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.

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Hackaday Links: March 29, 2020

It turns out that whacking busted things to fix them works as well on Mars as it does on Earth, as NASA managed to fix its wonky “mole” with a little help from the InSight lander’s robotic arm. Calling it “percussive maintenance” is perhaps a touch overwrought; as we explained last week, NASA prepped carefully for this last-ditch effort to salvage the HP³ experiment, and it was really more of a gentle nudge that a solid smack with the spacecraft’s backhoe bucket. From the before and after pictures, it still looks like the mole is a little off-kilter, and there was talk that the shovel fix was only the first step in a more involved repair. We’ll keep an ear open for more details — this kind of stuff is fascinating, and beats the news from Earth these days by a long shot.

Of course, the COVID-19 pandemic news isn’t all bad. Yes, the death toll is rising, the number of cases is still growing exponentially, and billions of people are living in fear and isolation. But ironically, we’re getting good at community again, and the hacker community is no exception. People really want to pitch in and do something to help, and we’ve put together some resources to help. Check out our Hackaday How You Can Help spreadsheet, a comprehensive list of what efforts are currently looking for help, plus what’s out there in terms of Discord and Slack channels, lists of materials you might need if you choose to volunteer to build something, and even a list of recent COVID-19 Hackaday articles if you need inspiration. You’ll also want to check out our calendar of free events and classes, which might be a great way to use the isolation time to better your lot.

Individual hackers aren’t the only ones pitching in, of course. Maybe of the companies in the hacker and maker space are doing what they can to help, too. Ponoko is offering heavy discounts for hardware startups to help them survive the current economic pinch. They’ve also enlisted other companies, like Adafruit and PCBWay, to join with them in offering similar breaks to certain customers.

More good news from the fight against COVID-19. Folding@Home, the distributed computing network that is currently working on folding models from many of the SARS-CoV-2 virus proteins, has broken the exaFLOP barrier and is now the most powerful computer ever built. True, not every core is active at any given time, but the 4.6 million cores and 400,000-plus GPUs in the network pushed it over from the petaFLOP range of computers like IBM’s Summit, until recently the most powerful supercomputer ever built. Also good news is that Team Hackaday is forming a large chunk of the soul of this new machine, with 3,900 users and almost a million work units completed. Got an old machine around? Read Mike Sczcys’ article on getting started and join Team Hackaday.

And finally, just because we all need a little joy in our lives right now, and because many of you are going through sports withdrawal, we present what could prove to be the new spectator sports sensation: marble racing. Longtime readers will no doubt recognize the mad genius of Martin and his Marble Machine X, the magnificent marble-dropping music machine that’s intended as a follow-up to the original Marble Machine. It’s also a great racetrack, and Martin does an amazing job doing both the color and turn-by-turn commentary in the mock race. It’s hugely entertaining, and a great tour of the 15,000-piece contraption. And when you’re done with the race, it’s nice to go back to listen to the original Marble Machine tune — it’s a happy little song for these trying times.

Hackaday Podcast 060: Counting Bees, DogBox Transmissions, And The Lowdown On Vents, BiPAP, And PCR

Hackaday editors Elliot Williams and Mike Szczys recount the past week in hardware hacking. There’s a new king of supercomputing and it’s everyone! Have you ever tried to count bees? Precision is just a cleverly threaded bolt away. And we dig into some of the technical details of the coronavirus response with a close look at PCR testing for the virus, and why ventilators are so difficult to build.

Take a look at the links below if you want to follow along, and as always tell us what you think about this episode in the comments!

Direct download (74.1 MB)

Places to follow Hackaday podcasts:

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Coronavirus And Folding@Home; More On How Your Computer Helps Medical Research

On Wednesday morning we asked the Hackaday community to donate their extra computer cycles for Coronavirus research. On Thursday morning the number of people contributing to Team Hackaday had doubled, and on Friday it had doubled again. Thank you for putting those computers to work in pursuit of drug therapies for COVID-19.

