From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: Re: Guix on clusters and in HPC Date: Wed, 2 Nov 2016 09:25:42 +1000 Message-ID: <9d899b54-934f-e98b-2464-8ccc2f8115c7@uq.edu.au> References: <87r37divr8.fsf@gnu.org> <8737jteh8z.fsf@gnu.org> <871szbazaa.fsf@gnu.org> <8760omujwc.fsf@elephly.net> <874m3zuy52.fsf@gnu.org> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------64BA77EE13A93BB1D6024A33" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:35512) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1c1iRJ-0007Y6-3r for guix-devel@gnu.org; Tue, 01 Nov 2016 19:25:58 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1c1iRF-0001mV-Kz for guix-devel@gnu.org; Tue, 01 Nov 2016 19:25:57 -0400 In-Reply-To: <874m3zuy52.fsf@gnu.org> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: =?UTF-8?Q?Ludovic_Court=c3=a8s?= , Ricardo Wurmus Cc: Guix-devel This is a multi-part message in MIME format. --------------64BA77EE13A93BB1D6024A33 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable X-MIME-Autoconverted: from 8bit to quoted-printable by newmailhub.uq.edu.au id uA1NPhuY007924 On 26/10/16 21:51, Ludovic Court=C3=A8s wrote: > Ricardo Wurmus skribis: > >> Ludovic Court=C3=A8s writes: >> >> What they suggest is to add Guix support simply by using Guix inside o= f >> Docker=E2=80=A6 Obviously, I=E2=80=99m not a fan of this because of h= ow inelegant this >> all seems. When it comes to bringing Guix to Galaxy I think we have >> cultural problems to overcome, not really technical issues. > Well, if this approach allows us to demonstrate the improvements Guix > can bring (and to sidestep the cultural differences), it may be a good > idea to try it. Has anyone ever managed to get Guix to work inside docker? I attempted=20 it as I intend on submitting some applications to kbase[0,1], where=20 developers submit docker files to run their applications within the=20 "narrative" interface i.e. web-facing interfaces to bioinformatic tools.=20 I failed I think because of docker's single-process restriction. Using=20 the attached (straightforward) dockerfile it fails at this step: RUN echo "nohup ~root/.guix-profile/bin/guix-daemon=20 --build-users-group=3Dguixbuild &" > /tmp/daemon-script.sh RUN bash /tmp/daemon-script.sh; guix pull ... guix pull: error: build failed: cloning builder process: Operation not=20 permitted That seems to suggest that we cannot run the daemon inside a docker=20 container, so I suppose we'd have to fall back on copying files from a=20 store built outside docker-land, right? Thanks, ben [0]: http://kbase.us/ [1]: https://github.com/kbase/user_docs/blob/master/kbase-architecture.md --------------64BA77EE13A93BB1D6024A33 Content-Type: text/plain; charset=UTF-8; name="Dockerfile" Content-Disposition: attachment; filename="Dockerfile" Content-Transfer-Encoding: base64 IyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMj IyMjIyMjIyMjIyMjIwojIERvY2tlcmZpbGUKIwojIFZlcnNpb246ICAgICAgICAgIDEKIyBT b2Z0d2FyZTogICAgICAgICBHTlUgR3VpeAojIFNvZnR3YXJlIFZlcnNpb246IDAuMTEuMC11 YnVudHUxNC4wNAojIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMj IyMjIyMjIyMjIyMjIyMjIyMjIyMjIyMjCgojIEJhc2UgaW1hZ2UgYXMgVW5idW50dQpGUk9N IHVidW50dToxNC4wNAoKUlVOIGFwdC1nZXQgdXBkYXRlClJVTiBhcHQtZ2V0IC15IGluc3Rh bGwgd2dldApSVU4gYXB0LWdldCAteSBpbnN0YWxsIGJ1aWxkLWVzc2VudGlhbAoKIyBJbnN0 YWxsIEd1aXggZnJvbSBiaW5hcnkKUlVOIGNkIC90bXAgJiYgd2dldCBmdHA6Ly9hbHBoYS5n bnUub3JnL2dudS9ndWl4L2d1aXgtYmluYXJ5LTAuMTEuMC54ODZfNjQtbGludXgudGFyLnh6 ClJVTiBjZCAvdG1wICYmIHdnZXQgZnRwOi8vYWxwaGEuZ251Lm9yZy9nbnUvZ3VpeC9ndWl4 LWJpbmFyeS0wLjExLjAueDg2XzY0LWxpbnV4LnRhci54ei5zaWcKClJVTiBncGcgLS1rZXlz ZXJ2ZXIgcGdwLm1pdC5lZHUgLS1yZWN2LWtleXMgMDkwQjExOTkzRDlBRUJCNQpSVU4gZ3Bn IC0tdmVyaWZ5IC90bXAvZ3VpeC1iaW5hcnktMC4xMS4wLng4Nl82NC1saW51eC50YXIueHou c2lnCgpSVU4gdGFyIC0td2FybmluZz1uby10aW1lc3RhbXAgLXhmIC90bXAvZ3VpeC1iaW5h cnktMC4xMS4wLng4Nl82NC1saW51eC50YXIueHoKClJVTiBsbiAtc2YgL3Zhci9ndWl4L3By b2ZpbGVzL3Blci11c2VyL3Jvb3QvZ3VpeC1wcm9maWxlIH5yb290Ly5ndWl4LXByb2ZpbGUK ClJVTiBncm91cGFkZCAtLXN5c3RlbSBndWl4YnVpbGQKUlVOIGZvciBpIGluIGBzZXEgLXcg MSAxMGA7IGRvIHVzZXJhZGQgLWcgZ3VpeGJ1aWxkIC1HIGd1aXhidWlsZCAtZCAvdmFyL2Vt cHR5IC1zIGB3aGljaCBub2xvZ2luYCAtYyAiR3VpeCBidWlsZCB1c2VyICRpIiAtLXN5c3Rl bSBndWl4YnVpbGRlciRpOyBkb25lCgpSVU4gbWtkaXIgLXAgL3Vzci9sb2NhbC9iaW4KUlVO IGxuIC1zIC92YXIvZ3VpeC9wcm9maWxlcy9wZXItdXNlci9yb290L2d1aXgtcHJvZmlsZS9i aW4vZ3VpeCAvdXNyL2xvY2FsL2JpbgoKIyBBdXRob3JpemUgaHlkcmEuIFBlcmhhcHMgdW5u ZWNlc3NhcnkgaW4gdGhlIGZ1dHVyZS4KUlVOIGd1aXggYXJjaGl2ZSAtLWF1dGhvcml6ZSA8 IH5yb290Ly5ndWl4LXByb2ZpbGUvc2hhcmUvZ3VpeC9oeWRyYS5nbnUub3JnLnB1YgoKIyBT dGFydCB0aGUgZGFlbW9uIG1hbnVhbGx5ClJVTiBlY2hvICJub2h1cCB+cm9vdC8uZ3VpeC1w cm9maWxlL2Jpbi9ndWl4LWRhZW1vbiAtLWJ1aWxkLXVzZXJzLWdyb3VwPWd1aXhidWlsZCAm IiA+IC90bXAvZGFlbW9uLXNjcmlwdC5zaApSVU4gYmFzaCAvdG1wL2RhZW1vbi1zY3JpcHQu c2g7IGd1aXggcHVsbAo= --------------64BA77EE13A93BB1D6024A33--