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

[Ragothaman Yennamalli]

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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