[gmx-users] specify node number in parallel simulation

[Itamar Kass]

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

132.64.65.123 user1
132.64.65.123 user1

to run lammpi write

 >lammpi -v bhost.def


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

* 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!
>
>Lianqing
>
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