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Subject:

Re: buying a cluster

From:

"[log in to unmask]" <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Sat, 1 Dec 2018 16:21:33 +0000

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HI James,



Re: dissenting opinion



I suspect that this conclusions depends very closely on (i) the shape of the problem and (ii) the extent to which the binary has been optimised for the given platform. 



I am pretty sure that there are some applications (heavily threaded, making extensive use of vector operations) which would be massively quicker on 2018 hardware than something a decade old. Certainly though, if you are comparing a not-highly-optimised single threaded binary then your conclusion is probably a valid one



Also how much power the machines take to get work done is a non-trivial factor… 



Cheerio Graeme







> On 30 Nov 2018, at 19:32, James Holton <[log in to unmask]> wrote:

> 

> I have a dissenting opinion about computers "moving on a bit".  At least when it comes to most crystallography software.

> 

> Back in the late 20th century I defined some benchmarks for common crystallographic programs with the aim of deciding which hardware to buy.  By about 2003 the champion of my refmac benchmark (https://bl831.als.lbl.gov/~jamesh/benchmarks/index.html#refmac) was the new (at the time) AMD "Opteron" at 1.4 GHz.  That ran in 74 seconds.

> 

> Last year, I bought a rather expensive 4-socket Intel Xeon E7-8870 v3 (turbos to 3.0 GHz), which is the current champion of my XDS benchmark.  The same old refmac benchmark on this new machine, however, runs in 68.6 seconds.  Only a smidge faster than that old Opteron (which I threw away years ago).

> 

> The Xeon X5550 in consideration here takes 74.1 seconds to run this same refmac benchmark, so price/performance wise I'd say that's not such a bad deal.

> 

> The fastest time I have for refmac to date is 41.4 seconds on a Xeon W-2155, but if you scale by GHz you can see this is mostly due to its fast clock speed (turbo to 4.5 GHz). With a few notable exceptions like XDS, HKL2k and shelx, which are multi-processing and optimized to take advantage of the latest processor features using intel compilers, most crystallographic software is either written in Python or compiled with gcc.  In both these cases you end up with performance pretty much scaling with GHz.  And GHz is heat.

> 

> Admittedly, the correlation is not perfect, and software has changed a wee bit over the years, so comparisons across the decades are not exactly fair, but the lesson I have learned from all my benchmarking is that single-core raw performance has not changed much in the last ~10 years or so.  Almost all the speed increase we have seen has come from parallelization.

> 

> And one should not be too quick to dismiss clusters in favor of a single box with a high core count. The latter can be held back by memory contention and other hard-to-diagnose problems.  Even with parallel execution many crystallography programs don't get any faster beyond using about 8-10 cores.  Don't let 100% utilization fool you!  Use a timer and you'll see.  I'm not really sure why that is, but it is the reason that same Xeon W-2155 that leads my refmac benchmark is also my champion system for running DIALS and phenix.refine.

> 

> My two cents,

> 

> -James Holton

> MAD Scientist

> 

> 

> On 11/26/2018 1:10 AM, V F wrote:

>> Dear all,

>> Thanks for all the off/list replies.

>> 

>>> To be honest, how much are they paying you to take it? Can you sell it for

>>> scrap?

>> May be I will give it a pass.

>> 

>>> To compare, two dual CPU servers with Skylake Gold 6148 - that is 40 cores -

>>> will probably beat the whole lot even if you could keep the cluster going.

>>> And keeping clusters busy is a time consuming challenge... I know!

>>> If they are 250W servers, then you are looking at £8000 per year to power

>>> and cool it. The two modern servers will be more like £1500 per year to run.

>>> And the servers will only cost about £6000... the economics and planet don't

>>> stack up!

>> By servers do you mean tower/standalone?

>> 

>> Thanks for the detailed explanation. From 2012, we already have many

>> dell precision T5600 with 2 x Xeon E5-2643 (8 Cores) (16 threads) and

>> I was hoping parallellisation with clusters maybe of some help. Looks

>> not.

>> 

>> These are running so well (takes about 45 min for a typical dataset

>> reduction with DIALS) I am not sure buying new ones is useful.

>> 

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