From unknown Mon Aug 18 22:11:31 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#53065] [PATCH] gnu: dealii: Update to 9.3.2. Resent-From: Felix Gruber Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 07 Jan 2022 07:40:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 53065 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 53065@debbugs.gnu.org Cc: Felix Gruber X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.164154118326896 (code B ref -1); Fri, 07 Jan 2022 07:40:01 +0000 Received: (at submit) by debbugs.gnu.org; 7 Jan 2022 07:39:43 +0000 Received: from localhost ([127.0.0.1]:42919 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n5jqZ-0006zL-Gm for submit@debbugs.gnu.org; Fri, 07 Jan 2022 02:39:43 -0500 Received: from lists.gnu.org ([209.51.188.17]:52712) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n5jqP-0006yl-Ml for submit@debbugs.gnu.org; Fri, 07 Jan 2022 02:39:33 -0500 Received: from eggs.gnu.org ([209.51.188.92]:32836) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n5jqO-0007Dt-DX for guix-patches@gnu.org; Fri, 07 Jan 2022 02:39:25 -0500 Received: from mout01.posteo.de ([185.67.36.65]:56075) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n5jqL-0008Tz-P1 for guix-patches@gnu.org; Fri, 07 Jan 2022 02:39:24 -0500 Received: from submission (posteo.de [89.146.220.130]) by mout01.posteo.de (Postfix) with ESMTPS id 0789E240028 for ; Fri, 7 Jan 2022 08:39:16 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=posteo.net; s=2017; t=1641541157; bh=6VtN2tNBdZky+dFUp8EDAx8jWo34Fuy6lRCPfF2rroI=; h=From:To:Cc:Subject:Date:From; b=Sh80tkTkoxhAnbtRpZYVUzZRm0Dz2Ex1wUS6U+MnzUcmzmdLh4VM9XLO0koIlsPo+ zNUszKyE5ANFL6+JtREOVnbNIAxN+sXP0sadY1PI602mUx97UKjfHG9R+2T1Ho+JYr G9FIBLrXjWvgRui833zWaNHurELH90aR5uuqqLxnVJ8b7FWOKM2HeLWTQfCmVao63N 3tYfGWfeDWDG2WIG4ZjlVGWEk1SW4mIOgSzYyJaRCUFscuyGi3NZ+rCPIUPRTfG5fe WRgjccthyQ8WnDUCicQ888q4orfUIWoejQkb4nzPrRgmUIjl6sFxlsznoQQ5NykbgR T4MZ4oymJUcmw== Received: from customer (localhost [127.0.0.1]) by submission (posteo.de) with ESMTPSA id 4JVZq830Ndz9rxL; Fri, 7 Jan 2022 08:39:16 +0100 (CET) From: Felix Gruber Date: Fri, 7 Jan 2022 07:39:05 +0000 Message-Id: <20220107073905.35503-1-felgru@posteo.net> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.65; envelope-from=felgru@posteo.net; helo=mout01.posteo.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H2=-0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.7 (/) 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: 2.0 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: * gnu/packages/maths.scm (dealii): Update to 9.3.2. [source]: Add dealii-fix-compiliation-with-boost-1.78.patch and dealii-fix-sundials.patch. [inputs]: Use simplified format. [native-inputs]: Use sim [...] Content analysis details: (2.0 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.0 SPF_HELO_PASS SPF: HELO matches SPF record 1.0 SPF_SOFTFAIL SPF: sender does not match SPF record (softfail) 2.0 PDS_OTHER_BAD_TLD Untrustworthy TLDs [URI: nixo.xyz (xyz)] -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager * gnu/packages/maths.scm (dealii): Update to 9.3.2. [source]: Add dealii-fix-compiliation-with-boost-1.78.patch and dealii-fix-sundials.patch. [inputs]: Use simplified format. [native-inputs]: Use simplified format. * gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch: New file. * gnu/packages/patches/dealii-fix-sundials.patch: New file. * gnu/local.mk: Add new patch files. --- gnu/local.mk | 4 +- gnu/packages/maths.scm | 24 ++++---- ...lii-fix-compiliation-with-boost-1.78.patch | 40 +++++++++++++ .../patches/dealii-fix-sundials.patch | 60 +++++++++++++++++++ 4 files changed, 115 insertions(+), 13 deletions(-) create mode 100644 gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch create mode 100644 gnu/packages/patches/dealii-fix-sundials.patch diff --git a/gnu/local.mk b/gnu/local.mk index 31354e413f..be5268b9e8 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -31,7 +31,7 @@ # Copyright © 2020 R Veera Kumar # Copyright © 2020 Nicolò Balzarotti # Copyright © 2020 Michael Rohleder -# Copyright © 2020, 2021 Felix Gruber +# Copyright © 2020, 2021, 2022 Felix Gruber # Copyright © 2020 Ryan Prior # Copyright © 2020 Jan Wielkiewicz # Copyright © 2020, 2021 Brice Waegeneire @@ -987,6 +987,8 @@ 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 b0944f307b..f4dba92c11 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -34,7 +34,7 @@ ;;; Copyright © 2019 Steve Sprang ;;; Copyright © 2019 Robert Smith ;;; Copyright © 2020 Jakub Kądziołka -;;; Copyright © 2020, 2021 Felix Gruber +;;; Copyright © 2020–2022 Felix Gruber ;;; Copyright © 2020 R Veera Kumar ;;; Copyright © 2020 Vincent Legoll ;;; Copyright © 2020 Nicolò Balzarotti @@ -5268,14 +5268,16 @@ A unique design feature of Trilinos is its focus on packages.") (define-public dealii (package (name "dealii") - (version "9.3.1") + (version "9.3.