<html>
<head>
<style>
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
</style>
</head>
<body class='hmmessage'>
Hi,<br><br>If your simulations no longer produce output, but still run<br>and there is no error or warning message,<br>my guess would be that they are waiting for MPI communication.<br>But the developers any many users are using 4.0 and I have<br>not heard from problems like this, so I wonder if the problem<br>could be somewhere else.<br><br>Could you (or have your tried to) continue your simulation<br>from the last checkpoint (mdrun option -cpi) before the hang,<br>to see if it crashes quickly then?<br><br>Berk<br><br>> Date: Fri, 12 Dec 2008 13:42:43 +0100<br>> From: bernhard.knapp@meduniwien.ac.at<br>> To: gmx-users@gromacs.org<br>> Subject: Subject: Re: Re: [gmx-users] Gromacs 4 bug?<br>> <br>> Mark wrote:<br>> <br>> > What's happening in the log files? What's the latest information in the <br>> > checkpoint files? Could there be some issue with file system availability?<br>> <br>> Hi Mark<br>> <br>> Unfortunaltey I already deleted the simulation files which got stuck <br>> after 847ps. But here is the output of another simulation done on the <br>> same system but with an other pdb file. This one gets stuck after 179ps <br>> with the following output:<br>> <br>> The latest thing the checkpoint file says is:<br>> <br>> "imb F 3% step 89700, will finish Wed Jul 1 09:11:00 2009<br>> imb F 3% step 89800, will finish Wed Jul 1 09:02:51 2009"<br>> <br>> The predcition for 1st of July is not surprising since I am always <br>> parameterizing the simulation with 200ns to avoid to restart it if <br>> something interesting happens in the last frames.<br>> <br>> for the .log file it is:<br>> <br>> "Writing checkpoint, step 88000 at Thu Dec 11 16:34:31 2008<br>> <br>> Energies (kJ/mol)<br>> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<br>> 7.83753e+03 3.64068e+03 2.45951e+03 1.29167e+03 5.13688e+04<br>> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.<br>> 3.82346e+05 -2.48883e+06 -3.51313e+05 -2.39119e+06 4.57648e+05<br>> Total Energy Temperature Pressure (bar) Cons. rmsd ()<br>> -1.93355e+06 3.10014e+02 1.09267e-01 2.14030e-05<br>> <br>> DD step 88999 load imb.: force 3.1%<br>> <br>> Step Time Lambda<br>> 89000 178.00002 0.00000<br>> <br>> Energies (kJ/mol)<br>> G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14<br>> 8.03089e+03 3.59681e+03 2.42628e+03 1.20942e+03 5.12341e+04<br>> LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.<br>> 3.81539e+05 -2.48602e+06 -3.51307e+05 -2.38929e+06 4.56901e+05<br>> Total Energy Temperature Pressure (bar) Cons. rmsd ()<br>> -1.93239e+06 3.09508e+02 1.64627e+01 2.08518e-05"<br>> <br>> <br>> the disk is also free df -h says 2.3G out of 666G used.<br>> <br>> The only difference between the system with gromacs 3.3 and gromacs 4 is <br>> that gromacs 4 is running under suse 11 while gromacs 3.3 is running on <br>> a node with suse 10. But I dont think this can be the problem?<br>> <br>> cheers<br>> Bernhard<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>
</html>