Galaxy generally defers to the DRM (torque in your case) for dealing with these things. In your job_conf.xml you can specify limits for memory or CPUs and Galaxy will pass these along to the DRM at which point it is up to the DRM to enforce these - details depend on if you are using the PBS runner or the DRMAA runner (let me know which and I can try to elobrate if that would be useful).
In your particular case - I don't believe torque "schedules" RAM so things will generally only be... throttled... by CPUs counts. This is what I was told by the admins at MSI when I worked there anyway. If you want to place hard limits on RAM I think you need to "upgrade" to the MOAB scheduler or switch over to a different DRM entirely like SLURM. Even for DRMs that deal more directly with memory - Galaxy doesn't provide a general mechanism for passing this along to the tool (https://trello.com/c/3RkTDnIn) - so it would be up to the tool to interact with the environment variables your DRM sets . This sounds really terrible in the abstract - but it reality it usually isn't an issue - most of Galaxy's multi-core mappers say have relatively low memory per CPU usage - and for things like assemblers where this is more important - one can usually just assign them to their own CPU or something like that to ensure they get all the memory available. Unlike memory - Galaxy will attempt to pass the number of slots allocated to a job to the tools by setting the GALAXY_SLOTS environment variable. All of the multiple core devteam Galaxy tools at this point use this and so should work - as should probably most multi-core tools from the tool shed - at least the most popular ones. Hope this helps, -John On Tue, Jan 13, 2015 at 11:52 AM, Fernandez Edgar <edgar.fernan...@umontreal.ca> wrote: > Hello gents, > > > > Hope everyone had a great holiday break! > > Wish you guys all the best for 2015! > > > > I have a couple of questions about how resources (CPU and memory) is > allocated when you have a galaxy and torque installation. > > > > So I’ve setup torque with some default and maximum amount of CPU and memory > allocations. > > However, I have some worries when it comes to application (like tophat for > example). > > By default, it takes half the CPU of a server unless specified otherwise. > > How is the CPU allocation is specified to application like tophat through > galaxy? > > > > Also, how does galaxy react if a job needs more memory than the limit set by > torque? > > > > Any information would help me a lot! > > > > My sincere salutations to you all!!! > > > > Cordialement / Regards, > > > > Edgar Fernandez > > System Administrator (Linux) > > Direction Générale des Technologies de l'Information et de la Communication > > ( Bur. : 1-514-343-6111 poste 16568 > > > > Université de Montréal > > PAVILLON ROGER-GAUDRY, bureau X-218 > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
