[phenixbb] Phenix 1.18 RSR runtime

Hannah Bridges hrb at mrc-mbu.cam.ac.uk
Thu Apr 30 00:19:34 PDT 2020

Hi Pavel,

Thank you for the rapid reply. We have tried increasing nproc, but it is 
still pretty slow. I will send my files privately so that you can check 
if something is awry.

Best wishes


On 30/04/2020 08:15, Pavel Afonine wrote:
> 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.
> Pavel
> 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
Dr Hannah Bridges
Investigator Scientist
MRC Mitochondrial Biology Unit
The Keith Peters Building
University of Cambridge
Cambridge Biomedical Campus
Hills Road
United Kingdom

Telephone : 01223 252812

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