Hi Graeme, 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 do hope some of these info are analyzed and either published or at least put at ccp4 wiki.
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 > > I really request all the program developers (in the ccp4bb) to clearly have a table in the website mentioning if certain program is purely GHz dependent and not multi-threaded. > Also how much power the machines take to get work done is a non-trivial > factor… But what about the environment? Trashing a decent machine from 2015 for the latest threadripper2? These old maches have 80-90 + gold power supply. Many (like Apple's planned obsolescence) are *forcibly* destroyed not refurbished at all. Does DIALS run that much quicker? How much time is saved for a phd student in their career if data processing speeds up from 15 min to 10 min? Sure perfect for use @synchrotron but otherwise? May the beamlines/synchrotons should allow for remote data processing and even refinement. May be all program devs need to put benchmarks - will help users greatly. These days i have a feeling science copied the typical electron/website framework programmers? Programs/website getting fatter not efficient and hoping everyone has 128GB RAM. Markus > Cheerio Graeme > > > > > On 30 Nov 2018, at 19:32, James Holton < > 0000270165b9f4cf-dmarc-requ...@jiscmail.ac.uk> 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. > >> > >> ############################################################ > ############ > >> > >> To unsubscribe from the CCP4BB list, click the following link: > >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > > ######################################################################## > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. 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