[phenixbb] Optimal Linux configuration for Phenix.refine

[Jim Fairman]

Xiao,

I can't comment much on refinement with phenix.den as it is a feature I
haven't used before.

There is indeed an input for number of processors.  If you are running via
command line, add --nproc=# to your command, where # is the number of
processors.  If you are using the GUI, there is a box in the bottom
right-hand corner where you can select number of CPUs.

For hyper threaded CPUs you can pick double the actual physical cores.  The
4770 chips have 4 hyper threaded physical cores, so you can run jobs with
up to eight.



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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>>
>
>


-- 
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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