<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>I also fixed a problem with unitialized variables for pbc calculations in trilinic boxes.<br>But up till now I have not observed any effect of this bug.<br>Is your box triclinic?<br><br>Berk<br><br><br>> Date: Tue, 6 Jan 2009 17:08:57 +0100<br>> From: patrick.fuchs@univ-paris-diderot.fr<br>> To: gmx-users@gromacs.org<br>> Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?<br>> <br>> Hi Berk,<br>> no I don't have virtual sites so this might not be the cause of my problem.<br>> Ciao,<br>> <br>> Patrick<br>> <br>> Berk Hess a écrit :<br>> > Hi,<br>> > <br>> > I just fixed a bug with virtual sites that were a single charge group.<br>> > Do you have virtual sites in your system?<br>> > <br>> > Berk<br>> > <br>> > > Date: Wed, 17 Dec 2008 16:55:55 +0100<br>> > > From: patrick.fuchs@univ-paris-diderot.fr<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?<br>> > ><br>> > > Hi Berk,<br>> > > thanks for the trick. Unfortunately I'm not in my lab right now and<br>> > > can't open easily xterms over the network. I'll try to catch up once I'm<br>> > > back (end of December), unless Bernhard or Antoine find the solution.<br>> > > Cheers,<br>> > ><br>> > > Patrick<br>> > ><br>> > > Berk Hess a écrit :<br>> > > > Hi,<br>> > > ><br>> > > > You can do something like:<br>> > > > mpirun -np 4 xterm -e gdb ~/check_gmx/obj/g_x86_64/src/kernel/mdrun<br>> > > ><br>> > > > with the appropriate settings for your system.<br>> > > ><br>> > > > You will have to type run in every xterm to make mdrun run.<br>> > > > Or you can make some scripts<br>> > > > (gdb -x gdb_cmds will read the gdb commands from the file gdb_cmds).<br>> > > ><br>> > > > When you think it hangs, type ctrl-c in an xterm<br>> > > > and type where to see where it hangs.<br>> > > > I would guess this would be in an MPI call.<br>> > > ><br>> > > > Berk<br>> > > ><br>> > > ><br>> > > > > Date: Mon, 15 Dec 2008 23:53:45 +0100<br>> > > > > From: patrick.fuchs@univ-paris-diderot.fr<br>> > > > > To: gmx-users@gromacs.org<br>> > > > > Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?<br>> > > > ><br>> > > > > Hi Berk,<br>> > > > > I used gcc version 4.3.0 20080428 (Red Hat 4.3.0-8) (GCC).<br>> > > > > I recompiled it with CFLAGS=-g and it still hangs...<br>> > > > > Now, how can we run it in the debugger ?<br>> > > > > Thanks,<br>> > > > ><br>> > > > > Patrick<br>> > > > ><br>> > > > > Berk Hess a écrit :<br>> > > > > > Hi,<br>> > > > > ><br>> > > > > > What compiler (and compiler version) are you using?<br>> > > > > ><br>> > > > > > Could you configure with CFLAGS=-g<br>> > > > > > and see if it still hangs?<br>> > > > > > If it also hangs in that case, we can run it in the debugger<br>> > > > > > and find out where it hangs.<br>> > > > > ><br>> > > > > > Berk<br>> > > > > ><br>> > > > > > > Date: Mon, 15 Dec 2008 16:32:31 +0100<br>> > > > > > > From: patrick.fuchs@univ-paris-diderot.fr<br>> > > > > > > To: gmx-users@gromacs.org<br>> > > > > > > Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?<br>> > > > > > ><br>> > > > > > > Hi,<br>> > > > > > > I have exactly the same problem under Fedora 9 on a <br>> > dual-quadricore<br>> > > > > > > (Intel Xeon E5430, 2.66 GHz) computer. Gromacs-4.0.2 is <br>> > hanging (same<br>> > > > > > > for gromacs-4.0.0) after a couple of minutes of simulation.<br>> > > > Sometimes,<br>> > > > > > > it even hangs very quickly before the simulation reaches the<br>> > > > writing of<br>> > > > > > > the first checkpoint file (in fact the time length before the <br>> > hang<br>> > > > > > > occurs is chaotic, sometimes a couple of minutes, or a few<br>> > > > seconds). The<br>> > > > > > > CPUs are still loaded but nothing goes to the output (on any <br>> > file<br>> > > > log,<br>> > > > > > > xtc, trr, edr...). All gromacs binaries were standardly <br>> > compiled with<br>> > > > > > > --enable-mpi and the latest lam-7.1.4. As Bernhard and Antoine I<br>> > > > don't<br>> > > > > > > see anything strange in the log file.<br>> > > > > > > I have another computer single quadricore (Intel Xeon E5430, <br>> > 2.66<br>> > > > GHz)<br>> > > > > > > under Fedora 8 and the same system (same mdp, topology etc...) is<br>> > > > > > > running fine with gromacs-4.0.2 (compiled with lam-7.1.4 as <br>> > well). So<br>> > > > > > > would it be possible that there's something wrong going on with<br>> > > > FC9 and<br>> > > > > > > lam-7.1.4...?