[phenixbb] Optimal Linux configuration for Phenix.refine

[Jim Fairman]

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 <C.Levy at manchester.ac.uk> wrote:

>  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
> c.levy at manchester.ac.uk
>
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-- 
Jim Fairman, Ph D.
Group Leader I - Crystallography
Beryllium <http://www.be4.com>
Tel: 206-780-8914
Cell: 240-479-6575
E-mail: fairman.jim at gmail.com jfairman at be4.com
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