AMBER Archive (2007)

Subject: AMBER: amber on AMD opteron-250

From: servaas michielssens (servaas.michielssens_at_student.kuleuven.be)
Date: Wed Dec 05 2007 - 14:10:22 CST

I ran a 20ps simulation of a system of 20000 atoms on an AMD opteron 250
cluster with 8 processors, I used amber8 and pmemd for the simulation. I
found some strange results:
proc time(min)
2 31
3 29
4 20
5 23
6 24
7 20
8 21

4 processors gives the optimum, it seems to be independent of how I
adress the processors. So for 5 processors 1-2-3-4-5 or 1-2-3-4-7 gives
the same results, always on for processors there is an optimum. Anyone
who experienced this scaling problem?

kind regards,

servaas michielssens

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