[GE users] error qhen using qsub

Reuti reuti at staff.uni-marburg.de
Wed Feb 23 17:47:34 GMT 2005


Try a short script:

#!/bin/sh
. /usr/sge/default/common/settings.sh

node=`head -n 1 $TMPDIR/machines`
export IS_IT_THERE="Some text."

echo $node

echo "With -V:"
qrsh -V -inherit -nostdin $node 'echo "Value: $IS_IT_THERE"'
echo "Without -V:"
qrsh    -inherit -nostdin $node 'echo "Value: $IS_IT_THERE"'
echo "Done."

exit 0


will give (be sure "job_is_first_task FALSE" in the PE, as we are not 
checking the hostname here):


node04
With -V:
Value: Some text.
Without -V:
Value:
Done.

CU - Reuti


lukacm at pdx.edu wrote:
> Thanks a lot for answer.
> I have directly a question to you as you was the one (i think) who did the
> tutorial for tight integration. I followd the second step (the second option).
> How can i verify if it is working? I mean i added the -V in the rcs wrapper but
> i am really not sure it is working.
> 
> 
> thanks a lot
> 
> martin
> 
> Quoting Reuti <reuti at staff.uni-marburg.de>:
> 
> 
>>lukacm at pdx.edu wrote:
>>
>>>Hello,
>>>
>>>we installed the PGI package with compilers. The person doing it disabled
>>
>>during
>>
>>>the compialation the head node as a exec host so to run a mpi job using
>>
>>mpirun
>>
>>>directly the '-nolocal' switch must be used.
>>
>>- To use a parallel (e.g. MPI) program, you have to define a PE in SGE
>>and request it with qsub. See man "sge_pe".
>>
>>- This will grant some slots on the machines, according to your request.
>>Don't use -nolocal, this would disable the head node of the job (this is
>>not related to the master node of the cluster).
>>
>>
>>>Now when i try to submit a job using qsub, and if i point to the mpirun
>>
>>binary
>>
>>>from PGI package i got this
>>>error:/opt/gridengine/default/spool/compute-0-0/job_scripts/269: line 7:
>>>/usr/pgi/linux86-64/5.2/bin/mpirun: No such file or directory.
>>
>>- Copy /usr/pgi to a shared directory. At least the mpirun from PGI and
>>maybe some dynamic libs also have to be available on the nodes.
>>
>>- When you have this working, you can look for a tight integration with
>>correct accounting. You can use mpirun from mpich to start PGI programs?
>>Then maybe the same integration applies, you can find at the Howto page.
>>
>>
>>>Does it mean taht SGE is not correctly integrated with the mpi run or
>>
>>something
>>
>>>else? If i refer to the original mpirun with ic in /opt/mpich/gnu/bin/ the
>>>process starts in parallel and everything is fine. however the PGI
>>>compiler/mpiruner is not even visible from the ccompute nodes.
>>>
>>>Does anyone using PGI had similar troubles or have some infomration about
>>
>>this
>>
>>>issue?
>>
>>Cheers - Reuti
>>
>>
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> 
> 
> 
> 
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