[phenixbb] Hardward phenix.refine

Ray Changrui Lu changrui at gmail.com
Tue Apr 12 21:47:34 PDT 2016

Dear Colin,

I agree with everything Tim and Kay said above. i5 or i7 of the same
frequency and core count will perform similarly with Xeons (even across all
generations of intel core/xeon processors). Adding more cores will help the
refining process (under linux and mac only), but unless the computer is
being used simultaneously by multiple users, I do not see the
cost-effectiveness in running a 36-core/72-thread dual Xeon E5.

As to the OS choice, another interesting point regarding cost arises. Top
performance Mac you can buy as of April 2016 is a 12-core 2.7Ghz Xeon (a
3-year old processor), setting you back a whooping 9000 USD. With the help
of a tech-savvy student or postdoc, you can easily build something that
runs circles around that mac pro with 1/3 of the cost. However you will
have to live with Linux, which is not half bad if you get used to it.

I personally still prefer OSX and I run an old dell optiplex with a
quad-core i5 (apple won't be happy but it is their fault for not updating
their product). It only took me half a day to put OSX and all
crystallization software I need on it and everything run like a dream. Due
to the lack of performance and high price of Mac Pros, if you want a fast
Mac, building a hackintosh is your only choice as of today.

Hope it helps.


On Wed, Apr 13, 2016 at 3:57 AM, Kay Diederichs <
kay.diederichs at uni-konstanz.de> wrote:

> Colin,
> check out the first option in the FAQ at
> https://www.phenix-online.org/documentation/faqs/refine.html
> A core i7 and a Xeon of the same generation are equally fast if their
> frequency is the same. The main differences are that
> - Xeon E3 supports ECC memory (most core i* don't)
> - Xeon E5 supports Dual-CPU (core i* is just one)
> - Xeon E7 supports multi-CPU and is very expensive
> - most Xeons don't have built-in graphics whereas most core i* do
> There are many other small differences but most of them irrelevant;
> inspect the Wikipedia pages!
> Xeons won't be faster with phenix.refine; a core i7 already has enough
> cores - to increase their usage you'll have to recompile as per the FAQ.
> HTH,
> Kay
> >
> > Message: 1
> > Date: Mon, 11 Apr 2016 07:56:39 +0000
> > From: Colin Levy <C.Levy at manchester.ac.uk>
> > To: "phenixbb at phenix-online.org" <phenixbb at phenix-online.org>
> > Subject: [phenixbb] Hardward phenix.refine
> > Message-ID: <773C4580-FA01-4246-86E9-2D73AFD98421 at manchester.ac.uk>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Dear all,
> >
> > Having read the FAQ regarding hardware I have a few ideas but would
> greatly appreciate any input from the community or developers.
> >
> > Would anyone like to suggest the best configuration of hardware for
> running phenix.refine? I mainly operate in OSX but have no issue with
> switching operating system if I can get a faster setup.  My current
> thoughts are either something running a 4GHz Quad core i7 or an alternative
> would be a 3.7GHz Quad-Core Intel Xeon E5 (iMac v Mac Pro) or equivalent
> Linux builds.
> >
> > I know that the i7 is reasonably fast as I have this setup in a
> different machine and phenix.refine runs reasonably quickly but as ever I
> would like it to be faster. Budget is not unlimited by any means but I
> would be interested in learning what an optimal setup might look like.
> >
> > 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<mailto:c.levy at manchester.ac.uk>
> >
> >  Manchester Institute of Biotechnology | University of Manchester |
> 3.020 Garside Building | 131 Princess Street | Manchester | M1 7DN
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