Hi,
Am 28.08.2013 um 10:40 schrieb Guillermo Marco Puche:
> I've been experiencing some weird behavior with Picard tools (bioinformatic
> tool on Java).
>
> • Job starts running
> • Job gets to T status (threshold)
Do you mean the process state "T" or the SGE job state "T"?
> • Job comes back to R status.
Do you use any checkpointing interface, to restart the job? If so, it should
output "Rr" in `qstat` instead of a plain "R" for the SGE job state.
> • Job stays in R status forever. The processes stay on compute node
> without using resources.
In the list I see only "S" states.
-- Reuti
NB: Maybe it could help, to run these "suspend-sensible" jobs with a nice value
of 19 ("priority 19" in the queue configuration), and normal job like usual at
0.
> You can see the real process inside compute node in the following picture. As
> I said they seem to do nothing, they just stay here.
>
> http://imm.io/1gmXT
>
> Thank you.
>
> Best regards,
> Guillermo.
> On 07/29/2013 01:35 PM, Reuti wrote:
>> Hi,
>>
>> Am 29.07.2013 um 13:07 schrieb Guillermo Marco Puche:
>>
>>
>>> I have set some subscribing rules. So cluster compute nodes have load
>>> balanced. This way, grid engine put some jobs to a T state when a compute
>>> node exceeds load rule.
>>>
>>> The problem is I've some perl scripts that use MySQL connection after
>>> resuming from a T state die because they lose the connection to MySQL.
>>>
>>> The question is.. Is there any way to exclude a job by name from suffering
>>> this rule? So It will never enter T status and die after resume.
>>>
>> unfortunately no.
>>
>> Nevertheless I saw the need for some kind of "suspensible y/n" flag for a
>> submitted job too:
>>
>>
>> https://arc.liv.ac.uk/trac/SGE/ticket/735
>>
>>
>> For your situation it could help to have a dedicated queue for these Perl
>> scripts only, which will never get suspended.
>>
>> -- Reuti
>>
>>
>>
>>> Thank you.
>>>
>>> Best regards,
>>> Guillermo.
>>> --
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>>> users mailing list
>>>
>>> [email protected]
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