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

[Berk Hess]

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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