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/dealii/dealii/releases/" "download/v" version "/dealii-" version ".tar.gz")) (sha256 - (base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6")) + (base32 "1s0kawnljg24jj6nibwrif5gxdgg2daqfylhqqpl1lvmzmmxfhak")) + (patches (search-patches "dealii-fix-compiliation-with-boost-1.78.patch" + "dealii-fix-sundials.patch")) (modules '((guix build utils))) (snippet '(begin @@ -5286,16 +5288,14 @@ A unique design feature of Trilinos is its focus on packages.") (outputs '("out" "doc")) (native-inputs ;; Required to build the documentation. - `(("dot" ,graphviz) - ("doxygen" ,doxygen) - ("perl" ,perl))) + (list graphviz doxygen perl)) (inputs - `(("arpack" ,arpack-ng) - ("blas" ,openblas) - ("gfortran" ,gfortran) - ("lapack" ,lapack) - ("muparser" ,muparser) - ("zlib" ,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 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 new file mode 100644 index 0000000000..1937aa9afc --- /dev/null +++ b/gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch @@ -0,0 +1,40 @@ +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 new file mode 100644 index 0000000000..7dd5df45da --- /dev/null +++ b/gnu/packages/patches/dealii-fix-sundials.patch @@ -0,0 +1,60 @@ +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 + -- 2.30.2 From unknown Mon Aug 18 22:11:31 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Felix Gruber Subject: bug#53065: closed (Re: [bug#53065] [PATCH] gnu: dealii: Update to 9.3.2.) Message-ID: References: <87lezm1u8g.fsf@nicolasgoaziou.fr> <20220107073905.35503-1-felgru@posteo.net> X-Gnu-PR-Message: they-closed 53065 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 53065@debbugs.gnu.org Date: Tue, 11 Jan 2022 09:46:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1641894362-14135-1" This is a multi-part message in MIME format... ------------=_1641894362-14135-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #53065: [PATCH] gnu: dealii: Update to 9.3.2. which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 53065@debbugs.gnu.org. --=20 53065: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D53065 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1641894362-14135-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 53065-done) by debbugs.gnu.org; 11 Jan 2022 09:45:36 +0000 Received: from localhost ([127.0.0.1]:54164 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n7Dib-0003f8-I7 for submit@debbugs.gnu.org; Tue, 11 Jan 2022 04:45:36 -0500 Received: from relay9-d.mail.gandi.net ([217.70.183.199]:33985) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n7Dia-0003eu-C4 for 53065-done@debbugs.gnu.org; Tue, 11 Jan 2022 04:45:28 -0500 Received: (Authenticated sender: admin@nicolasgoaziou.fr) by relay9-d.mail.gandi.net (Postfix) with ESMTPSA id 2D292FF808; Tue, 11 Jan 2022 09:45:20 +0000 (UTC) From: Nicolas Goaziou To: Felix Gruber Subject: Re: [bug#53065] [PATCH] gnu: dealii: Update to 9.3.2. References: <20220107073905.35503-1-felgru@posteo.net> Date: Tue, 11 Jan 2022 10:45:19 +0100 In-Reply-To: <20220107073905.35503-1-felgru@posteo.net> (Felix Gruber's message of "Fri, 7 Jan 2022 07:39:05 +0000") Message-ID: <87lezm1u8g.fsf@nicolasgoaziou.fr> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 53065-done Cc: 53065-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 (-) Hello, Felix Gruber writes: > * gnu/packages/maths.scm (dealii): Update to 9.3.2. > [source]: Add dealii-fix-compiliation-with-boost-1.78.patch and > dealii-fix-sundials.patch. > [inputs]: Use simplified format. > [native-inputs]: Use simplified format. > * gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch: > New file. > * gnu/packages/patches/dealii-fix-sundials.patch: New file. > * gnu/local.mk: Add new patch files. Applied. Thank you. 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Date: Fri, 7 Jan 2022 07:39:05 +0000 Message-Id: <20220107073905.35503-1-felgru@posteo.net> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Received-SPF: pass client-ip=185.67.36.65; envelope-from=felgru@posteo.net; helo=mout01.posteo.