From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp11.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms9.migadu.com with LMTPS id yPvZNKf6DmRN2wAASxT56A (envelope-from ) for ; Mon, 13 Mar 2023 11:27:51 +0100 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp11.migadu.com with LMTPS id SP/ONKf6DmStqwAA9RJhRA (envelope-from ) for ; Mon, 13 Mar 2023 11:27:51 +0100 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 6F38110406 for ; Mon, 13 Mar 2023 11:27:51 +0100 (CET) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pbfOR-0002Qm-Os; Mon, 13 Mar 2023 06:27:03 -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 1pbfO7-0002Ow-D4 for guix-science@gnu.org; Mon, 13 Mar 2023 06:26:46 -0400 Received: from smtphub1.cc.ic.ac.uk ([2a0c:5bc0:80:117::79]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1pbfO4-0006iP-Os for guix-science@gnu.org; Mon, 13 Mar 2023 06:26:43 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=imperial.ac.uk; s=main01; h=MIME-Version:Content-Transfer-Encoding: Content-Type:In-Reply-To:References:Message-ID:Date:Subject:CC:To:From:Sender :Reply-To:Content-ID:Content-Description:Resent-Date:Resent-From: Resent-Sender:Resent-To:Resent-Cc:Resent-Message-ID:List-Id:List-Help: List-Unsubscribe:List-Subscribe:List-Post:List-Owner:List-Archive; bh=x0hKIV0mCAW3r0Djrl5PKsWcrtXKAa4PGQ1H4SmJwDo=; b=IZsJdKITyBYSSvS43HTPpmOPQm XtKMMsqSlj3bJxkuQbo51gPbDkhxFCKOM8Zly99SPloLQpLmCHjK687MMj5uw7Y0ZuAfbx6xp79OL lKHukczRp1qC+tk0ecYmkXYZfKnYNkSUAuKEUwVpsamCWTAh3dpbODMgLEKSDl3jZdHI=; Received: from mail-cwlgbr01lp20207.outbound.protection.outlook.com ([2a01:111:f400:7e14::207] helo=GBR01-CWL-obe.outbound.protection.outlook.com) by smtphub1.cc.ic.ac.uk with esmtps (TLS1.2) tls TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384 (Exim 4.94.2) (envelope-from ) id 1pbfNw-0000vk-TS; Mon, 13 Mar 2023 10:26:33 +0000 ARC-Seal: i=1; a=rsa-sha256; s=arcselector9901; d=microsoft.com; cv=none; b=nbpDOEY5dizab6tjruleAfDpZ+JBQx116fxRrVQ1aTsvwcgrpaNkLkrKqLEmKgZM1GB0v19euizSGYz0b/vW52III5Wp7PQyJ5OHjdbsj+Xhuh2lvvYwNe05G3SyCp57uC2qQ1YXX2dmgmOpOOYY12vjpvCBr6xQ6+Ytbd+sIF+XoNZJf4TUG8BrTXq1rNRD226FzbC3SWMIiTcZPhup3usJrrT1dTisjnl4DJuXtiV1I+ySrnf+dqRbvADUc1DtTe5IlBpCR65vka0csxGWTMzlXKyE/bNAeR84qCRT39ZIV6XHzGDv7yyy8of0VnZc4xeKO9dhAIqNJbm1oTtkrw== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=microsoft.com; s=arcselector9901; h=From:Date:Subject:Message-ID:Content-Type:MIME-Version:X-MS-Exchange-AntiSpam-MessageData-ChunkCount:X-MS-Exchange-AntiSpam-MessageData-0:X-MS-Exchange-AntiSpam-MessageData-1; bh=x0hKIV0mCAW3r0Djrl5PKsWcrtXKAa4PGQ1H4SmJwDo=; b=MRaTogypnXLYgIWzuCAl/RSCbzr4+5Hgqx+rvEVTCMXsw6QhzV37i20Y8+LWgwkyhA3mOkhnrT8TrhBOba/jqEI38eHdez8OEVgb7x5lWy94bWTh0o+s+Aw1W1GwO/+dN7HxjU6aU9zAaXgvi9JJVgUpuNhNsg+4E0XS1myesGwfqAHTrJaxqPNywZBHli53rxNq/QdydquNAMBURsjR5tNcxQQ5c3s4cEEjgIeodW9QoYLkvqnv1bNpISNcG0CjZEYmC6LDEpkkOjiZFVOhdzblGem0yD6IO7Gq4L4jBhWv5/51awFTYb/tP9fekm06fw6ZSoOn5606YTFR0QA7sg== ARC-Authentication-Results: i=1; mx.microsoft.com 1; spf=pass smtp.mailfrom=imperial.ac.uk; dmarc=pass action=none header.from=imperial.ac.uk; dkim=pass header.d=imperial.ac.uk; arc=none DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=ImperialLondon.onmicrosoft.com; s=selector2-ImperialLondon-onmicrosoft-com; h=From:Date:Subject:Message-ID:Content-Type:MIME-Version:X-MS-Exchange-SenderADCheck; bh=x0hKIV0mCAW3r0Djrl5PKsWcrtXKAa4PGQ1H4SmJwDo=; b=o9i63I0ribjj6cH0zLXbx5FxnOoKydXzS8NIR4C4Y+Kco+BEUddmYvfNHEafbS4k9kR2pCbRv5jjEGhRU3cfYySMY77rqHctT/jbLIu2ei0r7pOMT3AlMmlrciz6ifd3vVl0ZGmmIaHw94pSzspwhSWT34xzO3dg9xxC1BZAHhQ= Received: from LO2P265MB0590.GBRP265.PROD.OUTLOOK.COM (2603:10a6:600:6a::19) by LO6P265MB6329.GBRP265.PROD.OUTLOOK.COM (2603:10a6:600:2d2::12) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.20.6178.24; Mon, 13 Mar 2023 10:26:30 +0000 Received: from LO2P265MB0590.GBRP265.PROD.OUTLOOK.COM ([fe80::54bb:e24f:f32d:87bc]) by LO2P265MB0590.GBRP265.PROD.OUTLOOK.COM ([fe80::54bb:e24f:f32d:87bc%4]) with mapi id 15.20.6178.024; Mon, 13 Mar 2023 10:26:30 +0000 From: "Lestang, Thibault" To: Simon Tournier , =?iso-8859-1?Q?Ludovic_Court=E8s?= CC: guix-science Subject: Re: Conda environments and reproducibility Thread-Topic: Conda environments and reproducibility Thread-Index: AQHZA1QdLKxEKK/fm0uz0N3vlviKx65UvUgAgAD35ACAACzBgIAAdKAAgBoR1oCAhaOks4AACq+AgAMHb+8= Date: Mon, 13 Mar 2023 10:26:30 +0000 Message-ID: References: <87pmd7ar8k.fsf@imperial.ac.uk> <87zgcayre2.fsf@imperial.ac.uk> <86y1rt5xoz.fsf@gmail.com> <87fsdfejfv.fsf@imperial.ac.uk> <87a60jy2e7.fsf@gnu.org> In-Reply-To: Accept-Language: en-GB, en-US Content-Language: en-GB X-MS-Has-Attach: X-MS-TNEF-Correlator: msip_labels: x-ms-publictraffictype: Email x-ms-traffictypediagnostic: LO2P265MB0590:EE_|LO6P265MB6329:EE_ x-ms-office365-filtering-correlation-id: fa1d04ec-adbb-438c-2347-08db23ad6909 x-ms-exchange-senderadcheck: 1 x-ms-exchange-antispam-relay: 0 x-microsoft-antispam: BCL:0; x-microsoft-antispam-message-info: 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 x-forefront-antispam-report: CIP:255.255.255.255; CTRY:; LANG:en; SCL:1; SRV:; IPV:NLI; SFV:NSPM; H:LO2P265MB0590.GBRP265.PROD.OUTLOOK.COM; PTR:; CAT:NONE; SFS:(13230025)(4636009)(376002)(366004)(39860400002)(346002)(136003)(396003)(451199018)(5660300002)(83380400001)(66574015)(186003)(478600001)(71200400001)(26005)(6506007)(7696005)(9686003)(38070700005)(8676002)(66476007)(76116006)(66446008)(33656002)(64756008)(66946007)(52536014)(66556008)(4326008)(41300700001)(8936002)(86362001)(786003)(110136005)(316002)(3480700007)(38100700002)(55016003)(122000001)(2906002); DIR:OUT; SFP:1102; x-ms-exchange-antispam-messagedata-chunkcount: 1 x-ms-exchange-antispam-messagedata-0: =?iso-8859-1?Q?zUq5FHbq+d9FL1EDACrMH6UqRBHkvW74qheMdIJhBMfcYlZsgIt3W2APEO?= =?iso-8859-1?Q?PRZKTXYXEgJRANRUhObE3h0pz0zq2zPaoPO0rCcUr2kkEVu9t0Hvuz7saR?= =?iso-8859-1?Q?Ngd3Jwt2DeY9SSbO4uOnIRTeQuoHLIuoyhR/4RcGa/0r4AukZXfMZwVgbs?= =?iso-8859-1?Q?TyzcFdovJUneCXn7qQm++N5twRSjERu3K3/RYEG+LDlZSQFJJDCZ+p7PpL?= =?iso-8859-1?Q?jBBdGlNX/eQ6CkZmmqGmCVWcKGsiDERnbFhcl/WfhBI2ZiAy79hxVXsEes?= =?iso-8859-1?Q?pWQ0KGt7lbhkAlA+GBtGaHn/EML9JNggxlwihxq+Hh0Hy/z2cn47mmSJAN?= =?iso-8859-1?Q?6/8Aw7ha++I8DqJrbxkFDpy2nDI/fm41M7v3PU+CGzH3AIkLYs3ObSG2To?= =?iso-8859-1?Q?BQmyH8vZm+DEEqcgM4ZxOXNoWToVSWQMM7AR1fcGR5cj72v9qfrgZuhi9U?= =?iso-8859-1?Q?Sg4s9TRJo6ST/1qqhi/H1PIKn+fJKDH5Ea8e0X4dDYWOKEzPYEfrrBiLwZ?= =?iso-8859-1?Q?yq6s90/geI9v2U2Pkcb/yXAc84DbFFB1OTJ9/fFvsXblMVXpsV4wTlNGUy?= =?iso-8859-1?Q?aqhaCCmd0ir1ii9e9oQRjhIcJt13CjRtdV4N/77pZlXYIjOBwgVTk4XnHj?= =?iso-8859-1?Q?U3mh1mYHHBPqhCsxiMLQACOJiVDxdnrYfUAE/wC3Pdhx0u4JD+GLpW3jB0?= =?iso-8859-1?Q?AiDSKiXuUFhe10qwPZ+G2+NTu6pZTSM8TTez9CX/2JYIoW3PXMcHv6IbB/?= =?iso-8859-1?Q?fOPafpeSAAIaflwoEmzp2ICY2SP7zPuWIEnbrPyp/j5sXwdzWFaaIQfE7q?= =?iso-8859-1?Q?qiTGlsY4tx2QfTbhVeTcdDTUT0t1JH+E6DxA/wVANl3Aa3jaWeYNRILhhp?= =?iso-8859-1?Q?HQNodLOKVrtLX3AL4n1TtZjoXjaQFzhFbyPPW5+iyWfo5Pphh4j6VFCKYg?= =?iso-8859-1?Q?zKd6KuTBm/L4rOEe4kCNKAJWNyk2PrAjAO+uwKGgdYSgYFgYrMyrW3o18T?= =?iso-8859-1?Q?0lH59MvA8tzKA25l/Qhx7ScOGoEA6/9yLyjUAyo2oYvPnXkLe+Pgi4elpW?= =?iso-8859-1?Q?GH5yQm4/KLwnKgW1Z2ROe7NBam6g0e2G6W69xKv3gZLT6i7SxDjDJVzERw?= =?iso-8859-1?Q?7ohZ3L3LrFWH06gStkn16ssomUDD28cRMpz8x+8VGQgpjuDtvAVfExyja3?= =?iso-8859-1?Q?l2weeR059yzpjQzKcm/pZmoQRd9vFv0ca+hd+IlDUH8gD6tAIMzzTk9YEP?= =?iso-8859-1?Q?zJ3i2m+ggyjpWd34T9oD+E+xIcfvYfy2rFw4G6yCexU9nvpBo5tpPI2Ctb?= =?iso-8859-1?Q?NjZ6wWVRCoYUnXT9ocoN39ILhuAB5o7AEe0Xm99Cn1Ua7gGsx9bxOhnvg9?= =?iso-8859-1?Q?GXGWsz5UgtNYH/MbKHQX51BGwE7kV/SREJ9kdp6SZ9tJ8oKtDQnc01LzWa?= =?iso-8859-1?Q?7aR0Re1NAFFqWeeFhDdaL5fCibVFhZCidCdTj2orzj+007fUbUyHADzIMQ?= =?iso-8859-1?Q?NkBn+R6BPbhYaCZYQEStRRdU5awXxifbAJHtWH66pinWfbE3QpOLbAmduE?