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Anubis author here. Tell me what I'm missing to implement protein folding without having to download gigabytes of scientific data to random people's browsers an

by xena 1y ago

Anubis author here. Tell me what I'm missing to implement protein folding without having to download gigabytes of scientific data to random people's browsers and I'll implement it today.

dijksterhuis 1y ago
Perhaps something along the lines of folding@home? https://foldingathome.org https://foldingathome.org https://github.com/FoldingAtHome/fah-client-bastet https://github.com/FoldingAtHome/fah-client-bastet seems like it would be possible to split the compute up. FAQ: https://foldingathome.org/faq/running-foldinghome/ https://foldingathome.org/faq/running-foldinghome/ What if I turn off my computer? Does the client save its work (i.e. checkpoint)? > Periodically, the core writes data to your hard disk so that if you stop the client, it can resume processing that WU from some point other than the very beginning. With the Tinker core, this happens at the end of every frame. With the Gromacs core, these checkpoints can happen almost anywhere and they are not tied to the data recorded in the results. Initially, this was set to every 1% of a WU (like 100 frames in Tinker) and then a timed checkpoint was added every 15 minutes, so that on a slow machine, you never lose more that 15 minutes work. > Starting in the 4.x version of the client, you can set the 15 minute default to another value (3-30 minutes). caveat: I have no idea how much data "1 frame" is.
- jerf 1y ago
  You can't do anything useful with checkpoints due to the same-site origin problem. Unless you can get browser support for some sort of proof of work that did something useful that whole line is a non-starter. No single origin involves a useful amount of work. The problem is that this problem is going to be all overhead. If you sit down and calmly work out the real numbers, trying to distribute computations to a whole bunch of consumer-grade devices, where you can probably only use one core for maybe two seconds at a time a few times an hour, you end up with it being cheaper to just run the computation yourself. My home gaming PC gets 16 CPU-hours per hour, or 56700 CPU-seconds. (Maybe less if you want to deduct a hyperthreading penalty but it doesn't change the numbers that much.) Call it 15,000 people needing to run 3-ish of these 2-second computations, plus coordination costs, plus serving whatever data goes with the computation, plus infrastructure for tracking all that and presumably serving, plus if you're doing something non-trivial a quite non-trivial portion of that "2 seconds" I'm shaving off for doing work will be wasted setting it up and then throwing it away. The math just doesn't work very well. Flat-out malware trying to do this on the web never really worked out all that well, adding the constraint of doing it politely and in such small pieces doesn't work. And that's ignoring things like you need to be able to prove-the-work for very small chunks. Basically not a practically solvable problem, barring a real stroke of genius somewhere.

by xena 1y ago

Anubis author here. Tell me what I'm missing to implement protein folding without having to download gigabytes of scientific data to random people's browsers and I'll implement it today.

dijksterhuis 1y ago

Perhaps something along the lines of folding@home? https://foldingathome.org https://foldingathome.org https://github.com/FoldingAtHome/fah-client-bastet https://github.com/FoldingAtHome/fah-client-bastet seems like it would be possible to split the compute up. FAQ: https://foldingathome.org/faq/running-foldinghome/ https://foldingathome.org/faq/running-foldinghome/ What if I turn off my computer? Does the client save its work (i.e. checkpoint)? > Periodically, the core writes data to your hard disk so that if you stop the client, it can resume processing that WU from some point other than the very beginning. With the Tinker core, this happens at the end of every frame. With the Gromacs core, these checkpoints can happen almost anywhere and they are not tied to the data recorded in the results. Initially, this was set to every 1% of a WU (like 100 frames in Tinker) and then a timed checkpoint was added every 15 minutes, so that on a slow machine, you never lose more that 15 minutes work. > Starting in the 4.x version of the client, you can set the 15 minute default to another value (3-30 minutes). caveat: I have no idea how much data "1 frame" is.

jerf 1y ago
You can't do anything useful with checkpoints due to the same-site origin problem. Unless you can get browser support for some sort of proof of work that did something useful that whole line is a non-starter. No single origin involves a useful amount of work. The problem is that this problem is going to be all overhead. If you sit down and calmly work out the real numbers, trying to distribute computations to a whole bunch of consumer-grade devices, where you can probably only use one core for maybe two seconds at a time a few times an hour, you end up with it being cheaper to just run the computation yourself. My home gaming PC gets 16 CPU-hours per hour, or 56700 CPU-seconds. (Maybe less if you want to deduct a hyperthreading penalty but it doesn't change the numbers that much.) Call it 15,000 people needing to run 3-ish of these 2-second computations, plus coordination costs, plus serving whatever data goes with the computation, plus infrastructure for tracking all that and presumably serving, plus if you're doing something non-trivial a quite non-trivial portion of that "2 seconds" I'm shaving off for doing work will be wasted setting it up and then throwing it away. The math just doesn't work very well. Flat-out malware trying to do this on the web never really worked out all that well, adding the constraint of doing it politely and in such small pieces doesn't work. And that's ignoring things like you need to be able to prove-the-work for very small chunks. Basically not a practically solvable problem, barring a real stroke of genius somewhere.