Subject: Re: Re: [gmx-users] Gromacs 4 bug?

[patrick fuchs]

Hi,
I have exactly the same problem under Fedora 9 on a dual-quadricore 
(Intel Xeon E5430, 2.66 GHz) computer. Gromacs-4.0.2 is hanging (same 
for gromacs-4.0.0) after a couple of minutes of simulation. Sometimes, 
it even hangs very quickly before the simulation reaches the writing of 
the first checkpoint file (in fact the time length before the hang 
occurs is chaotic, sometimes a couple of minutes, or a few seconds). The 
CPUs are still loaded but nothing goes to the output (on any file log, 
xtc, trr, edr...). All gromacs binaries were standardly compiled with 
--enable-mpi and the latest lam-7.1.4. As Bernhard and Antoine I don't 
see anything strange in the log file.
I have another computer single quadricore (Intel Xeon E5430, 2.66 GHz) 
under Fedora 8 and the same system (same mdp, topology etc...) is 
running fine with gromacs-4.0.2 (compiled with lam-7.1.4 as well). So 
would it be possible that there's something wrong going on with FC9 and 
lam-7.1.4...?
Cheers,

Patrick

Berk Hess a écrit :
> Hi,
> 
> If your simulations no longer produce output, but still run
> and there is no error or warning message,
> my guess would be that they are waiting for MPI communication.
> But the developers any many users are using 4.0 and I have
> not heard from problems like this, so I wonder if the problem
> could be somewhere else.
> 
> Could you (or have your tried to) continue your simulation
> from the last checkpoint (mdrun option -cpi) before the hang,
> to see if it crashes quickly then?
> 
> Berk
> 
>  > Date: Fri, 12 Dec 2008 13:42:43 +0100
>  > From: bernhard.knapp at meduniwien.ac.at
>  > To: gmx-users at gromacs.org
>  > Subject: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
>  >
>  > Mark wrote:
>  >
>  > > What's happening in the log files? What's the latest information in 
> the
>  > > checkpoint files? Could there be some issue with file system 
> availability?
>  >
>  > Hi Mark
>  >
>  > Unfortunaltey I already deleted the simulation files which got stuck
>  > after 847ps. But here is the output of another simulation done on the
>  > same system but with an other pdb file. This one gets stuck after 179ps
>  > with the following output:
>  >
>  > The latest thing the checkpoint file says is:
>  >
>  > "imb F 3% step 89700, will finish Wed Jul 1 09:11:00 2009
>  > imb F 3% step 89800, will finish Wed Jul 1 09:02:51 2009"
>  >
>  > The predcition for 1st of July is not surprising since I am always
>  > parameterizing the simulation with 200ns to avoid to restart it if
>  > something interesting happens in the last frames.
>  >
>  > for the .log file it is:
>  >
>  > "Writing checkpoint, step 88000 at Thu Dec 11 16:34:31 2008
>  >
>  > Energies (kJ/mol)
>  > G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
>  > 7.83753e+03 3.64068e+03 2.45951e+03 1.29167e+03 5.13688e+04
>  > LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
>  > 3.82346e+05 -2.48883e+06 -3.51313e+05 -2.39119e+06 4.57648e+05
>  > Total Energy Temperature Pressure (bar) Cons. rmsd ()
>  > -1.93355e+06 3.10014e+02 1.09267e-01 2.14030e-05
>  >
>  > DD step 88999 load imb.: force 3.1%
>  >
>  > Step Time Lambda
>  > 89000 178.00002 0.00000
>  >
>  > Energies (kJ/mol)
>  > G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14
>  > 8.03089e+03 3.59681e+03 2.42628e+03 1.20942e+03 5.12341e+04
>  > LJ (SR) Coulomb (SR) Coul. recip. Potential Kinetic En.
>  > 3.81539e+05 -2.48602e+06 -3.51307e+05 -2.38929e+06 4.56901e+05
>  > Total Energy Temperature Pressure (bar) Cons. rmsd ()
>  > -1.93239e+06 3.09508e+02 1.64627e+01 2.08518e-05"
>  >
>  >
>  > the disk is also free df -h says 2.3G out of 666G used.
>  >
>  > The only difference between the system with gromacs 3.3 and gromacs 4 is
>  > that gromacs 4 is running under suse 11 while gromacs 3.3 is running on
>  > a node with suse 10. But I dont think this can be the problem?
>  >
>  > cheers
>  > Bernhard
>  >
>  >
>  > _______________________________________________
>  > gmx-users mailing list gmx-users at gromacs.org
>  > http://www.gromacs.org/mailman/listinfo/gmx-users
>  > Please search the archive at http://www.gromacs.org/search before 
> posting!
>  > Please don't post (un)subscribe requests to the list. Use the
>  > www interface or send it to gmx-users-request at gromacs.org.
>  > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> ------------------------------------------------------------------------
> Express yourself instantly with MSN Messenger! MSN Messenger 
> <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
_________________________________________________________________
!!!! new E-mail address: patrick.fuchs at univ-paris-diderot.fr !!!!
!!!! new postal address !!!
Patrick FUCHS
Equipe de Bioinformatique Genomique et Moleculaire
INTS, INSERM UMR-S726, Université Paris Diderot,
6 rue Alexandre Cabanel, 75015 Paris
Tel : +33 (0)1-44-49-30-57 - Fax : +33 (0)1-47-34-74-31
Web Site: http://www.dsimb.inserm.fr/~fuchs