[gmx-users] mpi run in Gromacs

Erik Marklund erikm at xray.bmc.uu.se
Wed Mar 2 13:37:25 CET 2011

Selina Nawaz skrev 2011-03-02 11.54:
> Hi, I am a Phd student studying polymer membranes.
> I have installed Gromacs version 4.5.2 on our department cluster and 
> attempted to run a simulations on a DPPC bilayer membranes taken from 
> the tielleman website.
> I have set the system up in an NPT ensemble using a semi-isotropic 
> pressure coupling.
> The simulation seems to run perfect in serial however I am having 
> problems to run the simulation in parallel.
> I understand that this version of Gromacs uses threading to 
> parallelise the system. I wanted to know whether it is possible to run 
> this using openmpi and if not how do i use this thread base 
> parallelisation.
> Many Thanks
> Selina

It's slightly different than you think. Gromacs uses a thread based MPI 
implementation for communications between cores on the same machine. If 
you compile without threads it would use e.g. OpenMPI instead of threads 
as far as I know. Note that it will still use OpenMPI (or equivalent) 
for inter-node communication.


Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/

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