On Tue, Mar 26, 2013 at 10:15 AM, Alexander Kurze
<alexander.kurze@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