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?

>> 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.

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