Hi Peter,

thanks for your replies.

On 27.11.2012 11:44, Peter Cock wrote:
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?

This looks very promising. What I did not get from these messages is if that's already in galaxy-dist and where to put the dynamic job runner.

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.

I see the problem here. Especially since more and more tools are going into 
Tool Sheds.
I was just looking for some way to reduce my workload ;-)

Andreas Kuntzagk


Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany

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