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
Hi Alexander, There is a -t for PeakRanger to indicate the number of threads. I don't think macs14 or macs2 can run on mutltiple cores - I am cc'ing Tao Lui, the author of macs, who can confirm this.
Thanks,
Q
On Tue, Mar 26, 2013 at 6:15 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
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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
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.cock@googlemail.comwrote:
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
galaxy-dev@lists.galaxyproject.org
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Alexander Kurze -
Peter Cock -
Quang Trinh