[GE users] Job fragmentation of sge 6.0u8

Alessio Comisso alessio.comisso at gmail.com
Mon Jul 28 17:29:59 BST 2008



Il giorno 28/lug/08, alle ore 17:14, Reuti ha scritto:

Hello,
> Hi,
>
> Am 28.07.2008 um 17:28 schrieb Alessio Comisso:
>
>> Dear all,
>> This is the first time I am writing to this forum, I hope it is  
>> the right place where to ask for support.
>
> yes - sure :-)
>
>> I have a cluster running mpi jobs, but happens that more jobs are  
>> scheduled in the same node, for instance a qstat -f gives
>>
>> infini.q at node089.beowulf.clust BIP   4/4       4.00     lx26-amd64
>>   10568 0.53560 x88-PTCDA- toton        r     07/27/2008  
>> 08:50:15     2
>>   10632 0.62232 test-PAW   levita       r     07/28/2008  
>> 12:53:39     2
>
> You defined 4 slots on this node, anmd SGE scheduled 4 tasks to it.
>
>>
>> This in-homogeneous usage is not optimal, as the CPU usage is very  
>> low.
>>
>>                                                                       
>>       %CPU
>> 22190 levita    25   0  289m 182m 5772 R 53.3  2.3 108:12.66  
>> pwcapablanca.x
>> 22191 levita    25   0  289m 189m  13m R 51.3  2.4 110:20.80  
>> pwcapablanca.x
>> 12688 toton     25   0  459m 411m  13m R 48.6  5.2   1031:20 siesta
>> 12689 toton     25   0  207m 147m 6072 R 46.6  1.9   1037:39 siesta
>
> So, it looks like the machine has only 2 core, not 4. So what must  
> be adjusted is the number of slots in the queue configuration:

No no, the machine has 4 cores, I think that the communication  
patterns are limiting the performances. If the jobs are homogeneus  
you get 4 processes 99.9%.

Alessio

>
> qconf -mq infini.q
>
> and watch out for the line "slots" which should be 2 (at least for  
> the node "node089.beowulf.cluster".
>
> -- Reuti
>
>
>>
>>
>> How can I tell the nodes to accept only a single job (or a single  
>> user)? The installed version does not support the quotas.
>>
>> Kind Regards
>> Alessio
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>
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