[torqueusers] pbs job running slow

Abhishek Gupta abhig at Princeton.EDU
Tue Jul 14 14:10:26 MDT 2009


Hi Prakash,
The nuwa.py script looks like this:

#!/usr/bin/env python


if '__main__' == __name__:
    from DybPython.Control import main
    nuwa = main()
    nuwa.run()
    nuwa.finalize()
    pass #end

I believe it calls some other script too(FullChain.py i believe). I am 
not sure since I am testing this script on someone's behalf.
Thanks,
Abhi.


Prakash Velayutham wrote:
> Hi,
>
> I am not sure why you are seeing this difference. Without the actual 
> code (nuwa.py) I can't think of a way to reproduce or debug it. I can 
> confirm that the Torque scheduling happens as expected, so nothing 
> wrong with the PBS directives themselves. Sorry.
>
> Prakash
>
> On Jul 13, 2009, at 11:15 PM, Abhishek Gupta wrote:
>
>> Here is the script we are running. This is basically a test script of 
>> the actual script to test the performance.
>>
>> #!/bin/bash
>> #PBS -j oe
>> #PBS -o qsub1.out
>> #PBS -m ae
>> ###PBS -M abhig at princeton.edu
>> #PBS -l cput=36:0:0
>> ###PBS -l mem=1GB
>> #PBS -l nodes=node022
>>
>> date
>> echo "start"
>> export PATH=.:$PATH
>>
>> source /mnt/dayabay/trunk-source
>> cd /mnt/dayabay/project/speedtest
>>
>> time nuwa.py -l4 -n100 -H 345788 -o test1.root -m FullChain > test1.log
>>
>> echo "finish"
>> date
>>
>>
>> The command I run during interactively were
>> # qsub -I run.sh
>>
>> This took us to node022 and then
>> # run.sh
>> run.sh is the name of the script I wrote above.
>>
>> When job was finished, I run exit.
>>
>> Abhi.
>>
>> Prakash Velayutham wrote:
>>> Send your job commands when you run them interactively and also send 
>>> the contents of your batch file.
>>>
>>> Prakash
>>>
>>> On Jul 13, 2009, at 4:42 PM, abhig at Princeton.EDU 
>>> <mailto:abhig at Princeton.EDU> wrote:
>>>
>>>> Hi Prakash,
>>>> Thanks for your reply. I tried running job interactively and it 
>>>> seems that it is running normal. But ssh based job is running slow. 
>>>> Any further suggestion?
>>>> Abhi.
>>>>
>>>>
>>>>
>>>> On Mon 13/07/09 4:06 PM , Prakash Velayutham 
>>>> prakash.velayutham at cchmc.org <mailto:prakash.velayutham at cchmc.org> 
>>>> sent:
>>>>
>>>>     What is the job? And what does your batch file look like?
>>>>
>>>>     The best way to debug would be to use "qsub -I" and see if
>>>>     interactive PBS job also runs slow compared to a direct
>>>>     SSH-based job (job being the same). Then go from there.
>>>>
>>>>     Prakash
>>>>
>>>>     On Jul 13, 2009, at 3:55 PM, abhig at Princeton.EDU
>>>>     <javascript:top.opencompose('abhig at Princeton.EDU','','','')> wrote:
>>>>
>>>>>     Hi All,
>>>>>     The jobs with PBS are running very slow. Earlier I was
>>>>>     thinking that it might be because of rcp so I tried
>>>>>     configuring a node with usecp. The log file shows that it read
>>>>>     the usecp parameter but the speed is still slow. Can someone
>>>>>     suggest me anything? The same job running interactively take
>>>>>     almost half the time.
>>>>>     Thanks,
>>>>>     Abhi.
>>>>>     _______________________________________________
>>>>>     torqueusers mailing list
>>>>>     torqueusers at supercluster.org
>>>>>     <javascript:top.opencompose('torqueusers at supercluster.org','','','')>
>>>>>     http://www.supercluster.org/mailman/listinfo/torqueusers
>>>>
>>>
>
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