[GE users] can't start pthread with Gridengine

templedf dan.templeton at sun.com
Thu Jul 23 21:41:03 BST 2009


SGE doesn't do anything to your scripts other than execute them.  
Perhaps there's something different about the shell or environment that 
is being started on the exec node.  Try running "qrsh env" to see how 
the environment variables are set when you're job is executing on the 
remote machine.

Daniel

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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