[phenixbb] Phenix for CUDA?

Peter Zwart PHZwart at lbl.gov
Tue Jan 10 13:55:20 PST 2012


We have been developing tools that can leverage GPU technology. Have a look
at this:


Basically, the infracstructure is available for building the CCTBX with a
cuda compiler and calling those functions from within python using the
basic boost python wrappers.

There is not much there in the cudatbx yet, but in some other projects we
do have direct summation code that runs very nicely (not crystallographic
applications). As Nat mentioned however, it is unclear what the total
runtime impact would be though.


On 10 January 2012 11:56, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Tue, Jan 10, 2012 at 11:21 AM, Schubert, Carsten [JRDUS]
> <CSCHUBER at its.jnj.com> wrote:
> > are there any development plans for phenix in the works to take
> advantage of
> > NVIDIA’s CUDA platform?
> I was wondering when someone would ask about this.  Short answer is
> that there are cases where CUDA (and/or OpenCL) might be useful*, but
> it is unlikely to have a significant impact on the runtime of most
> existing programs in Phenix.  Various other algorithmic improvements
> are more likely to have a substantial impact on speed than optimizing
> our code for fancy hardware, especially for phenix.refine.
> -Nat
> (* and some work is actually being done on this in CCTBX, but not as
> part of Phenix per se.)
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P.H. Zwart
Research Scientist
Berkeley Center for Structural Biology
Lawrence Berkeley National Laboratories
1 Cyclotron Road, Berkeley, CA-94703, USA
Cell: 510 289 9246
BCSB:      http://bcsb.als.lbl.gov
PHENIX:   http://www.phenix-online.org
SASTBX:  http://sastbx.als.lbl.gov
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