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?
>>
>>
>>
>>> • 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?
-- 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>
>
_______________________________________________
users mailing list
[email protected]
https://gridengine.org/mailman/listinfo/users
