu/packages/maths.scm (dealii)[propagated-inputs]: Add sundials-5. Reformat list to clarify comment. (dealii-openmpi)[propagated-inputs]: Add sundials-openmpi-5. --- gnu/packages/maths.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) -- 2.36.0 diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index e6ebada82b..c74f055a07 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5205,7 +5205,11 @@ (define-public dealii ;; 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. - (list boost hdf5 suitesparse ; For UMFPACK. + (list boost + hdf5 + suitesparse ; For UMFPACK. + ;; SUNDIALS 6.0.0 and later will be supported in deal.II 9.4.0. + sundials-5 tbb)) (arguments `(#:build-type "DebugRelease" ; Supports only Debug, Release and DebugRelease. @@ -5255,12 +5259,13 @@ (define-public dealii-openmpi scalapack))) (propagated-inputs (modify-inputs (package-propagated-inputs dealii) - (delete "hdf5") + (delete "hdf5" "sundials") (prepend hdf5-parallel-openmpi openmpi p4est-openmpi petsc-openmpi slepc-openmpi + sundials-openmpi-5 trilinos-for-dealii-openmpi))) (arguments (substitute-keyword-arguments (package-arguments dealii) From patchwork Thu Apr 28 18:19:35 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: "Paul A. Patience" X-Patchwork-Id: 38991 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 2BDFD27BBE9; Thu, 28 Apr 2022 19:20:56 +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=unavailable 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 7584927BBEA for ; Thu, 28 Apr 2022 19:20:55 +0100 (BST) Received: from localhost ([::1]:39006 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1nk8l4-0000JU-HV for patchwork@mira.cbaines.net; Thu, 28 Apr 2022 14:20:54 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:38570) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1nk8kG-0007kn-TX for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:04 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:56026) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1nk8kG-0004vq-Jr for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:04 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1nk8kG-00038k-Fj for guix-patches@gnu.org; Thu, 28 Apr 2022 14:20:04 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#55170] [PATCH 5/5] gnu: dealii: Update to 9.3.3. 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Patience" Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 28 Apr 2022 18:20:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 55170 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 55170@debbugs.gnu.org Cc: ludovic.courtes@inria.fr, paul@apatience.com Received: via spool by 55170-submit@debbugs.gnu.org id=B55170.165116999212011 (code B ref 55170); Thu, 28 Apr 2022 18:20:04 +0000 Received: (at 55170) by debbugs.gnu.org; 28 Apr 2022 18:19:52 +0000 Received: from localhost ([127.0.0.1]:49919 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nk8k4-00037e-77 for submit@debbugs.gnu.org; Thu, 28 Apr 2022 14:19:52 -0400 Received: from mail-4022.proton.ch ([185.70.40.22]:10982) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1nk8jz-000373-EI for 55170@debbugs.gnu.org; Thu, 28 Apr 2022 14:19:48 -0400 Date: Thu, 28 Apr 2022 18:19:35 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=apatience.com; s=protonmail2; t=1651169981; bh=058B6tEF1RvyJ2m9IcPEbyJxihWny7k4utf0c6KxuW8=; h=Date:To:From:Cc:Reply-To:Subject:Message-ID:In-Reply-To: References:Feedback-ID:From:To:Cc:Date:Subject:Reply-To: Feedback-ID:Message-ID; b=ciNDbaqEgjJzbRu0otEcdmheHrlnelqVdt3qGfE9FxaNzyGyOtIegN710Jb8wXMgr f2Bhx9/W+eWGYZj1hS9w3QvvH1kIyeNfgaGf9k7oVAPEQ5jNV5VvkCQiO66Sc137/Z y/xIY6elQN8KrxEJPKybq6o5dDS11eEKLTA/f2MHKHMWF7diMp9kifGPCqNh9Ytrq8 GVy7HKt6PDe7G+vY/6wryTroJhi7GwDNCutwG9kdME802gfFmYLVEqBXH/PKx7Lz7l Ly0kEjtDsCQyWzbNtPHhvcjzr/Fk6zXM/j93rmjzO4FyjqK3yoPcdDq5lajdMMmGaA Bwk6HD9FlNt1Q== From: "Paul A. Patience" Message-ID: <20220428181919.281837-5-paul@apatience.com> In-Reply-To: <20220428181919.281837-1-paul@apatience.com> References: <20220428181919.281837-1-paul@apatience.com> 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: , 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 * gnu/packages/maths.scm (dealii): Update to 9.3.3. * gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch: Delete file. * gnu/packages/patches/dealii-fix-sundials.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Adjust accordingly. --- gnu/local.mk | 2 - gnu/packages/maths.scm | 6 +- ...lii-fix-compiliation-with-boost-1.78.patch | 40 ------------- .../patches/dealii-fix-sundials.patch | 60 ------------------- 4 files changed, 2 insertions(+), 106 deletions(-) delete mode 100644 gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch delete mode 100644 gnu/packages/patches/dealii-fix-sundials.patch -- 2.36.0 diff --git a/gnu/local.mk b/gnu/local.mk index 9bad87710c..d84d2bee3d 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -994,8 +994,6 @@ dist_patch_DATA = \ %D%/packages/patches/dbus-c++-gcc-compat.patch \ %D%/packages/patches/dbus-c++-threading-mutex.patch \ %D%/packages/patches/dbxfs-remove-sentry-sdk.patch \ - %D%/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch \ - %D%/packages/patches/dealii-fix-sundials.patch \ %D%/packages/patches/debops-constants-for-external-program-names.patch \ %D%/packages/patches/debops-debops-defaults-fall-back-to-less.patch \ %D%/packages/patches/dee-vapi.