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Computational chemistry, Locally? My rant on SSH

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Re: Computational chemistry, Locally? My rant on SSH

#31

Post by linksnapzz »

gregdaniels421 wrote: post #30
linksnapzz wrote: post #27

Earlier quoted context omitted.

>OP is not ready for corporate environments if "VPN + ssh + 2FA" already "feels like too much" lol Sad that it's necessary, but it's still a shitty environment. That employers foist it on their employees doesn't make it better. >I also wonder how they didn't come across X Forwarding at all? Xforwarding over VPN+residential broadband sounds like a great way to ...not use any sort of gui app.

> Xforwarding over VPN+residential broadband sounds like a great way to ...not use any sort of gui app. During COVID I had the wonderful opportunity to remote into a work computer that had a Matlab license and watch the screen slowly paint in. Each keystroke took multiple seconds to display for me.

X was never, ever, designed for high-latency networks. I don't understand what people are thinking when they recommend that use-case for X apps.

Re: Computational chemistry, Locally? My rant on SSH

#32

Post by gandreani »

n4r9 wrote: post #15

Recently Claude Code said my authentication credentials had become invalid and I needed to log in again. I recorded the ridiculous number of steps this took: - Copy-paste link to browser - Wait several minutes while page load hangs - Click refresh a couple of times, page finally loads - Type in work email - Redirect to work portal, type in work email again - Asked for work password: open KeepassXC and type in Keepass…

You can disable the laptop PIN requirement in keepassXC and store the OTP code in the app as well.

Not the best security practice but thought you should know!

Re: Computational chemistry, Locally? My rant on SSH

#33

Post by fxwin »

linksnapzz wrote: post #27
fxwin wrote: post #3

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 (Transfer…

>OP is not ready for corporate environments if "VPN + ssh + 2FA" already "feels like too much" lol Sad that it's necessary, but it's still a shitty environment. That employers foist it on their employees doesn't make it better. >I also wonder how they didn't come across X Forwarding at all? Xforwarding over VPN+residential broadband sounds like a great way to ...not use any sort of gui app.

Yea it's a shitty environment, it's just a "oh sweet summer child" kind of thing to say :)

I agree that X forwarding is a terrible way for GUI apps, but the OP read like they were just looking at logs or plots/visualizations without much interactivity. X forwarding is good enough for that (At least good enough to give it a try over scping files back and forth)

Re: Computational chemistry, Locally? My rant on SSH

#34

Post by linksnapzz »

NullifyNAN wrote: post #4

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 serv…

> 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.

This is an excellent way to have yr. campus infosec ppl shut the network port on said server, and then take the hardware to get its OS install scrutinized, and get your accounts locked in the process.

Don't do this.

Re: Computational chemistry, Locally? My rant on SSH

#35

Post by tjoff »

gregdaniels421 wrote: post #30
linksnapzz wrote: post #27

Earlier quoted context omitted.

>OP is not ready for corporate environments if "VPN + ssh + 2FA" already "feels like too much" lol Sad that it's necessary, but it's still a shitty environment. That employers foist it on their employees doesn't make it better. >I also wonder how they didn't come across X Forwarding at all? Xforwarding over VPN+residential broadband sounds like a great way to ...not use any sort of gui app.

> Xforwarding over VPN+residential broadband sounds like a great way to ...not use any sort of gui app. During COVID I had the wonderful opportunity to remote into a work computer that had a Matlab license and watch the screen slowly paint in. Each keystroke took multiple seconds to display for me.

x2go can be a bit janky but when setup correctly it can deliver the promise of x-forwarding with good performance even over internet.

Love the ability to just forward one or several applications directly instead of the whole desktop environment. Ability to resume connections are also a godsend.

Seems like that usecase isn't given a lot of effort nowadays.

Re: Computational chemistry, Locally? My rant on SSH

#37

Post by theideaofcoffee »

Qem wrote: post #11

> 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 disco…

Like another comment has mentioned, the field doesn't really lend itself to quick iterating jobs and loops and favors the long batch processes, for several reasons. Oftentimes, a structure calculation or optimization, if run using a "cheap" (computationally-speaking, say a semi-empirical or molecular mechanical) model, those can be done in seconds or minutes, sure. But for calculations that wish to approach or approximate characteristics of a structure seen in the real world, those can takes days or sometimes weeks, depending on the level of theory. There's also the interaction between different programs, or "codes" as they're called, feeding the output of one into another program to look at different phenomena, which is ideal for a batch system, especially if you are exploring a set of related structures or functionalities.

You will see a lot of similar procedures in, say, AI model training and refinement. Those depend on batch jobs as well, pretty heavily. So the batch process isn't really restricted to the weirdness of academia. My source there is actually working on the systems doing training for frontier models...

(Please forgive some of my hand-waviness or vagueness, it's been nearly 20 years since I last touched a lot of this).

Re: Computational chemistry, Locally? My rant on SSH

#38

Post by icedchai »

fxwin wrote: post #3

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 (Transfer…

Don't forget ZScaler and other corporate spyware.

Re: Computational chemistry, Locally? My rant on SSH

#39

Post by fragmede »

gandreani wrote: post #32
n4r9 wrote: post #15

Recently Claude Code said my authentication credentials had become invalid and I needed to log in again. I recorded the ridiculous number of steps this took: - Copy-paste link to browser - Wait several minutes while page load hangs - Click refresh a couple of times, page finally loads - Type in work email - Redirect to work portal, type in work email again - Asked for work password: open KeepassXC and type in Keepass…

You can disable the laptop PIN requirement in keepassXC and store the OTP code in the app as well. Not the best security practice but thought you should know!

Or just use a code and enter a couple of digits to log in and not do that dance.

Re: Computational chemistry, Locally? My rant on SSH

#40

Post by azalemeth »

jltsiren wrote: post #22
fxwin wrote: post #3

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 (Transfer…

The default VSCode configuration can cause problems in HPC clusters. VSCode likes to crawl the files it can see repeatedly. If you have a few users, it doesn't matter. But with many concurrent users and many files, it can destroy file system performance.

Most clusters I use are architected assuming you use vim and look at graphics locally. I do. I also use img-cat. I've never liked VSCode anything.
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