[GE users] Cleaning scratch files.

Baudilio Tejerina tejerina at chem.northwestern.edu
Thu Jun 29 03:59:00 BST 2006


Hi,

I had considered, and actually I tried, using $TMPDIR but, as you  
mentioned, I have observed that the variable is only used by the  
'master' node. I conclude that my job is not 'tightly integrated';  
isn't it?

Is there any procedure so that I can pass $TMPDIR to the slave nodes?  
I've tried via scripts but, as I suspected, it doesn't work.

Thanks so much for all,...

Baudilio


On Jun 28, 2006, at 6:30 PM, Reuti wrote:

> Hi,
>
> Am 29.06.2006 um 00:52 schrieb Baudilio Tejerina:
>
>> Hi,
>>
>> If in a parallel job, where several scratch files are created in  
>> the respective local-node disks, the job is deleted (qdel), the  
>> scratch files remain there. Is there any way to have 'sge' taking  
>> care of them (automatically removed them)?
>>
>> I've tried by inserting the appropriate 'rm' statement in the  
>> executing script but, these only work if the jobs successfully  
>> finish, obviously.
>
> in a tightly integrated parallel job the locally created $TMPDIR  
> with all stuff inside should also be deleted. The $TMPDIR will be  
> created by the first qrsh to the node. You just have to make sure,  
> that the $TMPDIR is used by all slave processes.
>
> If you want to do it for any reason on your own, you could use the - 
> notify in your qsub command and trap the warning, which the job  
> will get in this case. In the remaining time (defaults to 60 sec.)  
> you could also delete all the stuff in a custom way. Only a new  
> qrsh isn't allowed in this case, so you will end up with a loose  
> integration.
>
> HTH - Reuti
>
>
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