[GE users] can't start pthread with Gridengine

echoecho chrisbee at u.washington.edu
Fri Jul 24 00:58:45 BST 2009


Yes something is different about the environment when jobs are started by SGE.  I saved the output from env generated by a bash script submitted through qsub, then ssh'ed into a node directly, loaded the saved environemnt variables and tried my python pthreads test script.  It successfully created a thread so I don't think any difference in environment variables is the cause.

Are there any special configurations that need to be made to get Gridengine to play nice with libpthreads?

Chris

> 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
> >
> > ------------------------------------------------------
> > http://gridengine.sunsource.net/ds/viewMessage.do?dsForumId=38&dsMessageId=209228
> >
> > To unsubscribe from this discussion, e-mail: [users-unsubscribe at gridengine.sunsource.net].
> >

------------------------------------------------------
http://gridengine.sunsource.net/ds/viewMessage.do?dsForumId=38&dsMessageId=209269

To unsubscribe from this discussion, e-mail: [users-unsubscribe at gridengine.sunsource.net].



More information about the gridengine-users mailing list