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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 dual-quadricore <br>> (Intel Xeon E5430, 2.66 GHz) computer. Gromacs-4.0.2 is hanging (same <br>> for gromacs-4.0.0) after a couple of minutes of simulation. Sometimes, <br>> it even hangs very quickly before the simulation reaches the writing of <br>> the first checkpoint file (in fact the time length before the hang <br>> occurs is chaotic, sometimes a couple of minutes, or a few seconds). The <br>> CPUs are still loaded but nothing goes to the output (on any file log, <br>> xtc, trr, edr...). All gromacs binaries were standardly compiled with <br>> --enable-mpi and the latest lam-7.1.4. As Bernhard and Antoine I don't <br>> see anything strange in the log file.<br>> I have another computer single quadricore (Intel Xeon E5430, 2.66 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 well). So <br>> would it be possible that there's something wrong going on with 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 information in <br>> > the<br>> > > > checkpoint files? Could there be some issue with file system <br>> > 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 <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>> _______________________________________________<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? 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