[gmx-users] MPI runs on a local computer

[Carsten Kutzner]

Hi Jianqing,

On Sep 19, 2013, at 2:48 PM, "Xu, Jianqing" <xuj at MedImmune.com> wrote:
> Say I have a local desktop having 16 cores. If I just want to run jobs on one computer or a single node (but multiple cores), I understand that I don't have to install and use OpenMPI, as Gromacs has its own thread-MPI included already and it should be good enough to run jobs on one machine. However, for some reasons, OpenMPI has already been installed on my machine, and I compiled Gromacs with it by using the flag: "-DGMX_MPI=ON". My questions are:
> 
> 
> 1.       Can I still use this executable (mdrun_mpi, built with OpenMPI library) to run multi-core jobs on my local desktop? Or the default Thread-MPI is actually a better option for a single computer or single node (but multi-cores) for whatever reasons?
You can either use OpenMPI or Gromacs build-in thread MPI library. If you only want
to run on a single machine, I would recommend recompiling with thread-MPI, because 
this is in many cases a bit faster.

> 2.       Assuming I can still use this executable, let's say I want to use half of the cores (8 cores) on my machine to run a job,
> 
> mpirun -np 8 mdrun_mpi -v -deffnm md
> 
> a). Since I am not using all the cores, do I still need to "lock" the physical cores to use for better performance? Something like "-nt" for Thread-MPI? Or it is not necessary?
Depends on whether you get good scaling or not. Compare to a run on 1 core, for large
systems the 4 or 8 core parallel runs should be (nearly) 4 or 8 times as fast. If 
that is the case, you do not need to worry about pinning.

> 
> b). For running jobs on a local desktop, or single node having ...  say 16 cores, or even 64 cores, should I turn off the "separate PME nodes" (-npme 0)? Or it is better to leave as is?
You may want to check with g_tune_pme. Note that the optimum will depend on your
system, and for each MD system you should find that out.

> 
> 3.       If I want to run two different projects on my local desktop, say one project takes 8 cores, the other takes 4 cores (assuming I have enough memory), I just submit the jobs twice on my desktop:
> 
> nohup mpirun -np 8 mdrun_mpi -v -deffnm md1 >& log1&
> 
> nohup mpirun -np 4 mdrun_mpi -v -deffnm md2 >& log2 &
> 
> Will this be acceptable ? Will two jobs be competing the resource and eventually affect the performance?
Make some quick test runs (over a couple of minutes). Then you can check 
the performance of your 8 core run with and without another simulation running.

Best,
  Carsten

> 
> Sorry for so many detailed questions, but your help on this will be highly appreciated!
> 
> Thanks a lot,
> 
> Jianqing
> 
> 
> 
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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
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa