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

Carsten Kutzner ckutzne at gwdg.de
Mon Jan 17 16:36:57 CET 2011


On Jan 17, 2011, at 4:11 PM, Arnau Cordomi wrote:

> 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 ?
You should use the number of logical cores you have. This is normally
the number of physical cores, unless you use some kind of hyperthreading
or simultaneous multiprocessing in which case -nt is twice the number
of physical cores. mdrun reads the number of threads from your system
via sysconf().


> Any advice will be welcome.
> Thanks in advance.
> Best Regards,
> Arnau
> Cordomí
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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