[gmx-users] Parallelization scheme and terminology help

[Brad Van Oosten]

I have been lost in the sea of terminology for installing gromacs with 
multi-processors.   The plan is to upgrade from 4.5.5 to the 4.6 and i 
want the optimal install for my system.  There is a a nice explanaion at 
http://www.gromacs.org/Documentation/Acceleration_and_parallelization 
but the number of different options and terminology has confused me.

I currently have one computer with 2 processor sockets each with 4 cores 
each with 2 threads.  A mouthful which in the end allows for 16 
processes at once(2*4*2).

The way i read the documentation is that MPI is needed for the talk 
between the 2 physical processors, OpenMP does the talk between the 4 
cores in each processor and thread-MPI does the treading? or does 
thread-MPI do everything?

What would be the Parallelization scheme is required?