[phenixbb] GPU acceleration of phenix.real_space_refine?
pafonine at lbl.gov
Thu Jun 2 14:00:46 PDT 2016
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.
> 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
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