[gmx-users] parallelization

[Carsten Kutzner]

Hi,

On Oct 17, 2013, at 2:25 PM, pratibha kapoor <kapoorpratibha7 at gmail.com> wrote:

> Dear gromacs users
> 
> I would like to run my simulations on all nodes(8) with full utilisation of
> all cores(2 each). I have compiled gromacs version 4.6.3 using both thread
> mpi and open mpi. I am using following command:
> mpirun -np 8 mdrun_mpi -v -s -nt 2 -s *.tpr -c *.gro
> But I am getting following error:
> Setting the total number of threads is only supported with thread-MPI and
> Gromacs was compiled without thread-MPI .
> Although during compilation I have used:
> cmake .. -DGMX_MPI=ON -DGMX_THREAD_MPI=ON
you can either use MPI or thread_mpi. But you can use MPI and OpenMP with
-DGMX_MPI=ON -DGMX_OPENMP=ON

> If I dont use -nt option, I could see that all the processors(8) are
> utilised but I am not sure whether all cores are being utilised. For
You can run with 
mpirun -np 16 mdrun_mpi -v -s -nt 2 -s *.tpr -c *.gro

to use all 16 available cores.

> version 4.6.3 without mpi, I Know by default gromacs uses all the threads
> but not sure if mpi version uses all threads or not.
Take a look at the md.log output file, there it should be written
what Groamcs did use!

Best,
  Carsten

> Any help is appreciated.
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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