[GE users] can't start pthread with Gridengine

echoecho chrisbee at u.washington.edu
Mon Jul 27 20:48:36 BST 2009


Hi Christian,

This is Linux, CentOS 4.5, kernel 2.6.9-67.ELsmp.  Grid Engine version is 6.0u8.

> Hi,
> 
> on which architecture (and kernel version) you are running Grid Engine?
> Which Grid Engine version are you using?
> 
> Regards,
> 
> Christian
> 
> 
> On 07/23/09 20:26, echoecho wrote:
> > Hello,
> > 
> > I'd like to run multi-threaded applications on our cluster as Gridengine jobs, but it appears that Gridengine is not allowing the creation of pthreads.  I've tested two applications: BWA (short-read DNA sequence alignment) and a simple python script that makes one thread.  In both cases the programs cannot create pthreads.  I've tried with and without a parallel environment set up with this configuration:
> > 
> > $ qconf -sp smp
> > pe_name           smp
> > slots             999
> > user_lists        NONE
> > xuser_lists       NONE
> > start_proc_args   /bin/true
> > stop_proc_args    /bin/true
> > allocation_rule   $pe_slots
> > control_slaves    FALSE
> > job_is_first_task TRUE
> > urgency_slots     min
> > 
> > Both applications can create threads if started directly on a compute node outside of SGE.
> > 
> > Attached is the python script I've used to test thread creation and the bash script that creates the submit script and calls qsub.
> > 
> > Any help in troubleshooting this problem would be much appreciated.
> > 
> > Thanks,
> > Chris
> > 
> > --
> > Chris Berthiaume
> > University of Washington
> > Center for Environmental Genomics
> > 
> > ------------------------------------------------------
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> > 
> > To unsubscribe from this discussion, e-mail: [users-unsubscribe at gridengine.sunsource.net].
> > 
> 
> -- 
> Sun Microsystems GmbH             Christian Reissmann
> Dr.-Leo-Ritter-Str. 7             Software Engineer
> D-93049 Regensburg                Phone: +49 (0)941 3075 112
> Germany                           Fax:   +49 (0)941 3075 222
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>                                    http://www.sun.com/gridengine
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