From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 0/1] gnu: Add gromacs. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 17 Apr 2020 22:24:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.158716218316765 (code B ref -1); Fri, 17 Apr 2020 22:24:02 +0000 Received: (at submit) by debbugs.gnu.org; 17 Apr 2020 22:23:03 +0000 Received: from localhost ([127.0.0.1]:41845 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jPZO2-0004ML-Oe for submit@debbugs.gnu.org; Fri, 17 Apr 2020 18:23:02 -0400 Received: from lists.gnu.org ([209.51.188.17]:57523) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jPZO1-0004M0-PH for submit@debbugs.gnu.org; Fri, 17 Apr 2020 18:23:02 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:54612) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jPZO0-0002hX-Kb for guix-patches@gnu.org; Fri, 17 Apr 2020 18:23:01 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,FREEMAIL_FROM autolearn=disabled version=3.3.2 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1jPZNz-0003Wk-KI for guix-patches@gnu.org; Fri, 17 Apr 2020 18:23:00 -0400 Received: from mail-wr1-x431.google.com ([2a00:1450:4864:20::431]:37182) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1jPZNz-0003RE-DB for guix-patches@gnu.org; Fri, 17 Apr 2020 18:22:59 -0400 Received: by mail-wr1-x431.google.com with SMTP id k1so4789522wrx.4 for ; Fri, 17 Apr 2020 15:22:59 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=to:from:subject:message-id:date:user-agent:mime-version :content-language:content-transfer-encoding; bh=Jzr0COMI1L3fXghOyBoycR0+30ffkPJPD4aN1REhr9w=; b=UbYFoVHsluSX2p8Jf7wljncs5ABmwF8mdGdR5iBth6E67wE7imMIlq9ietaNEU4zMJ 6zGW3dslRkgku3kTLHwuZ9V/bI2dplz1XFzya1S7JB8WOeNFK9G690taE8qywnf5ugRj fIN7yGvh3jJlymEuN0oivmrPA8pVPi+9Y8WAvX3ThjSkiJphtDMf/rofNQ/Qi2/1/zuP NMjojoEFnZIvr7YXSrUBQkI1AODYK9UjT56rvogwn7w++Fwha9JHhe+YyAz0sDPQ727a 1avlp0JbKF6pTe2QOoGx55xdmJch2DntWpcACa6asvCmnnC9+ELV5f6aD7vH1ztbf8LE BXvQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:to:from:subject:message-id:date:user-agent :mime-version:content-language:content-transfer-encoding; bh=Jzr0COMI1L3fXghOyBoycR0+30ffkPJPD4aN1REhr9w=; b=arfZZ7nX3ZOy49Z2L/+MkH87gZdQSX2nel6BREFNoVqbr23NJpbyAzRuRw3shutjXI wPvMcGeSRNKHgh60BjuxJXRNBtHtU00rRlQDScK4Kwa2IxT6mqR67/eSWhs3VzbUEB53 AAeOmmEMBIaJ+ZOCiTmvNKYHGi1QfeOx5zEYcMdHjhSk70WMnAvAnc0LCaKZmuFIKH0m u0RpBwILJW/WSPkFz8B0iwK3TsVr7PdlcMIbIOU/KqqMbLLJtiKKs4Vgy8EO4pdFse+Q erKYsf8uCn3VZD24IbwxvxfiE0gF3aAB0UVkbmy/I9p2fTcy1QVYFXzp35sz1J/WeOtm D3KQ== X-Gm-Message-State: AGi0PuZRS1oI8NoEzh6Nbt2f/C18UiqoXd3qowZl+v6aE0ElI0SkExkm duXewYW6N/EE4nmalXpAiPabpCHJ X-Google-Smtp-Source: APiQypIfhg5V+WpszScjVEiejF7okoaeFJTnzAUWbOZ7n8sfH30P2DsT5eEsTjw0Y0E8BBL77iFW5Q== X-Received: by 2002:a5d:5386:: with SMTP id d6mr3969470wrv.222.1587162177706; Fri, 17 Apr 2020 15:22:57 -0700 (PDT) Received: from [10.0.0.2] (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id r20sm8996181wmh.26.2020.04.17.15.22.56 for (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Fri, 17 Apr 2020 15:22:56 -0700 (PDT) From: Vincent Legoll Message-ID: Date: Sat, 18 Apr 2020 00:22:54 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.7.0 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Language: en-US Content-Transfer-Encoding: 7bit X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2a00:1450:4864:20::431 X-Spam-Score: 2.3 (++) 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: Hello, following this is a patch to add gromacs. Description & synopsis taken from nix (hello Tobias) Content analysis details: (2.3 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.7 RCVD_IN_DNSWL_LOW RBL: Sender listed at https://www.dnswl.org/, low trust [209.51.188.17 listed in list.dnswl.org] 1.0 SPF_SOFTFAIL SPF: sender does not match SPF record (softfail) 0.0 FREEMAIL_FROM Sender email is commonly abused enduser mail provider (vincent.legoll[at]gmail.com) 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record 2.0 SPOOFED_FREEMAIL No description available. 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: -0.7 (/) Hello, following this is a patch to add gromacs. Description & synopsis taken from nix (hello Tobias) Linted, indent-code.el passed, and built OK with 2 rounds. Not sure if we want more cmake flags. problems reported by cmake: -- Found Doxygen: /gnu/store/k6albjaxkybsgshqyw6g44f5hz75l7q6-doxygen-1.8.15/bin/doxygen (found version "1.8.15") found components: doxygen missing components: dot -- Could NOT find Sphinx: Found unsuitable version "-real 2.3.1", but required is at least "1.6.1" (found /gnu/store/anyhb84x3mvyp11sbhmdnicbsa42m3x0-python-sphinx-2.3.1/bin/sphinx-build) -- Vincent Legoll From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH] gnu: Add gromacs. References: In-Reply-To: Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 17 Apr 2020 22:26:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Cc: Vincent Legoll Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158716230416990 (code B ref 40691); Fri, 17 Apr 2020 22:26:02 +0000 Received: (at 40691) by debbugs.gnu.org; 17 Apr 2020 22:25:04 +0000 Received: from localhost ([127.0.0.1]:41850 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jPZQ0-0004Py-3U for submit@debbugs.gnu.org; Fri, 17 Apr 2020 18:25:04 -0400 Received: from mail-wr1-f51.google.com ([209.85.221.51]:36314) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jPZPx-0004PG-SG for 40691@debbugs.gnu.org; Fri, 17 Apr 2020 18:25:02 -0400 Received: by mail-wr1-f51.google.com with SMTP id u13so4798316wrp.3 for <40691@debbugs.gnu.org>; Fri, 17 Apr 2020 15:25:01 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=D4ShfUxJEMdPA1NjWOFRhaJeSyCEWQZSZ1uNX97RXeE=; b=js8m69sCmEf/UPIKiNC7di702eTkyRGZAcV5Oupsge4x1Sv6RL2dPkBK9O5JnO9lhN xevk+j7RcjQzH5sbQOwCYYOHVf/l+dMItXH9RDUPQsPiVKe7Hb/O4iKeG+RTXg23yxgh 82ijoPFjm27ZKU9Gf70Mru1qFrjCXsvv15FJSc9K7Odd7g40IVzNSeZYzZ3mNt+ghHQH 9uhGXcIJadie0Uy7R7ZCUm4/iIbiy2goSzg9hwY8KVI3LVXHfDsxsiTfmdoEJ8W4t9QZ CHbPmxrh8B+9pyc4Jhw0Wwbdg1pltua+sJyx/hZEjO3/93kAixs8Mts5xjFvZ8qH9N3y iyfQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=D4ShfUxJEMdPA1NjWOFRhaJeSyCEWQZSZ1uNX97RXeE=; b=mgmkTK6W8028oVHBuNR6gR8WyvwVjNpxrUMLjHA7QYzE/wJZHsmwfDgz0/1J4FFDDJ d7I7GGLWfboDgAJlkKCnlFRXM1bEt+IKhuBny0D3GU3MuTr9pu6O9FfUyR8nAuJ/Kuja qxoUJ3R8lFJDbr7CP65fEBcNTo4uCMXyoKOeY+8zUsemi2CIMx030kBNhdQbFIn2lp2x njvTcgTD4YtNOaNLGzbranjOkfVg/1fZ4l8W10a0cYMtwuD9n3mQNNb/IK76U9rg/rNT kcnsiiu4zyXOCmq/E/QjEBqETuBIsE9A1PXFw8sNV6QR7Q7TCD0RAHTQAWPj3rWENml6 SHnQ== X-Gm-Message-State: AGi0PubkEGmTrpwcgMVU1qGMFNvcI9b9nOTOREzOAjn5IlMZoF18G6uY wzTzPc67CC56Zo1svMqgVYaUs9MK X-Google-Smtp-Source: APiQypLfKXy9apfalOPUSgIWsjdJmmTdvBAdc1lOPmzkPtwPe3YbKmSkUm1vBHe/0ByLldLLSWjTjA== X-Received: by 2002:adf:f4d1:: with SMTP id h17mr5900306wrp.69.1587162295749; Fri, 17 Apr 2020 15:24:55 -0700 (PDT) Received: from localhost.localdomain (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id q187sm9454774wma.41.2020.04.17.15.24.54 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 17 Apr 2020 15:24:55 -0700 (PDT) From: Vincent Legoll Date: Sat, 18 Apr 2020 00:24:44 +0200 Message-Id: <20200417222444.11115-1-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Spam-Score: -0.8 (/) 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: -1.8 (-) * gnu/packages/bioinformatics.scm (gromacs): New variable. --- gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b9be0c1918..f0fca30dd8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2019 Brett Gilio ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Jakub Kądziołka +;;; Copyright © 2020 Vincent Legoll ;;; ;;; This file is part of GNU Guix. ;;; @@ -785,6 +786,44 @@ input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.") (license license:x11))) +(define-public gromacs + (package + (name "gromacs") + (version "2020.1") + (source (origin + (method url-fetch) + (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-" + version ".tar.gz")) + (sha256 + (base32 + "1kwrk3i1dxp8abhqqsl049lh361n4910h0415g052f8shdc6arp1")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DGMX_DEVELOPER_BUILD=on"))) + (native-inputs + `(("doxygen" ,doxygen) ; need dot + ("python-sphinx" ,python-sphinx))) ; problem reported by cmake + (inputs + `(("fftwf" ,fftwf) + ("hwloc" ,hwloc-2 "lib") + ("imagemagick" ,imagemagick) + ("lapack" ,lapack) + ("openblas" ,openblas) + ("openmpi" ,openmpi) + ("perl" ,perl))) + (home-page "http://www.gromacs.org/") + (synopsis "Molecular dynamics software package") + (description "GROMACS is a versatile package to perform molecular dynamics, +i.e. simulate the Newtonian equations of motion for systems with hundreds to +millions of particles. It is primarily designed for biochemical molecules like +proteins, lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating the nonbonded +interactions (that usually dominate simulations) many groups are also using it +for research on non-biological systems, e.g. polymers. GROMACS supports all the +usual algorithms you expect from a modern molecular dynamics implementation.") + (license license:lgpl2.1+))) + (define-public python-pybedtools (package (name "python-pybedtools") -- 2.26.0 From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] gromacs - WIP, submitted References: In-Reply-To: Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 17 Apr 2020 22:49:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158716369219002 (code B ref 40691); Fri, 17 Apr 2020 22:49:01 +0000 Received: (at 40691) by debbugs.gnu.org; 17 Apr 2020 22:48:12 +0000 Received: from localhost ([127.0.0.1]:41858 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jPZmO-0004wP-3d for submit@debbugs.gnu.org; Fri, 17 Apr 2020 18:48:12 -0400 Received: from mail-wm1-f54.google.com ([209.85.128.54]:39194) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jPZmL-0004wC-NP for 40691@debbugs.gnu.org; Fri, 17 Apr 2020 18:48:10 -0400 Received: by mail-wm1-f54.google.com with SMTP id y24so4636639wma.4 for <40691@debbugs.gnu.org>; Fri, 17 Apr 2020 15:48:09 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=to:from:subject:message-id:date:user-agent:mime-version :content-language:content-transfer-encoding; bh=USZO/EMuKQPMXwrM30oq4rCiXPjqJ+T6VbZNops9o8o=; b=AkndzasustbB6+3k3ogaY1t9NnG8xMP6PcWR6/aLT/5vjP1JRVzUmUV6hJ5KHi2EPx 5lsIjhot1ALAwym1wpddaQES4yuLRVumXllAbLuKo9VBin2GMcu9i+3nUhnTMtrnN/+d 9K6qXFrdjTwz9LQAozVH2sAkleWBbmlEqB00l/XZe8m8y3gLjyMFwlN3BjxWuUVbIh7/ e0QBnt4BUTZ0e2cKxVqHMd8EiKoCwwgnRWT4eS3gHDuz91maRWPUQ4636pKmbgMGnjCN hQePTIlOVfoXlDyV9lhksPTwxpZNQ2YLax+g1AJQ8KGlRfsjZSHxC6jXidWrnbqNU96a KQyQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:to:from:subject:message-id:date:user-agent :mime-version:content-language:content-transfer-encoding; bh=USZO/EMuKQPMXwrM30oq4rCiXPjqJ+T6VbZNops9o8o=; b=lnA6yyfX/M9udwOKltWvHxGYVTkLyibxY7A7TVgkB6P8RYkuoiZpuWqsaqea1OejWs VgNNm512ghJZvryT6AHLklrAnvwej5nm+Yp0wEebCA8T4svIHuSL6M97ljgc/bsc4ksi slLpxiOsRSRYWIvs6q72haJNQpLoUeltIM4QYISf+jKCgu6s/82GF38OW5ZYTTc1W4nG dux3DngdQsqXEDDu1wP1y6NLH46mw6Rcem9w4pNVWHPTCyGM/gMa1OLw8lZV0G57g7g3 O1hGaZvU4Ko7+KSLRUJvvOQbiyJAqIyD8aITkYsfuhXVURLTBrJVZ0fm/Vab1DmAaRSl f7GA== X-Gm-Message-State: AGi0Pub01hD/H5+lTysBQy4qQqUe1zjCGrBFdlff5zUEpZsxfuylcHfJ qXsfiYJ/n1Bp/xb0HkNW43q6GkzX X-Google-Smtp-Source: APiQypKdiRMmsOblgeJ/xbVqkOVmp4XFrPkF70cTIG4GBOSU5zioTmxV66nOlALJNKQkWUVBsAqy+Q== X-Received: by 2002:a1c:ed18:: with SMTP id l24mr5415535wmh.122.1587163683180; Fri, 17 Apr 2020 15:48:03 -0700 (PDT) Received: from [10.0.0.2] (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id h2sm9044926wmb.16.2020.04.17.15.48.02 for <40691@debbugs.gnu.org> (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Fri, 17 Apr 2020 15:48:02 -0700 (PDT) From: Vincent Legoll Message-ID: <062db5ae-0377-8483-28ed-886dd97f33fc@gmail.com> Date: Sat, 18 Apr 2020 00:48:01 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.7.0 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Language: en-US Content-Transfer-Encoding: 7bit X-Spam-Score: -0.8 (/) 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: -1.8 (-) And now I see I've copy/pasted the fftwf input when I probably should have put one of the other fftws... WDYT ? From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 0/1] gnu: Add gromacs. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 19 Apr 2020 22:21:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Vincent Legoll Cc: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.15873348078878 (code B ref 40691); Sun, 19 Apr 2020 22:21:01 +0000 Received: (at 40691) by debbugs.gnu.org; 19 Apr 2020 22:20:07 +0000 Received: from localhost ([127.0.0.1]:46139 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jQIIJ-0002J8-H9 for submit@debbugs.gnu.org; Sun, 19 Apr 2020 18:20:07 -0400 Received: from eggs.gnu.org ([209.51.188.92]:60790 helo=eggs1p.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jQIII-0002IX-05 for 40691@debbugs.gnu.org; Sun, 19 Apr 2020 18:20:06 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:56527) by eggs1p.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jQIIC-0007Os-Fv; Sun, 19 Apr 2020 18:20:00 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=59278 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jQIIC-0005T1-04; Sun, 19 Apr 2020 18:20:00 -0400 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= References: Date: Mon, 20 Apr 2020 00:19:57 +0200 In-Reply-To: (Vincent Legoll's message of "Sat, 18 Apr 2020 00:22:54 +0200") Message-ID: <87k12b15ki.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable 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: -1.7 (-) Hi Vincent, Vincent Legoll skribis: > following this is a patch to add gromacs. > > Description & synopsis taken from nix (hello Tobias) Heheh. :-) > Not sure if we want more cmake flags. Could you add a comment explaining the reason for this flag? > problems reported by cmake: > > -- Found Doxygen: > /gnu/store/k6albjaxkybsgshqyw6g44f5hz75l7q6-doxygen-1.8.15/bin/doxygen > (found version "1.8.15") found components: doxygen missing > components: dot Perhaps add =E2=80=98graphviz=E2=80=99 as a native input? > -- Could NOT find Sphinx: Found unsuitable version "-real 2.3.1", but > required is at least "1.6.1" (found > /gnu/store/anyhb84x3mvyp11sbhmdnicbsa42m3x0-python-sphinx-2.3.1/bin/sphin= x-build) Oh, looks like it=E2=80=99s looking at argv[0] and the script is wrapped. = :-/ Can you somehow for CMake to think it=E2=80=99s fine, either with a flag or= by skipping the relevant check in =E2=80=98CMakeLists.txt=E2=80=99? Thanks, Ludo=E2=80=99. From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH v2 1/1] gnu: Add gromacs. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 20 Apr 2020 22:16:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ludovic =?UTF-8?Q?Court=C3=A8s?= Cc: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158742091632125 (code B ref 40691); Mon, 20 Apr 2020 22:16:02 +0000 Received: (at 40691) by debbugs.gnu.org; 20 Apr 2020 22:15:16 +0000 Received: from localhost ([127.0.0.1]:48620 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jQehA-0008M5-9y for submit@debbugs.gnu.org; Mon, 20 Apr 2020 18:15:16 -0400 Received: from mail-wm1-f47.google.com ([209.85.128.47]:37462) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jQeh7-0008Lr-Oz for 40691@debbugs.gnu.org; Mon, 20 Apr 2020 18:15:14 -0400 Received: by mail-wm1-f47.google.com with SMTP id z6so1385424wml.2 for <40691@debbugs.gnu.org>; Mon, 20 Apr 2020 15:15:13 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=subject:to:cc:references:from:message-id:date:user-agent :mime-version:in-reply-to:content-language; bh=aqejOvBn+FdQuTxejal5X0F1dB4J3gBavc7RxkSCmIE=; b=tN3EMKqVs++L4HFOGDDB6cZ+Evu42FslHOJaBSd8dBhPdj0BXK7TwTgPLOLGlWGGep hg8oGLyM77aUFGyVs0NkkMc3b/ifGU6MUA9rB1ITYwQe5wSpjl1yKD6B6iHBP+pIrNg/ Qx36IvbZb62I+XJMmTQOnb2h6NMIsQmjccXfZT4xEv5Cv+T8Lk0QyiKCz8dSX6ryhtdI weNSzcjGlJ91TPl9w0CPrIJxoNeb5THEV1QQwRPoham0gQmUpzq2kXJpynooT5HUxmsv UeM1+UAYH/F8d6bjsdJ2e20w99rlixSeJMXmcOplWYUWaQ1RO8LYk6kM/NT3YZOaYiEA L4jg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:subject:to:cc:references:from:message-id:date :user-agent:mime-version:in-reply-to:content-language; bh=aqejOvBn+FdQuTxejal5X0F1dB4J3gBavc7RxkSCmIE=; b=KFogvZHKrGKV2+D7QWhbCMf4kvkcykd5gsgLKWWtkHzf9M6qbjQ8jCouEStgTZc9BZ t7HdmyjxGIWUyXH3CddZg7j92LU8kT+9FjkhMCQB3WnsfuHbEdXE0kyk2WXQomLAjMaD i9ns4byFPQGoezdfY+NuT+fnKXuBXo6O6FycVYLsE9ReC0z5iBXZLegO7joMTQFOi0bp 59+RqSj1cRZT7+tsE7K6yLOuRh28Go+EDtYBEFrGK71QQ/7gOydTGOt6hyLtIc9opB/v gvPV50XKfiL5UYqDmmGhf4SkzaBb9dyBfaMg9qRBI/8TH7SnIG7l2mqMQpduk6QARjIx BpUA== X-Gm-Message-State: AGi0PuYn5ljbQ1BY4UY6H6Q2vJxYNIvhIF3t76Ww/yXc3kBujVZ0Hw1h stK2jblIlTcHXWTCIi5781/dd9sS X-Google-Smtp-Source: APiQypLJBNhKul0rJCTSh9gLvUSMghJGuvqbdoemTi1+nxo1UGlAj9hbgyhXJMVLVDWxxYPU9g8hrg== X-Received: by 2002:a1c:1f09:: with SMTP id f9mr1622579wmf.31.1587420907578; Mon, 20 Apr 2020 15:15:07 -0700 (PDT) Received: from [10.0.0.2] (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id q187sm921187wma.41.2020.04.20.15.15.05 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Mon, 20 Apr 2020 15:15:06 -0700 (PDT) References: <87k12b15ki.fsf@gnu.org> From: Vincent Legoll Message-ID: <36e8a145-1ca8-c380-9864-dbf8b1fd53cb@gmail.com> Date: Tue, 21 Apr 2020 00:15:05 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.7.0 MIME-Version: 1.0 In-Reply-To: <87k12b15ki.fsf@gnu.org> Content-Type: multipart/mixed; boundary="------------96D85335278C67436673ED76" Content-Language: en-US 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 (-) This is a multi-part message in MIME format. --------------96D85335278C67436673ED76 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit Hello, On 20/04/2020 00:19, Ludovic Courtès wrote: > Could you add a comment explaining the reason for this flag? Done, it'to build test executables. >> problems reported by cmake: >> >> -- Found Doxygen: >> /gnu/store/k6albjaxkybsgshqyw6g44f5hz75l7q6-doxygen-1.8.15/bin/doxygen >> (found version "1.8.15") found components: doxygen missing >> components: dot > > Perhaps add ‘graphviz’ as a native input? Yep, that fixed it >> -- Could NOT find