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[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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Received-From: 209.51.188.43 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: 0.09 Authentication-Results: aspmx1.migadu.com; dkim=fail (rsa verify failed) header.d=gmail.com header.s=20161025 header.b=h2i/PDuQ; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=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 [0.09 / 13.00]; RCVD_VIA_SMTP_AUTH(0.00)[]; GENERIC_REPUTATION(0.00)[-0.49501603108071]; TO_DN_SOME(0.00)[]; R_SPF_ALLOW(-0.20)[+ip6:2001:470:142::/48:c]; R_DKIM_REJECT(1.00)[gmail.com:s=20161025]; DWL_DNSWL_FAIL(0.00)[2001:470:142::17:server fail]; FREEMAIL_FROM(0.00)[gmail.com]; IP_REPUTATION_HAM(0.00)[asn: 22989(0.15), country: US(-0.00), ip: 2001:470:142::17(-0.50)]; DKIM_TRACE(0.00)[gmail.com:-]; RCPT_COUNT_TWO(0.00)[2]; MX_GOOD(-0.50)[cached: eggs.gnu.org]; MAILLIST(-0.20)[mailman]; FORGED_RECIPIENTS_MAILLIST(0.00)[]; RCVD_IN_DNSWL_FAIL(0.00)[2001:470:142::17:server fail]; MIME_TRACE(0.00)[0:+]; RCVD_TLS_LAST(0.00)[]; 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)[]; FROM_NEQ_ENVFROM(0.00)[vincentlegoll@gmail.com,guix-patches-bounces@gnu.org]; FROM_HAS_DN(0.00)[]; URIBL_BLOCKED(0.00)[fz-juelich.de:url,gromacs.org:url]; MIME_GOOD(-0.10)[text/plain]; PREVIOUSLY_DELIVERED(0.00)[40691@debbugs.gnu.org]; HAS_LIST_UNSUB(-0.01)[]; RCVD_COUNT_SEVEN(0.00)[10]; FORGED_SENDER_MAILLIST(0.00)[]; DMARC_POLICY_SOFTFAIL(0.10)[gmail.com : SPF not aligned (relaxed),none] X-TUID: 4UVYDhgF7Dug 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