[gmx-users] how to run parallel jobs in gromacs

[Mark Abraham]

Anupam Nath Jha wrote:
> Now i am using this much only:
> 
> #This is a PBS script for Parallel Jobs
> #!/bin/bash -f
> #PBS -o /home/anupam/MD/lyd
> #PBS -e /home/anupam/MD/lyd
> #PBS -q default
> 
> cd /home/anupam/MD/lyd
> 
> mpirun -np 4 /usr/local/gromacs/bin/mdrun_mpi -v -deffnm em
> 
> but still it's giving this error:
> totalnum=2  numhosts=1
> there are not enough hosts on which to start all processes

Why are you doing this? You've left alone the #PBS lines I thought might 
be producing a problem, and taken away the one where you tell the 
queueing system what processor topology you want. How is this ever going 
to work?

In any case, this problem has nothing to do with GROMACS, and everything 
to do with how your machine and PBS are configured. Please consult your 
system administrator.

Mark