[GE users] Help: Performance Test

Lee Amy openlinuxsource at gmail.com
Mon Jul 7 15:00:09 BST 2008


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2008/7/7 Reuti <reuti at staff.uni-marburg.de>:

> Am 07.07.2008 um 14:29 schrieb Lee Amy:
>
>
>  2008/7/7 Reuti <reuti at staff.uni-marburg.de>:
>> Hi,
>>
>> Am 07.07.2008 um 10:52 schrieb Lee Amy:
>>
>>
>> I built a small cluster with five nodes for the Bioinformatics Department
>> of my college. I've installed SGE 6.1 and set up integration parallel
>> environment properly. So I hope I can use some hints to exam whether SGE can
>> allocate the cluster resource perfectly. My main idea is following words.
>>
>> Every node has two Opteron 270HE processors so the total slots are 20.
>> What if I submit some jobs which take up 20 slots or more without SGE, I can
>> record their individual job running time. After that, I resubmit these jobs
>> with SGE and do some regulation(e.g. priority), then I record the job
>> running time again. I suppose that the total running time should be smaller
>> if I submit them using SGE. Because I believe that if I submit these jobs
>> normally they must seize resources and every job cannot run well. But with
>> SGE, it can allocate resources for jobs requirement.
>>
>> However, I'm afraid my idea is naive. So could anyone tell me some good
>> idea to have a test on SGE efficiency?
>>
>> the computing time should be the same. SGE will not speed up your
>> computation, but will take care of transferring the jobs to the nodes, built
>> an appropriate hostlist and so on.
>>
>> Unless you start your 20 slot job interactively only on one node and hence
>> oversubscribe this node, you shouldn't see any difference.
>>
>> -- Reuti
>>
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>>
>> Thank you for reply. And you mean that I should submit jobs on the cluster
>> to take up whole 20 slots or more, right? But still I got puzzled, what if I
>> oversubscribe this cluster with SGE, I can just use the default options of
>> SGE and I needn't change anything, is it okay?
>>
>> Furthermore, from your word I suppose that what I could have a performance
>> is just oversubscribe, is there any way to do test?
>>
>
> No. The opposite. You will have a slowdown if you start 20 processes on one
> and the same node instead of spreading it to 20 nodes (or more precise:
> cores). But whether you use 20 cores by hand or with SGE is no difference.
>
>
> -- Reuti
>
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>
> Reuti,

I'm sorry that I can't understand your word clearly. I submit jobs take up
more than 20 slots in the cluster(5 nodes) without SGE will slow down I know
this situation. If I submit the same jobs with SGE I think SGE can make a
hostlist then put them into appropriate nodes to run. So I have
*oversubscribe* the machine, SGE can do something to allocate the resource.

I don't know whether it's okay. But if I submit jobs even oversubscribe on 1
node, whether SGE can do something special?

Thank you again.

Regards,

Amy Lee



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