Hi Qiuye,
2x 12GB RTX-3060 will - for example - fit well with sufficient space
between cards on the MSI MEG *X570S* Unify-X Max (with two GPU slots at
16x/8x speed) and the Gigabyte X570S Aorus Master (with three slots at
8x/8x/4x if all are populated), but as you correctly noted, you will
need a really big case with plenty of fans to remove the heat such as an
Corsair 7000D Airflowor or the be quiet! silent base 802 or, for the
brave, build a water-cooled rig......
All cheaper X570S and all of the X570 boards do not support 16x/8x or
8x/8x speed (at least I did not find one).
Best,
Jeroen
Am 19.04.22 um 17:41 schrieb Qiuye Li:
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.
Best,
Qiuye
On Tue, Apr 19, 2022 at 7:47 AM mesters
<mest...@biochem.uni-luebeck.de> wrote:
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
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signature.html *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 *
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