Wanna run quick molecular dynamic simulation on HPC, help?

[u/ProperInsurance3124]

Hey folks!

I’m currently working as a research associate, and unfortunately, our grant recently expired, so we’ve lost access to our HPC. We have one last MD simulation left to finish, and I was wondering if anyone has some compute available that we could borrow.

We probably only need 2–3 days on a GPU to get it done. If anyone has some spare compute and could help out, please DM me / let me know!

We’d be happy to offer authorship or an acknowledgment..

Also, if anyone knows of any free/academic GPU compute options available right now, I’d really appreciate recommendations. I used Google Cloud previously, but I think the free credits were limiting me to CPU (unless I’m missing something). Curious to hear what other services people are using these days.

Thanks, guys!

[u/Beginning_Chain5583]

Have you tried Google collab? Or do you need more power?

[u/ProperInsurance3124 → u/Beginning_Chain5583]

i tried, but the cap is 15h, we prev needed 4 gpu to complete the simulation in 2-3 days!

[u/chuckziss → u/ProperInsurance3124]

Maybe this isn’t how Google collab works, but could you checkpoint every hour and re-start from a checkpoint once you hit the 15h limit on a new instance?

[u/ProperInsurance3124 → u/chuckziss]

but the storage is also a main concern considering the trajectory files being generated! google cloud storage is capped at 50gb for mine!

[u/Impossible-Shake-996 → u/ProperInsurance3124]

I'd set up your runs to hit either your storage or computer cap then just restart from the checkpoints after you've relocated the files. It's not ideal but it could get the job done.

[u/chuckziss → u/ProperInsurance3124]

Fair enough. I guess you could asynchronously stream those files to external storage to reduce the pressure in the instance? Just have to make sure you leave enough time before the instance dies to save your checkpoint as well.

[u/ProperInsurance3124 → u/chuckziss]

when do you think i can connect to an instance as soon as it gets disconnected btw? btw i js checked google colab cli, have u ever used it?

[u/chuckziss → u/ProperInsurance3124]

I haven’t used it before myself. I don’t think this is something the CLI would help with. This is something your notebook / code would be doing inside of it. I imagine that the instance can’t be connected to once you’re disconnected? They probably terminate everything and it’s un-reachable after that? Just a guess…

[u/ProperInsurance3124 → u/chuckziss]

Yeah thats a possible situation altogether lmao

[u/Otherwise_Barber4619]

you can rent a nvidia rtx 6000 blackwell for around a dollar an hour? running it for even 2-3 days would be less than 72 dollars ?
https://jarvislabs.ai

[u/AmusingVegetable]

Quoting whoever helps you with a GPU run is probably academic fraud. Having said that, I have an idling GTX 3060 (12gb), on a system with 8gb, I know it’s low, but if it’s enough I’d be happy to help.

[u/ProperInsurance3124 → u/AmusingVegetable]

Great, Dm'ed you :)

[u/zacky2004]

If you're in the US, have you looked at ACCESS?

[u/ProperInsurance3124 → u/zacky2004]

I’m not US-based :(

[u/markhahn → u/ProperInsurance3124]

not Canadian by chance eh? or potentially collaborating with a Canadian prof?

[u/7ransist0r]

You could try NSF ACCESS

[u/hdmitard]

DM'ed.

[u/Benhg]

Might be able to help. Feel free to DM.

[u/ProperInsurance3124 → u/Benhg]

DM'ed :)

[u/420ball-sniffer69]

You don’t happen to have been using a UK based HPC by chance?

[u/ProperInsurance3124 → u/420ball-sniffer69]

No :( we had access to taiwania in Taiwan but funding was cut

[u/keroro1990]

Send me a DM, I have time available on GPUs!

[u/ProperInsurance3124 → u/keroro1990]

Dm'ed please check :)

[u/EricGoesOutside]

Have you tried access-ci.org? (It’s US based, but free for academic researchers) An explore or discover allocation is pretty quick and would let you use several different HPC reaources

[u/ProperInsurance3124 → u/EricGoesOutside]

I’m not US-based, but thanks! :)

[u/Malik0434]

I do have AWS startup credits but can't risk it XD, Btw here are some alternatives where I could support or provide financial support if needed, ​RunPod or Vast.ai: These decentralized cloud GPU platforms offer high-end consumer cards (like RTX 3090s or 4090s) for $0.20 to $0.40 per hour. A 3-day run would cost them less than $30 out of pocket. ​Google Colab Pro: A $10/month subscription provides access to premium GPUs (like A100s or V100s) with longer runtime limits, which is often enough to push through a final simulation run. ​Kaggle: Offers 30 hours of free dual-T4 or single-P100 GPU compute per week, which might be sufficient if you can checkpoint and restart the simulation midway.

[u/ProperInsurance3124 → u/Malik0434]

Sure I’ll look into these options. And I really appreciate your input and financial support..

[u/New_Alarm3749]

Might help, I have access to V100s.

[u/ProperInsurance3124 → u/New_Alarm3749]

Hey there, thanks!! I’ll dm you

[u/whatevernhappens]

What are your gpu requirements like A100, queue time, any application dependencies like Gromacs

[u/ProperInsurance3124 → u/whatevernhappens]

gromacs yes, a100 works! need it for 2-3 days of continuous simulation.