Hello gents,

Once again I would like to convey my most sincere appreciation for your help!!!
And yes I would like to hear your elaboration on my DRMAA runner which is what 
I'm using.
So my installation looks like: galaxy --> pbs_drmaa --> torque

Cordialement / Regards, 
Edgar Fernandez

-----Message d'origine-----
De : John Chilton [mailto:jmchil...@gmail.com] 
Envoyé : January-18-15 8:59 PM
À : Fernandez Edgar
Cc : galaxy-...@bx.psu.edu
Objet : Re: [galaxy-dev] galaxy and torque - resource allocation

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
>
>
>
>
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