[gmx-users] Overflow problem with test-particle insertion

[Berk Hess]

Hi,

I realized now that this is an SSE issue.
Normally you would get NAN (or is it INF?). That is treated correctly in the GROMACS TPI code.
But in SSE a float "wraps around" when it overflows, which could, in very few cases, lead to a reasonably
looking energy value (I check for very high and very low values).
I found that you can check for overflows in SSE and committed a fix for 4.5.2.
I also filled the first 10 points (up to r=0.02 nm) of the potential/force tables, these used to be zero.
These values are only relevant for energy minimization or TPI with extreme atomic overlap.

Berk

From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] Overflow problem with test-particle insertion
Date: Thu, 9 Sep 2010 09:39:42 +0200








Hi,

This is an interesting issue.
The chance is quite small that this happens, but maybe not negligible.
In single precision the maximum a float can store is 2^127.
This gives a minimum distance of (2^127)^-1/12 = 6.5e-4 nm.
The chance of inserting a particle within this radius is dens*3e-10,
where dens is the number of particles per nm^3.
A typical density of LJ particles is 30 per nm^3, which leads to a chance of 1e-8.
Such insertion numbers can be reached, so we probably have to worry about this.

However, in your example the distance seems to be around 4e-3, which would
give r^-12 = 6e28. This still fits in a float and should not cause problems.
So we should make sure we understand what's going on here.
Could you file a bugzilla with the files to reproduce this and which insertion
is the problematic one?

I so two possible solutions:
Force tabulated potentials with TPI, this can currently be achieved by setting
the environment variable GMX_FORCE_TABLES
Or require double precision.
But I think both solutions would lead to about 40% lower performance.

Berk


Date: Wed, 8 Sep 2010 21:16:46 -0400
From: kdaly at princeton.edu
To: gmx-users at gromacs.org
Subject: [gmx-users] Overflow problem with test-particle insertion

Hello Gromacs users,

I sent a message to the list in June describing what appeared to be a float overflow issue with the energy calculation for test-particle insertions: http://lists.gromacs.org/pipermail/gmx-users/2010-June/052213.html. 


I have recently tried the test-particle insertion mode in Gromacs-4.5.1, and it seems the problem is still there. Does anyone know how to work around or fix this problem without using tabulated potentials?

-Kevin


-- 
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 		 	   		  

-- 
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100909/1e74ba46/attachment.html>