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

Carsten Kutzner ckutzne at gwdg.de
Mon Dec 15 12:57:53 CET 2014


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?


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

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