[gmx-developers] Gromacs 3.3.1 parallel benchmarking

[Michael Haverty]

Hello all,
  I'm doing some benchmarking of gromacs 3.3.1 on SUSE
9 systems using Intel Xeon processors on Gigabit
ethernet, but have been unable to reproduce the
scaling at 
http://www.gromacs.org/gromacs/benchmark/scaling-benchmarks.html
for Gromacs 3.0.0 and am trying to diagnose why.  I'm
getting sublinear scaling on distributed
single-processor 3.4 GHz Intel Xeon's with gigabit
connections.  I'm compiling using the 9.X versions of
Intel compilers and used a wide variety of FFT and
BLAS libraries with no success in reproducing the
linear scaling shown in the online benchmarking
results for the "large DPPC membrane system".
  Have any changes in the code been implemented since
3.0.0 that would likely change this scaling behavior
and/or has anyone done similar parallel benchmarking
with 3.3.1?  We'd like to start using this code for up
to 100's of millions of atoms system, but are
currently limited by this poor scaling.
  Thanks for any input or suggestions you can provide!
Mike

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