[phenixbb] Optimal Linux configuration for Phenix.refine

[Oleg Sobolev]

Hi All,

There is really not much is done in parallel in Phenix. The major parallel
thing is refinement with weights optimization. If you do this kind of
refinement you may see benefit of several processors.

Xiao: you may try both 8 and 4 processors and see what works for you best.
Please note, that you will need sufficient amount of memory on your machine
to run parallel refinements.

Apart from that, Intel i7 with maximum frequency seems the best option for
non-parallel refinements because of Intel TurboBoost technology which
allows increase frequency of a single core of the processor if it executes
only one (non-parallel) task.

Oleg Sobolev.

On Wed, Jun 24, 2015 at 10:21 AM, Xiao Lei <xiaoleiusc at gmail.com> wrote:

> 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
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>> Unsubscribe: phenixbb-leave at phenix-online.org
>>>
>>
>>
>>
>> --
>> 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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>
>
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