[GE users] [OT] Running R under SGE and OpenMPI

Rayson Ho rayrayson at gmail.com
Thu Oct 9 18:53:49 BST 2008


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Can you pass in "--mca pls_gridengine_verbose 1" to mpirun??

According to the OpenMPI FAQ, this should add the -verbose flag to
qrsh, and will help us debug the problem.

Rayson



On 10/9/08, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> On Thu, Oct 9, 2008 at 12:42 PM, Reuti <reuti at staff.uni-marburg.de> wrote:
> > Sean,
> >
> > Am 09.10.2008 um 17:47 schrieb Sean Davis:
> >
> >> On Thu, Oct 9, 2008 at 11:31 AM, Rayson Ho <rayrayson at gmail.com> wrote:
> >>>
> >>> On 10/9/08, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> >>>>
> >>>> I can confirm that there is no --with-sge in the configure --help
> >>>> output, even in 1.2.7.
> >>>
> >>> Yes, that's only in 1.3.
> >>>
> >>> BTW, how is your PE defined?? The error message tells you that the
> >>> remote execd is not starting the remote tasks:
> >>>
> >>>  error: got no connection within 60 seconds
> >>>  [octopus:21290] ERROR: A daemon on node shakespeare.nci.nih.gov failed
> >>>  to start as expected.
> >
> > is there any firewall installed on the machines?
>
> No.  And shakespeare is the qmaster of an otherwise working cluster.
>
> Sean
>
> >> Thanks, Rayson.
> >>
> >>> qconf -sp orte
> >>
> >> pe_name            orte
> >> slots              999
> >> user_lists         NONE
> >> xuser_lists        NONE
> >> start_proc_args    /bin/true
> >> stop_proc_args     /bin/true
> >> allocation_rule    $round_robin
> >> control_slaves     TRUE
> >> job_is_first_task  FALSE
> >> urgency_slots      min
> >> accounting_summary FALSE
> >>
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