[phenixbb] Optimal Linux configuration for Phenix.refine

[Xiao Lei]

Hi Jim,

Thanks for the information! I just got a HP with core i7 4771 (4 cores
3.5GHz), now I know it will be a good speed boost for phenix. I used DEN
refinement in phenix, which is very slow, I'm even thinking using
university cluster to do it. There is an "DEN parameter optimization"
choice in phenix, I do not know if this can be finished by parallel
computing with multiple processors.

I have one question, in the phenix refinement, there is an input for the
number of processor, is it the same number as cores CPU has? If a CPU is
hyper-threaded like core i7 4771 (8 threads but 4 cores), should I put
number of processors 8 or 4?


Xiao

On Wed, Jun 24, 2015 at 9:06 AM, Jim Fairman <fairman.jim at gmail.com> wrote:

> 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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