= =?iso-8859-1?Q?38oRb9++it7FuQsOcJ5NzJ1517hfJAeLMNGcdN5JIuBpxgrx7ghFajMJVu?= =?iso-8859-1?Q?tZUxvz2Dl+ti4=3D?= Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-OriginatorOrg: imperial.ac.uk X-MS-Exchange-CrossTenant-AuthAs: Internal X-MS-Exchange-CrossTenant-AuthSource: LO2P265MB0590.GBRP265.PROD.OUTLOOK.COM X-MS-Exchange-CrossTenant-Network-Message-Id: fa1d04ec-adbb-438c-2347-08db23ad6909 X-MS-Exchange-CrossTenant-originalarrivaltime: 13 Mar 2023 10:26:30.1265 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 2b897507-ee8c-4575-830b-4f8267c3d307 X-MS-Exchange-CrossTenant-mailboxtype: HOSTED X-MS-Exchange-CrossTenant-userprincipalname: ADzNiW50DxZ5EHkAu2nDtA7XsntYnsarLzGHBHUzv4SXaXxwgNbtc/vU3jn/WrX9hzn9VeVvczuZk5gPBYhx3Q== X-MS-Exchange-Transport-CrossTenantHeadersStamped: LO6P265MB6329 X-IC-MsgID: 1pbfNw-0000vk-TS Received-SPF: pass client-ip=2a0c:5bc0:80:117::79; envelope-from=t.lestang@imperial.ac.uk; helo=smtphub1.cc.ic.ac.uk X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 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, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: guix-science@gnu.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-science-bounces+larch=yhetil.org@gnu.org Sender: guix-science-bounces+larch=yhetil.org@gnu.org X-Migadu-Country: US X-Migadu-Flow: FLOW_IN ARC-Authentication-Results: i=2; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=imperial.ac.uk header.s=main01 header.b=IZsJdKIT; dkim=pass header.d=ImperialLondon.onmicrosoft.com header.s=selector2-ImperialLondon-onmicrosoft-com header.b=o9i63I0r; spf=pass (aspmx1.migadu.com: domain of "guix-science-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-science-bounces+larch=yhetil.org@gnu.org"; dmarc=fail reason="SPF not aligned (relaxed), DKIM not aligned (relaxed)" header.from=imperial.ac.uk (policy=none); arc=pass ("microsoft.com:s=arcselector9901:i=1") ARC-Seal: i=2; s=key1; d=yhetil.org; t=1678703271; a=rsa-sha256; cv=pass; b=G7gHszxBIvR8A4DiIvjMJr3ebQpfJW6kp0vagctb4CEsV+xTcqn6dswfOjUXzqx6eNxIoc YjYU1DxdALuEseehyayCNDvFa9nBsKjGa0qYdpp92cl+CLpgf4UutA7EP0CNrWuGihCLbd gPMtyM2aMNxX1uXW6CcvYwOrfsypTOAfUV3k3Jo/UMpdDxj+z/3PdYYXxg0tJo3N+p6y2B NnNtmNdA8TMUPyXBuiOWbhoTkpG7C7JShIWFqUe4rBnbToi9/sl+UnsDhBL7Ux/QgjY/Lt by8rXAP8Gx44KpPmT3clBGOYNzPEv3RzBPEd2cjigmRQ6u2DFgv6zqhd0Y2kRA== ARC-Message-Signature: i=2; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1678703271; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding: in-reply-to:in-reply-to:references:references:list-id:list-help: