From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp1 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id mrJ+OoCfrl4SLQAA0tVLHw (envelope-from ) for ; Sun, 03 May 2020 10:40:00 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp1 with LMTPS id mMgoJoufrl5LagAAbx9fmQ (envelope-from ) for ; Sun, 03 May 2020 10:40:11 +0000 Received: from lists.gnu.org (lists.gnu.org [IPv6:2001:470:142::17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 9E8A9943189 for ; Sun, 3 May 2020 10:40:09 +0000 (UTC) Received: from localhost ([::1]:36116 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jVC2a-00069Q-3L for larch@yhetil.org; Sun, 03 May 2020 06:40:08 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:35716) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jVC2U-00069G-Ix for guix-patches@gnu.org; Sun, 03 May 2020 06:40:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:43163) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1jVC2U-0002lc-9T for guix-patches@gnu.org; Sun, 03 May 2020 06:40:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1jVC2U-0008OQ-7c for guix-patches@gnu.org; Sun, 03 May 2020 06:40:02 -0400 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 X-Spam-Score: -3.3 (---) X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+larch=yhetil.org@gnu.org Sender: "Guix-patches" X-Scanner: scn0 X-Spam-Score: -1.01 Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=none; spf=pass (aspmx1.migadu.com: domain of guix-patches-bounces@gnu.org designates 2001:470:142::17 as permitted sender) smtp.mailfrom=guix-patches-bounces@gnu.org X-Scan-Result: default: False [-1.01 / 13.00]; RCVD_VIA_SMTP_AUTH(0.00)[]; GENERIC_REPUTATION(0.00)[-0.49358557686256]; TO_DN_SOME(0.00)[]; R_SPF_ALLOW(-0.20)[+ip6:2001:470:142::/48:c]; IP_REPUTATION_HAM(0.00)[asn: 22989(0.15), country: US(-0.00), ip: 2001:470:142::17(-0.49)]; DWL_DNSWL_FAIL(0.00)[2001:470:142::17:server fail]; MX_GOOD(-0.50)[cached: eggs.gnu.org]; RCPT_COUNT_TWO(0.00)[2]; MAILLIST(-0.20)[mailman]; FREEMAIL_TO(0.00)[gmail.com]; RCVD_IN_DNSWL_FAIL(0.00)[2001:470:142::17:server fail]; RCVD_TLS_LAST(0.00)[]; MIME_TRACE(0.00)[0:+]; ASN(0.00)[asn:22989, ipnet:2001:470:142::/48, country:US]; MID_RHS_MATCH_FROM(0.00)[]; TAGGED_FROM(0.00)[larch=yhetil.org]; ARC_NA(0.00)[]; FORGED_RECIPIENTS_MAILLIST(0.00)[]; FROM_NEQ_ENVFROM(0.00)[ludo@gnu.org,guix-patches-bounces@gnu.org]; FROM_HAS_DN(0.00)[]; URIBL_BLOCKED(0.00)[fz-juelich.de:url,gromacs.org:url]; TAGGED_RCPT(0.00)[]; MIME_GOOD(-0.10)[text/plain]; DMARC_NA(0.00)[gnu.org]; HAS_LIST_UNSUB(-0.01)[]; R_DKIM_NA(0.00)[]; RCVD_COUNT_SEVEN(0.00)[9]; FORGED_SENDER_MAILLIST(0.00)[] X-TUID: i3iywis3AEJu 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.