[gmx-users] mpi run in Gromacs
Mark.Abraham at anu.edu.au
Wed Mar 2 14:16:31 CET 2011
On 2/03/2011 11:37 PM, Erik Marklund wrote:
> 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.
You're going to have to be much more specific if you want useful help.
>> 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
>> Many Thanks
> 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.
Not in 4.5.x. You can configure with MPI or threads (the default) or
neither. The two cannot co-exist. Threading is only useful if a network
is not involved. OpenMPI will do approximately the same via
shared-memory as you can get from threading in the cases where it is useful.
The OP should consult the GROMACS webpage for MPI installation instructions.
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