[GE users] Job fragmentation of sge 6.0u8

Reuti reuti at staff.uni-marburg.de
Mon Jul 28 17:14:43 BST 2008


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:

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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