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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>That issue in 3.3.1 is completely unrelated to this issue in 4.0.<br><br>Was your problem in 3.3.1 with parrinello-rahman coupling?<br>If so, that problem is probably solved by a bug fix in the PR pressure coupling<br>I introduced in the 4.0 release.<br><br>Berk<br></div><br><br><hr id="stopSpelling">> Date: Thu, 16 Oct 2008 14:06:19 +0200<br>> From: till@bph.rub.de<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Unexplained crashes with Gromacs-4.0<br>> <br>> Hi,<br>> <br>> I think I had a similar error in GROMACS 3.3.1 (I posted it in June to <br>> the User List <br>> http://www.gromacs.org/pipermail/gmx-users/2008-June/034411.html). I <br>> also got a not reproducable error for the ci variable.<br>> <br>> I made some test and found out that for my system the error occures with <br>> semiisotropic pressure coupling and not with isotropic pressure <br>> coupling. Another way to avoid the error with semiisotropic pressure <br>> coupling was to change from double to single precision. By the way <br>> setting tau_p to 5 fs just shifts the error to a later time step. May <br>> be the mistake has something to do with the pressure coupling?<br>> <br>> Till<br>> <br>> <br>> Berk Hess wrote:<br>> ><br>> ><br>> ><br>> ><br>> > ------------------------------------------------------------------------<br>> > > Date: Tue, 14 Oct 2008 07:19:45 -0400<br>> > > From: jalemkul@vt.edu<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] Unexplained crashes with Gromacs-4.0<br>> > ><br>> > ><br>> > ><br>> > > Berk Hess wrote:<br>> > > > Hi,<br>> > > ><br>> > > > I don't really know what could be the problem here.<br>> > > ><br>> > > > 0..180 is (confusingly) not including the end, so 180 is out of range.<br>> > > ><br>> > > > The only thing I can think of (except for unknown bugs of coarse),<br>> > > > is that I corrected the coupling time of the Parrinello-Rahman <br>> > barostat<br>> > > > when going from 4.0 RC4 to the official 4.0 release.<br>> > > > I guess all your old simulations were with older Gromacs releases.<br>> > > > So to get the same coupling as before, so would need to multiply <br>> > tau_t<br>> > > > by 16.6.<br>> > > > I don't know if this would help.<br>> > ><br>> > > I did see this same error under RC2, but noticed that you fixed this <br>> > bug shortly<br>> > > after I saw it, and that's what I assumed it was. But now I have <br>> > seen it under<br>> > > the official 4.0 release.<br>> > ><br>> > > ><br>> > > > You did not get pressure coupling warnings before the crash?<br>> > > ><br>> > ><br>> > > There are no messages printed before this error pops up. What's really<br>> > > confusing is that if I simply try the same .tpr file again, it runs <br>> > without a<br>> > > problem. I know that's not terribly scientific, but it seemed odd to <br>> > me that my<br>> > > systems running for 40+ ns suddenly had a problem.<br>> > ><br>> > > Is there any diagnostic information I can provide? This problem <br>> > seems like it<br>> > > would be elusive, since even I can't fully reproduce it.<br>> > ><br>> > > -Justin<br>> ><br>> > If you run in parallel, the dynamic load balancing can affective <br>> > reprodibility.<br>> > You can turn it off with -dlb no<br>> ><br>> > Another source of non-reproducibility is FFTW (with PME).<br>> > By default FFTW times which of different codes is the fastest and uses <br>> > that.<br>> > Configuring FFTW with SSE makes all codes faster and the differences <br>> > smaller,<br>> > so you can configure Gromacs with --disable-fftw-measure to remove<br>> > the run time optimization without performance loss.<br>> > For debugging purposes the new -reprod switch of mdrun will try to turn<br>> > off all optimizations which might affect reproducibilty.<br>> ><br>> > Berk<br>> ><br>> ><br>> > ------------------------------------------------------------------------<br>> > Express yourself instantly with MSN Messenger! MSN Messenger <br>> > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > ------------------------------------------------------------------------<br>> ><br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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