[GE users] can't start pthread with Gridengine

crei crei at sun.com
Fri Jul 24 12:47:37 BST 2009


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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-- 
Sun Microsystems GmbH             Christian Reissmann
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