Sphinx: Found unsuitable version "-real 2.3.1", but >> required is at least "1.6.1" (found >> /gnu/store/anyhb84x3mvyp11sbhmdnicbsa42m3x0-python-sphinx-2.3.1/bin/sphinx-build) > > Oh, looks like it’s looking at argv[0] and the script is wrapped. :-/ > Can you somehow for CMake to think it’s fine, either with a flag or by > skipping the relevant check in ‘CMakeLists.txt’? Done, passing the version to cmake & adding pygments to inputs made it pass. Thanks for the help How's the attached v2 ? -- Vincent Legoll --------------96D85335278C67436673ED76 Content-Type: text/x-patch; charset=UTF-8; name="0001-gnu-Add-gromacs.patch" Content-Transfer-Encoding: 8bit Content-Disposition: attachment; filename="0001-gnu-Add-gromacs.patch" >From 650247f97a56f2967d068ee8b1911fae6412ce4d Mon Sep 17 00:00:00 2001 From: Vincent Legoll Date: Sat, 18 Apr 2020 00:14:56 +0200 Subject: [PATCH] gnu: Add gromacs. * gnu/packages/bioinformatics.scm (gromacs): New variable. --- gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b9be0c1918..1b643e29c8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2019 Brett Gilio ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Jakub Kądziołka +;;; Copyright © 2020 Vincent Legoll ;;; ;;; This file is part of GNU Guix. ;;; @@ -79,6 +80,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages glib) #:use-module (gnu packages graph) + #:use-module (gnu packages graphviz) #:use-module (gnu packages groff) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) @@ -785,6 +787,51 @@ input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.") (license license:x11))) +(define-public gromacs + (package + (name "gromacs") + (version "2020.1") + (source (origin + (method url-fetch) + (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-" + version ".tar.gz")) + (sha256 + (base32 + "1kwrk3i1dxp8abhqqsl049lh361n4910h0415g052f8shdc6arp1")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests + ;; Workaround for cmake/FindSphinx.cmake version parsing that does + ;; not understand the guix-wrapped `sphinx-build --version' answer + (string-append "-DSPHINX_EXECUTABLE_VERSION=" + ,(package-version python-sphinx))))) + (native-inputs + `(("doxygen" ,doxygen) + ("graphviz" ,graphviz) + ("python" ,python) + ("python-pygments" ,python-pygments) + ("python-sphinx" ,python-sphinx))) + (inputs + `(("fftwf" ,fftwf) + ("hwloc" ,hwloc-2 "lib") + ("imagemagick" ,imagemagick) + ("lapack" ,lapack) + ("openblas" ,openblas) + ("openmpi" ,openmpi) + ("perl" ,perl))) + (home-page "http://www.gromacs.org/") + (synopsis "Molecular dynamics software package") + (description "GROMACS is a versatile package to perform molecular dynamics, +i.e. simulate the Newtonian equations of motion for systems with hundreds to +millions of particles. It is primarily designed for biochemical molecules like +proteins, lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating the nonbonded +interactions (that usually dominate simulations) many groups are also using it +for research on non-biological systems, e.g. polymers. GROMACS supports all the +usual algorithms you expect from a modern molecular dynamics implementation.") + (license license:lgpl2.1+))) + (define-public python-pybedtools (package (name "python-pybedtools") -- 2.26.0 --------------96D85335278C67436673ED76-- From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH v2 1/1] gnu: Add gromacs. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 22 Apr 2020 15:39:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Vincent Legoll Cc: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.15875698997328 (code B ref 40691); Wed, 22 Apr 2020 15:39:01 +0000 Received: (at 40691) by debbugs.gnu.org; 22 Apr 2020 15:38:19 +0000 Received: from localhost ([127.0.0.1]:52943 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jRHS7-0001u8-Cs for submit@debbugs.gnu.org; Wed, 22 Apr 2020 11:38:19 -0400 Received: from eggs.gnu.org ([209.51.188.92]:38472) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jRHS5-0001tv-LZ for 40691@debbugs.gnu.org; Wed, 22 Apr 2020 11:38:18 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:60345) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jRHS0-0007PQ-Bt; Wed, 22 Apr 2020 11:38:12 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=52702 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jRHRz-0006rm-Ul; Wed, 22 Apr 2020 11:38:12 -0400 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= References: <87k12b15ki.fsf@gnu.org> <36e8a145-1ca8-c380-9864-dbf8b1fd53cb@gmail.com> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 4 =?UTF-8?Q?Flor=C3=A9al?= an 228 de la =?UTF-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Wed, 22 Apr 2020 17:38:09 +0200 In-Reply-To: <36e8a145-1ca8-c380-9864-dbf8b1fd53cb@gmail.com> (Vincent Legoll's message of "Tue, 21 Apr 2020 00:15:05 +0200") Message-ID: <87y2qnv8da.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable 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: -1.7 (-) Hi Vincent, Vincent Legoll skribis: > From 650247f97a56f2967d068ee8b1911fae6412ce4d Mon Sep 17 00:00:00 2001 > From: Vincent Legoll > Date: Sat, 18 Apr 2020 00:14:56 +0200 > Subject: [PATCH] gnu: Add gromacs. > > * gnu/packages/bioinformatics.scm (gromacs): New variable. This v2 looks alright to me, but I got this test failure on x86_64: --8<---------------cut here---------------start------------->8--- Start 13: HardwareUnitTests 13/52 Test #13: HardwareUnitTests ...................***Failed 0.04 sec [=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D] Running 5 tests from 2 test cases. [----------] Global test environment set-up. [----------] 1 test from CpuInfoTest [ RUN ] CpuInfoTest.SupportLevel [ OK ] CpuInfoTest.SupportLevel (0 ms) [----------] 1 test from CpuInfoTest (0 ms total) [----------] 4 tests from HardwareTopologyTest [ RUN ] HardwareTopologyTest.Execute [ OK ] HardwareTopologyTest.Execute (6 ms) [ RUN ] HardwareTopologyTest.HwlocExecute /tmp/guix-build-gromacs-2020.1.drv-0/gromacs-2020.1/src/gromacs/hardware/te= sts/hardwaretopology.cpp:88: Failure Expected: (hwTop.supportLevel()) >=3D (gmx::HardwareTopology::SupportLevel:= :Basic), actual: 4-byte object <01-00 00-00> vs 4-byte object <02-00 00-00> Cannot determine basic hardware topology from hwloc. GROMACS will still work, but it might affect your performance for large nodes. Please mail gmx-developers@gromacs.org so we can try to fix it. [ FAILED ] HardwareTopologyTest.HwlocExecute (5 ms) [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (6 ms) [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (5 ms) [----------] 4 tests from HardwareTopologyTest (22 ms total) [----------] Global test environment tear-down [=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D] 5 tests from 2 test cases ran. (22 ms tota= l) [ PASSED ] 4 tests. [ FAILED ] 1 test, listed below: [ FAILED ] HardwareTopologyTest.HwlocExecute 1 FAILED TEST [=E2=80=A6] The following tests FAILED: 13 - HardwareUnitTests (Failed) Errors while running CTest make: *** [Makefile:99: test] Error 8 --8<---------------cut here---------------end--------------->8--- Could you check what the test is doing? It may be reasonable to just skip it. Thanks, Ludo=E2=80=99. From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH v3 1/1] gnu: Add gromacs. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 23 Apr 2020 13:08:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ludovic =?UTF-8?Q?Court=C3=A8s?= Cc: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158764727412206 (code B ref 40691); Thu, 23 Apr 2020 13:08:01 +0000 Received: (at 40691) by debbugs.gnu.org; 23 Apr 2020 13:07:54 +0000 Received: from localhost ([127.0.0.1]:54236 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jRba5-0003Ao-FS for submit@debbugs.gnu.org; Thu, 23 Apr 2020 09:07:53 -0400 Received: from mail-wr1-f66.google.com ([209.85.221.66]:37167) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jRba3-0003AW-Fv for 40691@debbugs.gnu.org; Thu, 23 Apr 2020 09:07:52 -0400 Received: by mail-wr1-f66.google.com with SMTP id k1so6785099wrx.4 for <40691@debbugs.gnu.org>; Thu, 23 Apr 2020 06:07:51 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=subject:to:cc:references:from:message-id:date:user-agent :mime-version:in-reply-to:content-language; bh=twyao8TOZBG/YglYYomNPDWUWzIC28cwH+pbyZmB+T4=; b=jLhG5UKzzmaY/vnowPwoNgyTO5T9nrClw4Jhorkw/Kgf/cR6v9dTghSi9LZ5+VFlFq 0Fp8LhFIl6pB6KHRNMuNltjNE34cITxAgW7y2IH6LPolcdssEp8t2NndAayvnqbWegqd me+bHjh+CWonudm5QwJFst61sLB9hYplKpqcNXGdqzS2TZzsg/vPHaonuPbPpdjh8aUS IH75UsU638Q82OH2pcc2HThRW9IQkp+l96mlr2Jxz0NhKTUscnlvnCtSXTetPd13S+zo ULIm/JXKMJtee8doIwKE90PoAFLw8xJDnaHqsrf7k42kmuoKyoVEEd2JjIBsAxe52t+V 6zPw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:subject:to:cc:references:from:message-id:date :user-agent:mime-version:in-reply-to:content-language; bh=twyao8TOZBG/YglYYomNPDWUWzIC28cwH+pbyZmB+T4=; b=eTT9+u2f/b32x2y/k5bGzW+rqQ1u5lOJN/X+m4v+vRg/xk3uuJyYzpSlUulLhApKS6 bUncv0LGcSIU5JpXhdJgx1M/Z9ue1ePicn80AJy8Ky+pds8kHzcGDwfY6iNyF8quOUBq EDgcxtdpEIDgml0bRn+vdFUtEwtX6mlDuuZaizqGPnqdi3pdbuGTcvpzm6/arYGhQEhr N+RFwpr+0Nqi7F+p4s0iez/fKEwpDPXn0uy02QStH9nEPnLkD6HE2gIMY91BGjhMqSou 4o61u52QJbTemflNA13fmmW1SkX180HTbFk0gpuugkaB6M/HzZlYLhVwvmPc/BXaTRlj zgXg== X-Gm-Message-State: AGi0PubWqA3SawvV6lX9SYa4/EqzEaZC7Coga5OfSHhS8kU+2nPVOs5N Y0xGDGQFavhQHDsnL/4D9LKIG1Jg X-Google-Smtp-Source: APiQypIowC+xUAV5LyGzuPocKTHbLdgskuS9BfTlj3iQelsRbO8fu5hlqqWHa6IRec2HTEuwGG46bA== X-Received: by 2002:adf:cd0a:: with SMTP id w10mr4816682wrm.404.1587647265223; Thu, 23 Apr 2020 06:07:45 -0700 (PDT) Received: from [10.0.0.2] (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id s11sm3960036wrw.71.2020.04.23.06.07.43 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Thu, 23 Apr 2020 06:07:44 -0700 (PDT) References: <87k12b15ki.fsf@gnu.org> <36e8a145-1ca8-c380-9864-dbf8b1fd53cb@gmail.com> <87y2qnv8da.fsf@gnu.org> From: Vincent Legoll Message-ID: Date: Thu, 23 Apr 2020 15:07:42 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.7.0 MIME-Version: 1.0 In-Reply-To: <87y2qnv8da.fsf@gnu.org> Content-Type: multipart/mixed; boundary="------------2486E0B001B304112530357A" Content-Language: en-US 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 (-) This is a multi-part message in MIME format. --------------2486E0B001B304112530357A Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit On 22/04/2020 17:38, Ludovic Courtès wrote: > This v2 looks alright to me, but I got this test failure on x86_64: > > --8<---------------cut here---------------start------------->8--- > Start 13: HardwareUnitTests > 13/52 Test #13: HardwareUnitTests ...................***Failed 0.04 sec > [==========] Running 5 tests from 2 test cases. > [----------] Global test environment set-up. > [----------] 1 test from CpuInfoTest > [ RUN ] CpuInfoTest.SupportLevel > [ OK ] CpuInfoTest.SupportLevel (0 ms) > [----------] 1 test from CpuInfoTest (0 ms total) > > [----------] 4 tests from HardwareTopologyTest > [ RUN ] HardwareTopologyTest.Execute > [ OK ] HardwareTopologyTest.Execute (6 ms) > [ RUN ] HardwareTopologyTest.HwlocExecute > /tmp/guix-build-gromacs-2020.1.drv-0/gromacs-2020.1/src/gromacs/hardware/tests/hardwaretopology.cpp:88: Failure > Expected: (hwTop.supportLevel()) >= (gmx::HardwareTopology::SupportLevel::Basic), actual: 4-byte object <01-00 00-00> vs 4-byte object <02-00 00-00> > Cannot determine basic hardware topology from hwloc. GROMACS will still > > work, but it might affect your performance for large nodes. > Please mail gmx-developers@gromacs.org so we can try to fix it. > [ FAILED ] HardwareTopologyTest.HwlocExecute (5 ms) > [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency > [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (6 ms) > [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency > [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (5 ms) > [----------] 4 tests from HardwareTopologyTest (22 ms total) > > [----------] Global test environment tear-down > [==========] 5 tests from 2 test cases ran. (22 ms total) > [ PASSED ] 4 tests. > [ FAILED ] 1 test, listed below: > [ FAILED ] HardwareTopologyTest.HwlocExecute > > 1 FAILED TEST > > […] > > The following tests FAILED: > 13 - HardwareUnitTests (Failed) > Errors while running CTest > make: *** [Makefile:99: test] Error 8 > --8<---------------cut here---------------end--------------->8--- > > Could you check what the test is doing? I think it tries to get CPU topology from the linux kernel, which is not particularly useful to test on a build server, the package may run on completely different hardware. > It may be reasonable to just skip it. Hope you don't mind trading a test suite failure for a (harmless) test suite build warning... How's the crude disabling in the attached patch v3 look to you ? And does it fix the failure ? This test is not failing here (kvm on ryzen). -- Vincent Legoll --------------2486E0B001B304112530357A Content-Type: text/x-patch; charset=UTF-8; name="0001-gnu-Add-gromacs.v3.patch" Content-Transfer-Encoding: 8bit Content-Disposition: attachment; filename="0001-gnu-Add-gromacs.v3.patch" >From 660371d5a3e7c7c763fc123357ddd6c31f730553 Mon Sep 17 00:00:00 2001 From: Vincent Legoll Date: Sat, 18 Apr 2020 00:14:56 +0200 Subject: [PATCH] gnu: Add gromacs. * gnu/packages/bioinformatics.scm (gromacs): New variable. --- gnu/packages/bioinformatics.scm | 56 +++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b9be0c1918..62647d6146 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2019 Brett Gilio ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Jakub Kądziołka +;;; Copyright © 2020 Vincent Legoll ;;; ;;; This file is part of GNU Guix. ;;; @@ -79,6 +80,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages glib) #:use-module (gnu packages graph) + #:use-module (gnu packages graphviz) #:use-module (gnu packages groff) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) @@ -785,6 +787,60 @@ input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.") (license license:x11))) +(define-public gromacs + (package + (name "gromacs") + (version "2020.1") + (source (origin + (method url-fetch) + (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-" + version ".tar.gz")) + (sha256 + (base32 + "1kwrk3i1dxp8abhqqsl049lh361n4910h0415g052f8shdc6arp1")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests + ;; Workaround for cmake/FindSphinx.cmake version parsing that does + ;; not understand the guix-wrapped `sphinx-build --version' answer + (string-append "-DSPHINX_EXECUTABLE_VERSION=" + ,(package-version python-sphinx))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-hwloc-test + (lambda _ + ;; This test warns about the build host hardware + (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" + (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") + "void __guix_disabled()")) + #t))))) + (native-inputs + `(("doxygen" ,doxygen) + ("graphviz" ,graphviz) + ("python" ,python) + ("python-pygments" ,python-pygments) + ("python-sphinx" ,python-sphinx))) + (inputs + `(("fftwf" ,fftwf) + ("hwloc" ,hwloc-2 "lib") + ("imagemagick" ,imagemagick) + ("lapack" ,lapack) + ("openblas" ,openblas) + ("openmpi" ,openmpi) + ("perl" ,perl))) + (home-page "http://www.gromacs.org/") + (synopsis "Molecular dynamics software package") + (description "GROMACS is a versatile package to perform molecular dynamics, +i.e. simulate the Newtonian equations of motion for systems with hundreds to +millions of particles. It is primarily designed for biochemical molecules like +proteins, lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating the nonbonded +interactions (that usually dominate simulations) many groups are also using it +for research on non-biological systems, e.g. polymers. GROMACS supports all the +usual algorithms you expect from a modern molecular dynamics implementation.") + (license license:lgpl2.1+))) + (define-public python-pybedtools (package (name "python-pybedtools") -- 2.26.0 --------------2486E0B001B304112530357A-- From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH v3 1/1] gnu: Add gromacs. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 23 Apr 2020 19:54:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Vincent Legoll Cc: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158767158327586 (code B ref 40691); Thu, 23 Apr 2020 19:54:02 +0000 Received: (at 40691) by debbugs.gnu.org; 23 Apr 2020 19:53:03 +0000 Received: from localhost ([127.0.0.1]:55869 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jRhuB-0007Ar-CT for submit@debbugs.gnu.org; Thu, 23 Apr 2020 15:53:03 -0400 Received: from eggs.gnu.org ([209.51.188.92]:44972) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jRhu8-0007AM-85 for 40691@debbugs.gnu.org; Thu, 23 Apr 2020 15:53:01 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:54876) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jRhu2-0008Kx-TI; Thu, 23 Apr 2020 15:52:54 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=42096 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jRhu2-00072H-9p; Thu, 23 Apr 2020 15:52:54 -0400 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= References: <87k12b15ki.fsf@gnu.org> <36e8a145-1ca8-c380-9864-dbf8b1fd53cb@gmail.com> <87y2qnv8da.fsf@gnu.org> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 5 =?UTF-8?Q?Flor=C3=A9al?= an 228 de la =?UTF-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Thu, 23 Apr 2020 21:52:51 +0200 In-Reply-To: (Vincent Legoll's message of "Thu, 23 Apr 2020 15:07:42 +0200") Message-ID: <87lfmmnfn0.