[gmx-users] mpi run in Gromacs

[Erik Marklund]

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
Hi,

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.

Cheers,

-- 
-----------------------------------------------
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/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110302/8aad6c4b/attachment.html>