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>

and ...

  <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
<edgar.fernan...@umontreal.ca> wrote:
> 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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