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

[Jason Hill]

Hi Carsten,

Thank you for the advice. Using that as a starting point I think I now understand the Thread-MPI / OpenMP system a little better. Since my server does have 4 CPU sockets, 8 cores/socket, and 2 threads/core, -ntmpi 4 therefore designates 1 MPI-thread per socket, and 16 open MP threads per MPI-thread, does that sound right? Doing this doubles my simulation speed and I no longer get the warner of the GPU being so drastically underused. Now, as I monitor the run I see that GROMACS is still only using between 8-12 full time CPU threads, any idea why that is and if I can increase that?

Best,
Jason

> Date: Mon, 15 Dec 2014 12:57:19 +0100
> From: Carsten Kutzner <ckutzne at gwdg.de>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Trouble balancing GPU/CPU force calculation
> 	load,	ratio = 0.09
> Message-ID: <F1908832-1240-4BCF-9423-216C6C5307D3 at gwdg.de>
> Content-Type: text/plain; charset=windows-1252
> 
> 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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