Computational chemistry, Locally? My rant on SSH
chillphysicsenjoyer.substack.com20 points by crescit_eundo 3 days ago
20 points by crescit_eundo 3 days ago
OP is not ready for corporate environments if "VPN + ssh + 2FA" already "feels like too much" lol
I also wonder how they didn't come across X Forwarding at all? When i used a remote machine for my thesis that was one of the first things i set up, just so i could do small experiments on GPU and look at results more easily.
Basically every issue they seem to have is solved by using VSCode + Remote development (Transferring files, Customizing hotkeys, looking at outputs)
>And as for compute, I also realised that there are many small tasks that can actually be run on my machine
Yes, if you have a $3000 Computer, you can do many things that other people would need to use remote compute for. Depending on the "Cluster" they are talking about, the mac might even have better specs lol
Most issues can be solved by RTFM. They don't seem to have ever considered that...
> You know those really annoying shower controls in fancy hotels when you need to adjust two separate knobs for the pressure and temperature separately? That's clunky.
I like being able to control those two variables separately.
It seems like you’re so close but yet so far. It’s interesting that you concluded that Claude makes it easier to run tasks locally but did not conclude that claude makes it easier to use the cluster. Feels we’re in need of a part 2 where you use CC to automate all of the mundane cluster work.
Also just a hot tip, if you’re able to keep any always-only PC on a university subnet (your PI should have some form of a server) you can use tailscale as a jump proxy and bypass the whole VPN dance.
Yeah I came to the same conclusion.
Universities use all kinds of hard to setup stuff which are often custom built. Slurm configs, custom configured HPC servers etc. All of this pays off though if you need to do heavy computations which a local machine won't do.
IMO it would be better to make Claude build out something that makes interacting with the HPC much easier. A web UI, Tailscale whatever.
> There is also a layer of friction between doing the computations and then analysing the logs that comp chemistry programs spit out. If you want to visualise orbitals or look at the outputs of your simulations, it's really awkward to run Python whilst being in the cluster, and the cluster has no GUI display.
By the description it appears computational chemistry is stuck in batch processing era. They are yet to discover their equivalent to REPL tight feedback loop workflow.
You can fly by wire SLURM via Claude Code and bash fairly easily or run MATLAB batch over ssh tunnel etc
i think instead of trying to do more of the work locally, it might be worth considering trying to work more frictionlessly within the cluster environment instead? e.g. using claude to script visualizing the results and transferring them to your local environment for convenient inspection, or even designing a local GUI for running the jobs and inspecting the results?
it doesn't handle the VPN/2FA friction I guess, but I'd think unless most work can be done locally it would be better to invest in making cluster work more convenient
man 5 ssh_config
/ControlMasterhow would multiplexing ssh connections help for this?
Not a help for the VPN part, but I have to 2FA for SSH, with an app or YubiKey, and that would be tedious to set up with multiple shells. With a control channel it's instant login for subsequent shells, sshfs mounts, etc.
Living this dream with the CI/CD pipeline deploying to a cloud system.
It's really, really hard to shrink the problem and troubleshoot with large, opaque, containerized chunks of functionality and services.
Can I just connect to a DB in a terminal and run some SQL to figure out the problem?
Why, no: no, you cannot.
My work has the vpn simplified to just typing a single code from an app, just an 8 digit number. It's not that bad, but I despise the additional latency the VPN adds.