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So What Is Protein Folding, Anyway?:
The current COVID-19 pandemic is rife with problems that hackers have attacked with gusto. From 3D printed face shields and homebrew face masks to replacements for full-fledged mechanical ventilators, the outpouring of ideas has been inspirational and heartwarming. At the same time there have been many efforts in a different area: research aimed at fighting the virus itself.
Getting to the root of the problem seems to have the most potential for ending this pandemic and getting ahead of future ones, and that's the "know your enemy" problem that the distributed computing effort known as Folding@Home aims to address. Millions of people have signed up to donate cycles from spare PCs and GPUs, and in the process have created the largest supercomputer in history.
But what exactly are all these exaFLOPS being used for? Why is protein folding something to direct so much computational might toward? What's the biochemistry behind this, and why do proteins need to fold in the first place? Here's a brief look at protein folding: what it is, how it happens, and why it's important.
]...] Protein folding research is central to our understanding of so many diseases and infections that even once we figure out a way to beat COVID-19, the Folding@Home network, which as seen such explosive growth over the past month, will not go idle for long. The network is a research tool well-suited to exploring protein models central to dozens of diseases that are related to misfolded proteins, such as Alzheimer's and variant Cruetzfeldt-Jakob disease, often incorrectly called mad-cow disease. And when the next virus inevitably comes along, all that horsepower, and all the experience being gained in managing it, will be ready to go again.
I thought I had a good general idea of what protein folding was. And then this article made clear that there was much Much MUCH more to it than I had imagined! I found it to be written at just the right level to convey information without going into the weeds with too much detail; highly recommended!
For those who haven't heard of it before, folding@home is a way for people to donate unused CPU cycles towards protein folding calculations. If you decide to participate, soylentnews even has a team that you can join!
(Score: 3, Informative) by Runaway1956 on Wednesday April 15 2020, @06:55AM (6 children)
Oh - two computers, and two CPU's, with a total of four cores?
You can change that. Easiest is using FAHControl. Right click on one client on each machine. Probably whichever client is closest to being finished. In the dropdown, click "finish". When that client has finished and returned it's WU, go to slot control, and delete it. Now, go to the OTHER client on the same machine, go into configuration > slot control and adjust that number to -1 - that is negative 1. That slot will then recognize that it is running on a dual core, and make use of the resources available to that CPU.
When you examine that client in the future, it will APPEAR THAT the client is using a single core. But, in actuality, that second CPU core plays a support role for the core that is running.
If you were running a GPU on the same machine, that would be more obvious. A machine with two GPUS, and 32 CPU cores, the CPU client only uses 30 CPU cores, and the other two each supports the GPU clients.
I hope I haven't mangled that too badly.
(Score: 2) by RS3 on Wednesday April 15 2020, @02:33PM (2 children)
Thank you, makes absolute sense. I had played with the slot control, and used "task manager" to watch CPU utilization and it didn't change. I wonder if the work units are pre-programmed for single core and won't spread out to multiple cores? The bottom line is I didn't put much time into messing with it. And, my work units complete in much less time than allotted. All that said, I wonder if my machines are doing more good by doing 4 work units rather than 2?
So again, why are some of my points being given to some team that's not in any of my settings?
(Score: 3, Informative) by Runaway1956 on Wednesday April 15 2020, @03:06PM (1 child)
Time alloted is just a deadline. CPU or GPU, if you routinely butt up against the deadline, then there is most likely a problem. Most likely problem, is that the client is set to run only in idle, but the machine is never idle. The client looks for the screens to be shut off by power management, then it crunches, on windows.
As for giving points to other teams? Go into FAHControl > configure > Identity > first box gets your name, second box gets SoylentNews team number (230319) and the passkey gets whatever passkey was emailed to you when you filled out this page: https://apps.foldingathome.org/getpasskey [foldingathome.org]
If you make a typo in any of those boxes, your account won't be awarded the points, and SN may not get the points either. "Wasted" points aren't wasted, however. If FAH can't award the points any other way, they'll go to Anonymous. Example of an intentional "typo" is https://apps.foldingathome.org/teamstats/team230319.html, [foldingathome.org] scroll down far enough, and you will find Runaway1956NACL. That was a test account, to see how that Chrome native client worked, I made sure to get the points awarded to SN, but not to my main account.
NOTE: When requesting a passkey at the address above, you must use your SoylentNews team member ID, and you must use a valid email that you can access at least once to recover the passkey. Throwaway emails are fine, if you can get into once, and then save your passkey.
Not everyone may be aware of this, but the use of a passkey makes your work worth more points. I don't remember what the bonus is, but if interested, you can look it up.
The passkey is pretty long, it's best to copy and paste it into the client. If necessary, you can copy paste into a text file, and move it from machine to machine.
Hope that helps!
(Score: 2) by RS3 on Wednesday April 15 2020, @05:18PM
You're particularly good at explaining things. You will never be hired to write technical manuals. They're only meant to confuse and make work for tech support. :)
/s
Thank you again. I did most of that, but I didn't register and get a passkey. I might do that to get the bonus.
Again, I erased and re-entered the username (same as here) and SN's 230319, but it still gives some points to some odd team. I can't figure out where FAH stores that info. If I could find that secret hiding place, I might be able to edit out the other team's ID.
I'll uninstall FAH (after using "finish" command), try to clean up any "stuff" left behind, and try yet again.
Thanks again, and thanks for running it so much and the high points you've gotten.
(Score: 2) by RS3 on Friday April 17 2020, @05:10PM
Update: you may know there's a new FAH client to download 7.68.
So I let clients finish, uninstalled including removing "data" and installed new client. Only did the 1 CPU "slot" (-1). 1st machine got a Covid-19 work unit, and both cores are in use- total CPU utilization 100%. That's a good thing.
Tried to add a GPU "slot" and it just won't "take". I click "save" but it never shows up. And it has OpenCL API.
2nd computer: did same uninstall / install new client. Again, won't "take" a GPU. It's in the list, but disappears after I hit "save".
On 2nd computer, Covid-19 work unit only running on 1 core. "Slot" is -1.
I think this happened weeks ago when I started this, and that's why I added a 2nd CPU "slot", which I may do again because I have 1/4 of my available horsepower sitting idle.
(Score: 2) by RS3 on Friday April 17 2020, @05:18PM (1 child)
Correction: (wish we could edit posts here...) on 2nd machine, both CPU cores are in fact in use, but running at 50% total. I've set power to "full" and "priority" to "slightly higher".
Both machines are 99% identical- machine, OS, FAH client settings, etc.
As with all of my computers, most unnecessary "stuff" is turned off- many unneeded Windows processes, no automatic updaters running, no background cycle-stealers running.
When I had 2 CPU "slots", each core would get a "work unit" and run at 100%.
No clue right now...
(Score: 2) by Runaway1956 on Friday April 17 2020, @08:00PM
For "reasons", I don't run the Windows CPU's, so I can't look there for answers. That's 8 core, anyway. On Linux, this machine has 32 CPU cores, and 2 GPU's. FAHControl clearly shows that only 30 cores are normally in use, with one core supporting each of the GPU's.
Top, htop, and the like all show my CPU's being used 100%, all the time. At times, there will be less than 30 cores in use, due to vagaries of how the folding cores are programmed and work.
If I were in your position, I'd just leave both machines set on -1 and allow the client to choose what is best. Just watch it for some days, and see if it every uses the other cores. You may be seeing an intermittent "problem" that isn't really a problem. Let the client sort it out, and it should work fine.