[gmx-users] SMP/Parallel mdrun
Mark.Abraham at anu.edu.au
Thu Nov 27 03:21:27 CET 2008
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
> 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.
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