[phenixbb] Parallelization for optimization of wxu/wxc?

Nathaniel Echols nechols at lbl.gov
Fri Aug 26 05:14:55 PDT 2011

On Fri, Aug 26, 2011 at 2:09 PM, Francis E Reyes
<Francis.Reyes at colorado.edu> wrote:
> Isn't it parallelized in the nightlies?

Yes, Ralf and I added this a couple of months ago.  There are a few
more improvements that we'd like to make, such as setting 'nproc'
automatically (and adjusting to compensate for system load), and
fixing a couple of inefficiencies (e.g. after running a grid search to
identify optimal weight, it then refines *again* with that weight,
instead of saving the coordinates from the grid search result), but it
is already a significant improvement.

> - phenix.refine:
>  - grid searches parallelized: use 'nproc' parameter to set number of CPUs
>    to use
>    - this affects bulk solvent mask optimization, and XYZ and ADP weight
>      optimization (in addition to TLS identification)
>    - can reduce runtime by 75% or more depending on settings (see manual for
>      details)

FYI, in practice the largest number of CPUs that the weight
optimization routines will use appears to be 18 cores.  (The automatic
TLS identification will use as many as possible, but this won't have
much additional effect.)


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