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable 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: -1.7 (-) Hi Vincent, Vincent Legoll skribis: >> It may be reasonable to just skip it. > > Hope you don't mind trading a test suite failure for a (harmless) > test suite build warning... > > How's the crude disabling in the attached patch v3 look to you ? > > And does it fix the failure ? > This test is not failing here (kvm on ryzen). Oh that=E2=80=99s guix-daemon inside QEMU/KVM? Then what can happen, unlik= e on real hardware, is that hwloc doesn=E2=80=99t discrepancies between the actu= al number of cores and the info it gathers from /sys or whatever. > From 660371d5a3e7c7c763fc123357ddd6c31f730553 Mon Sep 17 00:00:00 2001 > From: Vincent Legoll > Date: Sat, 18 Apr 2020 00:14:56 +0200 > Subject: [PATCH] gnu: Add gromacs. > > * gnu/packages/bioinformatics.scm (gromacs): New variable. [...] > + (add-after 'unpack 'disable-hwloc-test > + (lambda _ > + ;; This test warns about the build host hardware > + (substitute* "src/gromacs/hardware/tests/hardwaretopology.c= pp" > + (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") > + "void __guix_disabled()")) I was thinking it=E2=80=99d be nice to use whatever mechanism gtest has to = mark a test as skipped but I didn=E2=80=99t find anything, so it=E2=80=99s proba= bly OK like this. However, there=E2=80=99s another issue I hadn=E2=80=99t noticed (apologies!= ): src/external bundles a few things like googletest, tinyxml2, zlib (indirectly), etc. Could you check if we can use our own dependencies instead of the bundled ones? For gtest it=E2=80=99s good if we can unpack the source of our =E2=80=98goo= gletest=E2=80=99 package in place of the bundled copy, but it=E2=80=99s optional (I think th= ere are cases where we found this wasn=E2=80=99t possible for some reason). Thank you! Ludo=E2=80=99. From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH v3 1/1] gnu: Add gromacs. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 01 May 2020 22:31:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ludovic =?UTF-8?Q?Court=C3=A8s?= Cc: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.15883722463539 (code B ref 40691); Fri, 01 May 2020 22:31:02 +0000 Received: (at 40691) by debbugs.gnu.org; 1 May 2020 22:30:46 +0000 Received: from localhost ([127.0.0.1]:50889 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUeBC-0000v1-CA for submit@debbugs.gnu.org; Fri, 01 May 2020 18:30:46 -0400 Received: from mail-wm1-f67.google.com ([209.85.128.67]:37810) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUeBB-0000uo-1w for 40691@debbugs.gnu.org; Fri, 01 May 2020 18:30:45 -0400 Received: by mail-wm1-f67.google.com with SMTP id z6so1511591wml.2 for <40691@debbugs.gnu.org>; Fri, 01 May 2020 15:30:44 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=subject:to:cc:references:from:message-id:date:user-agent :mime-version:in-reply-to:content-language:content-transfer-encoding; bh=WTkW06jRbgXwpvYAKBKJqy70hWOBpcti9tJ/PA8NrOo=; b=h4xFmVZQcUNSVsOUu4+1heUVPbgbUcOLn2YFs9YuJJBEou+ZLbs4NSY7qFFW4AiRZs Kr9EXd7HX3A9GdnKFkM4Z4AAAKWgA+9K60ee/udBw7ukY2owt5I6VZdSmweE8HORiG0Q NQs3hN/PJZjQ1SYAvh3g8j4x54JUBa1evWI/A2sjsiaHCMJDBocKzewtltws7X2OEtC2 uPmxYiu7LYn2V4JAUOsOExFTixdNj5mOp3QCD1yOC+0CsZlgS9cNa6CQ8LV4PV3BACJ3 d2tY7MmIAdFjsgtfynDlnLtx+1ekXxjQq+09zIsw/TTRDx7DfJYeegweKWUqkp1Ut8/L ClUg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:subject:to:cc:references:from:message-id:date :user-agent:mime-version:in-reply-to:content-language :content-transfer-encoding; bh=WTkW06jRbgXwpvYAKBKJqy70hWOBpcti9tJ/PA8NrOo=; b=rLO03tXZ/Dv9N1PPkhlWZlMPqbr06sN1IWvDz8KpHgFOLvp4EN1imDltX/3twJeK8+ yKFKzvjjfh5+Evw2eXL7atiWHhCBX1EQT8/X1Bl9LLTd+6QWuelDDL7opaTfGbyPmrVx 6aJZ4cWVsXNy86/o0Frk3pCWVzMMeqIADvRYbQcAoAIRGiIKz4Pyl8YgIqqrJEoQ4YX/ S9SwneIH6B/YjB097a0e3GucuV/Fcm797ASO0Dx5hmdN8F6R6DLzUkckXWxmfFPWi7/1 z8bccyndpExZ8jP4ZeZc/6E2GXy7lpQoLv+zDuvD1EeS3qIf1CS9eQQHKFmmWp+waJM4 IpvQ== X-Gm-Message-State: AGi0PuaHUtBdvOVH7RwLmkDEJ1qzMqQeW5ETbZND1MYUpnRtXQBLNp46 nTG97koxviZdqnamF12VMOTnI2mj X-Google-Smtp-Source: APiQypJ8OZfZfhe4RXcCIjyk0bbOmCDAoYsI6Um7RJrYSCVdVL75vGb9RnvXI9sDN9Vkz7jz+vUjng== X-Received: by 2002:a1c:ba82:: with SMTP id k124mr1776100wmf.66.1588372238556; Fri, 01 May 2020 15:30:38 -0700 (PDT) Received: from [10.0.0.2] (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id s14sm1344807wmh.18.2020.05.01.15.30.37 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Fri, 01 May 2020 15:30:37 -0700 (PDT) References: <87k12b15ki.fsf@gnu.org> <36e8a145-1ca8-c380-9864-dbf8b1fd53cb@gmail.com> <87y2qnv8da.fsf@gnu.org> <87lfmmnfn0.fsf@gnu.org> From: Vincent Legoll Message-ID: Date: Sat, 2 May 2020 00:30:35 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.7.0 MIME-Version: 1.0 In-Reply-To: <87lfmmnfn0.fsf@gnu.org> Content-Type: text/plain; charset=utf-8; format=flowed Content-Language: en-US Content-Transfer-Encoding: 8bit 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, On 23/04/2020 21:52, Ludovic Courtès wrote: > However, there’s another issue I hadn’t noticed (apologies!): > src/external bundles a few things like googletest, tinyxml2, zlib > (indirectly), etc. > > Could you check if we can use our own dependencies instead of the > bundled ones? I'm working on it but it is not trivial, some of the bundled versions are old enough that guix's are not compatible with the code using them. I'm trying to get some fixes upstream for that. > For gtest it’s good if we can unpack the source of our ‘googletest’ > package in place of the bundled copy, but it’s optional (I think there > are cases where we found this wasn’t possible for some reason). I'll try to fix this one also. -- Vincent Legoll From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH v3 1/1] gnu: Add gromacs. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 02 May 2020 13:36:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Vincent Legoll Cc: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158842651918891 (code B ref 40691); Sat, 02 May 2020 13:36:02 +0000 Received: (at 40691) by debbugs.gnu.org; 2 May 2020 13:35:19 +0000 Received: from localhost ([127.0.0.1]:51583 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUsIY-0004uc-RD for submit@debbugs.gnu.org; Sat, 02 May 2020 09:35:19 -0400 Received: from eggs.gnu.org ([209.51.188.92]:46598) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUsIW-0004uO-Ke for 40691@debbugs.gnu.org; Sat, 02 May 2020 09:35:17 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:57363) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jUsIR-0007DI-8L; Sat, 02 May 2020 09:35:11 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=46510 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jUsIN-00011o-CM; Sat, 02 May 2020 09:35:09 -0400 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= References: <87k12b15ki.fsf@gnu.org> <36e8a145-1ca8-c380-9864-dbf8b1fd53cb@gmail.com> <87y2qnv8da.fsf@gnu.org> <87lfmmnfn0.fsf@gnu.org> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 14 =?UTF-8?Q?Flor=C3=A9al?= an 228 de la =?UTF-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Sat, 02 May 2020 15:35:03 +0200 In-Reply-To: (Vincent Legoll's message of "Sat, 2 May 2020 00:30:35 +0200") Message-ID: <87v9le794o.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) 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, Vincent Legoll skribis: > On 23/04/2020 21:52, Ludovic Court=C3=A8s wrote: >> However, there=E2=80=99s another issue I hadn=E2=80=99t noticed (apologi= es!): >> src/external bundles a few things like googletest, tinyxml2, zlib >> (indirectly), etc. >> >> Could you check if we can use our own dependencies instead of the >> bundled ones? > > I'm working on it but it is not trivial, some of the bundled versions > are old enough that guix's are not compatible with the code using them. > > I'm trying to get some fixes upstream for that. Awesome, let us know how it goes. >> For gtest it=E2=80=99s good if we can unpack the source of our =E2=80=98= googletest=E2=80=99 >> package in place of the bundled copy, but it=E2=80=99s optional (I think= there >> are cases where we found this wasn=E2=80=99t possible for some reason). > > I'll try to fix this one also. Thank you! Ludo=E2=80=99. From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH v4 0/3] gnu: Add gromacs, tng & lmfit. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 02 May 2020 13:47:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ludovic =?UTF-8?Q?Court=C3=A8s?= Cc: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158842722120054 (code B ref 40691); Sat, 02 May 2020 13:47:02 +0000 Received: (at 40691) by debbugs.gnu.org; 2 May 2020 13:47:01 +0000 Received: from localhost ([127.0.0.1]:51608 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUsTs-0005DN-Pi for submit@debbugs.gnu.org; Sat, 02 May 2020 09:47:01 -0400 Received: from mail-wm1-f68.google.com ([209.85.128.68]:33834) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUsTp-0005DA-Re for 40691@debbugs.gnu.org; Sat, 02 May 2020 09:46:59 -0400 Received: by mail-wm1-f68.google.com with SMTP id v4so11781667wme.1 for <40691@debbugs.gnu.org>; Sat, 02 May 2020 06:46:57 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=subject:to:cc:references:from:message-id:date:user-agent :mime-version:in-reply-to:content-language:content-transfer-encoding; bh=6eHOUKAch4nqRDfaePeC39G1rrc0E7fZi4IKFHBIK5k=; b=h2i/PDuQN3RiNunJgIZ7+09iGmDEYk0YOAAVOfs7bAa9l1rmJZbe7hX2faQMMsIvvJ WvWwIrdwj1I/BqjvB7CSGNBeFho35MytRj5L5teUy73Ki6kLphE4vasVWhU/ICd2A6bF 2Scnbt0htLVJdLIVC2Iol0qHsS4AyVDRnQmV+rfZ2K9+9PWhickP+Bq6isFtXTpRVUF0 TZQl7sxwhCM4/dirMZQ4b1m1l896GPsf7mFot0TgT9gWdAsmNDdNwtTjVFacV0xIhITb zTM44pCt/lJYed3R3A1P7DbOlWrzATtd+wvncR+p7lzhP6pYzt4O2rXOw62fnp1m2sCC 3Jtw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:subject:to:cc:references:from:message-id:date :user-agent:mime-version:in-reply-to:content-language :content-transfer-encoding; bh=6eHOUKAch4nqRDfaePeC39G1rrc0E7fZi4IKFHBIK5k=; b=Mdd9XSRwpAHJUQfRanybdbOTXeq8OV9d8+jp3f2cgvhzlG74+fuzwLogF7b8J5tb66 yLk0RKPPQfydTViLAq+5KFzA8vw1p0jCvEKIfQWo8XwMnYf3g57nHKVKi3DLPg0FFS39 X/M4ATwTdk0B3G0gAAvL0HV29u8p5RtGZ5hZXhjzcm8N5b9xiOAEVTJZAcuLuigT89XC NglIB+q1ujiz2Emuwtvh8yKt7EOlSrZpp8Uxz5qPz/9SAoUNVlBrt+8LqGMv1e+CstR7 6gDVmDHTxbiw8Qmb4s35+ioUWZQLxOuBDWRnqiwVi5p24GOWYWkRWN/D6aBSBVLQJTTJ XdZw== X-Gm-Message-State: AGi0Pub27yQMi8NVDNh3JPsvfHJGo69kB2LwVtzfjB7Cw2M/hqeqm/1T zo1WIp5nn2WewfdNCk3Dqvu1wPk0 X-Google-Smtp-Source: APiQypKqaeTr1Rya55KWfH/E7jXmHC4+5EL+V2loVDQ43dMunWatUqYRfprJsCtpEmhRbz94t8JNcQ== X-Received: by 2002:a1c:9989:: with SMTP id b131mr4679381wme.176.1588427211570; Sat, 02 May 2020 06:46:51 -0700 (PDT) Received: from [10.0.0.2] (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id u188sm4409227wmg.37.2020.05.02.06.46.50 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Sat, 02 May 2020 06:46:51 -0700 (PDT) References: <87k12b15ki.fsf@gnu.org> <36e8a145-1ca8-c380-9864-dbf8b1fd53cb@gmail.com> <87y2qnv8da.fsf@gnu.org> <87lfmmnfn0.fsf@gnu.org> From: Vincent Legoll Message-ID: <5ff814d6-e0da-f5c9-8ae1-29cf40f87702@gmail.com> Date: Sat, 2 May 2020 15:46:49 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.7.0 MIME-Version: 1.0 In-Reply-To: <87lfmmnfn0.fsf@gnu.org> Content-Type: text/plain; charset=utf-8; format=flowed Content-Language: en-US Content-Transfer-Encoding: 7bit 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, here is my latest work on adding gromacs to guix. - rebased on latest guix master - gromacs had a new version - unbundling 3rdparties - packaged some 3rdparties to have our own I unbundled googletest by extracting our tarball in place of the bundled copy. Zlib got unbundled via packaging tng and unbundling it from there. Unbundled lmfit by packaging it separately and using that. I put it with gromacs, but its legitimate place may be elsewhere, like in maths.scm. Unbundled tinyxml2 to use our version, which is newer and broke code compatibility, so I added a patch to fix the fallout. I am trying to get those fixes upstream, but that may not be always practical, they may want to keep their well tested version. I'll follow up updating the patch in case parts of it get applied / released upstream. The remaining bundled 3rdparties are vmd_molfile & thread_mpi. Vmd_molfile source is behind a registration-only web form, I'm not going there. Thread_mpi looks like it is made to be bundled like that, and is part of the parallelizing of gromacs which is above my level of understanding (I'm only trying to package it, I'm not a user). More info here: http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multithreading_with_thread-MPI Latest license change for tng say "revised bsd", I don't know which one to choose, I put bsd-3. https://github.com/gromacs/tng/commit/65443992d81a8845ba3597620d84e8652e83a254 Lmfit is freebsd license, I choose bsd-2. https://jugit.fz-juelich.de/mlz/lmfit/-/blob/master/COPYING Gromacs itself is lgpl2.1+ and its copying file has bundled 3parties license explanations. https://github.com/gromacs/gromacs/blob/master/COPYING Please advise how to proceed further, this is already quite an adventure for me. -- Vincent Legoll From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 1/3] gnu: Add tng. References: In-Reply-To: Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 02 May 2020 13:49:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Cc: Vincent Legoll Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158842731420230 (code B ref 40691); Sat, 02 May 2020 13:49:01 +0000 Received: (at 40691) by debbugs.gnu.org; 2 May 2020 13:48:34 +0000 Received: from localhost ([127.0.0.1]:51616 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUsVO-0005GE-Fu for submit@debbugs.gnu.org; Sat, 02 May 2020 09:48:34 -0400 Received: from mail-wr1-f68.google.com ([209.85.221.68]:38178) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUsVM-0005Fy-Su for 40691@debbugs.gnu.org; Sat, 02 May 2020 09:48:33 -0400 Received: by mail-wr1-f68.google.com with SMTP id x17so15224693wrt.5 for <40691@debbugs.gnu.org>; Sat, 02 May 2020 06:48:32 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=y8nTGttrET5Hj7hEfv7HvRf4qZBPZFFmK88eZ/2pfF4=; b=px0ZcydiH0iwdCAy1tdfWkDDYZLVzkzmWSOQe1hULqLO1W92CuYRHeXiv/n5bOwo7S 5ZAxzdNOBnscqeOKZopU1eRh+DoeTBcYsobNlnDG2Wl2yMcIgioi4+y+mkKxxHWsfLq8 27lrkgwB/NU6SQRD/PUHhVEeXWaksFZsJsYZfwujP0S6xfE4mVWHRaU1KDnB3wjgITaQ TgPnaV22JVgh6Imc6RNoT2WQYsXzukXRpP44/eaJZ7kaSg84xfC7eh/uHecgNu4skO51 MLT4fvCU62ehVYb8jwi3s+3vrKZT8aiWLjksZZasgnsjZWlPA2UG6F5KNtaUcAPJrfSl qn/g== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=y8nTGttrET5Hj7hEfv7HvRf4qZBPZFFmK88eZ/2pfF4=; b=VjotfS8QgrzvAjb4sPDjKJhBSmxOZMzPUZsrvEVPMyHWoO9yfuJTjhDl+ZBcpWtonP dYEwaXe+xVxYYVu7ZKacco/eT7Tx1TSFLXmhJiaKFwc6SVLEnix5tECE0xLQB2+i351P RWgMxXxIIxi2fOFdTduTx4LONQLEY+3IVI9fZguQSod9tjoy42TmM1EKQyeht3qR9bKG uQ1Nt6mxUKtvxL/Lqzn8ILVNaDmYpQojwlmp44L+AZL1i5XaQQynxJZRpMTvxV3S2Uc9 FSMr/O74mwLKxPbrbrFyxOMaTMr+U81PH9iQ6nWl9QVqon4sZIwJ2Rlq6EoqsGGOEWfu nJAQ== X-Gm-Message-State: AGi0PubipUMJC5Zf1LKmI6LzLLOYWeedua//Mj2zLBrChidU59H7GbY2 UBJGPvRBaMVofCQeXR1spmH7Ji9A X-Google-Smtp-Source: APiQypJI+TL556G+aH59TKbdSd6hoMXipdIuywhm9aSsSrBrlE4vGijM/eOze65yJpsFMX7j2OvDEQ== X-Received: by 2002:a5d:4292:: with SMTP id k18mr9012929wrq.137.1588427306714; Sat, 02 May 2020 06:48:26 -0700 (PDT) Received: from localhost.localdomain (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id y70sm4574993wmc.36.2020.05.02.06.48.25 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 02 May 2020 06:48:26 -0700 (PDT) From: Vincent Legoll Date: Sat, 2 May 2020 15:48:13 +0200 Message-Id: <20200502134815.13390-1-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 (-) * gnu/packages/bioinformatics.scm (tng): New variable. --- gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 65b44568e0..f90401a560 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2019 Brett Gilio ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Jakub Kądziołka +;;; Copyright © 2020 Vincent Legoll ;;; ;;; This file is part of GNU Guix. ;;; @@ -785,6 +786,41 @@ input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.") (license license:x11))) +(define-public tng + (package + (name "tng") + (version "1.8.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gromacs/tng.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q")))) + (build-system cmake-build-system) + (inputs + `(("zlib" ,zlib))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-bundled-zlib + (lambda _ + (delete-file-recursively "external") + #t)) + (replace 'check + (lambda _ + (invoke "../build/bin/tests/tng_testing") + #t))))) + (home-page "https://github.com/gromacs/tng") + (synopsis "Trajectory Next Generation binary format manipulation library") + (description "TRAJNG (Trajectory next generation) is a program library for +handling molecular dynamics (MD) trajectories. It can store coordinates, and +optionally velocities and the H-matrix. Coordinates and velocities are +stored with user-specified precision.") + (license license:bsd-3))) + (define-public python-pybedtools (package (name "python-pybedtools") -- 2.26.0 From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 2/3] gnu: Add lmfit. