Thanks a lot for your answers. I tried to set the -t value to 32 in peakranger but nothing really happens...it 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! Alex On Tue, Mar 26, 2013 at 2:01 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote: > On Tue, Mar 26, 2013 at 10:15 AM, Alexander Kurze > <alexander.ku...@gmail.com> 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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