[gmx-users] Adding or modifying mpi-related files for better peformance

[Erik Lindahl]

On Thursday, Mar 13, 2003, at 07:17 US/Pacific, Taeho Kim wrote:

> hi,
> I'd like to add and modify some files, even might use a commercial mpi 
> software, to improve the scaling performance for Gromacs system since 
> our current Mac cluster hasn't provided better performance at all. 
> There is an interesting site, 
> http://exodus.physics.ucla.edu/appleseed/dev/developer.html, for Mac.
>
> How can I compile a new type of mpi software, not LAM-mpi nor mpich, 
> for Gromacs without too much problems ?
> Thanks,
>

Hi Taeho,

David just answered the question about using another mpi version; most 
mpi packages include a "mpicc" script for the compilation, and if this 
is in your path you can just run configure normally - there is nothing 
in Gromacs that is specific to LAM-MPI.

However, i doubt that you will get better performance with the 
appletalk-based versions of MPI included in pooch, since Appletalk is 
slower than TCP/IP - but do try their TCP/IP version if they have one!

You should also realize that there are significant differences between 
the "toy style" of parallelization used in many of the Pooch benchmarks 
and real parallel algorithms like MD. It is _trivial_ to write a 
parallel altivec fractal demo since you only have to send each 
processor a part of the problem, and then they don't need to talk 
anymore - that type of problem would scale to thousands of machines 
even over a modem line :-)

For molecular dynamics, we have to communicate thousands of forces and 
coordinates every single step, and we are running tens to hundreds of 
steps per second.

Sorry for the rant; I actually use Macs myself and have written altivec 
loops for Gromacs, but Apple have a tendency to "bend the rules" to get 
better looking benchmark results.

Now, the really interesting alternative is to use Firewire. I spoke 
with the Apple firewire hardware architect a couple of months ago - 
just before they published the draft IP-over-firewire specification. 
Firewire doesn't scale the same was as ethernet, but if you only have 
two machines you can get insanely good latencies with Firewire compared 
to ethernet!

Cheers,

Erik