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 02 May 2020 13:49:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Cc: Vincent Legoll Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158842732920256 (code B ref 40691); Sat, 02 May 2020 13:49:02 +0000 Received: (at 40691) by debbugs.gnu.org; 2 May 2020 13:48:49 +0000 Received: from localhost ([127.0.0.1]:51619 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUsVc-0005Gd-QM for submit@debbugs.gnu.org; Sat, 02 May 2020 09:48:49 -0400 Received: from mail-wm1-f50.google.com ([209.85.128.50]:53009) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUsVN-0005G0-J6 for 40691@debbugs.gnu.org; Sat, 02 May 2020 09:48:48 -0400 Received: by mail-wm1-f50.google.com with SMTP id 188so3111244wmc.2 for <40691@debbugs.gnu.org>; Sat, 02 May 2020 06:48:33 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=to+d1CKBVmG7ykW9ACQHbMpeRw9ktPHEHMH6Clr1iQ4=; b=S2oZJ7xdx06WxXNdu6K0Y3DK0NPyyQjBHDKBeSV+aWICcjOiiZBbjsr+Ia/uQBB/SQ z1+F20ibden6IYV2vC45C9mscFlL3xQF9T/tL8lD9JCoAFIXwllMT9105ThUZfAt3zBI 9XZIKWKDZEqgq4NDFNREbaU8Z19rQHzd9KSKmmFHLZZdGmxSzfPTXtj+PSsvKEa/D/Ow yGx3HVeyFb8dGd9ISucP8EbJeWnfzKkXVidxBm5j2xJ/58H/d6eWj0EldBzETGYuzhUM seH/Dv/WUNqbBwcp849mhbIMrOJEVeZZHTurD/GTmOwjNpoouptx3x7fgyQcXplC4iHb Pyrw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=to+d1CKBVmG7ykW9ACQHbMpeRw9ktPHEHMH6Clr1iQ4=; b=KF3h2oxBWGtEUGFR8wqKRG4LWOrVvUtZBjXxzOsXtqbbfW1vW1O8QYRI22AkRk5u5Y VAyDPDTQCHP29a0Y3rLJfbmeph//YRJSRHOquzCRNP0u4J8KMzQFe/XIHgOnAOkTcpxy eDcuczH5yJXXPjg+poZIpd50f0WAoEZ65TC7/d5D6SktZHSDgqqBUlzVw4yE3RP8KrJ4 KJYdxaL5Tr7vZKqGQBtwd8jAGIeIM3SGV/Iw/cYAfw3E2K6sfoAv8jITDOlt8gSr291e bH57i3q4OLutdsmOjLRhNPEyE0Eo4zMSgMy39gKeq+MttKqYdcxzxfPWXu/nwi3E6K5Z Gk4Q== X-Gm-Message-State: AGi0PuaCgzR4Y4ead/WiisQW0zxWyWYSruaiJK9VhlUpFCQJ03cUiTJS 3+4ZZP28xFXbldD62X1vJSEammAH X-Google-Smtp-Source: APiQypLtN+lUmOZs+vbq4tELK9l/ixBibrtP0ywSijhJv5ZJI92hOJxCrApE5mJPnIuRfYrjKCXUJA== X-Received: by 2002:a1c:770f:: with SMTP id t15mr4631015wmi.178.1588427307730; Sat, 02 May 2020 06:48:27 -0700 (PDT) Received: from localhost.localdomain (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id y70sm4574993wmc.36.2020.05.02.06.48.26 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 02 May 2020 06:48:27 -0700 (PDT) From: Vincent Legoll Date: Sat, 2 May 2020 15:48:14 +0200 Message-Id: <20200502134815.13390-2-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 In-Reply-To: <20200502134815.13390-1-vincent.legoll@gmail.com> References: <20200502134815.13390-1-vincent.legoll@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit 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 (-) * gnu/packages/bioinformatics.scm (lmfit): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f90401a560..02eae3b589 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -821,6 +821,30 @@ optionally velocities and the H-matrix. Coordinates and velocities are stored with user-specified precision.") (license license:bsd-3))) +(define-public lmfit + (package + (name "lmfit") + (version "8.2.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://jugit.fz-juelich.de/mlz/lmfit.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00bch77a6qgnw6vzsjn2a42n8n683ih3xm0wpr454jxa15hw78vf")))) + (build-system cmake-build-system) + (native-inputs + `(("perl" ,perl))) ; for pod2man + (home-page "https://jugit.fz-juelich.de/mlz/lmfit") + (synopsis "C library for Levenberg-Marquardt minimization and least-squares +fitting.") + (description "lmfit is a C library for Levenberg-Marquardt least-squares +minimization and curve fitting. It is mature code, based on decades-old +algorithms from the FORTRAN library MINPACK.") + (license license:bsd-2))) + (define-public python-pybedtools (package (name "python-pybedtools") -- 2.26.0 From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 3/3] gnu: Add gromacs. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 02 May 2020 13:49:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Cc: Vincent Legoll Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158842733420274 (code B ref 40691); Sat, 02 May 2020 13:49:02 +0000 Received: (at 40691) by debbugs.gnu.org; 2 May 2020 13:48:54 +0000 Received: from localhost ([127.0.0.1]:51621 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUsVf-0005Gr-4R for submit@debbugs.gnu.org; Sat, 02 May 2020 09:48:54 -0400 Received: from mail-wr1-f68.google.com ([209.85.221.68]:42684) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUsVO-0005G3-So for 40691@debbugs.gnu.org; Sat, 02 May 2020 09:48:50 -0400 Received: by mail-wr1-f68.google.com with SMTP id s8so4917155wrt.9 for <40691@debbugs.gnu.org>; Sat, 02 May 2020 06:48:34 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=x9v4BoI3sh37hkRykaE1fxyUCg7xKS8/VORT3CCtIzM=; b=qirPi9/R9lhSAcMNZjzjkFhotn5xZ607V+b0k+zW2c2PfQ37liNaTe2TJrRUqpfhIU Iwz/iRaGysv527cLYURCL8o3kdMPKlPuebPIOp496gSso55Ab0Hrk1oiasoS0pNyrZDw arjZ34lP8Fbu1rbcudh8CYG/RqXrhub5/jR16rK4RMRjDkPwyvdtNAE6M0/4OzovyIEd YOEGD9dOV1mF1Tbu9sFaqSeLUYSpBlA8NXwsnyqqYKkR8SHPQ2YAk9r8BPpO3IUb88q6 GY+5UxXF1aOfYSTrzaZu8xc8C2Vl3hiQ4saLPLlij5OS2Gab+hwBKZlQnrlD4QKoK0pb LIaQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=x9v4BoI3sh37hkRykaE1fxyUCg7xKS8/VORT3CCtIzM=; b=udNJahmq+b3HTLtZzhRpUxWyCmTzXHQmWe+AJ8ibrvvqemLwku3R0eQIn48HZ/B1FS aQwXeysdUMPS9N3WyTeZRsIy5sL+IW3bmVsVLXpx4ElkPSyyN9x/3tKbIF0MIF2GOVPY mPgjRrZx1qBHo0w4YhgRikA/F/nMX2KFnt7FRqfW+tBv54zJzO6xh3Lq8gwSvKKhG1fW BUvgSW+ivwRelbblbjDKzZWwRHfIIV0NcLpD6ZIt1O33kjeBWXK3MXKzNf6FnPGE+0gF oniyfnuM1i/6v/IZ5N6V3MQoTJTOHlBhVzcchlK9/0imyTyMIAs/H8zfyXj29XtjI9mc 9TQg== X-Gm-Message-State: AGi0PuY/DkiXwG0koa46cV6qQhvYN1Ns4HspIDJiW4/WpQTcpPSrLI6z 9JXoo5Z3PaGgO5I88CefrYS4yO8m X-Google-Smtp-Source: APiQypJr3RfVktCUiMgswMjHbbBtwrP6hcMb2c+jVpzxcK5KncTBStBmfzb+Yw66+uB84cKurA/CRA== X-Received: by 2002:adf:fe45:: with SMTP id m5mr10166164wrs.124.1588427308906; Sat, 02 May 2020 06:48:28 -0700 (PDT) Received: from localhost.localdomain (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id y70sm4574993wmc.36.2020.05.02.06.48.27 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 02 May 2020 06:48:28 -0700 (PDT) From: Vincent Legoll Date: Sat, 2 May 2020 15:48:15 +0200 Message-Id: <20200502134815.13390-3-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 In-Reply-To: <20200502134815.13390-1-vincent.legoll@gmail.com> References: <20200502134815.13390-1-vincent.legoll@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit 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 (-) * gnu/packages/bioinformatics.scm (gromacs): New variable. * gnu/packages/patches/gromacs-tinyxml2.patch: New file... * gnu/local.mk (dist_patch_DATA): ...add it here. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 84 +++++++++++++++++++++ gnu/packages/patches/gromacs-tinyxml2.patch | 50 ++++++++++++ 3 files changed, 135 insertions(+) create mode 100644 gnu/packages/patches/gromacs-tinyxml2.patch diff --git a/gnu/local.mk b/gnu/local.mk index 812253b192..70e8879284 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1004,6 +1004,7 @@ dist_patch_DATA = \ %D%/packages/patches/gpsbabel-qstring.patch \ %D%/packages/patches/grantlee-merge-theme-dirs.patch \ %D%/packages/patches/grep-timing-sensitive-test.patch \ + %D%/packages/patches/gromacs-tinyxml2.patch \ %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch \ %D%/packages/patches/grub-efi-fat-serial-number.patch \ %D%/packages/patches/gsl-test-i686.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 02eae3b589..0727d1bac8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -80,6 +80,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages glib) #:use-module (gnu packages graph) + #:use-module (gnu packages graphviz) #:use-module (gnu packages groff) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) @@ -845,6 +846,89 @@ minimization and curve fitting. It is mature code, based on decades-old algorithms from the FORTRAN library MINPACK.") (license license:bsd-2))) +(define-public gromacs + (package + (name "gromacs") + (version "2020.2") + (source (origin + (method url-fetch) + (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-" + version ".tar.gz")) + (sha256 + (base32 + "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl")) + (patches (search-patches "gromacs-tinyxml2.patch")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests + ; Unbundling + "-DGMX_USE_LMFIT=EXTERNAL" + "-DGMX_EXTERNAL_TNG=on" + "-DGMX_EXTERNAL_ZLIB=on" + "-DGMX_EXTERNAL_TINYXML2=on" + (string-append "-DTinyXML2_DIR=" + (assoc-ref %build-inputs "tinyxml2")) + ;; Workaround for cmake/FindSphinx.cmake version parsing that does + ;; not understand the guix-wrapped `sphinx-build --version' answer + (string-append "-DSPHINX_EXECUTABLE_VERSION=" + ,(package-version python-sphinx))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fixes + (lambda* (#:key inputs #:allow-other-keys) + ; The following has been submitted upstream + (substitute* "src/testutils/CMakeLists.txt" + (("target_link_libraries\\(testutils \\$") + "target_link_libraries(testutils PRIVATE $")) + ; Unbundling +; (delete-file-recursively "src/external/vmd_molfile") + (delete-file-recursively "src/external/lmfit") + (delete-file-recursively "src/external/clFFT") + (delete-file-recursively "src/external/fftpack") + (delete-file-recursively "src/external/build-fftw") +; (delete-file-recursively "src/external/thread_mpi") + (delete-file-recursively "src/external/tng_io") + (delete-file-recursively "src/external/tinyxml2") + (delete-file-recursively "src/external/googletest") + (copy-recursively (assoc-ref inputs "googletest-source") + "src/external/googletest") + ;; This test warns about the build host hardware, disable + (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" + (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") + "void __guix_disabled()")) + #t))))) + (native-inputs + `(("doxygen" ,doxygen) + ("googletest-source" ,(package-source googletest)) + ("graphviz" ,graphviz) + ("pkg-config" ,pkg-config) + ("python" ,python) + ("python-pygments" ,python-pygments) + ("python-sphinx" ,python-sphinx))) + (inputs + `(("fftwf" ,fftwf) + ("hwloc" ,hwloc-2 "lib") + ("imagemagick" ,imagemagick) + ("lapack" ,lapack) + ("lmfit" ,lmfit) + ("openblas" ,openblas) + ("openmpi" ,openmpi) + ("perl" ,perl) + ("tinyxml2" ,tinyxml2) + ("tng" ,tng))) + (home-page "http://www.gromacs.org/") + (synopsis "Molecular dynamics software package") + (description "GROMACS is a versatile package to perform molecular dynamics, +i.e. simulate the Newtonian equations of motion for systems with hundreds to +millions of particles. It is primarily designed for biochemical molecules like +proteins, lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating the nonbonded +interactions (that usually dominate simulations) many groups are also using it +for research on non-biological systems, e.g. polymers. GROMACS supports all the +usual algorithms you expect from a modern molecular dynamics implementation.") + (license license:lgpl2.1+))) + (define-public python-pybedtools (package (name "python-pybedtools") diff --git a/gnu/packages/patches/gromacs-tinyxml2.patch b/gnu/packages/patches/gromacs-tinyxml2.patch new file mode 100644 index 0000000000..3dace595d2 --- /dev/null +++ b/gnu/packages/patches/gromacs-tinyxml2.patch @@ -0,0 +1,50 @@ +diff -ruN gromacs-2020.2/src/testutils/CMakeLists.txt gromacs-2020.2-fixed/src/testutils/CMakeLists.txt +--- gromacs-2020.2/src/testutils/CMakeLists.txt 2020-04-30 18:33:44.000000000 +0200 ++++ gromacs-2020.2-fixed/src/testutils/CMakeLists.txt 2020-05-01 22:52:16.356000000 +0200 +@@ -73,7 +73,7 @@ + + if(HAVE_TINYXML2) + include_directories(SYSTEM ${TinyXML2_INCLUDE_DIR}) +- target_link_libraries(testutils ${TinyXML2_LIBRARIES}) ++ target_link_libraries(testutils PRIVATE ${TinyXML2_LIBRARIES}) + else() + include_directories(BEFORE SYSTEM "../external/tinyxml2") + endif() +diff -ruN gromacs-2020.2/src/testutils/refdata_xml.cpp gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp +--- gromacs-2020.2/src/testutils/refdata_xml.cpp 2020-04-30 18:33:44.000000000 +0200 ++++ gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp 2020-05-01 23:17:09.556000000 +0200 +@@ -206,21 +206,12 @@ + document.LoadFile(path.c_str()); + if (document.Error()) + { +- const char* errorStr1 = document.GetErrorStr1(); +- const char* errorStr2 = document.GetErrorStr2(); ++ const char* errorStr = document.ErrorStr(); + std::string errorString("Error was "); +- if (errorStr1) +- { +- errorString += errorStr1; +- } +- if (errorStr2) +- { +- errorString += errorStr2; +- } +- if (!errorStr1 && !errorStr2) +- { ++ if (errorStr) ++ errorString += errorStr; ++ else + errorString += "not specified."; +- } + GMX_THROW(TestException("Reference data not parsed successfully: " + path + "\n." + + errorString + "\n")); + } +@@ -371,7 +362,7 @@ + XMLElementPtr rootElement = createRootElement(&document); + createChildElements(rootElement, rootEntry); + +- if (document.SaveFile(path.c_str()) != tinyxml2::XML_NO_ERROR) ++ if (document.SaveFile(path.c_str()) != tinyxml2::XML_SUCCESS) + { + GMX_THROW(TestException("Reference data saving failed in " + path)); + } -- 2.26.0 From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH v4 0/3]: Add gromacs. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 02 May 2020 13:55:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158842764520817 (code B ref 40691); Sat, 02 May 2020 13:55:02 +0000 Received: (at 40691) by debbugs.gnu.org; 2 May 2020 13:54:05 +0000 Received: from localhost ([127.0.0.1]:51635 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUsaU-0005P2-K5 for submit@debbugs.gnu.org; Sat, 02 May 2020 09:54:05 -0400 Received: from mail-wm1-f66.google.com ([209.85.128.66]:35732) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUsaS-0005Op-Ge for 40691@debbugs.gnu.org; Sat, 02 May 2020 09:53:48 -0400 Received: by mail-wm1-f66.google.com with SMTP id r26so3353128wmh.0 for <40691@debbugs.gnu.org>; Sat, 02 May 2020 06:53:48 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=subject:to:references:from:message-id:date:user-agent:mime-version :in-reply-to:content-language:content-transfer-encoding; bh=L7SmUIuHl7uTX4PpN4f7PJCFI6gZHuAid/Dn5wIoKH4=; b=YlNpnN+5KrN+p+Kh4fChF4Q2oTWQ9ZpT5d/XDfy0KuoDNWevNX+gq86xD3kn2r+oAl lnn7Q2s+S7v9XhhkVd4YLBmN++SdSWUP1TjY7M9Sg6eX3PBLzmjtu4pfRAVsInkbSkSV hW+zSLmaWjHQTgd+CKpdyw1LWd/Ph1I8ejg32+hP9Ao9C0TYm6YsiFaE2h07jYEAJQKI z5H1A2y8S/nPUxayGWb6r1910K43ZwXcTIF0W0jNdQc8StUNSmwyvV99XAYIMweyfP1g YtL5k8wd9NxsbWnQILDZIKLdO2qaKco1ujG2TUFP0l3tTh1qrb++/bzBgI/z0oLdkRTa 7wTw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:subject:to:references:from:message-id:date :user-agent:mime-version:in-reply-to:content-language :content-transfer-encoding; bh=L7SmUIuHl7uTX4PpN4f7PJCFI6gZHuAid/Dn5wIoKH4=; b=h6dhKuulJPIGKmoTAEwL1wIfQ4vE1SlWs1QS1BivmG750u0pcdJS/L+C85Y4M5VpS1 8UXZEpf6qzlx+CpufBfRVd4OicDm7qw96HRKONADIDyK366aFI9E9QsJRPiSebkkXLDz rmOIK1iFrZSzTrOSHZtFdZ+AeKzfdMEnecrXFNEcoxvDdu3z/658cLHIHS/FQF/6kzEP PnSlhmXwWfOHWBwVVlyR4OUq6GBp6uA0nLw2jipX2RgeaXhJymlYXPKYk3MH0DR0jSNe lOcOUGec0v7VRrunZsX8f9XIslic2fD1OE8UdnMvmwsShfPVo1geDt+JK3dhcKjcKyL8 fxEQ== X-Gm-Message-State: AGi0PuZoAt1J1REF+hGEk5HWYhXxES7XQsZY8p0RRrEDIPa1pGHoKMHb 8OwDn7VkLX5yfTd+SbcjOkukKzG2 X-Google-Smtp-Source: APiQypL3V+Edgg1EvaksNP3mImAS/6S6haVpGLDjdfgNbKjEGtVOQiBNY6H2qpZDhKR2S2OA0k5DWQ== X-Received: by 2002:a1c:384:: with SMTP id 126mr4841163wmd.58.1588427622328; Sat, 02 May 2020 06:53:42 -0700 (PDT) Received: from [10.0.0.2] (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id w83sm4526431wmb.37.2020.05.02.06.53.41 for <40691@debbugs.gnu.org> (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Sat, 02 May 2020 06:53:41 -0700 (PDT) References: <20200502134815.13390-1-vincent.legoll@gmail.com> From: Vincent Legoll Message-ID: <0d82c5ad-a371-bdce-f435-957c7840f786@gmail.com> Date: Sat, 2 May 2020 15:53:40 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.7.0 MIME-Version: 1.0 In-Reply-To: <20200502134815.13390-1-vincent.legoll@gmail.com> Content-Type: text/plain; charset=utf-8; format=flowed Content-Language: en-US Content-Transfer-Encoding: 7bit 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 (-) I'll fix the lint warnings (and check indentation) then resend, but after getting feedback / fixing what's needed. From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 1/3] gnu: Add tng. References: In-Reply-To: Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 02 May 2020 16:45:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Cc: Vincent Legoll Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158843784423197 (code B ref 40691); Sat, 02 May 2020 16:45:01 +0000 Received: (at 40691) by debbugs.gnu.org; 2 May 2020 16:44:04 +0000 Received: from localhost ([127.0.0.1]:53768 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUvEx-000616-Us for submit@debbugs.gnu.org; Sat, 02 May 2020 12:44:04 -0400 Received: from mail-wr1-f67.google.com ([209.85.221.67]:42586) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUvEv-00060o-UG for 40691@debbugs.gnu.org; Sat, 02 May 2020 12:43:46 -0400 Received: by mail-wr1-f67.google.com with SMTP id s8so5296895wrt.9 for <40691@debbugs.gnu.org>; Sat, 02 May 2020 09:43:45 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=y8nTGttrET5Hj7hEfv7HvRf4qZBPZFFmK88eZ/2pfF4=; b=p7ZEjsa4kCWctSZhifLvFLiGWNJzxiJZlBhdqgExLMVpBtrd3ockvHEfPmUNyCdutw n/dXD9zYKPqGPXSCwt5Z5zviQUx6jMCEgLaZZVHBthuqjuoyEkOVMWfc6gAUOVc3CBw/ k3+xl7dydSndc32E0Vxq2R46qX8A9Ja2j6iGDboKsV3rkiSpSebyt1LHtzP9iVixLAXp ceWabneuCCX/NMiy8haSFRbToaWpkHR7afX9dOFF6FdhkUsVSLBLf8BVYAPiIjeyZZyu TXNU299NdhfjnyhQr1hHuEJbEPv4DN5XOIi/PpnYKZKpI8UwnWZsLc10WyCRKclKlErG ftBw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=y8nTGttrET5Hj7hEfv7HvRf4qZBPZFFmK88eZ/2pfF4=; b=WcNKLS9SuEX0ponRWUqXxsLBasMeaPH4WPGM1Iq9ZFVqxE/b+a1BNI8OfjPzqp9Jgt aaaxQaxpFUrttpH/wKoAX9sPifnfB6wa11LSYn6V89bv5VM9aCsfSyP+i09x21agR88z c0Rus7NjACo7tJkC+k7Mfv0oXIaGNsRfN2qhKEdOPSH2teST4X0Lo5s3r4+angwcgJGq aElCeCnsGRW6/4yqhjXT7oYaHB09sR6FL/r04QeG2lToL3fSwWvu2SJG+xApo9OLb3OD vUAsEUavAbOYf6S1x7FY7cpGydMABnEotE8O02RdXjLwY8G83nI9pMsY5jfZ9mQjppSf du5w== X-Gm-Message-State: AGi0PuZqggQP2Y7ZBy/iYkzC9wTp8iqTNul27VQGZwKl6Z4Yz646+RAl wpIi1E6FUQVsvQ8IwTjHkxRZJsrD X-Google-Smtp-Source: APiQypKMFasEqKPSIkMaSKlt46K6kK+TGKW7/T3lkIYUU9Gr3wWcOsqO5VklkeMg5JzF2GX1UBfb9g== X-Received: by 2002:adf:f884:: with SMTP id u4mr9781585wrp.171.1588437819660; Sat, 02 May 2020 09:43:39 -0700 (PDT) Received: from localhost.localdomain (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id q17sm4841598wmj.45.2020.05.02.09.43.38 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 02 May 2020 09:43:39 -0700 (PDT) From: Vincent Legoll Date: Sat, 2 May 2020 18:43:23 +0200 Message-Id: <20200502164325.2028-1-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 (-) * gnu/packages/bioinformatics.scm (tng): New variable. --- gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 65b44568e0..f90401a560 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2019 Brett Gilio ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Jakub Kądziołka +;;; Copyright © 2020 Vincent Legoll ;;; ;;; This file is part of GNU Guix. ;;; @@ -785,6 +786,41 @@ input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.") (license license:x11))) +(define-public tng + (package + (name "tng") + (version "1.8.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gromacs/tng.