Thanks a lot for your answers. I tried to set the -t value to 32 in
peakranger but nothing really still runs on 1 thread even so
it says -t 32 in the execution line  I guess I need to contact the author.

Thanks for your help!


On Tue, Mar 26, 2013 at 2:01 PM, Peter Cock <>wrote:

> On Tue, Mar 26, 2013 at 10:15 AM, Alexander Kurze
> <> wrote:
> > Hi there,
> >
> > we have a 32 core server but I realised that a lot of programs are only
> > using a fraction of that. I was able to adjust bowtie, bowtie2 and
> Tophat to
> > use all of the cores but couldn't find an thread/core option for Macs14,
> > Macs2 or PeakRanger. Does anyone know if these programs are capable of
> multi
> > threading?
> > If yes, where do I adjust it? Would be nice to have some global parameter
> > set in the universewgsi.ini file.
> >
> > Thanks,
> >
> > Alex
> A more configurable thread setting has come up several times -
> something that could integrate nicely with cluster back ends for
> scheduling would be ideal. Some of my wrappers use $NSLOTS
> if set, and if not default to four threads. This works very nicely
> under SGE where you can set the thread count via the runner
> settings in universewgsi.ini - but this is not really general enough.
> For now however, you do generally have to tweak the wrappers
> as you have done to edit any hard coded thread setting :(
> Peter

Alexander Kurze
70 Sunningwell Road
Oxford, OX1 4SX

Tel:   +44 1865-243-609
Mobile:  +44 7962-425-865
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