[GE users] Cleaning scratch files.

Reuti reuti at staff.uni-marburg.de
Thu Jun 29 15:28:38 BST 2006


Please have a look here:

http://gridengine.sunsource.net/servlets/ReadMsg? 
listName=users&msgNo=8769

HTH - Reuti


Am 29.06.2006 um 16:09 schrieb Baudilio Tejerina:

> It runs the Quantum Chemistry code GAMESS which uses the  
> Distributed Data Interface (DDI) as message-passing library. DDI  
> and GAMESS are developed at Iowa State University and Ames Laboratory.
>
>
> Baudilio
>
>
>
> On Jun 29, 2006, at 12:59 AM, Reuti wrote:
>
>> Am 29.06.2006 um 07:47 schrieb Baudilio Tejerina:
>>
>>> 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
>>
>> What is runscr doing? Is it MPICH, MPICH2, Linda, ... - Reuti
>>
>>
>>> ....
>>>
>>> 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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