[GE users] FW: Pick nodes from one queue plus 1 node from another queue

Reuti reuti at staff.uni-marburg.de
Wed Mar 30 12:23:08 BST 2005


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Hi,

you don't need a special queue to set up for the FatQueue machine. You 
can submit with "-masterq QueueA.q at myhost" in qsub.

Small problem: SGE may select another slot from this machine, unless you 
choose an allocation rule of 1. Then you can be sure, one slot (the 
special) one on the extra machine (so you may give this machine more 
slots than the other machines). The other slots will be on other 
machines this way. But as this can only be done for the head node of the 
parallel job, maybe you have to reorder any operation in your script, as 
you requested it to be the last machine.

Cheers - Reuti

William Burke wrote:
> Ultimately I would like to submit a parallel job that uses N-1 nodes 
> from QueueA.q and 1 node from FatQueueB.q as long as the node from 
> FatQueueB..q is the last node on the machinefile list
> 
>  
> 
> ------------------------------------------------------------------------
> 
> From: William Burke [mailto:wburke999 at msn.com]
> Sent: Wednesday, March 30, 2005 1:23 AM
> To: users at gridengine.sunsource.net
> Subject: RE: Pick nodes from one queue plus 1 node from another queue
> 
>  
> 
> There are M nodes in machine list and lets say that I want to submit a 
> job that can explicitly pick an exact amount of nodes from one 
> particular queue and  only one
> 
> node from another queue which equals the total # of nodes found in the 
> $pe_hostfile.
> 
>  
> 
> So for instance:
> 
>  
> 
> The user launches a parallel job that requests 33 processors. If two 
> queues exist, QueueA.q (consisting of 45 nodes) and FatQueueB.q 
> (consisting of 2 nodes from QueueA.q?s nodes) the user wants the ability 
> to specify 32 processors from QueueA.q and only 1 processor from 
> FatQueueB.q, what is the best way to implement that?
> 
>  
> 
> This is the situation:
> 
>  
> 
> 1.    The particular application needs N processors for a job
> 
> 2.    I request this in ?pe mpich N parameter
> 
> 3.    SGE generates M machines in its $pe_hostfile list based on the Nth 
> processor
> 
> 4.    As we already know the algorithm that creates $pe_hostfile says 
> create M nodes {if N is an even number then the Mth node should be N/2 
> else the Mth node should be (Nth+1)/2}
> 
> a.    I need some way to tell SGE that the Mth (or last) node of the 
> Machinefile list always has to be a node from the FatQueue.q which I use 
> those type of nodes for heavy io processing of the job.
> 
> b.    I do not want a job to run unless the Mth (or last) node in the 
> Machinefile is a node from FatQueue.q otherwise the job should wait 
> until that request is filled.
> 
> 5.    Ultimately the correctly formatted mpirun machinefile gets created 
> from the final $pe_hostfile of M nodes.
> 
>  
> 
> FWIW, usually the amount of processors is odd.
> 
> What is very important is that the last node of the mpirun machinefile 
> list is always from the FatQueueB.q.
> 
>  
> 
> Regards,
> 
>  
> 
> William
> 
>  
> 


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