[MMTK] symeig change to eigh

Konrad Hinsen research at khinsen.fastmail.net
Mon Apr 2 06:44:38 UTC 2012

ra.biehl writes:

 > I was trying to reduce a bit the memory usage of the normal mode
 > calculation of a large system.

That's not easy if you want to remain general. The only approaches I
know that can reduce memory use significantly are

- reduce the system size (coarse-grained models)

- reduce the number of modes (e.g. by using MMTK.Subspace)

- use iterative methods with a sparse representation of the force constant
  matrix to calculate selected modes

 > This project or better the source is not available anymore, but the wrapper for the
 > underlying lapack functions has moved to scipy and is included as scipy.linalg.eig
 > Changing the small pieces attached at the end allow the usage of scipy.linalg.eigh
 > instead of symeig in NormalModes/Core.py

I'll apply those modifications to MMTK, thanks!

 > Testing with AmberFF and insulin.pdb in mode='all' the Normal mode
 > calculation is a bit faster (232 s instead of 291s ) but
 > unfortunately the memory usage is not changed.

That's what I would expect.

If you want to try iterative approaches, I should still have some old
interface to ARPACK that does the job, assuming that ARPACK didn't
change too much over the last 10 years.

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net

More information about the mmtk mailing list