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

Mendez Giraldez, Raul rmendez at email.unc.edu
Mon Oct 27 15:34:21 CET 2014

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 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).

Thank you so much,


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