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

[Kevin Daly]

Hi,

Thank you for taking the time to fix the issue. I would be very
interested in testing out the modified code, but unfortunately I have
had some difficulties compiling the Gromacs code obtained straight
from GIT. In particular, I encounter the following error:

~/gromacs/src/tools/gmx_membed.c:1095: error: expected declaration
specifiers or ‘...’ before ‘gmx_global_stat_t’

If you are curious to see the log and CMake cache files from the
build, I sent them in a previous email to the list (though the text of
the message somehow got scrubbed). I could also just patch the
relevant parts of version 4.5.1 and test that out. If this would be
feasible, then what specific lines should I modify?

-Kevin

> Date: Thu, 9 Sep 2010 17:19:36 +0200
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] Overflow problem with test-particle insertion
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <COL113-W1513821AC701A1763B351B8E730 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> 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
>