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d="scan'208,223";a="72172475" From: To: Subject: [PATCH] fenics: Do not use mpirun for tests Thread-Topic: [PATCH] fenics: Do not use mpirun for tests Thread-Index: AQHYihiDt/XO5z75+U2c/n1SP0a9PA== Date: Mon, 27 Jun 2022 11:24:49 +0000 Message-ID: <87bkuefiwu.fsf@dlr.de> Accept-Language: de-DE, en-US Content-Language: en-US X-MS-Has-Attach: yes X-MS-TNEF-Correlator: Content-Type: multipart/mixed; boundary="_002_87bkuefiwufsfdlrde_" MIME-Version: 1.0 Received-SPF: pass client-ip=194.94.201.12; envelope-from=Ontje.Luensdorf@dlr.de; helo=mailin.dlr.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, SPF_HELO_NONE=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: -1.3 (-) X-Debbugs-Envelope-To: submit X-Mailman-Approved-At: Mon, 27 Jun 2022 08:31:51 -0400 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: -2.3 (--) --_002_87bkuefiwufsfdlrde_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi guix, the fenics package tests fail and it looks like the tests are run 3 times concurrently. Every test name is printed three times in the build log, for example here: https://ci.guix.gnu.org/build/1039880/log/raw This is the maximum number of parallel jobs of the test run and if I increase it, I get more print outputs. AFAIK, pytest doesn't support mpi, so I don't see why the tests are executed this way. Anyhow, in the attached patch, the tests are executed directly using pytest. This prevents the tests from getting stuck and subsequently I discovered a failure in XDMF tests. With this test also disabled, the package builds fine for me. Maybe a fenics or mpi expert can tell if this patch makes sense? Best regards, Ontje --_002_87bkuefiwufsfdlrde_ Content-Type: text/x-patch; name="0001-gnu-fenics-Do-not-mpirun-tests.patch" Content-Description: 0001-gnu-fenics-Do-not-mpirun-tests.patch Content-Disposition: attachment; filename="0001-gnu-fenics-Do-not-mpirun-tests.patch"; size=2010; creation-date="Mon, 27 Jun 2022 11:24:49 GMT"; modification-date="Mon, 27 Jun 2022 11:24:49 GMT" Content-ID: Content-Transfer-Encoding: base64 RnJvbSA4ZGQxMTU5Njg1MWFiNWE3YWUxZDQ4M2I5ODgzODk0YTliZDRkNGJhIE1vbiBTZXAgMTcg MDA6MDA6MDAgMjAwMQ0KRnJvbTogPT9VVEYtOD9xP09udGplPTIwTD1DMz1CQ25zZG9yZj89IDxv bnRqZS5sdWVuc2RvcmZAZGxyLmRlPg0KRGF0ZTogTW9uLCAyNyBKdW4gMjAyMiAxMTo1MToxMCAr MDIwMA0KU3ViamVjdDogW1BBVENIXSBnbnU6IGZlbmljczogRG8gbm90IG1waXJ1biB0ZXN0cy4N Cg0KKiBnbnUvcGFja2FnZXMvc2ltdWxhdGlvbi5zY20gKGZlbmljcylbcGhhc2VzXTogRG8gbm90 IHVzZSBtcGlydW4gZm9yIHRlc3RzDQogIGFuZCBza2lwIGZhaWxpbmcgWERNRiB0ZXN0Lg0KLS0t DQogZ251L3BhY2thZ2VzL3NpbXVsYXRpb24uc2NtIHwgMTcgKysrKysrKystLS0tLS0tLS0NCiAx IGZpbGUgY2hhbmdlZCwgOCBpbnNlcnRpb25zKCspLCA5IGRlbGV0aW9ucygtKQ0KDQpkaWZmIC0t Z2l0IGEvZ251L3BhY2thZ2VzL3NpbXVsYXRpb24uc2NtIGIvZ251L3BhY2thZ2VzL3NpbXVsYXRp b24uc2NtDQppbmRleCA5ZTkyZmJjYzViLi5kZjRkZDJkMTdhIDEwMDY0NA0KLS0tIGEvZ251L3Bh Y2thZ2VzL3NpbXVsYXRpb24uc2NtDQorKysgYi9nbnUvcGFja2FnZXMvc2ltdWxhdGlvbi5zY20N CkBAIC02NjUsMTUgKzY2NSwxNCBAQCAoZGVmaW5lLXB1YmxpYyBmZW5pY3MNCiAgICAgICAgICAg IChsYW1iZGEqICgjOmtleSB0ZXN0cz8gIzphbGxvdy1vdGhlci1rZXlzKQ0KICAgICAgICAgICAg ICAod2hlbiB0ZXN0cz8NCiAgICAgICAgICAgICAgICAod2l0aC1kaXJlY3RvcnktZXhjdXJzaW9u ICJ0ZXN0Ig0KLSAgICAgICAgICAgICAgICAgOzsgTm90ZTogVGhlIHRlc3QgdGVzdF9zbmVzX3Nl dF9mcm9tX29wdGlvbnMoKSBpbiB0aGUgZmlsZQ0KLSAgICAgICAgICAgICAgICAgOzsgdW5pdC9u bHMvdGVzdF9QRVRTY1NORVNfc29sdmVyLnB5IGZhaWxzIGFuZCBpcyBpZ25vcmVkLg0KLSAgICAg