[phenixbb] Phenix 1.18 RSR runtime

Pavel Afonine pafonine at lbl.gov
Thu Apr 30 00:15:42 PDT 2020

Hi Hannah,

it can be N times faster (N = number of available CPUs) if you use nproc 
to specify number of CPUs to use.

Alternatively you can disable the rotamer fitting step, which will bring 
the runtime back to previous "~1hrs" (but expect rotamer statistics go off).

If you send me files I am happy to check all is in order.


On 4/30/20 00:02, Hannah Bridges wrote:
> Dear Phenix developers,
> We have updated to phenix version 1.18-3845-000 and found that 
> realspace refinement (5 cycles) with minimization global, local grid 
> search and ADP is taking about 36 hours, compared to ~ 1hr in versions 
> 1.17 and 1.16. The slow step is the local grid search which is taking 
> >6 hours each cycle.
> We are very glad for the option to run the job detached, but I 
> wondered if this sort of timing was expected for this version?
> Best wishes
> Hannah

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