On Tue, Nov 27, 2012 at 10:38 AM, Andreas Kuntzagk
<andreas.kuntz...@mdc-berlin.de> wrote:
> Dear Peter,
>
>> As the author of several tool wrappers, I've been asking for a Galaxy
>> wide mechanism for Galaxy to tell the tool how many threads it can
>> use, for example via an environment variable. The value could then
>> be set with a general default, per runner default, or even per tool
>> using the existing runner configuration under [galaxy:tool_runners]
>> in universe_wsgi.ini
>
> This would be a possibility. Another would be to communicate the number
> of threads the other way. So the tool tells the runner how many threads.
> And the runner knows how to handle this.
>
> I can imagine universe_wsgi.ini having such lines:
>
> ncbi_blastp_wrapper  = drmaa://-V -pe smp $GALAXY_THREADS
>
> and then $GALAXY_THREADS is changed for the value given by the wrapper.
> Thinking again this is probably not goint to work because the runner comes
> first and the wrapper after. My idea was that the wrapper could decide what
> recources to request. So I could use lower memory settings for small mapping
> jobs ...

There is some work on dynamic job allocation you might be interested
in - have you seen this thread?
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-November/011759.html

>> In your example, and others like the BWA and BLAST+ wrappers where
>> the tool XML is hard coded to 8 threads, you would probably want to
>> use a custom runner in universe_wsgi.ini setting the cluster submission
>> to request that many slots/CPUs.
>
>
> A list of all these wrappers on the Wiki would be nice.

With many tools on the Tool Shed, I'm not sure how easy that would
be to co-ordinate. Doing it for the core tools would be more realistic.

Peter
___________________________________________________________
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:

  http://lists.bx.psu.edu/

Reply via email to