[gmx-users] mpi run in Gromacs

[Mark Abraham]

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 
>> 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.

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.

Mark
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