[gmx-users] Re: Help regarding Gromac installation with MPI

[Anton Feenstra]

sachin hegde wrote:
> Hey Anton,
> I am treying to run the Gromacs benchmark with ammasso 110o according
> to this doc :http://www.ammasso.com/tt_gromacs.pdf
> and am stuck at the last step, that is at the mpirun command. I was able to
> do
> 
> grompp -f cutoff.mdp
> -c conf.gro -p topol.top -po mdout.mdp -shuffle -sort -np 4
> 
> The next step is to run mpirun
> mpirun -np 4 ~/gromacs/g321/x86_64-unknown-linux-gnu/bin/mdrun -s topol.tpr
> -o traj.trr -c confout.gro -e ener.edr -g md.lot -np 4
> 
> This step doesnt seem to work as it says that the file or command was
> not found. I am pointing them to the correct paths, but dont know why
> its not recognizing it.

With some mpi installations, it happens that the command (in this case 
mdrun) is executed in the binary directory (~/gromacs/g321/...), which 
is not where your input files are. A solution that I use, is to make a 
link from the mdrun binary (~/gromacs/g321/.../mdrun) to the current 
directory (i.e., where your topol.tpr is), and then use 'mpirun -np 4 
./mdrun -s topol.tpr'.

Hope this helps. Also try you question(s) at the gromacs user list!


-- 
Groetjes,

Anton

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