[GE users] Cleaning scratch files.

Baudilio Tejerina tejerina at chem.northwestern.edu
Thu Jun 29 06:47:50 BST 2006


Hi,

I am using SGE 6.0, however my script does not contain any 'qrsh'. I   
just inserted

...
#$ -V
#
setenv RCMD_PREFIX TMPDIR=$TMPDIR
#
/opt/local/progs/runscr  data.in
....

into the script but, TMPDIR is unknown to the slaves nodes yet.


Baudilio


On Jun 29, 2006, at 12:08 AM, Reuti wrote:

> Am 29.06.2006 um 04:59 schrieb Baudilio Tejerina:
>
>> 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.
>
> If you are using SGE 6.0, just attach the PE to only one queue,  
> hence all the $TMPDIRs will have the same name. Then in the rsh- 
> wrapper add the -V switch to get "qrsh -inherit" call. So all slave  
> processes will also know bout it.
>
> Another option is setting
>
> export RCMD_PREFIX="TMPDIR=$TMPDIR"
>
> in your job script before the first qrsh call.
>
> HTH - Reuti
>
>
>> 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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