[torqueusers] pbs job running slow

Abhishek Gupta abhig at Princeton.EDU
Mon Jul 13 21:15:05 MDT 2009


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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