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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
