Poor scaling with MPI on many-core machines can also be due uneven job
distributions across cores or jobs being wastefully swapped between cores. You
might be able to fix this with some esoteric configuration options of mpirun
(--bind-to-core worked for me with openMPI), but the surest option is to switch
to gromacs 4.5 and run using thread-level parallelisation, bypassing MPI
entirely.
________________________________
From: Sara Campos <[email protected]>
To: [email protected]
Sent: Monday, 20 February 2012, 17:12
Subject: [gmx-users] Scaling/performance on Gromacs 4
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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