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q")))) + (build-system cmake-build-system) + (inputs + `(("zlib" ,zlib))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-bundled-zlib + (lambda _ + (delete-file-recursively "external") + #t)) + (replace 'check + (lambda _ + (invoke "../build/bin/tests/tng_testing") + #t))))) + (home-page "https://github.com/gromacs/tng") + (synopsis "Trajectory Next Generation binary format manipulation library") + (description "TRAJNG (Trajectory next generation) is a program library for +handling molecular dynamics (MD) trajectories. It can store coordinates, and +optionally velocities and the H-matrix. Coordinates and velocities are +stored with user-specified precision.") + (license license:bsd-3))) + (define-public python-pybedtools (package (name "python-pybedtools") -- 2.26.0 From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 2/3] gnu: Add lmfit. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 02 May 2020 16:45:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Cc: Vincent Legoll Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158843784523204 (code B ref 40691); Sat, 02 May 2020 16:45:01 +0000 Received: (at 40691) by debbugs.gnu.org; 2 May 2020 16:44:05 +0000 Received: from localhost ([127.0.0.1]:53770 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUvFE-000626-S6 for submit@debbugs.gnu.org; Sat, 02 May 2020 12:44:05 -0400 Received: from mail-wr1-f42.google.com ([209.85.221.42]:43607) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUvEw-00060q-DF for 40691@debbugs.gnu.org; Sat, 02 May 2020 12:43:50 -0400 Received: by mail-wr1-f42.google.com with SMTP id i10so15577247wrv.10 for <40691@debbugs.gnu.org>; Sat, 02 May 2020 09:43:46 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=OyUC+rWNb3RlHyyRtTx3Ii3iDXR9s6Pnu73y0PTM+0k=; b=UKHFasx69UmOY+lpo2m9KDxTLHwk1keP5suG0Vuau9h6rWduBRU12NDnFZBPJUptJE kbAz0cYGg3JlSUiSMPa6t67n/f+0fkzHW3wEQ0BkyfM6GbeT7VXnT4g+0B9j2M92oNGq DFDr2zh4GmxLPHq0evZ6l23t6opNDjkj2LwF/KhG3LvbWOmh+yzT41wO6+KK96H3h7r0 m25R3ClAYcSU3jmPFnExui7Wt21Jp1fX+HVFt6GMUYNCS0J9ryaU5AWIgVS5L1+g1s2R fhQnQpe0HHYcXSRwNSoroU/CcIry+hx/x1S2qQVZzW7DapjTvdyiEOoASTTw43wpbw4s hFLw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=OyUC+rWNb3RlHyyRtTx3Ii3iDXR9s6Pnu73y0PTM+0k=; b=kb+SJ4PD/CWHy4Wy8Qwq5Bul9x4of39gpcWfr9vuFuzUJ1UMg7cbjEVakkoINZHZ0v WCzqmqAfg9rES9PZ5Bqh2VzA6W6km2LBoU4vbwCu6IHosCRpR3Ujryxm5nMbY3cLCWK1 ORfx5NnK+BzD3jQWQu/IBb6l9/EiOrRt2szskerlG3qZ2Xgz5m5SgpsGoZFYhSpDvTn0 GjEhhL9WsfhgE/F8Y1hU7/fIC7v7x1hE8Z30LwuPlQIC1HEefLE65K09jT0iz1xAKPI0 Tnhu4bnptgakwKhO2ng47fhCwncdyZwDx8cOld6l+Uj1/lvapMrmJiPycgBBPnoCbTLq zzzA== X-Gm-Message-State: AGi0Puayhpgn+YbNfSEnJz1EKa47jnw/Lni1F38zd3+jXyz9Pe7WUA2C E9e720fTEmXvb+aAT7xFExmQh6HG X-Google-Smtp-Source: APiQypLagxBQyeTY5HQIcZL1w4guItWe0WyEBa0SYbeyEFmNedRgM8VI6eBVVfCIWjhePvjWGSPc2w== X-Received: by 2002:adf:cd12:: with SMTP id w18mr5981872wrm.341.1588437820537; Sat, 02 May 2020 09:43:40 -0700 (PDT) Received: from localhost.localdomain (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id q17sm4841598wmj.45.2020.05.02.09.43.39 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 02 May 2020 09:43:40 -0700 (PDT) From: Vincent Legoll Date: Sat, 2 May 2020 18:43:24 +0200 Message-Id: <20200502164325.2028-2-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 In-Reply-To: <20200502164325.2028-1-vincent.legoll@gmail.com> References: <20200502164325.2028-1-vincent.legoll@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit 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 (-) * gnu/packages/bioinformatics.scm (lmfit): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f90401a560..1e3e145500 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -821,6 +821,30 @@ optionally velocities and the H-matrix. Coordinates and velocities are stored with user-specified precision.") (license license:bsd-3))) +(define-public lmfit + (package + (name "lmfit") + (version "8.2.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://jugit.fz-juelich.de/mlz/lmfit.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00bch77a6qgnw6vzsjn2a42n8n683ih3xm0wpr454jxa15hw78vf")))) + (build-system cmake-build-system) + (native-inputs + `(("perl" ,perl))) ; for pod2man + (home-page "https://jugit.fz-juelich.de/mlz/lmfit") + (synopsis "C library for Levenberg-Marquardt minimization and least-squares +fitting") + (description "lmfit is a C library for Levenberg-Marquardt least-squares +minimization and curve fitting. It is mature code, based on decades-old +algorithms from the FORTRAN library MINPACK.") + (license license:bsd-2))) + (define-public python-pybedtools (package (name "python-pybedtools") -- 2.26.0 From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 3/3] gnu: Add gromacs. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 02 May 2020 16:45:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Cc: Vincent Legoll Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158843784723212 (code B ref 40691); Sat, 02 May 2020 16:45:02 +0000 Received: (at 40691) by debbugs.gnu.org; 2 May 2020 16:44:07 +0000 Received: from localhost ([127.0.0.1]:53772 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUvFF-00062D-5E for submit@debbugs.gnu.org; Sat, 02 May 2020 12:44:07 -0400 Received: from mail-wr1-f50.google.com ([209.85.221.50]:35859) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUvEx-00060s-IL for 40691@debbugs.gnu.org; Sat, 02 May 2020 12:43:51 -0400 Received: by mail-wr1-f50.google.com with SMTP id d15so15627800wrx.3 for <40691@debbugs.gnu.org>; Sat, 02 May 2020 09:43:47 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=E6jrLlRjDFTfJD1I5dHlZdvsWISdqO3GdhKtqgtbtCA=; b=bwIR5Vph4cZOZ/CR0fBmRW+GhGWdX0CMXfo2ZkdnjGPYPQpscAPI9gJB1nIh5FW+BN 01zsXfVqajRTMMXDp6JJNMRinYK2N9FdNs/9UWIby0QY80kIfCLVXvrFL36LcdAaZVI+ tcNApH3KGjxxt+saV8nE7HVfNAeP9P+4HZJ9fMHAVtlrvTPWW0WhP1ywWx3tMFFxG/7B 9MbbRWCZi7bRUe2cH0Vq2Ld4fSJUkhej57folUZ7zpLCTyMa1zCDaNqFhGUhe8LSaLwO jUEJqjshmXaeHdtxEMnGdx0ACQD7eA3AQsyi5JHzPsYxjlcSZie7CJk6FlQBeYED7wYO ksfA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=E6jrLlRjDFTfJD1I5dHlZdvsWISdqO3GdhKtqgtbtCA=; b=rSefCuSFwmZXz/wZqcLVayZ3oQVDFDMKvL5Oe7kmrrTOF+lUxxUfh+6UtXEisUOZWP uvGc0YDG0iKE/W8Rek3Nz0pykXlIGl4ZQwQHyQddvmzz4Nx9iqQvRE9Q0JcBOioIdLtc mwhYbGtmv4yfUu29PWgS1B9RwBp23dFB+L3DBx2RRAxTTfXtC4BN6y4PGNKW6AOSXPS4 g5beXYY+bQbol+4jCzLJcfdKb/0/ajTcIx/pahqZCbg+SclR6FAbdS3SlQkKHgeQ7nX4 Dvzh3GVDftP1d0VsccfxRebDwHtNWO5yXujk+CXhfLiPGrpzatTAbdGx29EmH0bMhrlU as6g== X-Gm-Message-State: AGi0PuZond1p358dLk/+O0Znvlo8QJCug2BPohFKAe8yiWr9Abdq5a4e hiEtv+DYV17rXsYGz+CfDwcRndNN X-Google-Smtp-Source: APiQypJTSgiTklcbcpgC3c1eAfnGbfxhMQ97hrgxvJHtUDy+F7P74SAzRSs+y2zeMm06zyi6Mwgwkg== X-Received: by 2002:a5d:6305:: with SMTP id i5mr11251000wru.60.1588437821543; Sat, 02 May 2020 09:43:41 -0700 (PDT) Received: from localhost.localdomain (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id q17sm4841598wmj.45.2020.05.02.09.43.40 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sat, 02 May 2020 09:43:41 -0700 (PDT) From: Vincent Legoll Date: Sat, 2 May 2020 18:43:25 +0200 Message-Id: <20200502164325.2028-3-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 In-Reply-To: <20200502164325.2028-1-vincent.legoll@gmail.com> References: <20200502164325.2028-1-vincent.legoll@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit 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 (-) * gnu/packages/bioinformatics.scm (gromacs): New variable. * gnu/packages/patches/gromacs-tinyxml2.patch: New file... * gnu/local.mk (dist_patch_DATA): ...add it here. --- gnu/local.mk | 1 + gnu/packages/bioinformatics.scm | 84 +++++++++++++++++++++ gnu/packages/patches/gromacs-tinyxml2.patch | 50 ++++++++++++ 3 files changed, 135 insertions(+) create mode 100644 gnu/packages/patches/gromacs-tinyxml2.patch diff --git a/gnu/local.mk b/gnu/local.mk index 812253b192..70e8879284 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1004,6 +1004,7 @@ dist_patch_DATA = \ %D%/packages/patches/gpsbabel-qstring.patch \ %D%/packages/patches/grantlee-merge-theme-dirs.patch \ %D%/packages/patches/grep-timing-sensitive-test.patch \ + %D%/packages/patches/gromacs-tinyxml2.patch \ %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch \ %D%/packages/patches/grub-efi-fat-serial-number.patch \ %D%/packages/patches/gsl-test-i686.patch \ diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1e3e145500..13d9c16c10 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -80,6 +80,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages glib) #:use-module (gnu packages graph) + #:use-module (gnu packages graphviz) #:use-module (gnu packages groff) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) @@ -845,6 +846,89 @@ minimization and curve fitting. It is mature code, based on decades-old algorithms from the FORTRAN library MINPACK.") (license license:bsd-2))) +(define-public gromacs + (package + (name "gromacs") + (version "2020.2") + (source (origin + (method url-fetch) + (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-" + version ".tar.gz")) + (sha256 + (base32 + "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl")) + (patches (search-patches "gromacs-tinyxml2.patch")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests + ; Unbundling + "-DGMX_USE_LMFIT=EXTERNAL" + "-DGMX_BUILD_OWN_FFTW=off" + "-DGMX_EXTERNAL_BLAS=on" + "-DGMX_EXTERNAL_LAPACK=on" + "-DGMX_EXTERNAL_TNG=on" + "-DGMX_EXTERNAL_ZLIB=on" + "-DGMX_EXTERNAL_TINYXML2=on" + (string-append "-DTinyXML2_DIR=" + (assoc-ref %build-inputs "tinyxml2")) + ;; Workaround for cmake/FindSphinx.cmake version parsing that does + ;; not understand the guix-wrapped `sphinx-build --version' answer + (string-append "-DSPHINX_EXECUTABLE_VERSION=" + ,(package-version python-sphinx))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fixes + (lambda* (#:key inputs #:allow-other-keys) + ; The following has been submitted upstream + (substitute* "src/testutils/CMakeLists.txt" + (("target_link_libraries\\(testutils \\$") + "target_link_libraries(testutils PRIVATE $")) + ; Unbundling +; (delete-file-recursively "src/external/vmd_molfile") + (delete-file-recursively "src/external/lmfit") + (delete-file-recursively "src/external/clFFT") + (delete-file-recursively "src/external/fftpack") + (delete-file-recursively "src/external/build-fftw") +; (delete-file-recursively "src/external/thread_mpi") + (delete-file-recursively "src/external/tng_io") + (delete-file-recursively "src/external/tinyxml2") + (delete-file-recursively "src/external/googletest") + (copy-recursively (assoc-ref inputs "googletest-source") + "src/external/googletest") + ;; This test warns about the build host hardware, disable + (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" + (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") + "void __guix_disabled()")) + #t))))) + (native-inputs + `(("doxygen" ,doxygen) + ("googletest-source" ,(package-source googletest)) + ("graphviz" ,graphviz) + ("pkg-config" ,pkg-config) + ("python" ,python) + ("python-pygments" ,python-pygments) + ("python-sphinx" ,python-sphinx))) + (inputs + `(("fftwf" ,fftwf) + ("hwloc" ,hwloc-2 "lib") + ("lmfit" ,lmfit) + ("openblas" ,openblas) + ("perl" ,perl) + ("tinyxml2" ,tinyxml2) + ("tng" ,tng))) + (home-page "http://www.gromacs.org/") + (synopsis "Molecular dynamics software package") + (description "GROMACS is a versatile package to perform molecular dynamics, +i.e. simulate the Newtonian equations of motion for systems with hundreds to +millions of particles. It is primarily designed for biochemical molecules like +proteins, lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating the nonbonded +interactions (that usually dominate simulations) many groups are also using it +for research on non-biological systems, e.g. polymers. GROMACS supports all the +usual algorithms you expect from a modern molecular dynamics implementation.") + (license license:lgpl2.1+))) + (define-public python-pybedtools (package (name "python-pybedtools") diff --git a/gnu/packages/patches/gromacs-tinyxml2.patch b/gnu/packages/patches/gromacs-tinyxml2.patch new file mode 100644 index 0000000000..3dace595d2 --- /dev/null +++ b/gnu/packages/patches/gromacs-tinyxml2.patch @@ -0,0 +1,50 @@ +diff -ruN gromacs-2020.2/src/testutils/CMakeLists.txt gromacs-2020.2-fixed/src/testutils/CMakeLists.txt +--- gromacs-2020.2/src/testutils/CMakeLists.txt 2020-04-30 18:33:44.000000000 +0200 ++++ gromacs-2020.2-fixed/src/testutils/CMakeLists.txt 2020-05-01 22:52:16.356000000 +0200 +@@ -73,7 +73,7 @@ + + if(HAVE_TINYXML2) + include_directories(SYSTEM ${TinyXML2_INCLUDE_DIR}) +- target_link_libraries(testutils ${TinyXML2_LIBRARIES}) ++ target_link_libraries(testutils PRIVATE ${TinyXML2_LIBRARIES}) + else() + include_directories(BEFORE SYSTEM "../external/tinyxml2") + endif() +diff -ruN gromacs-2020.2/src/testutils/refdata_xml.cpp gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp +--- gromacs-2020.2/src/testutils/refdata_xml.cpp 2020-04-30 18:33:44.000000000 +0200 ++++ gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp 2020-05-01 23:17:09.556000000 +0200 +@@ -206,21 +206,12 @@ + document.LoadFile(path.c_str()); + if (document.Error()) + { +- const char* errorStr1 = document.GetErrorStr1(); +- const char* errorStr2 = document.GetErrorStr2(); ++ const char* errorStr = document.ErrorStr(); + std::string errorString("Error was "); +- if (errorStr1) +- { +- errorString += errorStr1; +- } +- if (errorStr2) +- { +- errorString += errorStr2; +- } +- if (!errorStr1 && !errorStr2) +- { ++ if (errorStr) ++ errorString += errorStr; ++ else + errorString += "not specified."; +- } + GMX_THROW(TestException("Reference data not parsed successfully: " + path + "\n." + + errorString + "\n")); + } +@@ -371,7 +362,7 @@ + XMLElementPtr rootElement = createRootElement(&document); + createChildElements(rootElement, rootEntry); + +- if (document.SaveFile(path.c_str()) != tinyxml2::XML_NO_ERROR) ++ if (document.SaveFile(path.c_str()) != tinyxml2::XML_SUCCESS) + { + GMX_THROW(TestException("Reference data saving failed in " + path)); + } -- 2.26.0 From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] Fwd: Re: [PATCH v5 0/3] gnu: Add gromacs. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 02 May 2020 17:05:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158843904325380 (code B ref 40691); Sat, 02 May 2020 17:05:02 +0000 Received: (at 40691) by debbugs.gnu.org; 2 May 2020 17:04:03 +0000 Received: from localhost ([127.0.0.1]:53798 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUvYZ-0006bH-1b for submit@debbugs.gnu.org; Sat, 02 May 2020 13:04:03 -0400 Received: from mail-wm1-f67.google.com ([209.85.128.67]:54103) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jUvYY-0006an-Ao for 40691@debbugs.gnu.org; Sat, 02 May 2020 13:04:02 -0400 Received: by mail-wm1-f67.google.com with SMTP id k12so3485595wmj.3 for <40691@debbugs.gnu.org>; Sat, 02 May 2020 10:04:02 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=subject:references:to:from:message-id:date:user-agent:mime-version :in-reply-to:content-language:content-transfer-encoding; bh=/XmB6TjAiE9+tslZbeXofOHZ5nsUHtDLwRYpNGUO7lg=; b=IXaJ66cwuuTzEnu6OimvW1jVA7d5RihBAL3ZdVAC70De3kIwvMiMVkqUivZQtqHJSE EL47xaUH3u5FHJh2rB4I6Z1UcQJPyLWz4NwUqX0YppsZHhoVkm7splqGVxQAPQ8Y17Rs ZFA0TGJqA6VnmrkgX8SlDa6Eua0sK6E+rDT4FCm1jkJGyBgzVUk/6VxqaV8RCg5bJfDo 3DddtJp9PL1FrrvAP7lQV6wDvI/k64utcie86j+wpVyvIhahXoMsWmDqTzDEr3EDTXtt 8eBLXcTZMH0HiKbsN9OWPt4AQxDNfMVosCSU3DgUKwIisFl4o9VKX9+QpdEXv08sOA+G XzAQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:subject:references:to:from:message-id:date :user-agent:mime-version:in-reply-to:content-language :content-transfer-encoding; bh=/XmB6TjAiE9+tslZbeXofOHZ5nsUHtDLwRYpNGUO7lg=; b=LHkE0FowU3OiZf30gNarb3wMZIUZYODIOfvmnU3kxjYa0zLGkWV7qJ5J0QJsiDaND2 b/bqzWhubNVkAqgSuuBktsPE4EFDE2/sH9HqFA1PGH3v7tbHca+rEO5go77w3eDnpwwn fjuQIElV2B0SvRkyU7V2YNSHozXhd4oxqOvg4eCsgQbgXB7nnnowDmiwU7t0RiwfJ1BT mUuvim21KNjVYJ5JU5wEjLZ9mu2CQYE7ZM4I2sC1IApPYwzSpLkELpbGU+YWqf3Os0Cc aesnuSvjNjJs7Gzy3Yn95MF0FMMR0M89slL3hXkCBkJjupdVseRtzJoGEQCLT5haFQ36 em3A== X-Gm-Message-State: AGi0PuY7XtNMG/CiaohDk+gn88eLuTeGBX9z3GR9a0vFPgxrJE+LbaOR zc8mThi0kygUf9om40xIiqKjRfRy X-Google-Smtp-Source: APiQypKjHYJpGuVlF/mOQqlBGZ1R/bwQZg8RQMO4Q1gs6aU1LiT2c67/hDy971Xxax96uHYXxNR83Q== X-Received: by 2002:a05:600c:2046:: with SMTP id p6mr5362480wmg.177.1588439035869; Sat, 02 May 2020 10:03:55 -0700 (PDT) Received: from [10.0.0.2] (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id x23sm4870820wmj.6.2020.05.02.10.03.55 for <40691@debbugs.gnu.org> (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Sat, 02 May 2020 10:03:55 -0700 (PDT) References: From: Vincent Legoll X-Forwarded-Message-Id: Message-ID: Date: Sat, 2 May 2020 19:03:54 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.7.0 MIME-Version: 1.0 In-Reply-To: Content-Type: text/plain; charset=utf-8; format=flowed Content-Language: en-US Content-Transfer-Encoding: 7bit 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 (-) should have come before the last batch... -------- Forwarded Message -------- Subject: Re: [PATCH v5 0/3] gnu: Add gromacs. Date: Sat, 2 May 2020 18:43:11 +0200 From: Vincent Legoll To: Vincent Legoll - Removed unused inputs - tightened bundled 3rdparty usage by adding more cmake params - fixed lint warning - fixed one of the indent-code.el snippet (ignored the other ones as they make the comments look wrong) From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH v4 0/3] gnu: Add gromacs, tng & lmfit. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 03 May 2020 10:40:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Vincent Legoll Cc: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158850238332229 (code B ref 40691); Sun, 03 May 2020 10:40:02 +0000 Received: (at 40691) by debbugs.gnu.org; 3 May 2020 10:39:43 +0000 Received: from localhost ([127.0.0.1]:54709 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVC2A-0008Nl-St for submit@debbugs.gnu.org; Sun, 03 May 2020 06:39:43 -0400 Received: from eggs.gnu.org ([209.51.188.92]:60854) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVC28-0008NZ-Nf for 40691@debbugs.gnu.org; Sun, 03 May 2020 06:39:41 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:50281) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jVC23-0002J5-EY; Sun, 03 May 2020 06:39:35 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=49040 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jVC23-0004n8-29; Sun, 03 May 2020 06:39:35 -0400 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= References: <87k12b15ki.fsf@gnu.org> <36e8a145-1ca8-c380-9864-dbf8b1fd53cb@gmail.com> <87y2qnv8da.fsf@gnu.org> <87lfmmnfn0.fsf@gnu.org> <5ff814d6-e0da-f5c9-8ae1-29cf40f87702@gmail.com> Date: Sun, 03 May 2020 12:39:32 +0200 In-Reply-To: <5ff814d6-e0da-f5c9-8ae1-29cf40f87702@gmail.com> (Vincent Legoll's message of "Sat, 2 May 2020 15:46:49 +0200") Message-ID: <87y2q91evv.