I am comparing two portions of the same classical MD production (pore protein with a large ligand in a POPC hydrated membrane) for Amber9 vs Amber10 on the same hardware. As I found Amber 9 slower by some 5% (evaluated from either the "Total time" or the "Real time"), I am presenting the situation.
The in file reads:
prod protein ligand POPC membrane box 80x80
&cntrl
imin=0, irest=1, ntx=5,
nstlim=333334, dt=0.0015,
cut=10, ntb=2, ntp=1, taup=2.0,
ntc=2, ntf=2,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300.0,
/
Portion 4: Amber 10 compiled with ifor+MKL 10.1.015, support openmpi-1.2.6 (compiled same Intel).
Portion 3: with Amber 9 compiled with ifort 9.1.036, support openmpi-1.2.3 (compiled same Intel).
I expected little gain from MKL for classical MD because of the overhead, though I was surprised that Amber 10 has suffered so much to turn out to be slower.
That the MKL are installed correctly is proved by a 40% speed gain by using MKL in a heavy docking simulation (were ca 8GB MEM are used).
I assume that each nstlim=333334 run of MD should require the same time of execution. If this is not wrong, is the situation presented amenable to a comment?
Thanks
francesco pietra
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Sun May 25 2008 - 06:08:11 PDT
