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
architecture.
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) =
= http://www.pas.rochester.edu/~yildirim/ =
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Received on Sun Aug 31 2008 - 06:07:17 PDT