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) 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 Vincent, Vincent Legoll skribis: > here is my latest work on adding gromacs to guix. > > - rebased on latest guix master > - gromacs had a new version > - unbundling 3rdparties > - packaged some 3rdparties to have our own > > I unbundled googletest by extracting our tarball in > place of the bundled copy. > > Zlib got unbundled via packaging tng and unbundling > it from there. > > Unbundled lmfit by packaging it separately and using that. > I put it with gromacs, but its legitimate place may be > elsewhere, like in maths.scm. > > Unbundled tinyxml2 to use our version, which is newer and > broke code compatibility, so I added a patch to fix the > fallout. I am trying to get those fixes upstream, but that > may not be always practical, they may want to keep their > well tested version. I'll follow up updating the patch in > case parts of it get applied / released upstream. Woow, quite an achievement! Thanks for taking the time to go down this rabbit hole, I think it=E2=80=99s worth it. > The remaining bundled 3rdparties are vmd_molfile & thread_mpi. > > Vmd_molfile source is behind a registration-only web form, I'm > not going there. Sounds reasonable: the headers say it=E2=80=99s part of Gromacs, and it=E2= =80=99s definitely free software, so it=E2=80=99s OK to keep it here. > Thread_mpi looks like it is made to be bundled like that, and > is part of the parallelizing of gromacs which is above my > level of understanding (I'm only trying to package it, I'm not > a user). More info here: > http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Mul= tithreading_with_thread-MPI Sounds good. Perhaps a comment in the code to state that would be welcome, for our future selves. > Latest license change for tng say "revised bsd", I don't know > which one to choose, I put bsd-3. > > https://github.com/gromacs/tng/commit/65443992d81a8845ba3597620d84e8652e8= 3a254 > > Lmfit is freebsd license, I choose bsd-2. > > https://jugit.fz-juelich.de/mlz/lmfit/-/blob/master/COPYING > > Gromacs itself is lgpl2.1+ and its copying file has bundled > 3parties license explanations. > > https://github.com/gromacs/gromacs/blob/master/COPYING > > Please advise how to proceed further, this is already quite an > adventure for me. I=E2=80=99ll look at the individual patches but it looks like we=E2=80=99re= close to the end line! Ludo=E2=80=99. From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 1/3] gnu: Add tng. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 03 May 2020 10:42:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Vincent Legoll Cc: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158850247232404 (code B ref 40691); Sun, 03 May 2020 10:42:02 +0000 Received: (at 40691) by debbugs.gnu.org; 3 May 2020 10:41:12 +0000 Received: from localhost ([127.0.0.1]:54713 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVC3c-0008QY-BM for submit@debbugs.gnu.org; Sun, 03 May 2020 06:41:12 -0400 Received: from eggs.gnu.org ([209.51.188.92]:32990) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVC3b-0008QM-3D for 40691@debbugs.gnu.org; Sun, 03 May 2020 06:41:11 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:50299) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jVC3V-0003iD-RB; Sun, 03 May 2020 06:41:05 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=49042 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jVC3V-0004xl-FA; Sun, 03 May 2020 06:41:05 -0400 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= References: <20200502164325.2028-1-vincent.legoll@gmail.com> Date: Sun, 03 May 2020 12:41:04 +0200 In-Reply-To: <20200502164325.2028-1-vincent.legoll@gmail.com> (Vincent Legoll's message of "Sat, 2 May 2020 18:43:23 +0200") Message-ID: <87tv0x1etb.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) 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 (---) Vincent Legoll skribis: > * gnu/packages/bioinformatics.scm (tng): New variable. [...] > + (description "TRAJNG (Trajectory next generation) is a program libra= ry for > +handling molecular dynamics (MD) trajectories. It can store coordinates= , and I=E2=80=99d rather put it in chemistry.scm, next to =E2=80=98nmoldyn=E2=80= =99, which seems to do a similar job. WDYT? Otherwise LGTM! Ludo=E2=80=99. From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 2/3] gnu: Add lmfit. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 03 May 2020 10:45:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Vincent Legoll Cc: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158850264332711 (code B ref 40691); Sun, 03 May 2020 10:45:02 +0000 Received: (at 40691) by debbugs.gnu.org; 3 May 2020 10:44:03 +0000 Received: from localhost ([127.0.0.1]:54734 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVC68-0008Uv-Rt for submit@debbugs.gnu.org; Sun, 03 May 2020 06:44:03 -0400 Received: from eggs.gnu.org ([209.51.188.92]:33972) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVC67-0008Uj-Sk for 40691@debbugs.gnu.org; Sun, 03 May 2020 06:43:48 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:50377) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jVC62-0005fZ-Jw; Sun, 03 May 2020 06:43:42 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=49106 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jVC61-0005Hl-Nt; Sun, 03 May 2020 06:43:42 -0400 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= References: <20200502164325.2028-1-vincent.legoll@gmail.com> <20200502164325.2028-2-vincent.legoll@gmail.com> Date: Sun, 03 May 2020 12:43:40 +0200 In-Reply-To: <20200502164325.2028-2-vincent.legoll@gmail.com> (Vincent Legoll's message of "Sat, 2 May 2020 18:43:24 +0200") Message-ID: <87pnbl1eoz.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) 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 (-) Vincent Legoll skribis: > * gnu/packages/bioinformatics.scm (lmfit): New variable. [...] > + (home-page "https://jugit.fz-juelich.de/mlz/lmfit") > + (synopsis "C library for Levenberg-Marquardt minimization and least-= squares > +fitting") Perhaps remove =E2=80=9CC Library for=E2=80=9D to make it more concise. What about moving it to algebra.scm, next to Eigen & co.? Otherwise LGTM! Ludo=E2=80=99. From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 3/3] gnu: Add gromacs. Resent-From: Ludovic =?UTF-8?Q?Court=C3=A8s?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 03 May 2020 10:47:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Vincent Legoll Cc: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.1588502810542 (code B ref 40691); Sun, 03 May 2020 10:47:01 +0000 Received: (at 40691) by debbugs.gnu.org; 3 May 2020 10:46:50 +0000 Received: from localhost ([127.0.0.1]:54743 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVC94-00008g-0r for submit@debbugs.gnu.org; Sun, 03 May 2020 06:46:50 -0400 Received: from eggs.gnu.org ([209.51.188.92]:34896) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVC90-00008R-2z for 40691@debbugs.gnu.org; Sun, 03 May 2020 06:46:49 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:50436) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jVC8u-0008Sd-4u; Sun, 03 May 2020 06:46:40 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=49108 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jVC8t-0005i0-JZ; Sun, 03 May 2020 06:46:39 -0400 From: Ludovic =?UTF-8?Q?Court=C3=A8s?= References: <20200502164325.2028-1-vincent.legoll@gmail.com> <20200502164325.2028-3-vincent.legoll@gmail.com> Date: Sun, 03 May 2020 12:46:36 +0200 In-Reply-To: <20200502164325.2028-3-vincent.legoll@gmail.com> (Vincent Legoll's message of "Sat, 2 May 2020 18:43:25 +0200") Message-ID: <87lfm91ek3.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: -2.3 (--) 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 (---) Vincent Legoll skribis: > * gnu/packages/bioinformatics.scm (gromacs): New variable. > * gnu/packages/patches/gromacs-tinyxml2.patch: New file... > * gnu/local.mk (dist_patch_DATA): ...add it here. I wonder if chemistry.scm would be more appropriate, WDYT? > --- /dev/null > +++ b/gnu/packages/patches/gromacs-tinyxml2.patch > @@ -0,0 +1,50 @@ Could you add one or two sentences at the top of the file explaining what it does and what its upstream status is? It=E2=80=99s not obvious why= the reference data needs to be adjusted as a consequence of unbundling tinyxml2. That=E2=80=99s it! Could you send updated patches? I=E2=80=99ll be happy to commit them. :-) Thank you for all the work! Ludo=E2=80=99. From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH v6 0/3] gnu: Add gromacs, tng & lmfit. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 03 May 2020 22:32:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Ludovic =?UTF-8?Q?Court=C3=A8s?= Cc: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158854510315421 (code B ref 40691); Sun, 03 May 2020 22:32:02 +0000 Received: (at 40691) by debbugs.gnu.org; 3 May 2020 22:31:43 +0000 Received: from localhost ([127.0.0.1]:58332 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVN9D-00040f-D3 for submit@debbugs.gnu.org; Sun, 03 May 2020 18:31:43 -0400 Received: from mail-wm1-f66.google.com ([209.85.128.66]:35589) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVN9C-00040S-H0 for 40691@debbugs.gnu.org; Sun, 03 May 2020 18:31:42 -0400 Received: by mail-wm1-f66.google.com with SMTP id r26so6754881wmh.0 for <40691@debbugs.gnu.org>; Sun, 03 May 2020 15:31:42 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=subject:to:cc:references:from:message-id:date:user-agent :mime-version:in-reply-to:content-language:content-transfer-encoding; bh=lZwe56J0lmbsGqeUpCyfisEYCcLznrCddhEezRzwKhQ=; b=VZbKH5GlQWZUTYJGhLJRfxE9ABpLfCVpYcebmw3tOkjD5il+gFDs7efn1dxechRaFL ke6O7VWSe9uP/fohEGKQ8kErI/Zgsb2ZUTA0gVbRM1Pve7p5BQzfKJuNynPFsN7hSAEG kab14knAJgHUP747jGN7WMnMG5zUlaa0e6E79CpUIhENmo3yvYI632K7Cb0kXI0U45aA GIFPs8wX4CFkt1UfIf/BuSQzmnG1kEY1Sw87AMBJBEeQ62W19TeMlx4yMfog3mZvo8rK i8/PYcyTp2LBdpKsflBMPOckfWVRXITr/GGDRfyStwxpvu5N35gs6mucBesdt+DNdI3u gJDg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:subject:to:cc:references:from:message-id:date :user-agent:mime-version:in-reply-to:content-language :content-transfer-encoding; bh=lZwe56J0lmbsGqeUpCyfisEYCcLznrCddhEezRzwKhQ=; b=XTp5e4GwZDxGqCw0FG5RmkpXzDNUGPjsdCqiWQXgzg+CmOs5arODsg6F9q7i5yHh8+ qKGpiSbATGUjPAeBfnPHmVTXDOTrZixV9KaE/Lo8QEVPEWY/ogeEzmQ/+8iF2hQXJOoI j/uVnDTjnLliX1AquJjxpdnkh785vfaSwDNE8rIXYAwVoxBayd62dhdU9SBJ1ha0NJru DrT4cxvQss+Hql6iCjwfPuNNwsA2RpZ7SUuWf4sPGBY61JtN90vBYxFKDI29RnNARuko rGfXf5hNiFf8W4cBRzAn1yJseVOSeWUQG3K4oUdgFk//PVVctAL1PaE8Tb960CR3PR/X Saog== X-Gm-Message-State: AGi0Pua4LesPBN/7YLGJWVONd6+ooLTK3dkVIqLdwq2UQeCbdBB8mmTO toy3j7Xso8ll2Tb/o6J5jlvzSw3i X-Google-Smtp-Source: APiQypKl7vckLCyttjpuTtfJrp0L/rAxqJgXvGLb2NOKAXIzWzB8mvpWdqnzZCuHTFToUYQRz9s5DA== X-Received: by 2002:a1c:9e51:: with SMTP id h78mr12048024wme.177.1588545096267; Sun, 03 May 2020 15:31:36 -0700 (PDT) Received: from [10.0.0.2] (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id z16sm16906040wrl.0.2020.05.03.15.31.35 (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Sun, 03 May 2020 15:31:35 -0700 (PDT) References: <87k12b15ki.fsf@gnu.org> <36e8a145-1ca8-c380-9864-dbf8b1fd53cb@gmail.com> <87y2qnv8da.fsf@gnu.org> <87lfmmnfn0.fsf@gnu.org> <5ff814d6-e0da-f5c9-8ae1-29cf40f87702@gmail.com> <87y2q91evv.fsf@gnu.org> From: Vincent Legoll Message-ID: Date: Mon, 4 May 2020 00:31:34 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.7.0 MIME-Version: 1.0 In-Reply-To: <87y2q91evv.fsf@gnu.org> Content-Type: text/plain; charset=utf-8; format=flowed Content-Language: en-US Content-Transfer-Encoding: 8bit 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 Ludo, I removed the leftover scm code that was duplicating what is now in the patch, and added a patch header explaining what's going on. >> Vmd_molfile source is behind a registration-only web form, I'm >> not going there. > > Sounds reasonable: the headers say it’s part of Gromacs, and it’s > definitely free software, so it’s OK to keep it here. Added comment. >> Thread_mpi looks like it is made to be bundled like that, and >> is part of the parallelizing of gromacs which is above my >> level of understanding (I'm only trying to package it, I'm not >> a user). More info here: > > Sounds good. Perhaps a comment in the code to state that would be > welcome, for our future selves. Added comment. Put tng & gromacs in chemistry.scm, in fact gromacs sci domain is chemistry, even if also used in bioinfo. Added more comments for patch & still bundled 3rdparties. Moved lmfit to algebra.scm, shortened synopsis. I think I fixed all review comments. Thanks, patches follow. -- Vincent Legoll From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 1/3] gnu: Add tng. References: In-Reply-To: Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 03 May 2020 22:33:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Cc: Vincent Legoll Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158854518015538 (code B ref 40691); Sun, 03 May 2020 22:33:02 +0000 Received: (at 40691) by debbugs.gnu.org; 3 May 2020 22:33:00 +0000 Received: from localhost ([127.0.0.1]:58338 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVNAR-00042X-Pg for submit@debbugs.gnu.org; Sun, 03 May 2020 18:33:00 -0400 Received: from mail-wr1-f65.google.com ([209.85.221.65]:40424) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVNAQ-00042J-Bv for 40691@debbugs.gnu.org; Sun, 03 May 2020 18:32:58 -0400 Received: by mail-wr1-f65.google.com with SMTP id e16so13585411wra.7 for <40691@debbugs.gnu.org>; Sun, 03 May 2020 15:32:58 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=TQB2efBAPyJR623DG7yRR7Ysp0q65fdvgzber0o0tDg=; b=kzOG987AdTxkWC3lBpCX9DVjXp7MVfTa+p6IpmssWbng9o2rvvWKfYST1SJWHZsLFR I/09lPixdhT7sej1qZ/Div6Rrkv7fY6cmqjWZ/EXAaQwYM+DmjJuJD96oV33FyvJharL BUAuH2AblnItX67mX5gsR2VQxLERHSV3xIIi9fqrtA82F/jizSqi7VTx81fWBxY2D2ZR 9ptPVDfPWNz6x64W+2RQO+zZSvdMqToP3G4M5/5y7zQoPirOCLrJ9vut+r/V3Is74F6Q p0J6efaHyI2nOp8Q5IDq1eA40YNT5AwAR3MiaGhO7sRvATgXX35N7Pan3AaH90bDCfdF SQTQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=TQB2efBAPyJR623DG7yRR7Ysp0q65fdvgzber0o0tDg=; b=fmR8cc6I4oyXQ2sih3eaqBeZ+1YRQaZ7QnXnklHDvn+hEXscg4xasy7XsbHU+nLtGx /oPFmxXBW/Aamy9EyDcm0SuOBewf2/vE2n7KxC/lNjsWBdbLv8gdaO/csejR7pgcGv4m Ql9FsTWx7i/229l0FzaH1GIS2NjdjdT4e2gu0+/bVJCMbA0j9rYlV8LOczm/Ya+N6h/t 354S2We27WQN0en55vjch16+HxRBE0SRM13WXHlOOWRN3bipBICBmx/hdXN8BHskNf1k LwUxjU1N/E68STGDgNrGEG+60izssM4Awx6AB7agIX0XGJhhPGEDMZy+mq0V4QC3F3iZ YjTg== X-Gm-Message-State: AGi0PuZujxU41gZKe+/yQ9sSFUC2UCKvtEuMBn0iaXZ2Y3z86tqRxhcR v6jyyccnX3WSNVJlCk+WmikAf85q X-Google-Smtp-Source: APiQypLOwf0s9vee+uHAwMM1hkPY82wL6XGnO0yGmz0tS89jwV1JI1xFGChoBZ/omdro24f42lm3rw== X-Received: by 2002:a5d:4645:: with SMTP id j5mr15341738wrs.282.1588545172305; Sun, 03 May 2020 15:32:52 -0700 (PDT) Received: from localhost.localdomain (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id a205sm11211970wmh.29.2020.05.03.15.32.51 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 03 May 2020 15:32:51 -0700 (PDT) From: Vincent Legoll Date: Mon, 4 May 2020 00:32:38 +0200 Message-Id: <20200503223240.16408-1-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 (-) * gnu/packages/chemistry.scm (tng): New variable. --- gnu/packages/chemistry.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 855ae2df22..5b21e3309c 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -4,6 +4,7 @@ ;;; Copyright © 2018 Efraim Flashner ;;; Copyright © 2018 Tobias Geerinckx-Rice ;;; Copyright © 2020 Björn Höfling +;;; Copyright © 2020 Vincent Legoll ;;; ;;; This file is part of GNU Guix. ;;; @@ -300,6 +301,41 @@ is currently not actively maintained and works only with Python 2 and NumPy < 1.9.") (license license:cecill))) +(define-public tng + (package + (name "tng") + (version "1.8.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/gromacs/tng.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1apf2n8nb34z09xarj7k4jgriq283l769sakjmj5aalpbilvai4q")))) + (build-system cmake-build-system) + (inputs + `(("zlib" ,zlib))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'remove-bundled-zlib + (lambda _ + (delete-file-recursively "external") + #t)) + (replace 'check + (lambda _ + (invoke "../build/bin/tests/tng_testing") + #t))))) + (home-page "https://github.com/gromacs/tng") + (synopsis "Trajectory Next Generation binary format manipulation library") + (description "TRAJNG (Trajectory next generation) is a program library for +handling molecular dynamics (MD) trajectories. It can store coordinates, and +optionally velocities and the H-matrix. Coordinates and velocities are +stored with user-specified precision.") + (license license:bsd-3))) + (define-public openbabel (package (name "openbabel") -- 2.26.0 From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 2/3] gnu: Add lmfit. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 03 May 2020 22:34:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Cc: Vincent Legoll Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158854518315570 (code B ref 40691); Sun, 03 May 2020 22:34:01 +0000 Received: (at 40691) by debbugs.gnu.org; 3 May 2020 22:33:03 +0000 Received: from localhost ([127.0.0.1]:58341 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVNAU-00042o-2L for submit@debbugs.gnu.org; Sun, 03 May 2020 18:33:02 -0400 Received: from mail-wr1-f53.google.com ([209.85.221.53]:40783) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVNAR-00042L-5i for 40691@debbugs.gnu.org; Sun, 03 May 2020 18:33:00 -0400 Received: by mail-wr1-f53.google.com with SMTP id e16so13585432wra.7 for <40691@debbugs.gnu.org>; Sun, 03 May 2020 15:32:59 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=Mjhuk9Kc5PUHWtr6aItBEIft5yRm64OpFAr8QjbycNk=; b=BhtThuMAciPiFuNX6VodoLeTYEF5gSzNQbyNlZ9bRbyH4ZSG9HSoccKfVFEKhqKHla Z7Dp19qsKw3r4ISuUJv1dR5EY9OBqeqekVktVi6JJvQcTzfd2MyACe7zL3pTC1Qfu4Sh o7I8LC9EPheqP0M4krCenlE5UOhXI9OqabEkpEMK1vYAMGkjfO483B3zajzFAF/KfqYI x+IG5fWj2EBju1bemXaORk0Ul9SficqA+14NY2q0/SQLi3XrmOVqjpqfI+diWwEQFDnD GwD7lShrc5eJbEPmp7dG8izFitvbhwNKGP4XtmUJZ0lkU4wX2hgQNViJXFyGsEvM9o9T aaWg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=Mjhuk9Kc5PUHWtr6aItBEIft5yRm64OpFAr8QjbycNk=; b=mR1GT8dlE7HSTE5zilUCKKFj+7fQdKQBtTl7xrqeWtmktjk7RLxargblAld4Awy2Y4 +dU39RxAfF9j0KISq6Iand8wza5bzP559RRzJvJNo9y5y8dGXZnS3OppoC1YZ79bpe9W t+MghTAjSJ0M0LEyF0doZe7CEdFFHm+P5NiM1RfbRhdYZAxLDSfwysqRPojNmp/LEhxx 3dabKMbf9WrZAd8wGAf+kCA6fKjCJIWq3L2E7PcL7PY8rN/iJPD6Lk7/rLwImBxobiE9 6VPnJBaTdDZ6/Mjw8OWTjBo0ZWFDT+LE2uHLgBrEl5oclAqqtBsDKfzJsMbUWN+qh/8S XxZQ== X-Gm-Message-State: AGi0PuZ7Oq4l+yHQFVUCmndnJ6HiBS36Ti91n8tSgrmwElvk/7RzO5hm S0n6dxi/Ljb+3EIwzuoLUR6V0Qvn X-Google-Smtp-Source: APiQypKnRIYC3R8XyGgAOcDZs5fhvUSVlsACiX+4YKPXKRDbPvjE25Py8qI2/5vVL1k0u9WROGq4ig== X-Received: by 2002:adf:fed2:: with SMTP id q18mr17697176wrs.157.1588545173368; Sun, 03 May 2020 15:32:53 -0700 (PDT) Received: from localhost.localdomain (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id a205sm11211970wmh.29.2020.05.03.15.32.52 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 03 May 2020 15:32:52 -0700 (PDT) From: Vincent Legoll Date: Mon, 4 May 2020 00:32:39 +0200 Message-Id: <20200503223240.16408-2-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 In-Reply-To: <20200503223240.16408-1-vincent.legoll@gmail.com> References: <20200503223240.16408-1-vincent.legoll@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit 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 (-) * gnu/packages/algebra.scm (lmfit): New variable. --- gnu/packages/algebra.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index 34fb9ee4fd..d4f66d2ffd 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -10,6 +10,7 @@ ;;; Copyright © 2017, 2019 Eric Bavier ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Jakub Kądziołka +;;; Copyright © 2020 Vincent Legoll ;;; ;;; This file is part of GNU Guix. ;;; @@ -913,6 +914,29 @@ Fourier Transform} (DFT), @dfn{Discrete Cosine Transform} (DCT), @dfn{Discrete Sine Transform} (DST) and @dfn{Discrete Hartley Transform} (DHT).") (license license:bsd-2))) +(define-public lmfit + (package + (name "lmfit") + (version "8.2.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://jugit.fz-juelich.de/mlz/lmfit.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00bch77a6qgnw6vzsjn2a42n8n683ih3xm0wpr454jxa15hw78vf")))) + (build-system cmake-build-system) + (native-inputs + `(("perl" ,perl))) ; for pod2man + (home-page "https://jugit.fz-juelich.de/mlz/lmfit") + (synopsis "Levenberg-Marquardt minimization and least-squares fitting") + (description "lmfit is a C library for Levenberg-Marquardt least-squares +minimization and curve fitting. It is mature code, based on decades-old +algorithms from the FORTRAN library MINPACK.") + (license license:bsd-2))) + (define-public eigen (package (name "eigen") -- 2.26.0 From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 3/3] gnu: Add gromacs. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 03 May 2020 22:34:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Cc: Vincent Legoll Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158854518515591 (code B ref 40691); Sun, 03 May 2020 22:34:02 +0000 Received: (at 40691) by debbugs.gnu.org; 3 May 2020 22:33:05 +0000 Received: from localhost ([127.0.0.1]:58344 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVNAW-00043P-WE for submit@debbugs.gnu.org; Sun, 03 May 2020 18:33:05 -0400 Received: from mail-wr1-f51.google.com ([209.85.221.51]:42862) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVNAS-00042N-C6 for 40691@debbugs.gnu.org; Sun, 03 May 2020 18:33:03 -0400 Received: by mail-wr1-f51.google.com with SMTP id s8so8393654wrt.9 for <40691@debbugs.gnu.org>; Sun, 03 May 2020 15:33:00 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:in-reply-to:references :mime-version:content-transfer-encoding; bh=NwzvYY8MBDjsuRwKGsq2DZkFlH8CcjnFj+UehJdDCKY=; b=WK02JJGuDzaX9YSFePPPLs9zIXRrlh5syZ7uWHb7cTcmrBpMK2cELED0D2z9pAOlzp yYr83WXkVYrVRaemy5MBfMkl29ani841WQgbrDBF0dAa6s22tfIXfgaWYWQ1RAqiVSTF jLURYuR71pI86Qth2Q/Dlew/v3uElv2nLHK7IbUbw3Ino6ufYdR0NSN9Lo8waJ3SYhi7 YNhVRLxuM4zF7qMgVL2arVb6xLoz9dob95dzr1jc0JzFnzo/Ha+IjO6o8I0k382pyUNs jnPWYa0YnBak2uUcXCpILCNCgbzRgKegmM5PGGhSjW+zpGw7wJqbFdQLgqCG7v61jzkE FtDQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:in-reply-to :references:mime-version:content-transfer-encoding; bh=NwzvYY8MBDjsuRwKGsq2DZkFlH8CcjnFj+UehJdDCKY=; b=VehVr+cefg0PsLnbIX/zM4rZ2in+83nzFUtFNaOSAJT/jsrRAgJDNwboS0DC+Gpju8 p3uRFg94L5OuCwxhI9PBmcuWk4897sH87z2swel3JbYkAhpjiIxF4464uVYYrF7u3TZo pwiv9PXrNdk7YAFpFBrIAaN2uJdtbW0Us1ZTzEuTB+B1mFLgW4fsN1AshEKcSAiKysHG JvWnuY9gL++qDSGFaTqYFKvrGK1hgKapEEHZ6xRqlisskLr//06heFDGCwHSgOhc5zCn iy2dMyXe7bYXvY2Suy3eJImiuw/xElg63aQJ5Wfjmz+c7cLrm487Q0nE5MhzoTyPBrMy K6Nw== X-Gm-Message-State: AGi0PuaNDLA3yDvcb14LXk/Lx/uphGA+GJPYm8Wh73wIJufNBzQbbWJM GWUt+q4inp98CU1VUDcEohXsQdPG X-Google-Smtp-Source: APiQypJjEOPIE9x3nxdoiVFZqQEpeUOnsmMWiMbhVhnN3CvSeRTvozL38Qb7GSxcrRm5BrJafFiz3w== X-Received: by 2002:a5d:414f:: with SMTP id c15mr6917668wrq.61.1588545174356; Sun, 03 May 2020 15:32:54 -0700 (PDT) Received: from localhost.localdomain (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id a205sm11211970wmh.29.2020.05.03.15.32.53 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 03 May 2020 15:32:53 -0700 (PDT) From: Vincent Legoll Date: Mon, 4 May 2020 00:32:40 +0200 Message-Id: <20200503223240.16408-3-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 In-Reply-To: <20200503223240.16408-1-vincent.legoll@gmail.com> References: <20200503223240.16408-1-vincent.legoll@gmail.com> MIME-Version: 1.0 Content-Transfer-Encoding: 8bit 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 (-) * gnu/packages/chemistry.scm (gromacs): New variable. * gnu/packages/patches/gromacs-tinyxml2.patch: New file... * gnu/local.mk (dist_patch_DATA): ...add it here. --- gnu/local.mk | 1 + gnu/packages/chemistry.scm | 86 +++++++++++++++++++++ gnu/packages/patches/gromacs-tinyxml2.patch | 67 ++++++++++++++++ 3 files changed, 154 insertions(+) create mode 100644 gnu/packages/patches/gromacs-tinyxml2.patch diff --git a/gnu/local.mk b/gnu/local.mk index 3c9a10b6bc..827e186501 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1006,6 +1006,7 @@ dist_patch_DATA = \ %D%/packages/patches/gpsbabel-qstring.patch \ %D%/packages/patches/grantlee-merge-theme-dirs.patch \ %D%/packages/patches/grep-timing-sensitive-test.patch \ + %D%/packages/patches/gromacs-tinyxml2.patch \ %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch \ %D%/packages/patches/grub-efi-fat-serial-number.patch \ %D%/packages/patches/gsl-test-i686.patch \ diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 5b21e3309c..42368cb482 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -33,6 +33,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages documentation) #:use-module (gnu packages gl) + #:use-module (gnu packages graphviz) #:use-module (gnu packages gv) #:use-module (gnu packages maths) #:use-module (gnu packages pkg-config) @@ -336,6 +337,91 @@ optionally velocities and the H-matrix. Coordinates and velocities are stored with user-specified precision.") (license license:bsd-3))) +(define-public gromacs + (package + (name "gromacs") + (version "2020.2") + (source (origin + (method url-fetch) + (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-" + version ".tar.gz")) + (sha256 + (base32 + "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl")) + ;; Our version of tinyxml2 is far newer than the bundled one and + ;; require fixing `testutils' code. See patch header for more info + (patches (search-patches "gromacs-tinyxml2.patch")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests + ;; Unbundling + "-DGMX_USE_LMFIT=EXTERNAL" + "-DGMX_BUILD_OWN_FFTW=off" + "-DGMX_EXTERNAL_BLAS=on" + "-DGMX_EXTERNAL_LAPACK=on" + "-DGMX_EXTERNAL_TNG=on" + "-DGMX_EXTERNAL_ZLIB=on" + "-DGMX_EXTERNAL_TINYXML2=on" + (string-append "-DTinyXML2_DIR=" + (assoc-ref %build-inputs "tinyxml2")) + ;; Workaround for cmake/FindSphinx.cmake version parsing that does + ;; not understand the guix-wrapped `sphinx-build --version' answer + (string-append "-DSPHINX_EXECUTABLE_VERSION=" + ,(package-version python-sphinx))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fixes + (lambda* (#:key inputs #:allow-other-keys) + ;; Still bundled: part of gromacs, source behind registration + ;; but free software anyways + ;;(delete-file-recursively "src/external/vmd_molfile") + ;; Still bundled: threads-based OpenMPI-compatible fallback + ;; designed to be bundled like that + ;;(delete-file-recursively "src/external/thread_mpi") + ;; Unbundling + (delete-file-recursively "src/external/lmfit") + (delete-file-recursively "src/external/clFFT") + (delete-file-recursively "src/external/fftpack") + (delete-file-recursively "src/external/build-fftw") + (delete-file-recursively "src/external/tng_io") + (delete-file-recursively "src/external/tinyxml2") + (delete-file-recursively "src/external/googletest") + (copy-recursively (assoc-ref inputs "googletest-source") + "src/external/googletest") + ;; This test warns about the build host hardware, disable + (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" + (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") + "void __guix_disabled()")) + #t))))) + (native-inputs + `(("doxygen" ,doxygen) + ("googletest-source" ,(package-source googletest)) + ("graphviz" ,graphviz) + ("pkg-config" ,pkg-config) + ("python" ,python) + ("python-pygments" ,python-pygments) + ("python-sphinx" ,python-sphinx))) + (inputs + `(("fftwf" ,fftwf) + ("hwloc" ,hwloc-2 "lib") + ("lmfit" ,lmfit) + ("openblas" ,openblas) + ("perl" ,perl) + ("tinyxml2" ,tinyxml2) + ("tng" ,tng))) + (home-page "http://www.gromacs.org/") + (synopsis "Molecular dynamics software package") + (description "GROMACS is a versatile package to perform molecular dynamics, +i.e. simulate the Newtonian equations of motion for systems with hundreds to +millions of particles. It is primarily designed for biochemical molecules like +proteins, lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating the nonbonded +interactions (that usually dominate simulations) many groups are also using it +for research on non-biological systems, e.g. polymers. GROMACS supports all the +usual algorithms you expect from a modern molecular dynamics implementation.") + (license license:lgpl2.1+))) + (define-public openbabel (package (name "openbabel") diff --git a/gnu/packages/patches/gromacs-tinyxml2.patch b/gnu/packages/patches/gromacs-tinyxml2.patch new file mode 100644 index 0000000000..cc7d7459a8 --- /dev/null +++ b/gnu/packages/patches/gromacs-tinyxml2.patch @@ -0,0 +1,67 @@ +Unbundling tinyxml2 from gromacs and using our own, which is newer, broke gromacs +build. + +This patch fixes three issues: + +- cmake now errors out if using multiple target_link_libraries with mixed styles + of signatures. + +- Error handling API changed, fix the testutils/refdata_xml.cpp code by using the + new API: document.ErrorStr() & tinyxml2::XML_SUCCESS. + +Those fixes will be submitted for inclusion to upstream, but may not be suitable +there as long as they still keep the old version bundled. + +First hunk has already been requested for merging. Third is in discussion. Second +will only be sent if third is OK'ed. + +diff -ruN gromacs-2020.2/src/testutils/CMakeLists.txt gromacs-2020.2-fixed/src/testutils/CMakeLists.txt +--- gromacs-2020.2/src/testutils/CMakeLists.txt 2020-04-30 18:33:44.000000000 +0200 ++++ gromacs-2020.2-fixed/src/testutils/CMakeLists.txt 2020-05-01 22:52:16.356000000 +0200 +@@ -73,7 +73,7 @@ + + if(HAVE_TINYXML2) + include_directories(SYSTEM ${TinyXML2_INCLUDE_DIR}) +- target_link_libraries(testutils ${TinyXML2_LIBRARIES}) ++ target_link_libraries(testutils PRIVATE ${TinyXML2_LIBRARIES}) + else() + include_directories(BEFORE SYSTEM "../external/tinyxml2") + endif() +diff -ruN gromacs-2020.2/src/testutils/refdata_xml.cpp gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp +--- gromacs-2020.2/src/testutils/refdata_xml.cpp 2020-04-30 18:33:44.000000000 +0200 ++++ gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp 2020-05-01 23:17:09.556000000 +0200 +@@ -206,21 +206,12 @@ + document.LoadFile(path.c_str()); + if (document.Error()) + { +- const char* errorStr1 = document.GetErrorStr1(); +- const char* errorStr2 = document.GetErrorStr2(); ++ const char* errorStr = document.ErrorStr(); + std::string errorString("Error was "); +- if (errorStr1) +- { +- errorString += errorStr1; +- } +- if (errorStr2) +- { +- errorString += errorStr2; +- } +- if (!errorStr1 && !errorStr2) +- { ++ if (errorStr) ++ errorString += errorStr; ++ else + errorString += "not specified."; +- } + GMX_THROW(TestException("Reference data not parsed successfully: " + path + "\n." + + errorString + "\n")); + } +@@ -371,7 +362,7 @@ + XMLElementPtr rootElement = createRootElement(&document); + createChildElements(rootElement, rootEntry); + +- if (document.SaveFile(path.c_str()) != tinyxml2::XML_NO_ERROR) ++ if (document.SaveFile(path.c_str()) != tinyxml2::XML_SUCCESS) + { + GMX_THROW(TestException("Reference data saving failed in " + path)); + } -- 2.26.0 From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH 3/3] gnu: Add gromacs. Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 03 May 2020 22:40:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158854557616181 (code B ref 40691); Sun, 03 May 2020 22:40:01 +0000 Received: (at 40691) by debbugs.gnu.org; 3 May 2020 22:39:36 +0000 Received: from localhost ([127.0.0.1]:58357 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVNGb-0004Ce-Bm for submit@debbugs.gnu.org; Sun, 03 May 2020 18:39:36 -0400 Received: from mail-wm1-f50.google.com ([209.85.128.50]:39619) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVNGa-0004CS-Jh for 40691@debbugs.gnu.org; Sun, 03 May 2020 18:39:20 -0400 Received: by mail-wm1-f50.google.com with SMTP id y24so6764537wma.4 for <40691@debbugs.gnu.org>; Sun, 03 May 2020 15:39:20 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=subject:to:references:from:message-id:date:user-agent:mime-version :in-reply-to:content-language:content-transfer-encoding; bh=M3Ohg9q3Qsi7B+82k6U+bQvW7f0UQSgir/YTQwQ3+jM=; b=aU0MSTU8ze20lbV2OnEfFi/rbx+yfxPNMi8qS/0SE2kfFZ+PIBNDcZ2tIgaDnMnZKR O0Ng8rsgPg2seqlCwt6jPw9aPgew0dUnhKJJTLEGVfK3l4p3TbOQI6rfbn0c06SK1NuO C2d30Pnddw1Nd+JMIDoAUkOVDF4/JpoPObeCOCxVTb9+Ex1DVgZBdDn6nf2mD8RzPc3A bVi90zBs8Fp2peGaQDxpi8k1Y5j/kDaWQcdIzTk8mRbAzr/f36Dp9jLA3Q+QmaD37u2i E/27h9MO5DuhOmTR+ASRde/wGPSqeOIOpb3n0YDnvypwPYMMAsouEEZ0qdPvr/QlCKkv STIA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:subject:to:references:from:message-id:date :user-agent:mime-version:in-reply-to:content-language :content-transfer-encoding; bh=M3Ohg9q3Qsi7B+82k6U+bQvW7f0UQSgir/YTQwQ3+jM=; b=P2D/FLse3mygO/w3T6IqpL7Zctgh1hdUYG1aCVaoyVJ509Bay8vdmHEwgtj7b0lO/c kGiFzwUosUCCyrbBB4STeXtNnOaD3FU4eVx1fNzPnkXY+Rx+Kv37WhEgCa0Wyu5oiNQ+ 3LukRJh5/wyANpl7/PlEn2v+zqFVZ9kRhvj3sgb7OjfE8GM4k8GID/vbV6K4X5n8qjae 1NvovcJbJL9FG/ld7G6bnaYqDYKJ0H9xGI/maj60S2fOC4XzynaSjuWk9oqSu+4jo0rF jkKvRI/ya9bJD/wu/GA08vmu6oGBXkUweH98+lYwV/nJ4vUFv2ecaSlaK//cSWHHP1su RQdw== X-Gm-Message-State: AGi0PuaJ/tLRUfwMT99IXBlXxLprp6VjBI8H9aG8HuqwWISQlLLFj+3W JBq+mz/F5T4ofKEIeKFcbmMdfkui X-Google-Smtp-Source: APiQypImrLIKUJ3w4xqbJWNH3PZZt7cUp4hliSyw6F7MruPfQtAS+x5Px0Eu8Zih/KPMS8Db6PON2w== X-Received: by 2002:a1c:b70a:: with SMTP id h10mr11346489wmf.172.1588545554553; Sun, 03 May 2020 15:39:14 -0700 (PDT) Received: from [10.0.0.2] (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id c20sm11011140wmd.36.2020.05.03.15.39.13 for <40691@debbugs.gnu.org> (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Sun, 03 May 2020 15:39:14 -0700 (PDT) References: <20200503223240.16408-1-vincent.legoll@gmail.com> <20200503223240.16408-3-vincent.legoll@gmail.com> From: Vincent Legoll Message-ID: Date: Mon, 4 May 2020 00:39:13 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.7.0 MIME-Version: 1.0 In-Reply-To: <20200503223240.16408-3-vincent.legoll@gmail.com> Content-Type: text/plain; charset=utf-8; format=flowed Content-Language: en-US Content-Transfer-Encoding: 7bit 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 (-) Will resend this one, as I forgot to amend the missing module inclusions due to the move from bioinformatics.scm. From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] [PATCH] gnu: Add gromacs. References: In-Reply-To: Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 03 May 2020 22:40:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Cc: Vincent Legoll Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.158854559916221 (code B ref 40691); Sun, 03 May 2020 22:40:02 +0000 Received: (at 40691) by debbugs.gnu.org; 3 May 2020 22:39:59 +0000 Received: from localhost ([127.0.0.1]:58360 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVNHC-0004DY-EP for submit@debbugs.gnu.org; Sun, 03 May 2020 18:39:58 -0400 Received: from mail-wm1-f48.google.com ([209.85.128.48]:56060) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVNH9-0004DH-72 for 40691@debbugs.gnu.org; Sun, 03 May 2020 18:39:57 -0400 Received: by mail-wm1-f48.google.com with SMTP id e26so6284504wmk.5 for <40691@debbugs.gnu.org>; Sun, 03 May 2020 15:39:55 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=PZk5IUMFZ8wj7A8ZIW42dAtll2zZjJGByKE4Or9As+o=; b=G6YWackgHoJAsM+lw2bQrOdsA3fM8oTd05Nq+Axq3Xgw0de85csFegemA8FZQGNQ8c d0worUIy4p1QVpOAjsnyCKbIGkt0Vz835+6H/YUiAfVbA8a9KHDepblsqJpCSC6jUu+n