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 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_DNSWL_MED=-2.3, RCVD_IN_MSPIKE_H2=-0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: 0.7 (/) X-Debbugs-Envelope-To: submit 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: 2.0 (++) X-Spam-Report: Spam detection software, running on the system "debbugs.gnu.org", has NOT identified this incoming email as spam. The original message has been attached to this so you can view it or label similar future email. If you have any questions, see the administrator of that system for details. Content preview: * gnu/packages/maths.scm (dealii): Update to 9.3.2. [source]: Add dealii-fix-compiliation-with-boost-1.78.patch and dealii-fix-sundials.patch. [inputs]: Use simplified format. [native-inputs]: Use sim [...] Content analysis details: (2.0 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.0 SPF_HELO_PASS SPF: HELO matches SPF record 1.0 SPF_SOFTFAIL SPF: sender does not match SPF record (softfail) 2.0 PDS_OTHER_BAD_TLD Untrustworthy TLDs [URI: nixo.xyz (xyz)] -1.0 MAILING_LIST_MULTI Multiple indicators imply a widely-seen list manager * gnu/packages/maths.scm (dealii): Update to 9.3.2. [source]: Add dealii-fix-compiliation-with-boost-1.78.patch and dealii-fix-sundials.patch. [inputs]: Use simplified format. [native-inputs]: Use simplified format. * gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch: New file. * gnu/packages/patches/dealii-fix-sundials.patch: New file. * gnu/local.mk: Add new patch files. --- gnu/local.mk | 4 +- gnu/packages/maths.scm | 24 ++++---- ...lii-fix-compiliation-with-boost-1.78.patch | 40 +++++++++++++ .../patches/dealii-fix-sundials.patch | 60 +++++++++++++++++++ 4 files changed, 115 insertions(+), 13 deletions(-) create mode 100644 gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch create mode 100644 gnu/packages/patches/dealii-fix-sundials.patch diff --git a/gnu/local.mk b/gnu/local.mk index 31354e413f..be5268b9e8 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -31,7 +31,7 @@ # Copyright © 2020 R Veera Kumar # Copyright © 2020 Nicolò Balzarotti # Copyright © 2020 Michael Rohleder -# Copyright © 2020, 2021 Felix Gruber +# Copyright © 2020, 2021, 2022 Felix Gruber # Copyright © 2020 Ryan Prior # Copyright © 2020 Jan Wielkiewicz # Copyright © 2020, 2021 Brice Waegeneire @@ -987,6 +987,8 @@ 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 b0944f307b..f4dba92c11 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -34,7 +34,7 @@ ;;; Copyright © 2019 Steve Sprang ;;; Copyright © 2019 Robert Smith ;;; Copyright © 2020 Jakub Kądziołka -;;; Copyright © 2020, 2021 Felix Gruber +;;; Copyright © 2020–2022 Felix Gruber ;;; Copyright © 2020 R Veera Kumar ;;; Copyright © 2020 Vincent Legoll ;;; Copyright © 2020 Nicolò Balzarotti @@ -5268,14 +5268,16 @@ A unique design feature of Trilinos is its focus on packages.") (define-public dealii (package (name "dealii") - (version "9.3.1") + (version "9.3.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/dealii/dealii/releases/" "download/v" version "/dealii-" version ".tar.gz")) (sha256 - (base32 "1f0sqvlxvl0myqcn0q6xrn1vnp5pgx143lai4a4jkh1dmdv4cbx6")) + (base32 "1s0kawnljg24jj6nibwrif5gxdgg2daqfylhqqpl1lvmzmmxfhak")) + (patches (search-patches "dealii-fix-compiliation-with-boost-1.78.patch" + "dealii-fix-sundials.patch")) (modules '((guix build utils))) (snippet '(begin @@ -5286,16 +5288,14 @@ A unique design feature of Trilinos is its focus on packages.") (outputs '("out" "doc")) (native-inputs ;; Required to build the documentation. - `(("dot" ,graphviz) - ("doxygen" ,doxygen) - ("perl" ,perl))) + (list graphviz doxygen perl)) (inputs - `(("arpack" ,arpack-ng) - ("blas" ,openblas) - ("gfortran" ,gfortran) - ("lapack" ,lapack) - ("muparser" ,muparser) - ("zlib" ,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 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 new file mode 100644 index 0000000000..1937aa9afc --- /dev/null +++ b/gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch @@ -0,0 +1,40 @@ +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 new file mode 100644 index 0000000000..7dd5df45da --- /dev/null +++ b/gnu/packages/patches/dealii-fix-sundials.patch @@ -0,0 +1,60 @@ +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 + -- 2.30.2 ------------=_1641894362-14135-1--