[gmx-users] gromacs 4.5.3 with threads instead of MPI

Arnau Cordomi arnau.cordomi at uab.cat
Mon Jan 17 16:11:58 CET 2011

Dear Gromacs Users,

We normally run gromacs 4.0.x mdrun with OpenMPI in a 24 core
shared-memory server (SunFire X4450).
i. e. the command we use for a 12 core run is : mpirun -np 12 mdrun -v
-c output_md.gro
This is working great so far.

Now we are trying to use  gromacs 4.5.x and I found this on the
release notes (http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.5.x)

“Running on a multi-core node now uses thread-based parallelization to
automatically spawn the optimum number of threads in the default
build. MPI is now only required for parallelization over the network.”

So, I guess now instead of “mpirun -np 12 mdrun -v -c output_md.gro”
we should use “mdrun -nt 12 -v -c output_md.gro” and expect the same
performance. Am I right?

Also, is this “automatically spawn the optimum number of threads”
reliable ? Does that mean that if the recommended number is 4 cores
(threads) there’s no way to make it run faster even if specifying -nt
12 or 24 ?

Any advice will be welcome.
Thanks in advance.

Best Regards,


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