[gmx-developers] non-contiguous memory access in Gromacs?
alantu9000 at hotmail.com
Wed Mar 17 03:52:13 CET 2004
Thanks for your information. Could you please give me more details such as
which file or function includes this kind of access? We are especially
interested in those hotspots.
----- Original Message -----
From: "David van der Spoel" <spoel at xray.bmc.uu.se>
To: <gmx-developers at gromacs.org>
Sent: Monday, March 15, 2004 1:50 AM
Subject: Re: [gmx-developers] non-contiguous memory access in Gromacs?
> On Mon, 2004-03-15 at 03:00, MailList wrote:
> > Hi, there,
> > I was just wondering if Gromacs have any non-contiguous memory access?
> > For example, suppose it has a 2D array A[i,j], in C, it is row-wise
> > access. Therefore, if the code needs to access the A[*,1] and A[*,3],
> > then this is actually non-contiguous access.
> Yes this happens a lot. You can notice that performance improves when
> you add cache memory.
> > Thank you so much.
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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