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 have attached them to this email. 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 <g...@hotmail.com> Subject: RE: [gmx-users] Overflow problem with test-particle insertion To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <COL113- w1513821ac701a1763b351b8e...@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: g...@hotmail.com To: gmx-users@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: kd...@princeton.edu To: gmx-users@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
build_output.tar.gz
Description: GNU Zip compressed data
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