From unknown Sat Aug 16 14:26:37 2025 X-Loop: help-debbugs@gnu.org Subject: bug#57143: python-dolfin-adjoint / FEniCS fails to build Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Thu, 11 Aug 2022 18:33:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 57143 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 57143@debbugs.gnu.org Cc: Paul Garlick X-Debbugs-Original-To: bug-guix@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.166024273824106 (code B ref -1); Thu, 11 Aug 2022 18:33:01 +0000 Received: (at submit) by debbugs.gnu.org; 11 Aug 2022 18:32:18 +0000 Received: from localhost ([127.0.0.1]:54992 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oMCyf-0006Gk-Qx for submit@debbugs.gnu.org; Thu, 11 Aug 2022 14:32:18 -0400 Received: from lists.gnu.org ([209.51.188.17]:33792) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oMCyc-0006GM-DU for submit@debbugs.gnu.org; Thu, 11 Aug 2022 14:32:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:56532) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oMCyb-0001HF-Uv for bug-guix@gnu.org; Thu, 11 Aug 2022 14:32:14 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:38482) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oMCyZ-00048z-1R for bug-guix@gnu.org; Thu, 11 Aug 2022 14:32:12 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 4F57BC96; Thu, 11 Aug 2022 20:32:07 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id zBTv6aQRjqW0; Thu, 11 Aug 2022 20:32:06 +0200 (CEST) Received: from jurong (unknown [IPv6:2001:861:c4:f2f0:1ce9:67cd:7487:edd5]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 9E31F3CE; Thu, 11 Aug 2022 20:32:06 +0200 (CEST) Date: Thu, 11 Aug 2022 20:32:02 +0200 From: Andreas Enge Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Received-SPF: pass client-ip=185.233.100.1; envelope-from=andreas@enge.fr; helo=hera.aquilenet.fr X-Spam_score_int: -18 X-Spam_score: -1.9 X-Spam_bar: - X-Spam_report: (-1.9 / 5.0 requ) BAYES_00=-1.9, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.6 (-) 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: -2.6 (--) Hello, when updating python-sympy, I noticed that its dependent python-dolfin-adjoint fails to build. Probably this was also true before, since we do not have a substitute. I think the problem was in FEniCS, with an assertion failure, so my impression was that the code computed a wrong solution. It would be nice if someone with special knowledge could have a look; some of the packages in the family also have updates available (but not dolfin itself if I saw correctly). Andreas From unknown Sat Aug 16 14:26:37 2025 X-Loop: help-debbugs@gnu.org Subject: bug#57143: Test failure in python-dolfin-adjoint References: In-Reply-To: Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Mon, 24 Jul 2023 11:56:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 57143 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 57143@debbugs.gnu.org Cc: Paul Garlick Received: via spool by 57143-submit@debbugs.gnu.org id=B57143.1690199744483 (code B ref 57143); Mon, 24 Jul 2023 11:56:01 +0000 Received: (at 57143) by debbugs.gnu.org; 24 Jul 2023 11:55:44 +0000 Received: from localhost ([127.0.0.1]:41986 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qNuAC-00007i-0X for submit@debbugs.gnu.org; Mon, 24 Jul 2023 07:55:44 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:58904) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1qNuA7-00007L-Hd for 57143@debbugs.gnu.org; Mon, 24 Jul 2023 07:55:42 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 59206F92; Mon, 24 Jul 2023 13:55:33 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id qzRBxhnuAg61; Mon, 24 Jul 2023 13:55:32 +0200 (CEST) Received: from jurong (unknown [IPv6:2001:861:c4:f2f0::c64]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 83F5DEB; Mon, 24 Jul 2023 13:55:32 +0200 (CEST) Date: Mon, 24 Jul 2023 13:55:31 +0200 From: Andreas Enge Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline X-Spam-Score: -0.0 (/) 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: -1.0 (-) Hello, below are more details on the current test failure of python-dolfin-adjoint version 2019.1.0. Maybe an option would be to try to update to a newer version? There is 2019.1.2. Andreas =================================== FAILURES =================================== _____________________________ test_read_checkpoint _____________________________ def test_read_checkpoint(): with stop_annotating(): N = 15 mesh = UnitSquareMesh(N, N) V = FunctionSpace(mesh, "CG", 1) x = SpatialCoordinate(mesh) v = project(x[0]*x[1]*cos(x[1]), V) out = XDMFFile(file_from_curr_dir("scalar.xdmf")) out.write_checkpoint(v, "u", 0.0) out.close() exact = assemble(v*dx) mesh = UnitSquareMesh(N, N) V = FunctionSpace(mesh, "CG", 1) v = Function(V) c = Control(v) J = assemble(v*dx) infile = XDMFFile(file_from_curr_dir("scalar.xdmf")) u = Function(V) > infile.read_checkpoint(u,'u', -1) tests/fenics_adjoint/test_io.py:38: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = args = (Coefficient(FunctionSpace(Mesh(VectorElement(FiniteElement('Lagrange', triangle, 1), dim=2), 38754), FiniteElement('Lagrange', triangle, 1)), 38769), 'u', -1) kwargs = {}, annotate = True def XDMFFile_read_checkpoint(self, *args, **kwargs): annotate = annotate_tape(kwargs) > output = __XDMFFile_read_checkpoint__(self, *args, **kwargs) E RuntimeError: basic_string::_M_construct null not valid /gnu/store/p7hjddizapgmdk62dpvmrdkac0d4l3r9-python-dolfin-adjoint-2019.1.0/lib/python3.10/site-packages/fenics_adjoint/types/io.py:48: RuntimeError ----------------------------- Captured stdout call ----------------------------- Calling FFC just-in-time (JIT) compiler, this may take some time. ------------------------------ Captured log call ------------------------------- Level 25 FFC:log.py:127 Calling FFC just-in-time (JIT) compiler, this may take some time. INFO FFC:log.py:127 Compiling form ffc_form_e905624fad7a62b101d5d4bc784070d31ec0cc46 INFO FFC:log.py:127 Compiler stage 1: Analyzing form(s) INFO FFC:log.py:127 ----------------------------------- DEBUG FFC:log.py:127 Preprocessing form using 'uflacs' representation family. INFO FFC:log.py:127 INFO FFC:log.py:127 Geometric dimension: 2 Number of cell subdomains: 0 Rank: 1 Arguments: '(v_0)' Number of coefficients: 0 Coefficients: '[]' Unique elements: 'CG1(?,?), Vector<2 x CG1(?,?)>' Unique sub elements: 'CG1(?,?), Vector<2 x CG1(?,?)>' INFO FFC:log.py:127 representation: auto --> uflacs INFO FFC:log.py:127 quadrature_rule: auto --> default INFO FFC:log.py:127 quadrature_degree: auto --> 6 INFO FFC:log.py:127 quadrature_degree: 6 INFO FFC:log.py:127 INFO FFC:log.py:127 Compiler stage 1 finished in 0.00596237 seconds. INFO FFC:log.py:127 Compiler stage 2: Computing intermediate representation INFO FFC:log.py:127 ------------------------------------------------------- INFO FFC:log.py:127 Computing representation of 0 elements INFO FFC:log.py:127 Computing representation of 0 dofmaps INFO FFC:log.py:127 Computing representation of 0 coordinate mappings INFO FFC:log.py:127 Computing representation of integrals INFO FFC:log.py:127 Computing uflacs representation DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG FFC:log.py:127 Reusing element from cache DEBUG UFL:log.py:127 Blocks of each mode: 1 full INFO FFC:log.py:127 Computing representation of forms INFO FFC:log.py:127 INFO FFC:log.py:127 Compiler stage 2 finished in 0.0164835 seconds. INFO FFC:log.py:127 Compiler stage 3: Optimizing intermediate representation INFO FFC:log.py:127 -------------------------------------------------------- INFO FFC:log.py:127 Optimizing uflacs representation INFO FFC:log.py:127 INFO FFC:log.py:127 Compiler stage 3 finished in 0.000202894 seconds. INFO FFC:log.py:127 Compiler stage 4: Generating code INFO FFC:log.py:127 --------------------------------- INFO FFC:log.py:127 Generating code for 0 finite_element(s) INFO FFC:log.py:127 Generating code for 0 dofmap(s) INFO FFC:log.py:127 Generating code for 0 coordinate_mapping(s) INFO FFC:log.py:127 Generating code for integrals INFO FFC:log.py:127 Generating code from ffc.uflacs representation INFO FFC:log.py:127 Generating code for forms INFO FFC:log.py:127 INFO FFC:log.py:127 Compiler stage 4 finished in 0.00399137 seconds. INFO FFC:log.py:127 Compiler stage 4.1 finished in 9.53674e-07 seconds. INFO FFC:log.py:127 Compiler stage 5: Formatting code INFO FFC:log.py:127 --------------------------------- INFO FFC:log.py:127 INFO FFC:log.py:127 Compiler stage 5 finished in 0.000437498 seconds. INFO FFC:log.py:127 FFC finished in 0.0274181 seconds. =============================== warnings summary =============================== ../../../gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:96 /gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:96: PytestDeprecationWarning: @pytest.yield_fixture is deprecated. Use @pytest.fixture instead; they are the same. @pytest.yield_fixture(scope="function") ../../../gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:230 /gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:230: PytestDeprecationWarning: @pytest.yield_fixture is deprecated. Use @pytest.fixture instead; they are the same. @pytest.yield_fixture(scope="function") ../../../gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:255 /gnu/store/v36c8jmb0316czxkqajpkai70kjkmkfy-fenics-2019.1.0.post0/lib/python3.10/site-packages/dolfin_utils/test/fixtures.py:255: PytestDeprecationWarning: @pytest.yield_fixture is deprecated. Use @pytest.fixture instead; they are the same. def pushpop_parameters(): -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/fenics_adjoint/test_io.py::test_read_checkpoint - RuntimeError: ... = 1 failed, 125 passed, 9 skipped, 1 xfailed, 3 warnings in 839.66s (0:13:59) == From unknown Sat Aug 16 14:26:37 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: Andreas Enge Subject: bug#57143: closed (Close) Message-ID: References: X-Gnu-PR-Message: they-closed 57143 X-Gnu-PR-Package: guix Reply-To: 57143@debbugs.gnu.org Date: Mon, 31 Mar 2025 21:56:03 +0000 Content-Type: multipart/mixed; boundary="----------=_1743458163-27948-1" This is a multi-part message in MIME format... ------------=_1743458163-27948-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #57143: python-dolfin-adjoint / FEniCS fails to build which was filed against the guix package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 57143@debbugs.gnu.org. --=20 57143: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D57143 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1743458163-27948-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 57143-done) by debbugs.gnu.org; 31 Mar 2025 21:55:29 +0000 Received: from localhost ([127.0.0.1]:43265 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tzN6O-0007Dt-D3 for submit@debbugs.gnu.org; Mon, 31 Mar 2025 17:55:28 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:45004) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tzN6E-0007AJ-Kj for 57143-done@debbugs.gnu.org; Mon, 31 Mar 2025 17:55:19 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 826523F4; Mon, 31 Mar 2025 23:55:12 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id rRItMYOZMt_u; Mon, 31 Mar 2025 23:55:12 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 7E17E1B6; Mon, 31 Mar 2025 23:55:10 +0200 (CEST) Date: Mon, 31 Mar 2025 23:55:08 +0200 From: Andreas Enge To: 57143-done@debbugs.gnu.org Subject: Close Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline X-Rspamd-Queue-Id: 826523F4 X-Spamd-Result: default: False [8.40 / 15.00]; SPAM_FLAG(5.00)[]; NEURAL_SPAM(3.00)[0.999]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; FROM_EQ_ENVFROM(0.00)[]; MIME_TRACE(0.00)[0:+]; RCPT_COUNT_ONE(0.00)[1]; ARC_NA(0.00)[]; TO_DN_NONE(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; RCVD_VIA_SMTP_AUTH(0.00)[]; FROM_HAS_DN(0.00)[]; RCVD_TLS_ALL(0.00)[] X-Spam-Level: ******** X-Rspamd-Action: add header X-Spamd-Bar: ++++++++ X-Rspamd-Server: hera X-Spam: Yes X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 57143-done 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: -1.0 (-) This will be handled in https://issues.guix.gnu.org/77195 . Andreas ------------=_1743458163-27948-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 11 Aug 2022 18:32:18 +0000 Received: from localhost ([127.0.0.1]:54992 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oMCyf-0006Gk-Qx for submit@debbugs.gnu.org; Thu, 11 Aug 2022 14:32:18 -0400 Received: from lists.gnu.org ([209.51.188.17]:33792) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oMCyc-0006GM-DU for submit@debbugs.gnu.org; Thu, 11 Aug 2022 14:32:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:56532) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oMCyb-0001HF-Uv for bug-guix@gnu.org; Thu, 11 Aug 2022 14:32:14 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:38482) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oMCyZ-00048z-1R for bug-guix@gnu.org; Thu, 11 Aug 2022 14:32:12 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 4F57BC96; Thu, 11 Aug 2022 20:32:07 +0200 (CEST) X-Virus-Scanned: Debian amavisd-new at aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id zBTv6aQRjqW0; Thu, 11 Aug 2022 20:32:06 +0200 (CEST) Received: from jurong (unknown [IPv6:2001:861:c4:f2f0:1ce9:67cd:7487:edd5]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 9E31F3CE; Thu, 11 Aug 2022 20:32:06 +0200 (CEST) Date: Thu, 11 Aug 2022 20:32:02 +0200 From: Andreas Enge To: bug-guix@gnu.org Subject: python-dolfin-adjoint / FEniCS fails to build Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Received-SPF: pass client-ip=185.233.100.1; envelope-from=andreas@enge.fr; helo=hera.aquilenet.fr X-Spam_score_int: -18 X-Spam_score: -1.9 X-Spam_bar: - X-Spam_report: (-1.9 / 5.0 requ) BAYES_00=-1.9, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.6 (-) X-Debbugs-Envelope-To: submit Cc: Paul Garlick 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: -2.6 (--) Hello, when updating python-sympy, I noticed that its dependent python-dolfin-adjoint fails to build. Probably this was also true before, since we do not have a substitute. I think the problem was in FEniCS, with an assertion failure, so my impression was that the code computed a wrong solution. It would be nice if someone with special knowledge could have a look; some of the packages in the family also have updates available (but not dolfin itself if I saw correctly). Andreas ------------=_1743458163-27948-1--