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

Jason Hill jason.hill at zoologi.su.se
Mon Dec 15 12:45:16 CET 2014

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 Hill, Ph.D.
Wheat Lab
Zoologiska Institutionen
Stockholms Universitet
D-419 Svante Arrhenius v 18B
S-10691 Stockholm Sweden

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