Subject: Re: Re: [gmx-users] Gromacs 4 bug?
patrick fuchs
patrick.fuchs at univ-paris-diderot.fr
Wed Dec 17 16:55:55 CET 2008
Hi Berk,
thanks for the trick. Unfortunately I'm not in my lab right now and
can't open easily xterms over the network. I'll try to catch up once I'm
back (end of December), unless Bernhard or Antoine find the solution.
Cheers,
Patrick
Berk Hess a écrit :
> 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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> > > > >
> > >
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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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> > > _______________________________________________
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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
> >
> > _______________________________________________
> > 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!
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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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