On Fri, Oct 10, 2008 at 12:57 PM, Brock Palen <brockp_at_[hidden]> wrote:
> Actually I had a much differnt results,
> gromacs-3.3.1 one node dual core dual socket opt2218 openmpi-1.2.7
> mpich2 gcc
For some reason, the difference in minutes didn't come through, it seems,
but I would guess that if it's a medium-large difference, then it has its
roots in PGI7.2 vs. GCC rather than MPICH2 vs. OpenMPI. Though, to be fair,
I find GCC vs. PGI (for C code) is often a toss-up - one may beat the other
handily on one code, and then lose just as badly on another.
I think my install of mpich2 may be bad, I have never installed it before,
> only mpich1, OpenMPI and LAM. So take my mpich2 numbers with salt, Lots of
I think the biggest difference in performance with various MPICH2 install
comes from differences in the 'channel' used.. I tend to make sure that I
use the 'nemesis' channel, which may or may not be the default these days.
If not, though, most people would probably want it. I think it has issues
with threading (or did ages ago?), but I seem to recall it being
considerably faster than even the 'ssm' channel.
Sangamesh: My advice to you would be to recompile Gromacs and specify, in
the *Gromacs* compile / configure, to use the same CFLAGS you used with
MPICH2. Eg, "-O2 -m64", whatever. If you do that, I bet the times between
MPICH2 and OpenMPI will be pretty comparable for your benchmark case -
especially when run on a single processor.