[gmx-users] Scaling/performance on Gromacs 4

[Sara Campos]

Dear GROMACS users

My group has had access to a quad processor, 64 core machine (4 x Opteron
6274 @ 2.2 GHz with 16 cores)
and I made some performance tests, using the following specifications:

System size: 299787 atoms
Number of MD steps: 1500
Electrostatics treatment: PME
Gromacs version: 4.0.4
MPI: LAM
Command ran: mpirun -ssi rpi tcp C mdrun_mpi ...

#CPUS          Time (s)   Steps/s
64             195.000     7.69
32             192.000     7.81
16             275.000     5.45
8              381.000     3.94
4              751.000     2.00
2             1001.000     1.50
1             2352.000     0.64

The scaling is not good. But the weirdest is the 64 processors performing
the same as 32. I see the plots from Dr. Hess on the GROMACS 4 paper on JCTC
and I do not understand why this is happening. Can anyone help?

Thanks in advance,
Sara
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