ICAgICAgICAgICAgOzsgTGltaXQgdGhlIG51bWJlciBvZiBqb2JzIHRvIDMgYXMgNTAwIE1pQiBv ZiBtZW1vcnkgaXMgdXNlZA0KLSAgICAgICAgICAgICAgICAgOzsgcGVyIHByb2Nlc3MuDQotICAg ICAgICAgICAgICAgICAoaW52b2tlICJtcGlydW4iICItbnAiIChudW1iZXItPnN0cmluZw0KLSAg ICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgKG1pbiAzIChwYXJhbGxlbC1q b2ItY291bnQpKSkNCi0gICAgICAgICAgICAgICAgICAgICAgICAgInB5dGhvbiIgIi1CIiAiLW0i DQotICAgICAgICAgICAgICAgICAgICAgICAgICJweXRlc3QiICJ1bml0IiAiLS1pZ25vcmUiDQot ICAgICAgICAgICAgICAgICAgICAgICAgICJ1bml0L25scy90ZXN0X1BFVFNjU05FU19zb2x2ZXIu cHkiKSkpKSkNCisgICAgICAgICAgICAgICAgIChpbnZva2UNCisgICAgICAgICAgICAgICAgICAi cHl0ZXN0IiAidW5pdCINCisgICAgICAgICAgICAgICAgICA7OyBUaGUgdGVzdCB0ZXN0X3NuZXNf c2V0X2Zyb21fb3B0aW9ucygpIGluIHRoZSBmaWxlDQorICAgICAgICAgICAgICAgICAgOzsgdW5p dC9ubHMvdGVzdF9QRVRTY1NORVNfc29sdmVyLnB5IGZhaWxzIGFuZCBpcyBpZ25vcmVkLg0KKyAg ICAgICAgICAgICAgICAgICItLWlnbm9yZSIgInVuaXQvbmxzL3Rlc3RfUEVUU2NTTkVTX3NvbHZl ci5weSINCisgICAgICAgICAgICAgICAgICA7OyBGYWlscyB3aXRoIGEgc2VnZmF1bHQuDQorICAg ICAgICAgICAgICAgICAgIi0taWdub3JlIiAidW5pdC9pby90ZXN0X1hETUYucHkiDQorICAgICAg ICAgICAgICAgICAgKSkpKSkNCiAgICAgICAgICAoYWRkLWFmdGVyICdpbnN0YWxsICdpbnN0YWxs LWRlbW8tZmlsZXMNCiAgICAgICAgICAgIChsYW1iZGEqICgjOmtleSBvdXRwdXRzICM6YWxsb3ct b3RoZXIta2V5cykNCiAgICAgICAgICAgICAgKGxldCogKChkZW1vcyAoc3RyaW5nLWFwcGVuZA0K DQpiYXNlLWNvbW1pdDogOTc3NjYzMjNiYzZlMmI0ZGNmYmE0ZDZiNDY3NDlhNDI4MGJjYTcwOQ0K LS0gDQoyLjM2LjENCg0K --_002_87bkuefiwufsfdlrde_-- From debbugs-submit-bounces@debbugs.gnu.org Mon Jul 04 06:18:46 2022 Received: (at 56257) by debbugs.gnu.org; 4 Jul 2022 10:18:46 +0000 Received: from localhost ([127.0.0.1]:46124 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o8JAE-0006N2-IH for submit@debbugs.gnu.org; Mon, 04 Jul 2022 06:18:46 -0400 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]:50022) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o8JAB-0006MY-EX for 56257@debbugs.gnu.org; Mon, 04 Jul 2022 06:18:44 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=inria.fr; s=dc; h=from:to:cc:subject:references:date:in-reply-to: message-id:mime-version:content-transfer-encoding; bh=0kyu4oJzbNbG8dyqYSKw6e79hSEZE3px8+zuxMmWWK0=; b=nKMv2KD8bZn37s2tekhjk13hGhKAYrd+gkhEI47duf2fZ6ZnvNhuiCaS qx3/ERRHRDVRzRd03mX/Su1in6wM2oOTjI3lPQlmMToa5T4+/Sd6u8NYt F7riC63cTCSK5X+sljl6T2SpVYRXvG03kkQEszSnO65yr7ee57vFQOAcO M=; Authentication-Results: mail2-relais-roc.national.inria.fr; dkim=none (message not signed) header.i=none; spf=SoftFail smtp.mailfrom=ludovic.courtes@inria.fr; dmarc=fail (p=none dis=none) d=inria.fr X-IronPort-AV: E=Sophos;i="5.92,243,1650924000"; d="scan'208";a="44099027" Received: from unknown (HELO ribbon) ([193.50.110.235]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 04 Jul 2022 12:18:37 +0200 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Subject: Re: bug#56257: [PATCH] fenics: Do not use mpirun for tests References: <87bkuefiwu.fsf@dlr.de> Date: Mon, 04 Jul 2022 12:18:36 +0200 In-Reply-To: <87bkuefiwu.fsf@dlr.de> (Ontje Luensdorf's message of "Mon, 27 Jun 2022 11:24:49 +0000") Message-ID: <87fsjhfaf7.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/28.