I’m writing today for two reasons, we want to keep up this trend, and also answer some of the most common questions out there. Folding@Home (FAH) is an initiative that simulates proteins associated with several diseases, searching for indicators that will help medical researchers identify treatments. These are complex problems and your efforts right now are incredibly important to finding treatments faster. FAH loads the research pipeline, generating a data set that researchers can then follow in every step of the process, from identifying which chemical compounds may be effective and how to deliver them, to testing they hypothesis and moving toward human trials.

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Join Team Hackaday To Crunch COVID-19 Through Folding@Home

Donate your extra computer cycles to combat COVID-19. The Folding@Home project uses computers from all over the world connected through the Internet to simulate protein folding. The point is to generate the data necessary to discover treatments that can have an impact on how this virus affects humanity. The software models protein folding in a search for pharmaceutical treatments that will weaken the virus’ ability to attack the human immune system. Think of this like mining for bitcoin but instead we’re mining for a treatment to Coronavirus.

Initially developed at Standford University and released in the year 2000, this isn’t the first time Hackaday has advocated for Folding@Home. The “Team Hackaday” folding group was started by readers back in 2005 and that team number is still active, so let’s pile on and work our way up the rankings. At the time of writing, we’re ranked 267 in the world, can we get back up to number 30 like we were in 2008? To use the comparison to bitcoin once again, this is like a mining pool except what we end up with is a show of goodwill, something I think we can all use right about now.

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Hackaday Links: March 8, 2020

A lot of annoying little hacks are needed to keep our integer-based calendar in sync with a floating-point universe, and the big one, leap day, passed us by this week. Aside from the ignominy of adding a day to what’s already the worst month of the year, leap day has a tendency to call out programmers who take shortcuts with their code. Matt Johnson-Pint has compiled a list of 2020 leap day bugs that cropped up, ranging from cell phones showing the wrong date on February 29 to an automated streetlight system in Denmark going wonky for the day. The highest-profile issue may have been system crashes of Robinhood, the online stock trading platform. Robinhood disagrees that the issues were caused by leap day code issues, saying that it was a simple case of too many users and not enough servers. That seems likely given last week’s coronavirus-fueled trading frenzy, but let’s see what happens in 2024.

Speaking of annoying time hacks, by the time US readers see this, we will have switched to Daylight Saving Time. Aside from costing everyone a precious hour of sleep, the semiannual clock switch always seems to set off debates about the need for Daylight Saving Time. Psychologists think it’s bad for us, and it has elicited a few bugs over the years. What will this year’s switch hold? Given the way 2020 has been going so far, you’d better buckle up.
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CRAYFIS Hijacks Our Cellphones For A Worldwide Cosmic Ray Detector

Although scientists have known about Ultra-High Energy Cosmic Rays (UHECRs) for years, nobody can pinpoint their origin. When these UHECRs hit the ground, however, they cause a widespread local disturbance called an air shower. This air shower is a wide dispersion of photons, muons, and electrons at sea level. The means of observing this air shower mandates a widespread geographic region for detecting them. One solution would be a very big detector. Physicists [Daniel] and [Michael] discovered an alternative to pricey hardware, though. By leveraging the CMOS sensors in our smartphones, they can borrow some CPU cycles on our phones to create a worldwide detector network.

According to their paper, the CMOS camera in our smartphones is sensitive to the spectrum of radiation induced by muons and photons from these air showers. With an app running on our phones, [Daniel], [Michael], and other scientists can aggregate the data from multiple detections in a similar region to better understand their origins.

If you’re concerned about CRAYFIS taking away from your talk or web-browsing time, fear not; it runs in the background when a power source has been detected, hopefully, when you are asleep. It’s not the first time we see scientists tap into our computing resources, but this is certainly an achievement made possible in only the last few years by the sensor-loaded smartphone that charges on many of our night stands. With over 1.5 billion smartphones active in the world, we’re thrilled to see a team cleverly leveraging a ubiquitous and already-well-distributed resource.

via [NPR]