JOO4rl1UCuVv909mAtURVZgpkZ/jAlOgfEd0MQZ49SZ2b3YoezoyUUKUvFbCKg2YtV46 gwJuyjT9Tzr9jpUwh9SCP8mz4XLhSlXbBmvyGjf/47UOs4iWLMcRhK+LjAyN8gnfbT/C RXOycV2XyNVTEeFjcWb6NZe4GZraL99yj8q+YllmnzJN579eg4oAMeRiFaVk77a6CRSv wDxQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:cc:subject:date:message-id:mime-version :content-transfer-encoding; bh=PZk5IUMFZ8wj7A8ZIW42dAtll2zZjJGByKE4Or9As+o=; b=Uuur2jwdf0Of+TDcT2SadCe0SYb2pPxaOJ7U/XulgBdRX+j6+EKG2LoNPGj/6zeDoh nDkUzIMrTwqixxp1P0usxI4+kj293FlYy+5rG4wZ6o/Eaw4biVNnbguJD8xjdlbDD3fX QI/3+PX9fl8BmW/IBjVIiPKeNpjahjG++1iupjnN9zzrCLle9EerrbaFSb/HKiBC6HG5 BMYzqds0oaq3S70IuwMVqEnDpztc8IgzrCc34FL+9QVARycZcdz5NDv0j90ajx9qCPxm opUk8F+29GodEKL0Jx7tzO5GlLYqjUbZanoee8HJYJjQx4K2glY1BZ8Xjexke+nZxqUi pCIA== X-Gm-Message-State: AGi0PuYqql4rD64dFwkruOaGBXXqKQmf/1W8ZsevEAVlXofExVoGdcUF OfhF9TUX56/CNB0Zn76+NgbG2dVo X-Google-Smtp-Source: APiQypKr4rWO6CyLY3vBdriLEf/+sD+jwqq/sKpDm+EaES9ZmBZsh3pME4XFrktxAwNCkZX8wn7fnw== X-Received: by 2002:a7b:c456:: with SMTP id l22mr10970852wmi.148.1588545589200; Sun, 03 May 2020 15:39:49 -0700 (PDT) Received: from localhost.localdomain (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id l5sm10260796wmi.22.2020.05.03.15.39.48 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 03 May 2020 15:39:48 -0700 (PDT) From: Vincent Legoll Date: Mon, 4 May 2020 00:39:36 +0200 Message-Id: <20200503223936.16554-1-vincent.legoll@gmail.com> X-Mailer: git-send-email 2.26.1 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit 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 (-) * gnu/packages/chemistry.scm (gromacs): New variable. * gnu/packages/patches/gromacs-tinyxml2.patch: New file... * gnu/local.mk (dist_patch_DATA): ...add it here. --- gnu/local.mk | 1 + gnu/packages/chemistry.scm | 90 +++++++++++++++++++++ gnu/packages/patches/gromacs-tinyxml2.patch | 67 +++++++++++++++ 3 files changed, 158 insertions(+) create mode 100644 gnu/packages/patches/gromacs-tinyxml2.patch diff --git a/gnu/local.mk b/gnu/local.mk index 3c9a10b6bc..827e186501 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1006,6 +1006,7 @@ dist_patch_DATA = \ %D%/packages/patches/gpsbabel-qstring.patch \ %D%/packages/patches/grantlee-merge-theme-dirs.patch \ %D%/packages/patches/grep-timing-sensitive-test.patch \ + %D%/packages/patches/gromacs-tinyxml2.patch \ %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch \ %D%/packages/patches/grub-efi-fat-serial-number.patch \ %D%/packages/patches/gsl-test-i686.patch \ diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 5b21e3309c..0540dfceb6 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -30,15 +30,20 @@ #:use-module (gnu packages) #:use-module (gnu packages algebra) #:use-module (gnu packages boost) + #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages documentation) #:use-module (gnu packages gl) + #:use-module (gnu packages graphviz) #:use-module (gnu packages gv) #:use-module (gnu packages maths) + #:use-module (gnu packages mpi) + #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) + #:use-module (gnu packages sphinx) #:use-module (gnu packages xml) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) @@ -336,6 +341,91 @@ optionally velocities and the H-matrix. Coordinates and velocities are stored with user-specified precision.") (license license:bsd-3))) +(define-public gromacs + (package + (name "gromacs") + (version "2020.2") + (source (origin + (method url-fetch) + (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-" + version ".tar.gz")) + (sha256 + (base32 + "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl")) + ;; Our version of tinyxml2 is far newer than the bundled one and + ;; require fixing `testutils' code. See patch header for more info + (patches (search-patches "gromacs-tinyxml2.patch")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests + ;; Unbundling + "-DGMX_USE_LMFIT=EXTERNAL" + "-DGMX_BUILD_OWN_FFTW=off" + "-DGMX_EXTERNAL_BLAS=on" + "-DGMX_EXTERNAL_LAPACK=on" + "-DGMX_EXTERNAL_TNG=on" + "-DGMX_EXTERNAL_ZLIB=on" + "-DGMX_EXTERNAL_TINYXML2=on" + (string-append "-DTinyXML2_DIR=" + (assoc-ref %build-inputs "tinyxml2")) + ;; Workaround for cmake/FindSphinx.cmake version parsing that does + ;; not understand the guix-wrapped `sphinx-build --version' answer + (string-append "-DSPHINX_EXECUTABLE_VERSION=" + ,(package-version python-sphinx))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fixes + (lambda* (#:key inputs #:allow-other-keys) + ;; Still bundled: part of gromacs, source behind registration + ;; but free software anyways + ;;(delete-file-recursively "src/external/vmd_molfile") + ;; Still bundled: threads-based OpenMPI-compatible fallback + ;; designed to be bundled like that + ;;(delete-file-recursively "src/external/thread_mpi") + ;; Unbundling + (delete-file-recursively "src/external/lmfit") + (delete-file-recursively "src/external/clFFT") + (delete-file-recursively "src/external/fftpack") + (delete-file-recursively "src/external/build-fftw") + (delete-file-recursively "src/external/tng_io") + (delete-file-recursively "src/external/tinyxml2") + (delete-file-recursively "src/external/googletest") + (copy-recursively (assoc-ref inputs "googletest-source") + "src/external/googletest") + ;; This test warns about the build host hardware, disable + (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" + (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") + "void __guix_disabled()")) + #t))))) + (native-inputs + `(("doxygen" ,doxygen) + ("googletest-source" ,(package-source googletest)) + ("graphviz" ,graphviz) + ("pkg-config" ,pkg-config) + ("python" ,python) + ("python-pygments" ,python-pygments) + ("python-sphinx" ,python-sphinx))) + (inputs + `(("fftwf" ,fftwf) + ("hwloc" ,hwloc-2 "lib") + ("lmfit" ,lmfit) + ("openblas" ,openblas) + ("perl" ,perl) + ("tinyxml2" ,tinyxml2) + ("tng" ,tng))) + (home-page "http://www.gromacs.org/") + (synopsis "Molecular dynamics software package") + (description "GROMACS is a versatile package to perform molecular dynamics, +i.e. simulate the Newtonian equations of motion for systems with hundreds to +millions of particles. It is primarily designed for biochemical molecules like +proteins, lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating the nonbonded +interactions (that usually dominate simulations) many groups are also using it +for research on non-biological systems, e.g. polymers. GROMACS supports all the +usual algorithms you expect from a modern molecular dynamics implementation.") + (license license:lgpl2.1+))) + (define-public openbabel (package (name "openbabel") diff --git a/gnu/packages/patches/gromacs-tinyxml2.patch b/gnu/packages/patches/gromacs-tinyxml2.patch new file mode 100644 index 0000000000..cc7d7459a8 --- /dev/null +++ b/gnu/packages/patches/gromacs-tinyxml2.patch @@ -0,0 +1,67 @@ +Unbundling tinyxml2 from gromacs and using our own, which is newer, broke gromacs +build. + +This patch fixes three issues: + +- cmake now errors out if using multiple target_link_libraries with mixed styles + of signatures. + +- Error handling API changed, fix the testutils/refdata_xml.cpp code by using the + new API: document.ErrorStr() & tinyxml2::XML_SUCCESS. + +Those fixes will be submitted for inclusion to upstream, but may not be suitable +there as long as they still keep the old version bundled. + +First hunk has already been requested for merging. Third is in discussion. Second +will only be sent if third is OK'ed. + +diff -ruN gromacs-2020.2/src/testutils/CMakeLists.txt gromacs-2020.2-fixed/src/testutils/CMakeLists.txt +--- gromacs-2020.2/src/testutils/CMakeLists.txt 2020-04-30 18:33:44.000000000 +0200 ++++ gromacs-2020.2-fixed/src/testutils/CMakeLists.txt 2020-05-01 22:52:16.356000000 +0200 +@@ -73,7 +73,7 @@ + + if(HAVE_TINYXML2) + include_directories(SYSTEM ${TinyXML2_INCLUDE_DIR}) +- target_link_libraries(testutils ${TinyXML2_LIBRARIES}) ++ target_link_libraries(testutils PRIVATE ${TinyXML2_LIBRARIES}) + else() + include_directories(BEFORE SYSTEM "../external/tinyxml2") + endif() +diff -ruN gromacs-2020.2/src/testutils/refdata_xml.cpp gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp +--- gromacs-2020.2/src/testutils/refdata_xml.cpp 2020-04-30 18:33:44.000000000 +0200 ++++ gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp 2020-05-01 23:17:09.556000000 +0200 +@@ -206,21 +206,12 @@ + document.LoadFile(path.c_str()); + if (document.Error()) + { +- const char* errorStr1 = document.GetErrorStr1(); +- const char* errorStr2 = document.GetErrorStr2(); ++ const char* errorStr = document.ErrorStr(); + std::string errorString("Error was "); +- if (errorStr1) +- { +- errorString += errorStr1; +- } +- if (errorStr2) +- { +- errorString += errorStr2; +- } +- if (!errorStr1 && !errorStr2) +- { ++ if (errorStr) ++ errorString += errorStr; ++ else + errorString += "not specified."; +- } + GMX_THROW(TestException("Reference data not parsed successfully: " + path + "\n." + + errorString + "\n")); + } +@@ -371,7 +362,7 @@ + XMLElementPtr rootElement = createRootElement(&document); + createChildElements(rootElement, rootEntry); + +- if (document.SaveFile(path.c_str()) != tinyxml2::XML_NO_ERROR) ++ if (document.SaveFile(path.c_str()) != tinyxml2::XML_SUCCESS) + { + GMX_THROW(TestException("Reference data saving failed in " + path)); + } -- 2.26.0 From unknown Sat Aug 16 18:44:12 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: Vincent Legoll Subject: bug#40691: closed (Re: [bug#40691] [PATCH v6 0/3] gnu: Add gromacs, tng & lmfit.) Message-ID: References: <87k11st7ni.fsf@gnu.org> X-Gnu-PR-Message: they-closed 40691 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 40691@debbugs.gnu.org Date: Mon, 04 May 2020 08:41:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1588581662-8795-1" This is a multi-part message in MIME format... ------------=_1588581662-8795-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #40691: [PATCH 0/1] gnu: Add gromacs. 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 40691@debbugs.gnu.org. --=20 40691: http://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D40691 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1588581662-8795-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 40691-done) by debbugs.gnu.org; 4 May 2020 08:40:42 +0000 Received: from localhost ([127.0.0.1]:58916 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVWeX-0002HD-Rk for submit@debbugs.gnu.org; Mon, 04 May 2020 04:40:42 -0400 Received: from eggs.gnu.org ([209.51.188.92]:38170) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jVWeW-0002H2-Vv for 40691-done@debbugs.gnu.org; Mon, 04 May 2020 04:40:41 -0400 Received: from fencepost.gnu.org ([2001:470:142:3::e]:52918) by eggs.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jVWeR-0000qH-NR; Mon, 04 May 2020 04:40:35 -0400 Received: from [2a01:e0a:1d:7270:af76:b9b:ca24:c465] (port=51418 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1jVWeR-0005ju-Ay; Mon, 04 May 2020 04:40:35 -0400 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Vincent Legoll Subject: Re: [bug#40691] [PATCH v6 0/3] gnu: Add gromacs, tng & lmfit. References: <87k12b15ki.fsf@gnu.org> <36e8a145-1ca8-c380-9864-dbf8b1fd53cb@gmail.com> <87y2qnv8da.fsf@gnu.org> <87lfmmnfn0.fsf@gnu.org> <5ff814d6-e0da-f5c9-8ae1-29cf40f87702@gmail.com> <87y2q91evv.fsf@gnu.org> Date: Mon, 04 May 2020 10:40:33 +0200 In-Reply-To: (Vincent Legoll's message of "Mon, 4 May 2020 00:31:34 +0200") Message-ID: <87k11st7ni.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/26.3 (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: 40691-done Cc: 40691-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: -3.3 (---) Hi Vincent, Vincent Legoll skribis: >>> Vmd_molfile source is behind a registration-only web form, I'm >>> not going there. >> >> Sounds reasonable: the headers say it=E2=80=99s part of Gromacs, and it= =E2=80=99s >> definitely free software, so it=E2=80=99s OK to keep it here. > > Added comment. > >>> Thread_mpi looks like it is made to be bundled like that, and >>> is part of the parallelizing of gromacs which is above my >>> level of understanding (I'm only trying to package it, I'm not >>> a user). More info here: >> >> Sounds good. Perhaps a comment in the code to state that would be >> welcome, for our future selves. > > Added comment. > > Put tng & gromacs in chemistry.scm, in fact gromacs sci domain is > chemistry, even if also used in bioinfo. Added more comments for > patch & still bundled 3rdparties. > > Moved lmfit to algebra.scm, shortened synopsis. > > I think I fixed all review comments. Thanks a lot, applied! (Will push shortly.) 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[82.242.148.1]) by smtp.gmail.com with ESMTPSA id r20sm8996181wmh.26.2020.04.17.15.22.56 for (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Fri, 17 Apr 2020 15:22:56 -0700 (PDT) To: guix-patches@gnu.org From: Vincent Legoll Subject: [PATCH 0/1] gnu: Add gromacs. Message-ID: Date: Sat, 18 Apr 2020 00:22:54 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.7.0 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Language: en-US Content-Transfer-Encoding: 7bit X-detected-operating-system: by eggs.gnu.org: Genre and OS details not recognized. X-Received-From: 2a00:1450:4864:20::431 X-Spam-Score: 2.3 (++) 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: Hello, following this is a patch to add gromacs. Description & synopsis taken from nix (hello Tobias) Content analysis details: (2.3 points, 10.0 required) pts rule name description ---- ---------------------- -------------------------------------------------- -0.7 RCVD_IN_DNSWL_LOW RBL: Sender listed at https://www.dnswl.org/, low trust [209.51.188.17 listed in list.dnswl.org] 1.0 SPF_SOFTFAIL SPF: sender does not match SPF record (softfail) 0.0 FREEMAIL_FROM Sender email is commonly abused enduser mail provider (vincent.legoll[at]gmail.com) 0.0 SPF_HELO_NONE SPF: HELO does not publish an SPF Record 2.0 SPOOFED_FREEMAIL No description available. X-Debbugs-Envelope-To: submit 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: -0.7 (/) Hello, following this is a patch to add gromacs. Description & synopsis taken from nix (hello Tobias) Linted, indent-code.el passed, and built OK with 2 rounds. Not sure if we want more cmake flags. problems reported by cmake: -- Found Doxygen: /gnu/store/k6albjaxkybsgshqyw6g44f5hz75l7q6-doxygen-1.8.15/bin/doxygen (found version "1.8.15") found components: doxygen missing components: dot -- Could NOT find Sphinx: Found unsuitable version "-real 2.3.1", but required is at least "1.6.1" (found /gnu/store/anyhb84x3mvyp11sbhmdnicbsa42m3x0-python-sphinx-2.3.1/bin/sphinx-build) -- Vincent Legoll ------------=_1588581662-8795-1-- From unknown Sat Aug 16 18:44:12 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#40691] Upstream patches are being merged References: In-Reply-To: Resent-From: Vincent Legoll Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 05 May 2020 21:28:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 40691 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 40691@debbugs.gnu.org Received: via spool by 40691-submit@debbugs.gnu.org id=B40691.15887140636183 (code B ref 40691); Tue, 05 May 2020 21:28:02 +0000 Received: (at 40691) by debbugs.gnu.org; 5 May 2020 21:27:43 +0000 Received: from localhost ([127.0.0.1]:37743 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jW56M-0001bf-Jn for submit@debbugs.gnu.org; Tue, 05 May 2020 17:27:42 -0400 Received: from mail-wm1-f52.google.com ([209.85.128.52]:36902) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1jW56K-0001bK-Mb for 40691@debbugs.gnu.org; Tue, 05 May 2020 17:27:41 -0400 Received: by mail-wm1-f52.google.com with SMTP id z6so88758wml.2 for <40691@debbugs.gnu.org>; Tue, 05 May 2020 14:27:40 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=to:from:subject:message-id:date:user-agent:mime-version :content-language:content-transfer-encoding; bh=RvIdj33eFutQ8r8x/9x2hdfXVxKttft/Nkw6f17qyuI=; b=T+uuDTIaOY4VaVrvYSGbwvI/fJFsMnCpoZl4MiAnwJjfv5kjDcxKbal2ElzvvOKb+t laukgaFvjXqYV4uOTlrXww19sMKrB5deW7ts9aSiCgwVXCw5EYr3NVztWv2EXURemnal x5XqdpOfNgJgfrl7JDtGvFphURx1c+oCb+c6T5IBlnf73ARIaSSNloN2oEJWfM9Y5x06 ey/c4naJsy0Uwl21ODnaWvAQTCHpWLOvhMqv0hboJ7UlOe42zUX03f7ANExheRfUB6j7 10Jz6UWyBCnlI4BCpd4ZsUDKH1OIF5m1eQELN1WinX3YnBSnqnX7tbbeNzzz8dF9mCqA rBxg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:to:from:subject:message-id:date:user-agent :mime-version:content-language:content-transfer-encoding; bh=RvIdj33eFutQ8r8x/9x2hdfXVxKttft/Nkw6f17qyuI=; b=Ha3CsQy5vIgCOmvrEa+T9s3n666Q958HAPdUx9EMKVjIMhweyJDy3lrS2TzXQ/XNe7 OAsiEtgQnr4EkHqTqTTyvewUWspH+2+G9Vup5KuvfUC2BxsxwSAo/nclrqDsKmoZCNSv fk5ybPM/zXRVUyztsyc0akpU0PR1z6bkFB8XYAxmH6j1RzkL5iqW2LA+m8u1aMgoIrnt l137d5ZaDaBtCfTu9+cmk+BPGj8AUO+KCtUNSNIxcTn9xeP2xFXq1KJ6cXIfp0dAI2zx aG4hgAVuyADp5FNz87w+TEoD6emkNIhMLdcq1fVlj224aZUPANwjxXVNOueR4K3Ova5k X0zQ== X-Gm-Message-State: AGi0PuaEyWyA2PvzBc6LOXb+wW3Rh0Zw1MTolXpX+LW98JA0qd/NkeYS qCdthiihnHTxyNL9w1TS0oat5jMr X-Google-Smtp-Source: APiQypLLSnTFd7QtoQJzDT5o8WkO1uuxv6+JfqitokhsDQ7cmNt8tLqEJ4NyfdHgVBpWr5M7imvFPw== X-Received: by 2002:a1c:f20c:: with SMTP id s12mr671642wmc.83.1588714054283; Tue, 05 May 2020 14:27:34 -0700 (PDT) Received: from [10.0.0.2] (se167-1-82-242-148-1.fbx.proxad.net. [82.242.148.1]) by smtp.gmail.com with ESMTPSA id x24sm5671516wrd.51.2020.05.05.14.27.33 for <40691@debbugs.gnu.org> (version=TLS1_3 cipher=TLS_AES_128_GCM_SHA256 bits=128/128); Tue, 05 May 2020 14:27:33 -0700 (PDT) From: Vincent Legoll Message-ID: <92f2572a-7660-b4c4-69e6-cca5ec9b4c82@gmail.com> Date: Tue, 5 May 2020 23:27:31 +0200 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:68.0) Gecko/20100101 Thunderbird/68.7.0 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8; format=flowed Content-Language: en-US Content-Transfer-Encoding: 7bit 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, the first hunk the the gromacs patch has been merged, and they are interested in the remaining bits, I'll work with them to that end, and update guix package accordingly. https://gitlab.com/gromacs/gromacs/-/merge_requests/153 -- Vincent Legoll