[cctbxbb] New top-level module: fast_linalg

Nicholas Sauter nksauter at lbl.gov
Sun Mar 6 12:38:58 PST 2016


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 at 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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