Hi guys,
I’m a grad student in a lab that is using Cryo-EM to essentially take pictures of large proteins and then using those pictures, piece together a 3D structure. The software we are using to do that is Relion, and it will be running on CentOS. The way it works is we basically flash freeze purified proteins onto a laser grid, and then film them with an electron microscope. Then we have to piece together the 2D averages that we took pictures of into our 3D model, and that part is very very resource intensive. Our budget is up to $6000 or so.
Looking at the Relion benchmarks, it looks like a Threadripper 2950X should be enough with its 16 cores and 32 threads, to feed the GPUs, since there’s a benchmark of a 1950X feeding two Voltas, and benching 2:43, which is the fastest time on the benchmarks page. So it seems like a 2950X should prevent any kind of CPU bottlenecking.
Similarly, that system is running 128GB RAM, so I think we will be fine with that. How much of an impact will the RAM speed have on the CPU performance? Also, if the motherboard supports quad channel, will any RAM work in quad channel, or does it have to be quad channel specific memory?
We would like to go the 4 GPU route, so I need to find a motherboard that supports 4 GPUs, preferably at full speeds. Does such a thing exist? Everything I’m finding says 2xPCI-E 16 and 2xPCI-E 8, when running 4. Is there enough bandwidth to run 4x16?
As far as the GPUs go, I was thinking 2080s. They don’t support more than 2-Way SLI, but I think I can run them independently for Relion, they will be doing compute, not video rendering, so I want 4 of them. I was thinking MSI-VENTUS, if anyone has any experience with those.
Additionally, I’ll be running probably a 1TB SSD and a pair of 4 TB HDDs. I don’t know who makes a decent hard drive nowadays. WD Red Pro’s?
As for power, it will go through spurts of heavy use most likely, a day or two under constant load, followed by weeks of nothing, etc. I’m thinking 1500W, and so the EVGA SuperNOVA 1600 caught my eye. I’m just trying to figure out the power connectors. The 2080s need an 8+6 (at least teh ones I was looking at do) and so I was looking at the SuperNOVA. It has 9 8-pin VGA plugs, which I assume should be enough. Does each plug go to an 8+8 configuration, or would I need two plugs per 2080?
Finally, for a case and cooling, well, it’s going to be in a separate room so I’m not worried about noise. I was thinking something like a Define XL R2, but the truth is I’m not sure about how to manage the heat from those 4 cards. Does anyone have any case recommendations for keeping them cool? And is the 2950X difficult to keep cool? Would a simple fan be good enough for it, since it won’t be overclocked?
Here is my PC Part Picker list, if anyone wanted to take a quick gander and let me know if something is really off:
https://pcpartpicker.com/user/ccgauvin94/saved/#view=ZW6nHx
And if anyone (@wendell maybe?) is feeling ambitious and wanted to try booting up a TR machine with a couple of video cards and seeing how it handled the Relion benchmark, that would be a huge, huge help!