Antw: [gmx-developers] Gromacs 3.3.1 parallel benchmarking

Peter Friedel friedel at
Tue Aug 15 09:55:54 CEST 2006

hello, all,
I am trying to do some benchmarking on SLES 9 system with AMD opteron dual core processors (2.2 GHz) too, but there are still some crashes when performing the DPPC test with 2 or 8 processors. I try to find the subroutine where the crash happens. I am using the infiniband network applying the MPICH derivative mvapich. Nevertheless, the test with 16 processors had a benchmark of 13.335 GFlops and with one processor 1.175 GFlops. 
sincerely peter

Dr. Peter Friedel
Hohe Str. 6, 01069 Dresden
Institut für Polymerforschung Dresden e.V.
Tel.: 0351-4658289
Fax: 0351-4658565
email: friedel at
>>> mghav at 15.08.06 1.05 >>>
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
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!

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