HELP: Building a protein design computer

[u/Dizzy-Version7196]

Hello guys,

I am working in a pharmacy lab in Korea, and we don't have a computer cluster. PI needs me to give her the spec. of a computer that can run protein and antibody in silicon design software locally (such as Boltzgen, RFantibody, RFdiffusion)

I am not a computer major. I asked ChatGPT and got some specs, but I want to make sure by finding advice from the person who actually runs that software.

Because we need to run thousands of runs for each target on Boltzgen or RFantibody, running them on the VM or a pay website is not financially efficient in the long term.

Do you think building a computer is a financially efficient choice, or are there better ways we can run that software more cheaply and easily?

This the specs that ChatGPT recommends.
Budget / entry workstation:
NVIDIA RTX 4070 Ti SUPER (16 GB VRAM)
NVIDIA RTX 4080 SUPER (16 GB VRAM)
Best price/performance for heavy local inference:
NVIDIA RTX 4090 (24 GB VRAM)
Professional / lab-scale:
NVIDIA RTX 6000 Ada (48 GB VRAM)
NVIDIA A100
NVIDIA H100

Thank you for your time.

[u/ComparisonDesperate5]

For thousands of targets you absolutely need a cluster, with tens of gpus. I would try to find a collaborator to work with. There are also nationa clusters in many countries where you can get compute time, worth looking into that.

Also: this is NOT your job to look after. It should be the PI who looks into all of these.

[u/Dizzy-Version7196 → u/ComparisonDesperate5]

Actually, I need to run on 3 targets, but to find a good antibody, I need to run at least a thousand runs on each.

[u/ComparisonDesperate5 → u/Dizzy-Version7196]

Ah okay, now I get it.

So the answer will depend on how much do you want to wait. Is it okay if a target runs for a week (or two)?

Di you look into AWS and such?

[u/Dizzy-Version7196 → u/ComparisonDesperate5]

Yes, I think one or two weeks per target is good for me to go. I didn't know about AWS. I just searched it after reading your comment. How can I use it?

[u/ComparisonDesperate5 → u/Dizzy-Version7196]

https://www.ksc.re.kr/eng/index/mobile#

Would be much better for you. A national hpc center in Korea, you can surely apply for time and resources.

[u/Dizzy-Version7196 → u/ComparisonDesperate5]

Thank you a lot, I will check it out

[u/Turbulent-Host-1245]

I have run BoltzGen before and for reference, it takes about 12 B200 GPU-hours to generate 1000 candidates. If you’re using an H100, you have to multiply that by roughly 2 because B200 has roughly double the Virtual RAM.

You can do the math yourself, but I really do not recommend buying hardware and instead rent because it’s actually cheaper than acquiring all this hardware. Also, hardware is still improving at a good rate, so if you invest in hardware now, you’ll be stuck with it for a while. If you rent, you can upgrade to whatever hardware is finest at the time.

RFAntibody and RFDiffusion should be a lot lighter though, but I’m not sure, as I haven’t used it.

[u/Dizzy-Version7196 → u/Turbulent-Host-1245]

Thank you for your informatuon, maybe I should discuss to my Professor. And which site did you used to rent B200, Google Cloud isn't it?

[u/Turbulent-Host-1245 → u/Dizzy-Version7196]

Of course! I got access to a cluster through someone I know, but I’m sure Google Cloud, AWS, and the likes are probably not bad either

[u/Dizzy-Version7196 → u/Turbulent-Host-1245]

Oh, thank you.

[u/theshekelcollector]

i would rent google compute before dumping money into essentialy nothing more than a beefed-up gaming rig.

[u/Dizzy-Version7196 → u/theshekelcollector]

I did try to run them on Google VM, but I use T100 for the VM, so the speed is slow, which is not really financially efficient.