A few years back one of the PHENIX devs referenced Amdahl's Law and how it
affects the performance of PHENIX:
https://en.wikipedia.org/wiki/Amdahl's_law
Even though some parts of the refinement are done in parallel on multiple
processors, the really time-consuming calculations are done in serial,
which ends up governing the overall speed of the process.
I have found that Intel Haswell-class processors like the Core i7 4770
perform refinements significantly speedier than our brand new 12-core Xeon
server that is less than 6 months old. So it is my naive guess that
getting the fastest "single processor performance" will get you maximal
refinement speeds on PHENIX.
If you want to up the ante a bit more, you can always try overclocking
with liquid
nitrogen to hit 7.2 Ghz http://valid.canardpc.com/240rw0.
Cheers, Jim
On Wed, Jun 24, 2015 at 8:20 AM, Colin Levy
Apologies for the slightly off topic question.
I am configuring a Linux workstation and would like your thoughts on an optimal setup for running Phenix. A lot of my computing time is spent in refinement and I am keen to put something together that will see a considerable increase in speed from my creaking Mac Pro (2 2.4GHz Quad core Intel Xeon with 24Gb RAM).
Many thanks,
Colin
Manchester Protein Structure Facility
Dr. Colin W. Levy MIB G034 Tel. 0161 275 5090 Mob.07786 197 554 [email protected]
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