[gmx-users] MPIRUN error while running position restrained MD

[Tsjerk Wassenaar]

Hi Ragu,

The tail of the .log file is not very informative here. Please try to
find in the log where it first went wrong. It may well start out with
a LINCS warning.
Besides, please be more specific in what you're trying to simulate,
and what protocol you used.

Cheers,

Tsjerk

On 1/19/07, Ragothaman Yennamalli <ymr79in at yahoo.co.in> wrote:
> Hi,
> This is the tail of the .log file
> new box (3x3):
>    new box[    0]={-4.13207e+15,  0.00000e+00,
> -0.00000e+00}
>    new box[    1]={ 0.00000e+00, -5.17576e+15,
> -0.00000e+00}
>    new box[    2]={ 0.00000e+00,  1.51116e+23,
> -1.14219e+16}
> Correcting invalid box:
> old box (3x3):
>    old box[    0]={-4.13207e+15,  0.00000e+00,
> -0.00000e+00}
>    old box[    1]={ 0.00000e+00, -5.17576e+15,
> -0.00000e+00}
>    old box[    2]={ 0.00000e+00,  1.51116e+23,
> -1.14219e+16}
> THe log files have generated as huge files (approx
> 20GB) which have used all the disk space.
> Raghu
> --- Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
> > Ragothaman Yennamalli wrote:
> > > Dear all,
> > > I am running gromacs3.2 version. When I am running
> > the
> > > position restraint md for the protein, the process
> > > stops within 100 steps with the following error:
> > >
> >
> -----------------------------------------------------------------------------
> > > One of the processes started by mpirun has exited
> > with
> > >       nonzero exit
> > > code.  This typically indicates that the process
> > > finished in error.
> > > If your process did not finish in error, be sure
> > to
> > > include a "return
> > > 0" or "exit(0)" in your C code before exiting the
> > > application.
> > >
> > > PID 16200 failed on node n0 (10.10.0.8) due to
> > signal
> > > 9.
> > >
> >
> -----------------------------------------------------------------------------
> > >
> > > I searched the mailing list and google and
> > understood
> > > that the pressure coupling parameter "tau_p" value
> > in
> > > the .mdp file has to be more than 1.0 and I did
> > the
> > > same.
> >
> > This is likely irrelevant. What do the ends of the
> > .log files say?
> >
> > Mark
> > _______________________________________________
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>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623