[gmx-users] "nstlist=-1" and performance problem

XAvier Periole x.periole at rug.nl
Wed Jan 28 23:28:25 CET 2009


Any documentation on how this is actually done?

Sounds interesting!


On Jan 28, 2009, at 11:12 PM, LuLanyuan wrote:

> Hi Berk,
> Thanks very much. I've found the problem. As you said I forgot to  
> increase rvdw. So the buffer is zero and the system needs to update  
> the nblist every step, which is obviously wrong. After I corrected  
> the mistake, the speed for "nstlist=-1" is roughly three times  
> faster as I expected.
> Lanyuan
> From: gmx3 at hotmail.com
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] "nstlist=-1" and performance problem
> Date: Wed, 28 Jan 2009 10:42:59 +0100
> Hi,
> I assume you did not only change nstlist, but also other mdp  
> settings, or not?
> Changing only nstlist from 1 to -1 should result in nearly equal or  
> much faster speeds.
> For efficient simulations with nslist=-1 you need to set an  
> appropriate
> buffer region (rlist > rcoulomb=rvdw). In 4.0 you have to optimize  
> this by hand.
> It would be nice to have this automated.
> At the end of the log file (a run of a few minutes is enough) you  
> can see what
> the neighborlist lifetime is. Optimal is usually something between  
> 10 and 20.
> Play with rlist to optimize the performance (also printed at the end  
> of the log file).
> Berk
> From: lulanyuan at msn.com
> To: gmx-users at gromacs.org
> Date: Mon, 26 Jan 2009 17:31:43 -0500
> Subject: [gmx-users] "nstlist=-1" and performance problem
> Hello,
> Could Berk or someone else answer my question regarding the new  
> "nstlist=-1" option in gmx4? In my understanding, the algorithm for  
> this option is the one used in DLPOLY/LAMMPS. However, When I was  
> trying two gromacs runs with "nstlist=-1" and "nstlist=1", I found  
> the speeds were basically the same. Isn't this automatic nblist  
> checking supposed to be faster than updating the nblist every step?  
> I also did similar tests on LAMMPS for the same system and found the  
> speed for automatical updating was several times faster. As a  
> result, although Gromacs is about 60% faster if we choose  
> nstlist=1,  it's much slower than LAMMPS if we choose the automatic  
> nblist updating.
> Thanks in advance for any ideas about it.
> Lanyuan Lu
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