Am 28.08.2013 um 16:39 schrieb Guillermo Marco Puche:
> On 08/28/2013 04:33 PM, Reuti wrote:
>> Am 28.08.2013 um 11:00 schrieb Guillermo Marco Puche:
>>
>>
>>> On 08/28/2013 10:57 AM, Reuti wrote:
>>>
>>>> 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"?
>>>>
>>> T in SGE.
>>>
>> Ok, the Threshold was triggered by the load being too high?
>>
> Indeed, that's exactly what happened.
>>>>
>>>>> • 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.
>>>>
>>>>
>>>>
>>> No, I don't use any checkpointing interface.
>>>
>> Then the state should be "r".
>>
>> In total: the processes are suspended in the correct way (and reach state
>> "T" also in `ps -e f), but after the `kill -cont ...` to wake them up they
>> become sleeping?
>>
> Correct. That's why I don't understand. Other processes after being in a T
> state because the load was too high they resume correctly and finish.
>
> But it seems that Java doesn't like being in a non running status. Or at
> leasts that's my pov.
This depends on the particular program. In principle it's possible to stop/cont
a java application.
-- Reuti
> Best regards,
> Guillermo.
>> -- Reuti
>>
>>
>>
>>>>> • 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.
>>>>>>> --
>>>>>>> _______________________________________________
>>>>>>> users mailing list
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> [email protected]
>>>>>>> https://gridengine.org/mailman/listinfo/users
>>> --
>>> Guillermo Marco Puche
>>>
>>> Bioinformatician, Computer Science Engineer.
>>> Sistemas Genómicos S.L.
>>> Phone: +34 902 364 669
>>> Fax: +34 902 364 670
>>>
>>> www.sistemasgenomicos.com
>>>
>>>
>>> <bioinfo.png>
>>>
>>>
>
>
> --
> Guillermo Marco Puche
>
> Bioinformatician, Computer Science Engineer.
> Sistemas Genómicos S.L.
> Phone: +34 902 364 669
> Fax: +34 902 364 670
> www.sistemasgenomicos.com
>
> <Mail-Anhang.png>
>
>
>
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