list-unsubscribe:list-subscribe:list-post:dkim-signature; bh=x0hKIV0mCAW3r0Djrl5PKsWcrtXKAa4PGQ1H4SmJwDo=; b=Ygf0eoqXLQiXRnChTkMrUbW6QH43RtGQ78XWmVwbwdhMTcWgDj+9VXOboOKxeyFYlDxr0f Djk7S2YjPUajU9aKCOXwekZ6GJRN3BmvNWgVoMlKUCTrOaTvjz9GsA8+bVD5D4Wxq6Cnh6 OX05gqtnHNrTsjP2h5lETdBRg4KADgX2anpUBDTCOR0n9lEbpn/BOpuLmVHdWdyF1HRpUl 2Sg98TeZzN60qxeIwrsp2rfVhLc9H5Tv48CQT70AKm9Flmr0oy1ypwUoRLAvLqQKDqHHy9 8fatcEuvlSlqkezVjwLa6mZUxzuogsb2Q/pAWlLIS6+uW4tWd8xf39unrFqYWw== X-Migadu-Spam-Score: -6.90 X-Spam-Score: -6.90 X-Migadu-Queue-Id: 6F38110406 X-Migadu-Scanner: scn1.migadu.com Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=imperial.ac.uk header.s=main01 header.b=IZsJdKIT; dkim=pass header.d=ImperialLondon.onmicrosoft.com header.s=selector2-ImperialLondon-onmicrosoft-com header.b=o9i63I0r; spf=pass (aspmx1.migadu.com: domain of "guix-science-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-science-bounces+larch=yhetil.org@gnu.org"; dmarc=fail reason="SPF not aligned (relaxed), DKIM not aligned (relaxed)" header.from=imperial.ac.uk (policy=none); arc=pass ("microsoft.com:s=arcselector9901:i=1") X-TUID: zBjmuL00kpLB Ludovic Court=E8s writes:=0A= =0A= > Any findings so far? Looking at the pipelines, it seems to be all=0A= > green, right?=0A= =0A= Timely reply - all green until 3 days ago when the job timed out after 70mi= n. =0A= However, I re-ran the job manually this morning and it succeeded within a c= ouple of minutes. Not =0A= quite sure what happened but probably not related to conda. Not logs availa= ble unfortunately.=0A= =0A= If the process of reproducing the environment is going to fail at some poin= t, I =0A= wonder if we could accelerate this process by defining a more complex envir= onment. =0A= Any ideas?=0A= =0A= Simon Tournier writes:=0A= =0A= > 1. also use the image continuumio/miniconda3:latest=0A= > 2. install Miniconda on the top of the Docker image of Debian=0A= > unstable and run "apt update && apt upgrade"=0A= > =0A= > And I expect that #2 will break first, then #1 and last the current=0A= > one.=0A= =0A= Could you elaborate on this? For context the current pipeline =0A= pulls a pinned miniconda image then updates conda (=3Dconda update conda=3D= ). =0A= Do you expect system libraries (I mean software installed through apt, not = =0A= managed by conda) to influence the conda environment creation? My current = =0A= understanding is that conda brings its own copies of these libraries witho= ut relying =0A= on whatever was/will be installed through other ways (e.g. apt).=0A= =0A= Anyways very happy to set these two cases up as well.=0A= =0A= Thibault=0A=