[gmx-users] Problem about thread based MPI in Gromacs-4.5.1

[Szilárd Páll]

Hi,

> But when use "mdrun -h", the -nt does not exist.
> So can the -nt option be used in mdrun?

Just checked and If you have threads turned on (!) when building
gromacs then on the help page (mdrun -h) -nt does show up! Otherwise,
it's easy to check if you have thread-enabled build or not: just start
mdrun on a multicore node and see if it uses one thread or all threads
;)

> And if can, how do I use thread based MPI in mdrun?
> Can someone show me an mdrun execution example, please?

As already the information quoted by you underlines, threading is
useful _only_ for multicore parallelism. However, it is not possible
to combine threading and MPI at the moment, if that's what you mean by
"thread based MPI". If you want to parallelize over multiple machines
you'll need to use MPI to parallelize over a single machine's cores as
well.

I hope this helps!

Cheers,
--
Szilárd