Re: [galaxy-dev] Multicore
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 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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Multicore
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 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Multicore
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 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 > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
