Re: Conceptual questions about GPU acceleration

From: Axel Kohlmeyer (
Date: Sat Apr 27 2013 - 12:20:06 CDT

Simply put a GPU is a multi-core processor with hundreds of cores and very efficient hyper-threading, thread management and high memory bandwith.

If you cannot extract the knowlege you are looking for from the references you mentioned, then you will have to learn more fundamentals first. It doesn't get more general than those. The CUDA SDK has well commented examples. Look for the many-body example as a precursor to MD codes.


Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.
-----Original Message-----
From: "Andrew DeYoung" <>
Sender: owner-namd-l_at_ks.uiuc.eduDate: Sat, 27 Apr 2013 12:46:49 
To: <>
Subject: namd-l: Conceptual questions about GPU acceleration
Hi NAMD experts, 
I am a graduate student and have used MD codes on a Linux CPU cluster for
the past 2 years.  However, I am a complete beginner when it comes to GPUs
and GPU acceleration of MD.
This is a very basic question, and I am a little embarassed to be asking it,
but I will ask it anyway.  Do you know of any good review articles that
would help me to understand what a GPU is and how it can be used to improve
the performance of MD codes such as NAMD?
Even after reading articles on Wikipedia and Nvidia websites, I am still
confused as to what a GPU is (I have no background in computer
architecture).  I understand that GPUs were originally designed for graphics
computations, but in the last 10 or 15 years, they have been used for
high-performance applications because they are efficient at floating point
arithmetic.  I think that GPUs must be used in tandem with at least one CPU.
I have read the following excellent review article by Stone et al. from
Stone, John E.; Hardy, David J.; Ufimtsev, Ivan S.; Schulten, Klaus. Journal
of Molecular Graphics and Modelling 2010, 29, 116-125. "GPU-accelerated
molecular modeling comes of age."
But, I feel that it would help me to read an even more basic tutorial/review
of GPUs and their application to, for example, MD.  Do you know of such
tutorials, reviews, or websites?  Thank you for considering this somewhat
off-topic question!
Andrew DeYoung
Carnegie Mellon University

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