[gmx-users] SMP/Parallel mdrun

[Mark Abraham]

Ian Stokes-Rees wrote:
> I am a computational scientist working with a physical chemist to try to 
> parallelize her use of gromacs -- today is my first day using the 
> application and I am not succeeding in getting multiple threads.

Terminology - GROMACS is not threaded, but uses MPI processes for 
parallelism.

> I have an MPI-compiled version of gromacs v4.0 and am attempting to get 
> parallel execution on a 2x2 core AMD Opteron system via:
> 
> $ lamboot
> $ mdrun -np 4 -s ../1WOM.tpr -v -N 4

-N does nothing, and -np is no longer accepted - as you'd know from 
reading mdrun -h, right?

Like most MPI parallel codes, you need to use mpirun. If your lam 
environment is correctly configured, then I think you will not need -np 
4 as an argument to mpirun.

Also, probably you are actually running a non-MPI gromacs, since by 
default, using --enable-mpi will suffix mdrun to be mdrun_mpi.

> however there is then only a single thread executing.  Do I need to 
> preprocess the topology file?

Not with gromacs 4.

Mark