[gmx-users] mdrun : fatal error with 8 CPUs

[David]

On Thu, 2003-10-30 at 11:33, sophie.vilarem at laposte.net wrote:
> Hi,
> 
> I've got a fatal error (Fatal error: ci = -2147483648 should
> be in 0 .. 1727 [FILE nsgrid.c, LINE 210]) when I try to run
> Gromacs on 8 CPUs, on a xeon cluster (bi-processors,
> MPICH-1.2.5). It ran without any problem on 1, 2 and 4 CPUs.
> Can anybody help me please?
> 
> Thanks a lot!
> Sophie Vilarem
> 
> 
> Here are the command line and the results :
> grompp -np 8 -shuffle
> mpirun -np 8 -machinefile hostfile
> /works/work6/theogone/Gromacs/usr/local/Gromacs/i686-pc-linux-gnu/bin/mdrun
> -g pc2_8
> 
> Parts of the results :
> etc....
> 
> 
> creating statusfile for 8 nodes...
>  
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 3 of the 3 non-bonded parameter combinations
> Excluding 3 bonded neighbours for PE6000 1
> Moltype    PE6000    #atoms
> CPU   0         1     12000
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
All your atoms are on CPU 0. You'll have to turn off constraints (and
reduce the timestep to 1 fs) for this to parallellize. That doesn't mean
it should crash when you do it anyway..



-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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