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

Stephan Grell - Sun Germany - SSG - Software Engineer stephan.grell at sun.com
Wed Mar 30 15:45:34 BST 2005


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Reuti wrote:

> Stephan,
>
> I was thinking of the same. But wouldn't this allow to get additional 
> slots from the wrong queue as slaves?
>
Yes. You are right. I did not find a way to prevent that.  Hm.. Could 
one use sequence numbers for it? Or maybe
soft requests, which are only full filed on hosts in the "other" host group?

Just an idea. It could work.

Stephan

> I think, he means an allocation in PBS like:
>
> -l nodes=ionode:1+compute:5
>
> to get 6 CPUs - one from the nodes with the feature ionode and 5 with 
> the feature compute. - Reuti
>
>
> Stephan Grell - Sun Germany - SSG - Software Engineer wrote:
>
>> William Burke wrote:
>>
>>> Hi,
>>>
>>> <Snip>
>>>  
>>>
>>>> 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.
>>>>   
>>>
>>>
>>>
>>> The thing is if I pick myhost to be masterq what happens if that 
>>> host is
>>> busy with another job and there are other host that can be picked.
>>>
>>> The robustness that I need in SGE is for it to arbitrarily pick 
>>> those M-1
>>> nodes from the QueueA.q and the Mth one from FatQueueB.q. I do not 
>>> see how
>>> the "-masterq QueueA.q at myhost" in qsub will achieve this. Help me to
>>> understand your suggestion.
>>>  
>>>
>> You can put the M-1 hosts in one cluster queue and the other hosts 
>> into another cluster queue.
>>
>> A simple approach would be to put all M-1 hosts into the M-1 
>> hostgroup and all other hosts
>> into a second hostgroup (others).
>>
>> You than define a cluster queue on the M-1 and other hostgroup.
>>
>> The qsub command would like like:
>>
>> qsub -pe .... -masterq "cluster_queue@@M-1" .....
>>
>> This ensures, that the master task is started on one of teh M-1 
>> machines.
>>
>> Does it help?
>>
>> Stephan
>>
>>> I think that PBS's qsub has a way to specify a queue and the number 
>>> of nodes
>>> from that queue - Queue:Num_nodes Does SGE have this built in 
>>> functionality?
>>>
>>> William
>>>
>>> -----Original Message-----
>>> From: Reuti [mailto:reuti at staff.uni-marburg.de] Sent: Wednesday, 
>>> March 30, 2005 6:23 AM
>>> To: users at gridengine.sunsource.net
>>> Subject: Re: [GE users] FW: Pick nodes from one queue plus 1 node from
>>> another queue
>>>
>>> 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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>>>  
>>>
>>
>>
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