AMBER Archive (2008)

Subject: AMBER: Re: Dell 2 Quad Core System Performance

From: Ilyas Yildirim (
Date: Wed Aug 27 2008 - 16:04:14 CDT

Dear All,

I did a benchmarking to see the performance of a dual quad core system.
The system I tested have 3359 atoms in it (an RNA solvated with Na+ ions,
and ~1000 water molecules). I used sander.MPI in the simulations. The
machine is a dual quad core system with Intel Xeon CPUs (E5430,
2.66GHz) and 16 GB RAM. I did 4-5 test simulations for each case and here
are the results:

1 CPU X 1
2 CPU X 1.88
4 CPU X 3.49
8 CPU X 5.78

I have to say, I am very disappointed with the results. I had the same
question a year ago, and Ross Walker gave a really nice answer. I am
surprised that we cannot, still, get a full performance due to the bad cpu

Is it possible that if I use pmemd, I can increase the efficiency? In any
case, just wanted to share my experience with you.

Best regards,

> Did any of you have experience with running sander in dell 2 quad core
> systems? We are going to buy a system for the lab to run sander in
> parallel, and I was wondering how the performances of DELL 2 quad core
> systems are. Can we get a x8 performance when we use all the CPU for one
> simulation? Thanks in advance for your answers.

  Ilyas Yildirim
  = Department of Physics        -                              =
  = University of Rochester      -                              =
  = 585-275-6766 (office)        - 585-267-5644 (home)          =
  =                     =

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