Luc,

Are you also aware that we've implemented sparse Cholesky decomposition by wrapping the Eigen C++ header library? We use it now within DIALS for true sparse-matrix decomposition. One modality is that we take a Jacobian expressed in terms of the sparse::matrix data structure that you defined within scitbx, but then we use Eigen to actually solve the normal matrix.

David Waterman & I can provide more details as needed.

Nick

Nicholas K. Sauter, Ph. D.
Computer Staff Scientist, Molecular Biophysics and Integrated Bioimaging Division

Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720
(510) 486-5713

On Sun, Mar 6, 2016 at 5:06 AM, Luc Bourhis <luc_j_bourhis@mac.com> wrote:

Hi,

this is an advanced warning for the introduction of a new top-level module named fast_linalg. In a couple of days, I will push it in one go as 25 commits but don’t be scared, nothing is changed outside the top directory fast_linalg, which also means it is not configured by default. Thus there cannot be any disruption but I thought it would be polite to warn all cctbx developers.

The module features the automatic installation and integration of OpenBLAS which I have used to speed up smtbx refinement. I will commit that work later.

Best wishes,

Luc J. Bourhis

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