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Hi,<br><br>You should use the release-4-5-patches branch.<br>After git clone do:<br><pre wrap="">git branch --track release-4-5-patches origin/release-4-5-patches<br>git checkout release-4-5-patches<br><br>Berk<br></pre>> Date: Thu, 9 Sep 2010 19:38:00 -0400<br>> From: kdaly@princeton.edu<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Overflow problem with test-particle insertion<br>> <br>> Hi,<br>> <br>> Thank you for taking the time to fix the issue. I would be very<br>> interested in testing out the modified code, but unfortunately I have<br>> had some difficulties compiling the Gromacs code obtained straight<br>> from GIT. In particular, I encounter the following error:<br>> <br>> ~/gromacs/src/tools/gmx_membed.c:1095: error: expected declaration<br>> specifiers or ‘...’ before ‘gmx_global_stat_t’<br>> <br>> If you are curious to see the log and CMake cache files from the<br>> build, I sent them in a previous email to the list (though the text of<br>> the message somehow got scrubbed). I could also just patch the<br>> relevant parts of version 4.5.1 and test that out. If this would be<br>> feasible, then what specific lines should I modify?<br>> <br>> -Kevin<br>> <br>> > Date: Thu, 9 Sep 2010 17:19:36 +0200<br>> > From: Berk Hess <gmx3@hotmail.com><br>> > Subject: RE: [gmx-users] Overflow problem with test-particle insertion<br>> > To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> > Message-ID: <COL113-W1513821AC701A1763B351B8E730@phx.gbl><br>> > Content-Type: text/plain; charset="iso-8859-1"<br>> ><br>> ><br>> > Hi,<br>> ><br>> > I realized now that this is an SSE issue.<br>> > Normally you would get NAN (or is it INF?). That is treated correctly in the GROMACS TPI code.<br>> > But in SSE a float "wraps around" when it overflows, which could, in very few cases, lead to a reasonably<br>> > looking energy value (I check for very high and very low values).<br>> > I found that you can check for overflows in SSE and committed a fix for 4.5.2.<br>> > I also filled the first 10 points (up to r=0.02 nm) of the potential/force tables, these used to be zero.<br>> > These values are only relevant for energy minimization or TPI with extreme atomic overlap.<br>> ><br>> > Berk<br>> ><br>> > From: gmx3@hotmail.com<br>> > To: gmx-users@gromacs.org<br>> > Subject: RE: [gmx-users] Overflow problem with test-particle insertion<br>> > Date: Thu, 9 Sep 2010 09:39:42 +0200<br>> ><br>> ><br>> ><br>> ><br>> ><br>> ><br>> ><br>> ><br>> > Hi,<br>> ><br>> > This is an interesting issue.<br>> > The chance is quite small that this happens, but maybe not negligible.<br>> > In single precision the maximum a float can store is 2^127.<br>> > This gives a minimum distance of (2^127)^-1/12 = 6.5e-4 nm.<br>> > The chance of inserting a particle within this radius is dens*3e-10,<br>> > where dens is the number of particles per nm^3.<br>> > A typical density of LJ particles is 30 per nm^3, which leads to a chance of 1e-8.<br>> > Such insertion numbers can be reached, so we probably have to worry about this.<br>> ><br>> > However, in your example the distance seems to be around 4e-3, which would<br>> > give r^-12 = 6e28. This still fits in a float and should not cause problems.<br>> > So we should make sure we understand what's going on here.<br>> > Could you file a bugzilla with the files to reproduce this and which insertion<br>> > is the problematic one?<br>> ><br>> > I so two possible solutions:<br>> > Force tabulated potentials with TPI, this can currently be achieved by setting<br>> > the environment variable GMX_FORCE_TABLES<br>> > Or require double precision.<br>> > But I think both solutions would lead to about 40% lower performance.<br>> ><br>> > Berk<br>> ><br>> ><br>> > Date: Wed, 8 Sep 2010 21:16:46 -0400<br>> > From: kdaly@princeton.edu<br>> > To: gmx-users@gromacs.org<br>> > Subject: [gmx-users] Overflow problem with test-particle insertion<br>> ><br>> > Hello Gromacs users,<br>> ><br>> > 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.<br>> ><br>> ><br>> > 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?<br>> ><br>> > -Kevin<br>> ><br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br>                                            </body>
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