Hi everyone,
I am testing pmemd.MPI (of amber12) on parallel machines (e.g. 72 CPUs),
and trying to tweak parameters to improve parallel efficiency.
My .in is like:
Plain MD
&cntrl
ntx=5, irest=1,
ntpr=500, ntwx=5000, ntwe=5000, ntwr=5000,
ntc=2, ntf=2, ntb=2, igb=0, cut=10, nsnb=10, skinnb=2, column_fft=1,
nstlim=50000000, dt=0.002, t=0,
ntt=1, tautp=1, temp0=298.0,
ntp=1, taup=2.0, pres0=1,
&end
But I got something like "amber invalid reference to variable in NAMELIST
input, unit 5, ...", pointing to my setting of column_fft=1, by which I
thought could make parallel runs faster. The Manual does say "The column
method can be faster for larger processor counts since..."
So does anyone know why did I get such error message?
And which parameters should I play with to improve parallel efficiency?
Best,
Yun
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Received on Sun Nov 17 2013 - 15:30:02 PST
