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

Berk Hess gmx3 at hotmail.com
Tue Dec 16 14:04:21 CET 2008 

Hi,

You can do something like:
 mpirun -np 4 xterm -e gdb ~/check_gmx/obj/g_x86_64/src/kernel/mdrun

with the appropriate settings for your system.

You will have to type run in every xterm to make mdrun run.
Or you can make some scripts
(gdb -x gdb_cmds will read the gdb commands from the file gdb_cmds).

When you think it hangs, type ctrl-c in an xterm
and type where to see where it hangs.
I would guess this would be in an MPI call.

Berk


> Date: Mon, 15 Dec 2008 23:53:45 +0100
> From: patrick.fuchs at univ-paris-diderot.fr
> To: gmx-users at gromacs.org
> Subject: Re: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
> 
> 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.fuchs at univ-paris-diderot.fr
> >  > To: gmx-users at 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.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
> >  > > >
> >  > > >
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> -- 
> _________________________________________________________________
> !!!! 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
> 
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