[gmx-developers] Problem with g_covar diagonalizing large covariance matrices

Mark Abraham mark.j.abraham at gmail.com
Mon Oct 27 20:48:45 CET 2014

On Mon, Oct 27, 2014 at 2:19 PM, Mendez Giraldez, Raul <
rmendez at email.unc.edu> wrote:

>  Dear Gromacs developers,
>  I am trying to compute PCA on a 46464x46464 matrix (15488 atoms).
> g_covar produces segmentation fault. We thought it was a lack of physical
> memory, but when our computer cluster system administrator, Shubin Liu,
> looked into the system logs, found that the maximum RAM used by the program
> was 16 Gb, while I had booked up to 800 Gb of RAM. Shubin realized that the
> actual problem arises at the eigensolver call within covar routine. So it
> looks like eigensolver is unable to handle big matrices, but not because
> of lack of physical memory (is it based on LAPACK libraries, still 32-bit
> coded?).

I've no idea if there are any limits, but you can choose the LAPACK
implementation with which to link GROMACS (see install guide), so you
should find out what you've been using (e.g. inspect CMakeCache.txt in your
build tree), and explore alternatives.

I am using Gromacs 4.6.3.
>  Do you know an alternative to that? The reason I want to do that is
> to have some ion atoms in addition to my protein and see how they move
> along the low frequency modes (large variance PCs).

How many of your protein atoms do you really need for that analysis? I
presume you're already excluding the hydrogen atoms, since they're not
doing much at low frequencies. Even if you think you really do need them, I
suggest you start with something small that works.


>  Thank you so much,
>  Raul
> Raul Mendez Giraldez, PhD
> Dokholyan Lab
> Dept. Biophysics & Biochemistry
> Genetic Medicine
> University of North Carolina
> 120 Mason Farm Road
> Chapel Hill, NC 27599
> US
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