[gmx-users] GTX980 performance

Carmen Di Giovanni cdigiova at unina.it
Fri Feb 27 10:59:29 CET 2015

Szilárd thank you for the useful adivices about the configuration of the new 
server machine.

I report the changes made to improve the performance of a molecular dynamics 
on a  protein of 1925 running on GPU INVIDIA K20 Tesla :

  a.. To limit the number of cores used in the calculation (option -pin on) 
and to have a better performance:
          "gmx_mpi mdrun ... -ntomp 16 -pin on"

         where ntomp is the number of OpenMP threads

  a.. clock frequency using the NVDIA management tool is been increased from 
the default 705 MHz to 758 MHz.

  a.. to reduce runtime  to calculate energies every step in mdp file:

        nstcalcenergy option = -1

The actual performance is about 7ns /day against 2ns/day without these 


----- Original Message ----- 
From: "Szilárd Páll" <pall.szilard at gmail.com>
To: "Carmen Di Giovanni" <cdigiova at unina.it>
Cc: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, February 26, 2015 2:37 PM
Subject: Re: GTX980 performance

On Wed, Feb 25, 2015 at 1:21 PM, Carmen Di Giovanni <cdigiova at unina.it> 
> A special thank you to Szilárd Páll for the good advices in "GPU low
> performance discussion".
> The perfomance calculation is much improved after its suggestions.

I'm glad it helped. Could you post the changes you made to your
mdp/command line and the results these gave? It would allow others to
learn from it.

> Dear GROMACS users and developers,
> we are thinking to buy a new tyan server machine with  these features:
> SERVER SYSTEM TYAN FT48 - Tower/Rack,Dual Xeon ,8xSATA
> N. 2 CPU INTEL XEON E5-2620 2.0Ghz - 6 CORE 15MCache LGA2011
> N. 4 Scheda Video Nvidia GTX980, 4GB GDDR5,PCIE 3.0 , 2DVI, HD
> N. 4 DDR3 8 GB 1600 Mhz
> I known that the GTX980 offer good performance for GROMACS 5.0
> What are your views about this ?

That CPU-GPU combination will give heavily CPU-bound GROMACS runs,
those GTX 980s are 1.5-2x faster than what you can use with those CPUs
- conversely, if you'd get 6-core 3 GHz CPUs, you'll see a huge,
nearly 50% improvement in performance.

This will change in the futur, but at least with GROMACS v5.1 and
earlier, the performance on this machine won't be much higher than
with a single fast CPU and one GTX 980.

For better performance with GROMACS, consider getting better CPUs in
this machine or for the same (or less) money get two workstations with
i7 4930K or 4960X CPUs.


> Thank you in advance
> Carmen
> Carmen Di Giovanni, PhD
> Postdoctoral Researcher
> Dept. of Pharmacy
> "Drug Discovery Lab"
> University of Naples "Federico II"
> Via D. Montesano, 49
> 80131 Naples
> Tel.: ++39 081 678623
> Fax: ++39 081 678100
> Email: cdigiova at unina.it

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