AMBER Archive (2008)

Subject: AMBER: Amber9 vs Amber10+MKL benchmark

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat May 24 2008 - 08:48:12 CDT

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

      
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