My two cents, if one has access to centralized computing power i.e. CPUs
and GPUs for doing the heavy calculations, one will hardly need a
64-core threadripper 3990X (4300 €) in the office especially since most
programs profit from quality (speed), not quantity (total number of
cores). A 3960x will do just fine and will provide 75% computing power
of an 3990x (both are rated at 280 wattswhich sets the total performance
level for the major part) at just 33% of the costs. Extra money is much
better spent on other components such as sufficient ram, M.2 SSDs,
sufficient HDDs, a professional CUDA card such as the 20GB, 7168
CUDA-core RTX 4500 (2300 €) and most of all, *two* (!) 1440p displays
Happy easter wishes (holidays) to everybody,
Jeroen
Am 17.04.22 um 01:38 schrieb Paul Emsley:
On 15/04/2022 16:32, Qiuye Li wrote:
We recently centralized our high-end workstations and no longer have
easy access to their displays,
Someone drew the short straw there :-(
I found coot 0.9/wincoot 0.9 are a bit laggy on our less frequently
updated office computers,
You mean hardware updates? Yes, if you go back a gen or two, you will
notice this.
and the all-new coot 1 probably requires even more hardware resources?
It was my intention that Coot 1 be faster than 0.9.x in Basic mode -
Coot 1 is using the GPU in the way it was intended to be used - not
transferring the map line by line from the CPU to the GPU each frame.
So, with my machine, in the coot spin test, with a sampling rate of
2.5 and a radius of 99, Coot 0.9.8.1 spins at 5fps, and Coot 1 spins
at 60fps for all render modes (limited by monitor sync).
Coot 1 has three render modes: Basic, Standard and Fancy. Basic mode
draws models with lines (like Coot 0.x does), Standard mode uses
(only) ambient, diffuse and specular lighting, Fancy mode adds
brightness, gamma, depth blur, SSAO and shadows.
Fancy mode in 4K fullscreen with a ribosome drops the frame rate to
less than 60 fps on my computer (RTX 2070 Super).
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. [] Any suggestions are
appreciated!
OK, so Coot 1 now takes more than 1 second to open in graphics mode on
my computers (SSD and m.2 NVMe PCIe 4). Coot 0.9.x was 0.35s. I
haven't tested it from a hard drive, but I can believe that Coot 1
would take more than 10 seconds - that could be irritating. So m.2
NVMe 4 or 5 it is.
Since 2017 any function/algorithm that I've written that takes more
than 1 second to complete is now written as multi-threaded (and I have
refactored several older algorithms to be multi-threaded also). So
the more of and faster the cores the better. I only have access to
workstation/Xeon processor at work - they are less speedy (and more
expensive (reliable though)). Although I haven't tried them myself I'd
recommend AMD Ryzen 5900X, 5950X or (the new) 5800X3D (the increased
size of the L3 cache could improve contouring and FFT speed).
Process size: I've seen coot get up to more than 20Gb - typically when
using map masking for cryo-EM maps. I have 32 Gb RAM on my main
machine and I haven't see Coot crash due to lack of memory. So I'd
recommend at least that especially if you have a multi-tabbed browser
and other graphics going also.
If you have a 4K monitor (if you don't have one, you should get one)
and want fullscreen 4K Fancy mode goodness (and to make pretty
screenshots) you'd want something better than my card, so the 3000
series, RTX 3070 or 3080. I don't follow AMD graphics cards sad to
say. I intend to make the interface to Blender increasingly powerful
and easy to use - that also will benefit from big memory and a fast
graphics card.
So, get yourself a ballin gamer rig, and you'll have a ballin Coot
workstation :-)
The Best Coot Workstation today would be build around the AMD
Threadripper 3990X and Nvidia RTX 3090 Ti card and Dell UltraSharp
U4320Q monitor.
Paul.
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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 *
*jeroen.mest...@uni-luebeck.de
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https://orcid.org/0000-0001-8532-6699
*Ratzeburger Allee 160
23538 Lübeck, Schleswig-Holstein
Germany*
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