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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jan 22 20:52:27 CET 2007


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



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