[phenixbb] Optimal Linux configuration for Phenix.refine
fairman.jim at gmail.com
Wed Jun 24 10:32:51 PDT 2015
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?
> On Wed, Jun 24, 2015 at 9:06 AM, Jim Fairman <fairman.jim at gmail.com>
>> A few years back one of the PHENIX devs referenced Amdahl's Law and how
>> it affects the performance of PHENIX:
>> 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>
>>> 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,
>>> 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
>>> 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
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> Unsubscribe: phenixbb-leave at phenix-online.org
Jim Fairman, Ph D.
Group Leader I - Crystallography
E-mail: fairman.jim at gmail.com jfairman at be4.com
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