[gmx-users] specify node number in parallel simulation

Itamar Kass ikass at cc.huji.ac.il
Sat Nov 20 06:12:58 CET 2004

you have to create a file (bhost.def) which "tells" lammpi on which 
nodes you wish to run, e.g.: user1 user1

to run lammpi write

 >lammpi -v bhost.def

* You can run lammpi only from a computer which will be include in the 

* Each user might have only one lammpi process at a time (every lammpi 
process might run any number of subprocess).

Lianqing Zheng wrote:

>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!
>gmx-users mailing list
>gmx-users at gromacs.org
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