[cctbxbb] Install OpenBLAS or MKL in base

Nicholas Sauter nksauter at lbl.gov
Fri Jun 22 13:07:24 PDT 2018

Hi Luc,

I thought that non_linear_ls was a derived class from linear_ls, so yes we
do use that base class for DIALS, cctbx.xfel, samosa, and probably other
things.  However, I do not think I've ever touched


Nicholas K. Sauter, Ph. D.
Senior Scientist, Molecular Biophysics & Integrated Bioimaging Division
Lawrence Berkeley National Laboratory
1 Cyclotron Rd., Bldg. 33R0345
Berkeley, CA 94720
(510) 486-5713

On Fri, Jun 22, 2018 at 1:00 PM, Graeme.Winter at Diamond.ac.uk <
Graeme.Winter at diamond.ac.uk> wrote:

> Folks,
> Optional use could be interesting for dials... I find for big rotation
> sets the refinement can be rate limiting... faster algorithms are of
> interest but I agree optional better. Also dials scaling...
> Also with the use of git and branches and stuff we can test this very
> carefully before merging back
> Best wishes Graeme
> ________________________________
> From: cctbxbb-bounces at phenix-online.org <cctbxbb-bounces at phenix-online.org>
> on behalf of Luc Bourhis <luc_j_bourhis at mac.com>
> Sent: 22 June 2018 20:28:19
> To: cctbx mailing list
> Subject: Re: [cctbxbb] Install OpenBLAS or MKL in base
> Nicholas,
> > Please make sure that any new dependencies are optional, and that
> existing users can continue to use the existing code.  LSTBX is a
> fundamental component of CCTBX, and I wouldn't be keen on suddenly changing
> all the underlying implementations!
> Yes, I had noticed it is used by xfel and by a few tests. Only the class
> non_linear_ls is used though, and that I did not optimise in my current
> attempt, that can be found on the branch reworked_fast_lstbx. I only
> optimised the L.S. I needed for smtbx, i.e. where the scale between model
> and data is unknown and needs to be fitted. The class is
> non_linear_ls_with_separable_scale_factor. So, right now, there is
> nothing to worry about as far as the smtbx is not concerned! Unless I
> missed something…
> Would that be acceptable then, if we don’t touch the features of
> scitbx.lstbx used outside of smtbx? The thing is that keeping both BLAS 2
> and 3 implementations significantly increased the complexity of it all.
> Moreover it makes some alternative solutions we are considering, like
> moving part of the code to Python, more difficult. So we would prefer to
> have the freedom to break code using non_linear_ls_with_separable_
> scale_factor.
> > Also, we cannot include anything GPL in CCTBX.
> Yes, sure. The discussion went on a tangent, sorry.
> Best wishes,
> Luc
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