[GE users] Cleaning scratch files.

Baudilio Tejerina tejerina at chem.northwestern.edu
Thu Jun 29 04:01:55 BST 2006


Rayson, Craig,

Thanks for the suggestions. I am not familiar with prolog/epilog  
scripts but, I'll study this alternative too.

Baudilio



On Jun 28, 2006, at 6:02 PM, Craig Tierney wrote:

> Rayson Ho wrote:
>> AFAIK, the prolog & epilog are only run on the first node, even for
>> tight PE integration...
>
> You are correct.  Use your favorite distributed shell command (pdsh  
> for instance) to run the rm command on all of the nodes  
> simultaneously based
> on the provided host list.
>
> This is how our large clusters have been running for over 4 years.
>
> Craig
>
>
>> Rayson
>> On 6/28/06, Craig Tierney <ctierney at hypermall.net> wrote:
>>> Baudilio Tejerina wrote:
>>> > 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.
>>> >
>>>
>>> Add the rm statement in the job prologue.  That is guaranteed to run
>>> before every job, and and clean up the tmp space if there are  
>>> stale files.
>>>
>>> Craig
>>>
>>>
>>> > Thanks for any help anyone might bring.
>>> >
>>> > Regards.
>>> >
>>> > Baudilio
>>> >
>>> >  
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