Behind The Scenes Of Folding@Home: How Do You Fight a Virus with Distributed Computing?

A great big Thank You to everyone who answered the call to participate in Folding@Home, helping to understand proteins interactions of SARS-CoV-2 virus that causes COVID-19. Some members of the FAH research team hosted an AMA (Ask Me Anything) session on Reddit to provide us with behind-the-scenes details. Unsurprisingly, the top two topics are “Why isn’t my computer doing anything?” and “What does this actually accomplish?”

The first is easier to answer. Thanks to people spreading the word — like the amazing growth of Team Hackaday — there has been a huge infusion of new participants. We could see this happening on the leader boards, but in this AMA we have numbers direct from the source. Before this month there were roughly thirty thousand regular contributors. Since then, several hundred thousands more started pitching in. This has overwhelmed their server infrastructure and resulted in what’s been termed a friendly-fire DDoS attack.

The most succinct information was posted by a folding support forum moderator.

Here’s a summary of current Folding@Home situation :
* We know about the work unit shortage
* It’s happening because of an approximately 20x increase in demand
* We are working on it and hope to have a solution very soon.
* Keep your machines running, they will eventually fold on their own.
* Every time we double our server resources, the number of Donors trying to help goes up by a factor of 4, outstripping whatever we do.

Why don’t they just buy more servers?

The answer can be found on Folding@Home donation FAQ. Most of their research grants have restrictions on how that funding is spent. These restrictions typically exclude capital equipment and infrastructure spending, meaning researchers can’t “just” buy more servers. Fortunately they are optimistic this recent fame has also attracted attention from enough donors with the right resources to help. As of this writing, their backend infrastructure has grown though not yet caught up to the flood. They’re still working on it, hang tight!

Computing hardware aside, there are human limitations on both input and output sides of this distributed supercomputer. Folding@Home need field experts to put together work units to be sent out to our computers, and such expertise is also required to review and interpret our submitted results. The good news is that our contribution has sped up their iteration cycle tremendously. Results that used to take weeks or months now return in days, informing where the next set of work units should investigate.

As promised, here is our first glimpse of the #COVID19 spike protein (aka the demogorgon) in action, courtesy of @foldingathome . More to come! pic.twitter.com/iD2crCMHcX

— Greg Bowman (@drGregBowman) March 16, 2020

Is this work actually useful?

In a word, yes. Folding@Home results are available to researchers at no cost, and this data has contributed to many published papers and even more in the pipeline. For more details on publishing see our earlier update, but there were a few new questions in this AMA beyond papers.

This global pandemic has attracted attention at all levels, so there are many other computational research projects running like AlphaFold and efforts at Oak Ridge National Laboratory. Folding@Home isn’t even the only distributed computing platform, with Rosetta@Home on BOINC also vying for time on people’s personal computers. Are we all just duplicating effort? The team assured us that we are not. All of these are complementary efforts attacking the challenge from different sides. They are coordinating with, not competing against, all of these other researchers.

They do acknowledge it’s hard to make their work understandable outside of medical researchers. But public outreach is something they very much want to improve upon. They haven’t found a way to condense such a complex field into a single tweet, but in the meantime they’ll settle for efforts like this eleven-part thread summarizing how Folding@Home helps drug discovery and development.

What does the future hold?

We’re big fans of open source here at Hackaday, and thankfully someone brought up that topic. There is intent to open-source the Folding@Home client but that hasn’t happened yet and obviously not their top priority at the moment. They hope opening their source will attract contributors to bring Folding@Home to more platforms. BOINC is an obvious candidate, and we can also think of upcoming powerful video game consoles with teraflops to spare. Software developers who have a newfound interest in this field can get started by looking over the existing open-source foundations: GROMACS for their CPU folding core, and OpenMM for their GPU folding core. Additional technical background can be found on the folding support forum.

We’d love to have you join in the effort, if you do, use the team code #44851 to track your stats as part of Team Hackaday. And, we encourage all participants to continue even after this specific crisis is over, whenever that may be. After the original SARS subsided, research attention withered and in hindsight that might have been a mistake. Yes, we need to focus on SARS-CoV-2 today, but researchers want a better general understanding of the whole family. It’s only a matter of time before SARS-CoV-3 (or whatever its name will be) makes its appearance, how prepared will we be? Your support of Folding@Home will continue to be valuable long after this pandemic has been retired to the history books.

[Main image source: Simulation of millisecond protein folding: NTL9 (from Folding@home)]

from Hackaday https://ift.tt/2R1sXNg