[GE users] use only N out of M cores per node?

mbay2002 jeff at haferman.com
Wed Feb 3 15:50:19 GMT 2010


Both of the proposed solutions require administrative fixes, which is
fine... I was hoping there was something I was overlooking that would
allow this to work "out of the box" in the default config...


dagru wrote:
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> With a newer SGE you can also make use of the exclusive complex in order to
> prevent interference with other jobs even if you are using 4 out of 8 slots.
> 
> See: 
> http://wikis.sun.com/display/gridengine62u3/Configuring+Exclusive+Scheduling
> 
> Together with core binding you can enforce the job distribution over 2 
> sockets.
> 
> Daniel
> 
> On 02/03/10 08:30, mlelstv wrote:
>> On Tue, Feb 02, 2010 at 06:41:48PM -0800, mbay2002 wrote:
>>   
>>> This is on a machine using SGE 6.1u5 (I can upgrade but this has served
>>> has well)...
>>>
>>> I'd like our users to be able to submit jobs and tell SGE that only
>>> N out of M cores per node should be used, for example, we have 8 cores
>>> per node but because of memory constraints certain users want to submit
>>> jobs and request that only 4 out of the 8 cores be used per node and, 
>>> they may need 16 cores total, so the qsub needs to tel sge to use
>>> 4 cores on 4 nodes.
>>>     
>>
>> You can create a parallel environment that allocates 4 slots per node.
>> This will cause the job to be split over 4 nodes.
>>
>> However, this will leave the other 4 slots per node free for other
>> jobs. Since your reason is memory constraints, this may not be what
>> you want.
>>
>> A flexible approach would ask for a memory ressource, then it is
>> possible that in parallel to the 16 slot job you may still run
>> small jobs. This requires that all your jobs ask for the memory
>> ressource correctly so that SGE can manage memory usage.
>>
>> If the goal is to use the complete nodes but only take 4 cores
>> for computation (and let the others idle), you can ask for all
>> cores (make it a 32 slot job) and tell your application to
>> use only half of the allocated slots on each node. Your jobscript
>> needs then to modify the $PE_HOSTFILE and needs to be careful about
>> the $NSLOTS parameter.
>>
>>

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