[GE users] can't start pthread with Gridengine

echoecho chrisbee at u.washington.edu
Thu Jul 23 19:26:01 BST 2009


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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