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

fabio affinito fabio.affinito at tiscali.it
Fri Jul 9 13:42:08 CEST 2004

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 
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

What am I doing wrong!?!



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