Hi Jeroen,
Thanks for the kind suggestions, they definitely help me as well as many
others a lot!
I recently tested coot0.9 on a 11800H+64G+A2000+1600p mobile workstation
and am quite OK with the performance. I guess the same gen desktop-level
hardware and configuration--something around 5950X+64G+3060 with my
existing 27' 2k display--should do the work well, and can be picked up
today in a local store. We already have more than a dozen consumer cards in
our workstations so we'll probably worry about NVIDIA's policy later. The
idea of a dual-GPU machine sounds wonderful, I need to dig a bit more
myself to see if there are decent chassis and board to fit those gamer
cards' little hot fans, and still be reasonably quiet in an office.


On Tue, Apr 19, 2022 at 7:47 AM mesters <mest...@biochem.uni-luebeck.de>

> Hi Qiuye,
> somehow the one-million-dollar* "budget vs. program specs vs.
> current/future applications** vs. access to central computing facilities*"
> question, is it not?
> As Paul indicated, for a personal/office graphics workstation (maximally
> 128GB ram memory), a 8-16 core CPU with a passmark
> <https://www.cpubenchmark.net/high_end_cpus.html> of >27.500 and for <600
> US$ will do (intel i9-12900, i7-12700, i5-12600k; Ryzen 5950x, 5900x or
> 5800x). As heat dissipation is a major problem, AMD is a good choice for
> the moment (i9-12900k TDP 241 watts vs. 3950x TDP 105 watts). If there is a
> reasonable chance, the system is to be upgraded in the future to a
> small/medium 2x GPU CryoSpark workstation, plan for a 16-core CPU from the
> beginning and make sure to choose a motherboard that offers the possibility
> of 2x PCIe 4.0 at *8x/8x* speed mode (MSI MPG Z690 FORCE / Gygabyte X570
> *S* Aorus PRO) as many standard boards only offer 16x/4x speed mode (read
> the technical description carefully; most if not all boards <300 US$ offer
> 16x/4x only).
> As for the graphics card, it depends mainly on program specs,
> structure-model-size / e.d.-map-size and screen resolution.
> For a 4K screen in combination with rendering, you will indeed require a
> >4000 cuda-cores GPU card such as a 8GB RTX3060ti (600 €; 4864 cuda-cores;
> 200 watt and sadly no FE model available) or a 16GB RTX A4000 (1100 €; 6144
> cuda-cores; 140 watt). Again, as heat dissipation is a major problem, the
> A4000 is a very good pick with 16GB memory! I recommend a professional RTX
> *A*xx00-series over the wide-spread 3x00-series consumer cards (*FE*
> models if at all!) as for the moment, Nvidia still allows the installation
> of the CUDA-package (AlphaFold, etc., etc.) on consumer cards outside of
> any central university computing facility without restrictions (read the
> small print in the cuda software documention), but I would not be surprized
> this might change in the future (recall the LHR measures taken by the
> company)! Nvidia can tell from the IP-adress who-is-who (office, home or
> central computing facility).
> For a 1440p screen and small- to mid-sized models/maps, an A2000 (3328
> cuda-cores, 30% more cores than a 2070 super; 650-750€; 70 watt) with 6 or
> 12GB GDDR is good although not a bargain compared to the A4000 that offers
> a much better price/performance ratio.
> Paul's dream-machine - an 3990X combined with a Nvidia RTX 3090 Ti - will
> cost you, build-it-yourself, at least 8.000 €, which is just too expensive
> in my eyes.....
> A build-it-yourself machine around a Ryzen 5800x, 12GB RTX A2000, 2TB M.2,
> 12TB HDD and 32GB ram including power-supply and case will cost about 2600
> €, and with a Ryzen 5950x and 16GB RTX A4000 about 3100 €.
> A minimal system for about 1100€ can be build around a Ryzen 5600x or
> intel i5-12500 (passmark > 20.000), 16Gb ram and a 6GB GTX 1660 super (1408
> cuda-cores; max. 1440p resolution; we run AlphaFold v2 on such a card, not
> superfast but it gets the job done), for smaller models/maps of course and
> with slower Coot1 fancy mode I guess ....
> It all boiles down to budget in the end I guess, good luck at taking the
> right decision!
> Jeroen
> Am 15.04.22 um 17:32 schrieb Qiuye Li:
> Dear all,
> We recently centralized our high-end workstations and no longer have easy
> access to their displays, and thus need a modeling computer. I found coot
> 0.9/wincoot 0.9 are a bit laggy on our less frequently updated office
> computers, and the all-new coot 1 probably requires even more hardware
> resources? With this recent launch of coot 1, it is probably a good time to
> kindly ask for hardware suggestions, like CPU, RAM, SSD, and dGPU.
> With coot, I typically visualize a .mrc map using a radius of ~25 A and
> work with real-space refinement/other simple manual adjustments. Other than
> coot, I often have  1-2 active chimera/Phenix windows open, a few SSH
> tunnels, and some web pages. I'll be happy to provide more details if
> needed. Any suggestions are appreciated!
> Best,
> Qiuye
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> --
> *Dr. math. et dis. nat. Jeroen R. Mesters *Deputy, Lecturer, Program
> Coordinator Infection Biology
> <https://www.uni-luebeck.de/en/university-education/degree-programmes/infection-biology.html>
> Visiting Professorship (South Bohemian University
> <https://www.jcu.cz/?set_language=en>) in Biophysics
> *University of Lübeck*
> Center for Structural and Cell Biology in Medicine
> * Institute of Biochemistry*
> Tel  +49 451 3101 3105 (Secretariate 3101)
> Fax +49 451 3101 3104
> jeroen.mest...@uni-luebeck.de
> https://www.biochem.uni-luebeck.de
> https://orcid.org/0000-0001-8532-6699
> *Ratzeburger Allee 160 23538 Lübeck, Schleswig-Holstein Germany*
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