[gmx-users] Horrendous scaling

Senthil Kandasamy senthilk at engin.umich.edu
Tue Jun 24 16:34:01 CEST 2003

I guess this topic has been beaten to death, but here it is again.
My machines are dual processor Athlon 2600+ using ethernet.
The system is a reasonably large lipid bilayer with proteins(~40000
atoms.) with PME electrostatics. I use fft_optimize, fft_order=4,
shuufle and sort options

1 processor 		:  in 1 hour walltime, 13.3 ps  of simulation
2 processors(1 node)	:  in 1 hour walltime, 17.7 ps of simulation
4 processors (2 nodes)	:  in 1-hour walltime, 8.7 ps of simulation!!

I can live with running on two processors if I can improve scaling by a
little bit more.

I will try to increase the fft_order to 6 and see what happens.

Also, these machines are part of a super cluster using mpich-1.2.5
Are there any compilation options for mpich  and fftw that would improve
performance? I do see a lot of suggestions for LAM., but none for mpich.



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