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

[Brad Aagaard]

Hongfeng,

Scheduler refers to submitting to the batch system and launcher refers 
to launching the MPI job.

--scheduler.dry shows you the shell script submitted to the batch system

--launcher.dry shows you how the MPI job is launched

Brad


On 2/29/12 8:54 AM, Hongfeng Yang wrote:
> 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
>>>
>>>
>>
>
>