Phenix 1.18 RSR runtime
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 Cambridge CB2 0XY United Kingdom Telephone : 01223 252812
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
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 Hannah 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 Cambridge CB2 0XY United Kingdom Telephone : 01223 252812
Thanks Hannah, thanks for quick reply and sharing files! It really is expected to be N times faster with nproc.. So I'm really keen to check this! I will investigate right away once I have files. Best, Pavel On 4/30/20 00:19, Hannah Bridges wrote:
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
Hannah
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
Hi Hannah, thanks for sharing files. I managed to bring it down to 4300 seconds running on my laptop using 1 CPU. It may take another few days before it is available in Phenix nightly builds. 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
participants (2)
-
Hannah Bridges -
Pavel Afonine