<br>> > > > > > > Cheers,<br>> > > > > > ><br>> > > > > > > Patrick<br>> > > > > > ><br>> > > > > > > Berk Hess a écrit :<br>> > > > > > > > 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<br>> > > > > > information in<br>> > > > > > > > the<br>> > > > > > > > > > checkpoint files? Could there be some issue with file <br>> > system<br>> > > > > > > > availability?<br>> > > > > > > > ><br>> > > > > > > > > Hi Mark<br>> > > > > > > > ><br>> > > > > > > > > Unfortunaltey I already deleted the simulation files which<br>> > > > got stuck<br>> > > > > > > > > after 847ps. But here is the output of another simulation<br>> > > > done on the<br>> > > > > > > > > same system but with an other pdb file. This one gets stuck<br>> > > > after<br>> > > > > > 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<br>> > > > always<br>> > > > > > > > > parameterizing the simulation with 200ns to avoid to restart<br>> > > > 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 <br>> > 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 <br>> > 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<br>> > > > > > gromacs 4 is<br>> > > > > > > > > that gromacs 4 is running under suse 11 while gromacs 3.3 is<br>> > > > > > running on<br>> > > > > > > > > a node with suse 10. But I dont think this can be the <br>> > 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 <br>> > http://www.gromacs.org/search before<br>> > > > > > > > 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 <br>> > http://www.gromacs.org/mailing_lists/users.php<br>> > > > > > > ><br>> > > > > > > ><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>> > ------------------------------------------------------------------------<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 <br>> > before<br>> > > > > > 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>> > > > > > > !!!! new E-mail address: patrick.fuchs@univ-paris-diderot.fr !!!!<br>> > > > > > > !!!! new postal address !!!<br>> > > > > > > Patrick FUCHS<br>> > > > > > > Equipe de Bioinformatique Genomique et Moleculaire<br>> > > > > > > INTS, INSERM UMR-S726, Université Paris Diderot,<br>> > > > > > > 6 rue Alexandre Cabanel, 75015 Paris<br>> > > > > > > Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31<br>> > > > > > > Web Site: http://www.dsimb.inserm.fr/~fuchs<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<br>> > > > > > 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>> > > > > > Express yourself instantly with MSN Messenger! MSN Messenger<br>> > > > > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > > > > ><br>> > > > > ><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<br>> > > > 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>> > > > > !!!! new E-mail address: patrick.fuchs@univ-paris-diderot.fr !!!!<br>> > > > > !!!! new postal address !!!<br>> > > > > Patrick FUCHS<br>> > > > > Equipe de Bioinformatique Genomique et Moleculaire<br>> > > > > INTS, INSERM UMR-S726, Université Paris Diderot,<br>> > > > > 6 rue Alexandre Cabanel, 75015 Paris<br>> > > > > Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31<br>> > > > > Web Site: http://www.dsimb.inserm.fr/~fuchs<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<br>> > > > 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>> > > > Express yourself instantly with MSN Messenger! MSN Messenger<br>> > > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/><br>> > > ><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 <br>> > 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>> > > !!!! new E-mail address: patrick.fuchs@univ-paris-diderot.fr !!!!<br>> > > !!!! new postal address !!!<br>> > > Patrick FUCHS<br>> > > Equipe de Bioinformatique Genomique et Moleculaire<br>> > > INTS, INSERM UMR-S726, Université Paris Diderot,<br>> > > 6 rue Alexandre Cabanel, 75015 Paris<br>> > > Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31<br>> > > Web Site: http://www.dsimb.inserm.fr/~fuchs<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 <br>> > 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>> > 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>> !!!! new E-mail address: patrick.fuchs@univ-paris-diderot.fr !!!!<br>> !!!! new postal address !!!<br>> Patrick FUCHS<br>> Equipe de Bioinformatique Genomique et Moleculaire<br>> INTS, INSERM UMR-S726, Université Paris Diderot,<br>> 6 rue Alexandre Cabanel, 75015 Paris<br>> Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31<br>> Web Site: http://www.dsimb.inserm.fr/~fuchs<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>