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 eBf1Ee0X/F5lVgAA0tVLHw (envelope-from ) for ; Wed, 01 Jul 2020 04:58:21 +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 iFCNDe0X/F6XEAAAbx9fmQ (envelope-from ) for ; Wed, 01 Jul 2020 04:58:21 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id B85349403D2 for ; Wed, 1 Jul 2020 04:58:19 +0000 (UTC) Received: from localhost ([::1]:48754 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jqUp8-0004Bq-CF for larch@yhetil.org; Wed, 01 Jul 2020 00:58:18 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53556) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jqUoc-0004Bi-DJ for guix-devel@gnu.org; Wed, 01 Jul 2020 00:57:46 -0400 Received: from mail.thebird.nl ([94.142.245.5]:47796) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1jqUoa-0005GJ-93; Wed, 01 Jul 2020 00:57:45 -0400 Received: by mail.thebird.nl (Postfix, from userid 1000) id 4363D1B65; Wed, 1 Jul 2020 06:57:40 +0200 (CEST) Date: Tue, 30 Jun 2020 23:57:40 -0500 From: Pjotr Prins To: simon tournier Subject: Re: Reproducible Research Hackathon: Friday, July 3rd Message-ID: <20200701045740.o67v64d3bhljmzoz@thebird.nl> References: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: NeoMutt/20170113 (1.7.2) Received-SPF: pass client-ip=94.142.245.5; envelope-from=pjotr2020@thebird.nl; helo=mail.thebird.nl X-detected-operating-system: by eggs.gnu.org: First seen = 2020/07/01 00:57:40 X-ACL-Warn: Detected OS = Linux 3.11 and newer [fuzzy] X-Spam_score_int: -18 X-Spam_score: -1.9 X-Spam_bar: - X-Spam_report: (-1.9 / 5.0 requ) BAYES_00=-1.9, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, URIBL_BLOCKED=0.001 autolearn=_AUTOLEARN X-Spam_action: no action X-BeenThere: guix-devel@gnu.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: guix-devel@gnu.org, guix-hpc@gnu.org Errors-To: guix-devel-bounces+larch=yhetil.org@gnu.org Sender: "Guix-devel" X-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=none; spf=pass (aspmx1.migadu.com: domain of guix-devel-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=guix-devel-bounces@gnu.org X-Spam-Score: -1.01 X-TUID: FXnv6gvpz6Mw We at UTHSC are game. We are struggling with an old version of the GeneNetwork web service 1.x which is now running on a 10 year old CentOS. The backup time machine server died recently. GenNetwork1 depends on Python 2.4(!) with modules that have not been updated this century, and an older version of Apache with mod_python, amongst other things. We would like to use the guix time-machine feature to run older versions on demand in containers, also for the recent GeneNetwork2 version which runs on a modern Guix stack. When we get it to work I would like to push the older packages in Guix-Past. Bit much for one day, but let's see where it ends. There is no point in updating the older GeneNetwork1 instances, I mean the code. The point really is that it is a reproducible version tied to older scientific publications that people still can explore. Note that GeneNetwork requires a largisch MySQL/MariaDB (170GB) which is also a snapshot in time. We have 5+ snapshots of that database that go with 5+ versions of the code. We want to run them all under Guix so we no longer have to care about the underlying Linux distro. With the newer GeneNetwork2 stack we are thinking of making use of Guix timemachine to run snapshots, firing containers up on demand. These will have to be tied with a certain version of the database, so we have to force time points maintained outside the package Guix git repo. The databases can be ready to run - listening on a different port for each version. Nice challenge and it will make a great story when it works. Pj. On Tue, Jun 30, 2020 at 02:40:12PM +0200, simon tournier wrote: > Hello, > > We are pleased to announce a Hackathon about Reproducible Science. > > We propose to collectively tackle some issues on *Friday, July 3rd*: > > - identify stumbling blocks in using Guix to write end-to-end > pipelines, > - document how to achieve this, > - feed the Guix-Past channel by other old packages, > - provide guix.scm for some of the ReScience C submissions. > > Feel free to contact us at guix-hpc@gnu.org if you would like to hack > with us. > > We will meet at *9:30 CEST* on the #guix-hpc channel of > irc.freenode.net. You can use this web client to reach us: > > http://guix.gnu.org/contact/irc/ > > (tweaking the channel name). > > Read more details at: > > https://hpc.guix.info/blog/2020/06/reproducible-research-hackathon > > Hope to see you on Friday.