Hi Berk,
I used gcc version 4.3.0 20080428 (Red Hat 4.3.0-8) (GCC).
I recompiled it with CFLAGS=-g and it still hangs...
Now, how can we run it in the debugger ?
Thanks,

Patrick

Berk Hess a écrit :
Hi,

What compiler (and compiler version) are you using?

Could you configure with CFLAGS=-g
and see if it still hangs?
If it also hangs in that case, we can run it in the debugger
and find out where it hangs.

Berk

 > Date: Mon, 15 Dec 2008 16:32:31 +0100
 > From: patrick.fu...@univ-paris-diderot.fr
 > To: gmx-users@gromacs.org
 > Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
 >
 > 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.kn...@meduniwien.ac.at
 > > > To: gmx-users@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
 > > >
 > > >
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