[GE users] Help: How to configurate the program output

Chris Dagdigian dag at sonsorol.org
Tue Aug 7 15:15:53 BST 2007



Hi Amy,

The root home directory (/root/) is not usually shared on beowulf  
clusters. You should be running your job as a non-root user with a  
home directory that is shared cluster wide or you should use the SGE  
qsub "-o" and "-e" switches to write the program output to a shared  
filesystem location.

Regards,
Chris


On Aug 7, 2007, at 10:09 AM, Lee Amy wrote:

> Hello,
>
> I'm a newbie in SGE. I build a Linux beowulf cluster for the  
> Bioinformatics Department for my college.
> The Linux is Cent OS4 and I have 5 nodes from gnode1 to gnode5.  
> Gnode1 is the Administration Host.
> Follow words is the situation of the problem which I faced.
>
> The directory /usr/local in gnode1 has been exported by NFS for  
> gnode2 to gnode5. And I make a directory called jobs, there's a  
> shell script job1.sh in jobs dir. The job1.sh is like this:
>
> #!/bin/bash
>
> exec /usr/local/tgicl_linux/tgicl  /usr/local/sequence/pataa -c 4
>
> In gnode1, I use qsub to submit job1.sh
>
> # qsub /usr/local/jobs/job1.sh [Enter]
>
> Then qsub show that it's okay, the job is processed in gnode[2-5].  
> After finished the job, for example, it's running on gnode4, the  
> program output (not the SGE output) is in /root directory in gnode4.
> But I hope the program output is in /usr/local/jobs in gnode1.
>
> How can I do with SGE can change the output?
>
> Please forgive my poor English.
>
> Thanks very much~
>
> Regards,
>
> Amy Lee

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