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index c74f055a07..2d3e67a6b4 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -5171,16 +5171,14 @@ (define trilinos-for-dealii-openmpi (define-public dealii (package (name "dealii") - (version "9.3.2") + (version "9.3.3") (source (origin (method url-fetch) (uri (string-append "https://github.com/dealii/dealii/releases/" "download/v" version "/dealii-" version ".tar.gz")) (sha256 - (base32 "1s0kawnljg24jj6nibwrif5gxdgg2daqfylhqqpl1lvmzmmxfhak")) - (patches (search-patches "dealii-fix-compiliation-with-boost-1.78.patch" - "dealii-fix-sundials.patch")) + (base32 "0a8s4yxcbvzmfgv5qcg27h2ss4fcnyhrhhs35glqj59l9cbmkysx")) (modules '((guix build utils))) (snippet ;; Remove bundled boost, muparser, TBB and UMFPACK. diff --git a/gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch b/gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch deleted file mode 100644 index 1937aa9afc..0000000000 --- a/gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch +++ /dev/null @@ -1,40 +0,0 @@ -From cbef761731627cece2a6f0276b87dacabbdc8a72 Mon Sep 17 00:00:00 2001 -From: David Wells -Date: Tue, 4 Jan 2022 12:46:30 -0500 -Subject: [PATCH] Fix compilation with boost 1.78. - -I bisected (fortunately Boost.Geometry a header-only library so adding the -include directory sufficed) and -https://github.com/boostorg/geometry/commit/6eb9e238bcb37e26dc31d16acf826784a2ba30f4 -is where this problem starts for us. See also -https://github.com/boostorg/geometry/issues/792 - the easiest fix for all such -issues is to just include the project header `boost/geometry/geometry.hpp`. - -In this particular case, if you look at the commit which causes grid_tools.cc -fails to compile, its because we were relying on some implicit includes. In -particular, we need the distance header to find the distance between points and -boxes, but that was previously included in another file. - -This patch has been adapted from -e0e76835519d122fd12b5858e16d08641a641c6a to apply to dealii 9.3.2. - -See https://github.com/dealii/dealii/pull/13165. ---- - include/deal.II/numerics/rtree.h | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/include/deal.II/numerics/rtree.h b/include/deal.II/numerics/rtree.h -index 1b9d04dacd..1e1bfd2932 100644 ---- a/include/deal.II/numerics/rtree.h -+++ b/include/deal.II/numerics/rtree.h -@@ -26,6 +26,7 @@ - #include - - DEAL_II_DISABLE_EXTRA_DIAGNOSTICS -+#include - #include - #include - DEAL_II_ENABLE_EXTRA_DIAGNOSTICS --- -2.30.2 - diff --git a/gnu/packages/patches/dealii-fix-sundials.patch b/gnu/packages/patches/dealii-fix-sundials.patch deleted file mode 100644 index 7dd5df45da..0000000000 --- a/gnu/packages/patches/dealii-fix-sundials.patch +++ /dev/null @@ -1,60 +0,0 @@ -From af73f368f7f9d4a00df075d1a9f50fc495f8e87a Mon Sep 17 00:00:00 2001 -From: Timo Heister -Date: Sat, 25 Dec 2021 12:30:45 -0500 -Subject: [PATCH] fix sundials compilation - ---- - include/deal.II/sundials/n_vector.templates.h | 11 ++++++----- - 1 file changed, 6 insertions(+), 5 deletions(-) - -diff --git a/include/deal.II/sundials/n_vector.templates.h b/include/deal.II/sundials/n_vector.templates.h -index 2b49e3efc9..746f63a03b 100644 ---- a/include/deal.II/sundials/n_vector.templates.h -+++ b/include/deal.II/sundials/n_vector.templates.h -@@ -253,13 +253,13 @@ namespace SUNDIALS - template < - typename VectorType, - typename std::enable_if_t::value, int> = 0> -- MPI_Comm -+ const MPI_Comm & - get_communicator(N_Vector v); - - template < - typename VectorType, - typename std::enable_if_t::value, int> = 0> -- MPI_Comm -+ const MPI_Comm & - get_communicator(N_Vector v); - - /** -@@ -481,7 +481,7 @@ SUNDIALS::internal::NVectorOperations::destroy(N_Vector v) - - template ::value, int>> --MPI_Comm -+const MPI_Comm & - SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v) - { - return unwrap_nvector_const(v)->block(0).get_mpi_communicator(); -@@ -491,7 +491,7 @@ SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v) - - template ::value, int>> --MPI_Comm -+const MPI_Comm & - SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v) - { - return unwrap_nvector_const(v)->get_mpi_communicator(); -@@ -519,7 +519,8 @@ SUNDIALS::internal::NVectorOperations::get_communicator_as_void_ptr(N_Vector v) - (void)v; - return nullptr; - # else -- return get_communicator(v); -+ // We need to cast away const here, as SUNDIALS demands a pure `void *`. -+ return &(const_cast(get_communicator(v))); - # endif - } - --- -2.30.2 -