On 05/31/2016 12:29 PM, Michael Crusoe wrote: > Reminder: you can make fake chroots without root privileges (can also > be used to convert Docker images and run software within them): > https://github.com/common-workflow-language/common-workflow-language/wiki/Userspace-Container-Review#getting-userspace-containers-working-on-ancient-rhel > > If your kernel version is new enough and your security people are fine > with Docker then there are various efforts to ease administration of > Docker on top of HPC schedulers. For Docker, I have created a script that creates a Docker image for all DebianMed packages. they are available at https://docker-ui.genouest.org/app/#/ with container debian/xxx
Basically we fetch debianmed packages and create a docker with a simple "apt-get install". I also extract a few meta-data that are added to Dockerfile labels for additional info. Olivier > > On Tue, May 31, 2016 at 11:10 AM, Steffen Möller > <[email protected] <mailto:[email protected]>> wrote: > > Hello, > > If I can remember correctly, one reason we are doing this Debian > packaging is that we find not all but many packages not ultimately > straight-forward to compile. It is not the "configure && make install" > that bothers us, but the manifold dependencies and dependencies of > those > dependencies that also need to be maintained. And this effort can be > shared, obviously. > > Now, for a single binary I would not mind, but we are about to > transition all our "evolving routine" workflows over to the > University's > central HPC cluster . And the suggestion is to just recompile what one > needs and automate that recompilation if it is any cumbersome - > somewhat > surprisingly they did not say "package it". It is some > Jessie-analogous > CentOS, i.e. not a .deb distro and they feature the typical module > environments to get functionality in and out, together with slurm. > Would > it be worthwhile to try installing the packages to $HOME/debroot > as with | > dpkg-deb -x app.deb $HOME/debroot| > and fiddle with the $PATH environment not too different from how > module > is doing it? This would certainly raise my interest in backports. > > Our next (first real) meeting is on Thursday. Docker and chroot > environments will certainly be discussed. We could also just not > completely migrate everything but constrain ourselves, e.g., on short > read alignments, and self-compile those "typical suspect" binaries > only. > Not ideal. What do you folks do out there? Just not bother and use > some > commercial cloud service? There would be single VMware instances > for us, > but not tens or hundreds as in OpenStack or Eucalyptus. I presume that > this situation is rather common and I would very much like to hear > your > opinions/experiences about it. > > Cheers, > > Steffen > > > > > > -- > Michael R. Crusoe > Community Engineer & Co-founder > Common Workflow Language project > https://impactstory.org/u/0000-0002-2961-9670 > [email protected] <mailto:[email protected]> > +32 (0) 2 808 25 58 > +1 480 627 9108 -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
