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<body class='hmmessage'><div style="text-align: left;">Hi,<br><br>I have no clue what the problem could be.<br>But now I thought a bit longer, I realized that with domain decomposition<br>the ci error should never occur, since the domain decomposition<br>puts the charge groups inside the DD cells, so also inside the ns cells.<br>This seems to indicate that there is a bug somewhere.<br><br>We will need all the information we can get, so please file a bugzilla<br>and include the details on the machine, compiler,<br>attach the tpr file, log file and mdrun debug files.<br></div><br>Thanks,<br><br>Berk<br><br><hr id="stopSpelling">> Date: Wed, 15 Oct 2008 22:14:28 -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>> <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>> I have a situation now that, without fail, has crashed with the same issues I've <br>> described before while using "-dlb auto." Using "-dlb no" the run does not <br>> fail. The .tpr file has now produced that strange error three times, and I have <br>> run mdrun with the "-debug 1" flag. Would providing these .log files and .xvg <br>> files provide any useful information?<br>> <br>> I can also provide the .tpr file in a bugzilla, if that would be useful.<br>> <br>> Please let me know and I will upload whatever files you might need.<br>> <br>> -Justin<br>> <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 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>> > <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>> ========================================<br>> <br>> Justin A. Lemkul<br>> Graduate Research Assistant<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<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 /><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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