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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