[GE users] can't start pthread with Gridengine

rayson rayrayson at gmail.com
Tue Jul 28 17:14:16 BST 2009


Also check the resource limit, so run limit (csh) or ulimit -a (sh,
bash) inside and outside of the SGE environment and see if there is
any difference.

Rayson



On 7/23/09, echoecho <chrisbee at u.washington.edu> wrote:
> 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
> > >
> > > ------------------------------------------------------
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> > >
> > > To unsubscribe from this discussion, e-mail: [users-unsubscribe at gridengine.sunsource.net].
> > >
>
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