[gmx-users] Trouble balancing GPU/CPU force calculation load, ratio = 0.09

[Szilárd Páll]

Even 4 ranks x 16 theads is too much for AMD CPUs! In my experience
the optimal is typically 2-8 threads/rank (depending on DD / imbalance
behavior), so I suggest that you try these lower thread/rank counts.

Also, make sure that the application clocks are set to max on that
K40, otherwise you're missing 20% GPU performance!

--
Szilárd


On Mon, Dec 15, 2014 at 12:57 PM, Carsten Kutzner <ckutzne at gwdg.de> wrote:
> Hi,
>
> from the log file it seems that you were actually using 64 OpenMP threads.
> This is not very efficient, you could try to start mdrun with 4 thread-MPI
> ranks (instead of 1), e.g.
>
> mdrun -ntmpi 4 -gpu_id 0000 -s …
>
> Could it be that another process was running on your node while you
> ran the simulation?
>
> Carsten
>
>
> On 15 Dec 2014, at 12:45, Jason Hill <jason.hill at zoologi.su.se> wrote:
>
>> Hello list,
>>
>> I am simulating a protein in water and am concerned that I am not using my hardware to the best of it’s abilities. Here (https://drive.google.com/file/d/0BwAaTxAET7c5VkZERkFsa1cyRlk/view?usp=sharing <https://drive.google.com/file/d/0BwAaTxAET7c5VkZERkFsa1cyRlk/view?usp=sharing>) is the log file from a 1 nanosecond simulation. The only piece of information missing from it that may be of use is that I am using the OPLS/AA force field. Additionally, GROMACS only seems to be using 8-12 cores of the 64 available despite it’s complaint that the GPU is being underutilized. Please take a look and if you can, give me some advice about improving my simulation efficiency.
>>
>> Best regards,
>> Jason
>>
>>
>>
>> Jason Hill, Ph.D.
>> Wheat Lab
>> Zoologiska Institutionen
>> Stockholms Universitet
>> D-419 Svante Arrhenius v 18B
>> S-10691 Stockholm Sweden
>>
>>
>>
>>
>>
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>
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/grubmueller/kutzner
> http://www.mpibpc.mpg.de/grubmueller/sppexa
>
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