Was hoping someone with an actual torque cluster would respond. I think the way you would configure this might be for instance might be setting native_specification like "-l nodes=1:ppn=n". Depending on how things are configured or simply because I am ignorant - this may be wrong - but I think what you really want should look a lot like your arguments to qsub. So let say you have defined a job runner plugin called pbs_drmaa at the top of your job_conf.xml file. Then you could default everything to a single core by default and send "big" jobs to a destination with 8 cores with destinations and tool sections that look something like this...
<destinations default="singlecore"> <destination id="singlecore" runner="pbs_drmaa"> <param id="native_specification">-l nodes=1:ppn=1</param> </destination> <destination id="multicore" runner="pbs_drmaa"> <param id="native_specification">-l nodes=1:ppn=8</param> </destination> </destinations>
<tools> <tool id="bowtie2" destination="multicore" /> <tool id="bowtie" destination="multicore" /> <tool id="deeptools" destination="multicore" /> <tool id="cufflinks"destination="multicore" /> <tool id="cuffdiff" destination="multicore" /> <tool id="cuffmerge" destination="multicore" /> <tool id="tophat2" destination="multicore" /> </tools>
Again - that native specification could be wrong - probably best to test it out locally (or maybe Nate or JJ will step in and correct me).
Hope this helps, -John
On Mon, Jan 19, 2015 at 8:05 AM, Fernandez Edgar email@example.com wrote:
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:firstname.lastname@example.org] Envoyé : January-18-15 8:59 PM À : Fernandez Edgar Cc : email@example.com 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,
On Tue, Jan 13, 2015 at 11:52 AM, Fernandez Edgar firstname.lastname@example.org wrote:
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,
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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