Re: AW: "Beefier" benchmark

From: Maxime Boissonneault (maxime.boissonneault_at_calculquebec.ca)
Date: Wed Aug 20 2014 - 09:20:15 CDT

Le 2014-08-20 02:38, Norman Geist a écrit :
> Hi,
>
> the timings you get with 0.01 s/step doesn't seem to be very good. Before
> you move to a higher benchmark pls try in namd script:
>
> twoawayx yes
>
> if the above helps also try in addition:
>
> twoawayy yes
>
> if that helps try in addition:
>
> twoawayz yes
>
> This options artificially increase the number of patches (box slices) so
> that the large amount of cores a GPU has can be better utilized.
Any one of those reduces the time to 0.0074s/step.
Any two of those makes the time ~0.0087s/step
If I put all 3, the time goes up to 0.013s/step

So, those parameters do not change the results ?
> Also to the namd2 command try:
>
> +ignoresharing
This either does not make a difference or slightly increase the times.

Thanks,

Maxime

>
> To come back to your original question, the stmv benchmark is quite large.
>
> Mit freundlichen Grüßen
>
> Norman Geist.
>
>
>> -----Ursprüngliche Nachricht-----
>> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
>> Auftrag von Phil Greer
>> Gesendet: Dienstag, 19. August 2014 18:31
>> An: Maxime Boissonneault
>> Cc: Namd Mailing List
>> Betreff: Re: namd-l: "Beefier" benchmark
>>
>> 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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-- 
---------------------------------
Maxime Boissonneault
Analyste de calcul - Calcul Québec, Université Laval
Ph. D. en physique

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