[gmx-users] when grompp and mdrun disagree about processor numbers

[David van der Spoel]

On Fri, 2004-07-09 at 13:42, fabio affinito wrote:
> Hi...
> When I submit a job on my Linux Beowulf cluster (with PBS), I receive 
> this error message:
> 
> 
> Fatal error: run input file 2_4_topol.tpr was made for 4 nodes,
>               while mdrun_mpi expected it to be for 1 nodes.
> 
> 
> and the job is killed...
> 
> I use this script to submit the job:
> 
> [I cut the PBS instructions]
> grompp_mpi -np 4 -f 2_4_cav300pr.mdp -po mdout300pr.mdp -c 
> 2_4_cav_ini.gro -r 2_4_cav_out.gro -n 2_4_cav.ndx -p 2_4_cav.top -o 
> 2_4_topol.tpr
> mdrun_mpi -np 4 -s 2_4_topol.tpr -o traiettorie.trr -x traj300.xtc -c 
> 2_4_cav_out.gro -e energy.edr -g Sim.log
> 

mpirun -np 4 mdrun_mpi

> What am I doing wrong!?!
> 
> Bye
> 
> Fabio
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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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