Subject: Re: Re: [gmx-users] Gromacs 4 bug?
patrick fuchs
patrick.fuchs at univ-paris-diderot.fr
Tue Jan 6 18:37:20 CET 2009
Hi,
> I also fixed a problem with unitialized variables for pbc calculations
> in trilinic boxes.
> But up till now I have not observed any effect of this bug.
> Is your box triclinic?
Yes it is. So shall I test your corrected version ?
Patrick
>
> Berk
>
>
> > Date: Tue, 6 Jan 2009 17:08:57 +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,
> > no I don't have virtual sites so this might not be the cause of my
> problem.
> > Ciao,
> >
> > Patrick
> >
> > Berk Hess a écrit :
> > > Hi,
> > >
> > > I just fixed a bug with virtual sites that were a single charge group.
> > > Do you have virtual sites in your system?
> > >
> > > Berk
> > >
> > > > Date: Wed, 17 Dec 2008 16:55:55 +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,
> > > > 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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> _________________________________________________________________
> > > > > > > > !!!! 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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> > > > > > --
> > > > > > _________________________________________________________________
> > > > > > !!!! 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
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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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> > --
> > _________________________________________________________________
> > !!!! 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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_________________________________________________________________
!!!! 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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