[gmx-users] specify node number in parallel simulation

Lianqing Zheng lzheng at me.rochester.edu
Fri Nov 19 23:05:57 CET 2004

Dear GMX-pals,

We have a linux cluster (36 nodes and each node with duel CUP) and I'm
wondering how to do to let gromacs run on given nodes, say 21 to 24. I
tried the following commands:
grompp -f water.mdp -p water.top -c spc216.gro -o water.tpr -np 4

mpirun n21-24 /home/lzheng/gromacs-3.2.1/i686-pc-linux-gnu/bin/mdrun -s
water.tpr -o water.trr -c water_out.gro -v -g water.log -np 4

But it didn't work, giving an error like:

Fatal error: run input file water.tpr was made for 4 nodes,
             while mdrun expected it to be for 1 nodes.
[0] MPI Abort by user Aborting program !
[0] Aborting program!

How to solve this problem? Thank you very much!


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