From: Phil Greer (pgreer_at_structbio.pitt.edu)
Date: Tue Aug 19 2014 - 11:30:38 CDT
Sometimes, the number of seconds/step is off if the run completes too quickly. This happened on a GPU system we were building in my department. Increasing the number of steps gives a bigger sample for computing seconds per step. In reality, that is just a fist pass test without finding a bigger system. If it is still claiming ~0.01s/step then a bigger system is needed.
-Phil Greer
On Aug 19, 2014, at 12:14 PM, Maxime Boissonneault <maxime.boissonneault_at_calculquebec.ca> wrote:
> That will increase the total run time, but why would it change the number of seconds per step ?
>
> Maxime Boissonneault
>
> Le 2014-08-19 12:10, Phil Greer a écrit :
>> In the apoa1.namd file edit the numsteps parameter to 10000 or higher.
>>
>> -Phil Greer
>>
>> On Aug 19, 2014, at 11:48 AM, Maxime Boissonneault <maxime.boissonneault_at_calculquebec.ca> wrote:
>>
>>> Hi,
>>> I am running the apoa1 benchmark on our GPU cluster. Each node has 8 GPUs and 20 cores. I am compiling Namd with MPI and SMP support. It seems I reach a limit of about ~0.01s/step with one node, and cannot go quicker with more than one node.
>>>
>>> Is there a larger benchmark out there that would scale better on this type of system ?
>>>
>>> Thanks,
>>>
>>> --
>>> ---------------------------------
>>> Maxime Boissonneault
>>> Analyste de calcul - Calcul Québec, Université Laval
>>> Ph. D. en physique
>>>
>
>
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