[CIG-SHORT] Running PyLith on a cluster with the Sun Grid Engine batch system

[Hongfeng Yang]

Hi Brad,

I generated a sgebatch.cfg following the instruction on the wiki website,

[pylithapp]
scheduler = sge

[pylithapp.sge]
shell = /bin/bash
#pe-name = orte
qsub-options = -V -m bea -M email at uni.edu -j y

[pylithapp.launcher]
#command = mpirun -np ${nodes}
# Use the options below if not using the OpenMPI ORTE Parallel Environment
command = mpirun -np ${nodes}-machinefile ${PE_HOSTFILE} -n ${NSLOTS}

Then I run pylith by
pylith sgebatch.cfg step01.cfg --nodes=48 --job.name=sgetest --launcher.dry

However, the following error occurs
   Unable to run job: No project specified.
   Exiting.
  /scratch/h/hyang/cig/executable/bin/pylith: qsub: signal 1

Doesn't --launcher.dry suppose to give me the command line than actually 
submitting the job? Should I use --scheduler.dry?

Hongfeng

On 02/27/2012 11:12 AM, Brad Aagaard wrote:
> Hongfeng,
>
> PyLith does support the Sun Grid Engine batch system. It also supports 
> the PBS and LSF batch systems as discussed in the manual. I have added 
> some notes on using PyLith with the PBS/Torque and Sun Grid Engine 
> batch systems on the PyLith wiki
> http://www.geodynamics.org/cig/community/workinggroups/short/workarea/pylith-wiki/ 
>
>
> We will add the Sun Grid Engine information to the PyLith manual.
>
> Brad
>
>
>
> On 2/24/12 1:54 PM, Hongfeng Yang wrote:
>>
>> On 2/16/12 4:26 PM, Brad Aagaard wrote:
>>> Hongfeng,
>>>
>>> Note: There is a very easy way to submit a PyLith job to the PBS batch
>>> queue system. Create a batch.cfg file with the lines
>>>
>>> [pylithapp]
>>> scheduler = pbs
>>>
>>> [pylithapp.pbs]
>>> shell = /bin/bash
>>> qsub-options = -V -m bea -M MYEMAIL_ADDRESS
>>>
>>> [pylithapp.launcher]
>>> command = mpirun -np ${nodes} -machinefile ${PBS_NODEFILE}
>>>
>>> and then run PyLith via
>>>
>>> pylith batch.cfg step14.cfg --nodes=16 --scheduler.ppn=8
>>> --job.name=YOURJOBNAME --job.stdout=YOURJOBNAME.log
>> Our cluster uses SGE batch. Does pylith support SGE? I did not find it
>> in the manual. If so, how to set it up in a cfg file for pylith?
>>
>> Thanks,
>>
>> Hongfeng
>>
>>
>


-- 
Postdoc Investigator
Woods Hole Oceanographic Institution
Dept. Geology and Geophysics
360 Woods Hole Rd, MS 24
Woods Hole, MA 02543