[gmx-developers] non-contiguous memory access in Gromacs?

David van der Spoel spoel at xray.bmc.uu.se
Mon Mar 15 08:50:09 CET 2004

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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