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

[Mark Abraham]

Anupam Nath Jha wrote:
> Dear all
> 
> i am new in gromacs. i have installed gromacs-3.3.3 in our cluster(mpi is
> already there) with parallel version (using the following command):
> 
> 
> make clean
> ./configure --enable-mpi --disable-nice --program-suffix="_mpi"
> make mdrun
> make install-mdrun
> 
> it went fine.
> 
> but when i ran the command -
> qsub pbs_submit
> 
> it's the pbs_submit file:
> 
> #This is a PBS script for Parallel Jobs
> #!/bin/bash -f
> #PBS -l nodes=2:ppn=2
> #PBS -o /home/anupam/MD/lyd
> #PBS -e /home/anupam/MD/lyd

These latter two should probably be file names, not directory names...

> #PBS -q default
> 
> cd /home/anupam/MD/lyd

... since this seems to be a directory? Check out the #PBS -wd option too...

> mpirun grompp -f em.mdp -p topol.top -c solvated.gro -np 4 -o em.tpr

grompp is not an MPI code, run it without mpirun

> mpirun mdrun_mpi -v -deffnm -np 4 em

Unless you have a PBS-customized install of mpirun, you should use 
"mpirun -np 4 mdrun_mpi -v deffnm em" since mdrun_mpi will pick up the 
four processors from the environment, but mpirun won't.

> but it's not doing anything,except writing this:
> 
> totalnum=3  numhosts=2
> there are not enough hosts on which to start all processes
> totalnum=3  numhosts=2
> there are not enough hosts on which to start all processes

First get grompp working interactively, then get grompp working in a 
script, (neither of which need MPI), and only then worry about mpirun 
-np 4 mdrun

Mark