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 56257 Cc: 56257@debbugs.gnu.org, 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: -3.3 (---) Hi, skribis: > the fenics package tests fail and it looks like the tests are run 3 > times concurrently. Every test name is printed three times in the build > log, for example here: > > https://ci.guix.gnu.org/build/1039880/log/raw > > This is the maximum number of parallel jobs of the test run and if I > increase it, I get more print outputs. > > AFAIK, pytest doesn't support mpi, so I don't see why the tests are > executed this way. Good question. Paul, do you remember the reasons for doing so? > Anyhow, in the attached patch, the tests are executed directly using > pytest. This prevents the tests from getting stuck and subsequently I > discovered a failure in XDMF tests. With this test also disabled, the > package builds fine for me. Let=E2=80=99s see what Paul thinks, and otherwise I=E2=80=99ll apply the pa= tch shortly so fenics can be installed again. Thanks, Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Tue Jul 05 08:43:27 2022 Received: (at 56257) by debbugs.gnu.org; 5 Jul 2022 12:43:27 +0000 Received: from localhost ([127.0.0.1]:49623 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o8htm-0003jg-V3 for submit@debbugs.gnu.org; Tue, 05 Jul 2022 08:43:27 -0400 Received: from mail-40136.proton.ch ([185.70.40.136]:32161) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o8htk-0003jP-2Q for 56257@debbugs.gnu.org; Tue, 05 Jul 2022 08:43:26 -0400 Date: Tue, 05 Jul 2022 12:43:10 +0000 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=apatience.com; s=protonmail2; t=1657024996; x=1657284196; bh=Kh7C5mMhKtLzvLV4zqYMcnEaTv6dwgSmCXIxV2sodes=; h=Date:To:From:Reply-To:Subject:Message-ID:Feedback-ID:From:To:Cc: Date:Subject:Reply-To:Feedback-ID:Message-ID; b=oIyZkDcScEQo5QcBl9MjhGmDtPBszPZFWn4yAYMsjFEEAXFmZglTj0F6lB5rP0lid 3yrspn7tQ0tJOLy1O+5CT27bcDCrdN/lb99MjIbnTIL9+ZFM0RKDRzR4qv2w1XjOrZ OKbfTegNfaYRzD5wCQvl1L1A+Sh9CxtIfW88+5dd7hQoYM6YwDdYkh2hvEL48NkjSB MFG5fgg9um+aYGfvVUoRc+2A7kVDw7rcCsBFJPYSmCgRogqukMDJyg8zI6XAOe208M 4pRkeIh+H7GzYSJ3QZJ6odLdrLYwp4fOnDwc4gbDzeigEd6Bfh3a75SxqaS1RnUk4o fqp/8wmicPbeA== To: 56257@debbugs.gnu.org From: "Paul A. Patience" Subject: [bug#56257] [PATCH] fenics: Do not use mpirun for tests Message-ID: <87mtdnu4af.fsf@apatience.com> Feedback-ID: 19227857:user:proton MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 56257 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: , Reply-To: "Paul A. Patience" Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi, Ludovic Court=C3=A8s writes: > Good question. Paul, do you remember the reasons for doing so? If I'm the Paul you're referring to, it would be better to CC me in the future, as I'm not subscribed to the list and only intermittently check it (which happens more often when I'm submitting patches). >> Anyhow, in the attached patch, the tests are executed directly using >> pytest. This prevents the tests from getting stuck and subsequently I >> discovered a failure in XDMF tests. With this test also disabled, the >> package builds fine for me. > > Let=E2=80=99s see what Paul thinks, and otherwise I=E2=80=99ll apply the = patch shortly > so fenics can be installed again. Actually, I'm not the original author of the fenics package; I just added support for #:tests? (and fixed the sanity check), so I don't know why the tests are run with mpirun. However, the reason I had added support for the #:tests? flag is to skip the fenics tests, which were failing for me. I'm no expert in MPI and pytest, but it does seem that pytest_mpi [1] is recommended when