[phenixbb] GPU acceleration of phenix.real_space_refine?

Pavel Afonine pafonine at lbl.gov
Thu Jun 2 14:00:46 PDT 2016

Hi Oliver,

unlike reciprocal-space refinement (phenix.refine), real-space 
refinement (phenix.real_space_refine) is much easier to parallelize and 
it will benefit a lot from parallelization.

Making use of multiple processors is in my list of things to do. No GPU 


On 5/24/16 09:28, Oliver Clarke wrote:
> Hi all,
> phenix.real_space_refine takes a very long time to run on large 
> systems when using any of the more computationally expensive options 
> (e.g. morphing).
> I was wondering if there has been any consideration towards optimizing 
> this code (and maybe that of phenix.map_to_model) for GPU 
> acceleration? There is somewhat of a shift occuring in the EM 
> community towards using GPU workstations for data processing - if we 
> could use already purchased capabilities to accelerate model 
> refinement as well that would be a huge bonus.
> I saw a discussion on the bb from a while back concerning the same 
> question applied to phenix.refine, and the conclusion was that in that 
> case the benefits would be minimal, but I'm not sure whether the same 
> applies to real space operations.
> Cheers,
> Oli.
> PS has there been any consideration of including an option to allow 
> users to supply two half maps at run time, one "work" and one "test" 
> map for cross validation purposes? It is possible to do this with two 
> separate runs right now but having the option integrated would be 
> wonderful.

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