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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>  > > > _________________________________________________________________
>  > > > !!!! 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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>  > --
>  > _________________________________________________________________
>  > !!!! 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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