combining the two, and there are no instances of @pytest.mark.mpi in the fenics repository. Further, running pytest tests under MPI is accomplished with [2]: mpirun -n 2 python -m pytest --with-mpi In other words, it seems as if the current tests are repeated in parallel, as Ontje discovered. The patch looks good to me. Best regards, Paul [1]: https://pypi.org/project/pytest-mpi/ [2]: https://pytest-mpi.readthedocs.io/en/latest/usage.html From debbugs-submit-bounces@debbugs.gnu.org Wed Aug 03 06:05:00 2022 Received: (at 56257-done) by debbugs.gnu.org; 3 Aug 2022 10:05:00 +0000 Received: from localhost ([127.0.0.1]:46166 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJBFL-0003dX-VU for submit@debbugs.gnu.org; Wed, 03 Aug 2022 06:05:00 -0400 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]:51356) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oJBFJ-0003dI-HB for 56257-done@debbugs.gnu.org; Wed, 03 Aug 2022 06:04:58 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=inria.fr; s=dc; h=from:to:cc:subject:references:date:in-reply-to: message-id:mime-version:content-transfer-encoding; bh=UpSiWwFPYABa4bU5elfmCElB84u3/Eum3sgrjjPWbAo=; b=AUwTtw/UdANV9ym3VLYxUE7jc+CIpZwhJdESO3HQ1OJ43zPdZuFi1UBa 6Ra/qlnTe7avnwn+BA/UuVu7phJrkf1NUO2okpRVQg5puE4t3g8lDFp0O d+mqJ48bwkXukY2tToYANhNFwDws0nZY1chmMThnOI7U4eHWnx5xASpsx c=; Authentication-Results: mail2-relais-roc.national.inria.fr; dkim=none (message not signed) header.i=none; spf=SoftFail smtp.mailfrom=ludovic.courtes@inria.fr; dmarc=fail (p=none dis=none) d=inria.fr X-IronPort-AV: E=Sophos;i="5.93,213,1654552800"; d="scan'208";a="47833389" Received: from 91-160-117-201.subs.proxad.net (HELO ribbon) ([91.160.117.201]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 03 Aug 2022 12:04:51 +0200 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: "Paul A. Patience" Subject: Re: bug#56257: [PATCH] fenics: Do not use mpirun for tests References: <87bkuefiwu.fsf@dlr.de> <87mtdnu4af.fsf@apatience.com> Date: Wed, 03 Aug 2022 12:04:50 +0200 In-Reply-To: <87mtdnu4af.fsf@apatience.com> (Paul A. Patience's message of "Tue, 05 Jul 2022 12:43:10 +0000") Message-ID: <87a68lve0t.fsf_-_@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/28.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) X-Debbugs-Envelope-To: 56257-done Cc: 56257-done@debbugs.gnu.org, Ontje.Luensdorf@dlr.de 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: -3.3 (---) Hi, (Sorry for the delay.) "Paul A. Patience" skribis: > Ludovic Court=C3=A8s writes: >> Good question. Paul, do you remember the reasons for doing so? > > If I'm the Paul you're referring to, it would be better to CC me in the > future, as I'm not subscribed to the list and only intermittently check > it (which happens more often when I'm submitting patches). I actually Cc=E2=80=99d Paul Garlick, but maybe Debbugs ate the Cc: field? > I'm no expert in MPI and pytest, but it does seem that pytest_mpi [1] is > recommended when combining the two, and there are no instances of > @pytest.mark.mpi in the fenics repository. > Further, running pytest tests under MPI is accomplished with [2]: > > mpirun -n 2 python -m pytest --with-mpi > > In other words, it seems as if the current tests are repeated in > parallel, as Ontje discovered. > > The patch looks good to me. Alright, applied. Thanks! Ludo=E2=80=99. 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