Folding@Home And Rosetta, For ARM

Most readers will be aware of the various distributed computing projects that provide supercomputer-level resources to researchers by farming out the computing tasks across a multitude of distributed CPUs and GPUs. The best known of these are probably Folding@Home and Rosetta, which have both this year been performing sterling service in the quest to understand the mechanisms of the SARS COVID-19 virus. So far these two platforms have remained available nearly exclusively for Intel-derived architectures, leaving the vast number of ARM-based devices out in the cold. It’s something the commercial distributed-computing-on-your-phone company Neocortix have addressed, as they have successfully produced ARM64 clients for both platforms that will be incorporated into the official clients in due course.

So it seems that mundane devices such as mobile phones and the more capable Raspberry Pi boards will now be able to fold proteins like a boss, and the overall efforts to deliver computational research will receive a welcome boost. But will there be any other benefits? It’s a Received Opinion that ARM chips are more power-efficient than their Intel-derived cousins, but will this deliver more energy-efficient distributed computing? The answer is “probably”, but the jury’s out on that one as computationally intensive tasks are said to erode the advantage significantly.

Folding@Home was catapulted by the influx of COVID-19 volunteers into first place as the world’s largest supercomputer earlier this year, and we’re pleased to say that Hackaday readers have played their part in that story. As this is being written the July 2020 stats show our team ranked at #39 worldwide, having racked up 14,005,664,882 points across 824,842 work units. Well done everybody, and we look forward to your ARM phones and other devices boosting that figure. If you haven’t done so yet, download the client and join us..

Via HPCwire. Thanks to our colleague [Sophi] for the tip.

Help Us Throw More Cycles At The Coronavirus Problem

The Hackaday community has answered the call and put their computers put to work folding proteins found in the coronavirus. Team_Hack-a-Day ranks #44 in the world so far this month, and I’ve seen us rank as high as #19 on 24-hour leaderboards.

Want to join the fight? Donate some of those computing cycles you’re not using to battling SARS‑CoV‑2. You’re probably not an epidemiologist or a vaccine researcher, but you can make their jobs easier by providing them with the data they need through the Folding@home Project.

As Dan Maloney explained in his excellent article on protein folding, understanding the incredibly complex folding behavior of the proteins in the virus will be key to finding treatments and possibly a vaccine. Folding@home connects countless computers via the internet and is now the largest supercomputer in the world, consisting of over 3.5 million CPUs and over half a million GPUs. The resulting data is freely available to researchers.

Let’s take a look at how easy it is to get up and running, how a GPU can supercharge a setup, and dip into the stats for Team_Hack-a-Day’s effort.

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Turn Folds Into Flowers, But Not With Origami

It is said that you’re not a sysadmin if you haven’t warmed up a sandwich on server. OK, it’s not widely said; we made it up, and only said it once, coincidentally enough after heating up a sandwich on a server. But we stand by the central thesis: never let a good source of excess thermal energy go to waste.

[Joseph Marlin] is in the same camp, but it’s not lunch that he’s warming up. Instead, he’s using the heat generated by his Folding@Home rig to sprout seeds for beautiful tropical flowers. A native of South Africa Strelitzia reginae, better known as the striking blue and orange Bird of Paradise flower, prefers a temperature of at least 80° F (27° C) for the two months its seeds take to sprout. With all the extra CPU cycles on a spare laptop churning out warm air, [Joseph] rigged an incubator of sorts from a cardboard box. A 3D-printed scoop snaps over the fan output on the laptop and funnels warm air into the grow chamber. This keeps the interior temperature about 15 degrees above ambient, which should be good enough for the seeds to sprout. He says that elaborations for future versions could include an Arduino and a servo-controlled shutter to regulate the temperature, which seems like a good idea.

The Bird of Paradise is a spectacular flower, but if growing beautiful things isn’t your style, such a rig could easily sprout tomatoes or peppers or get onions off to a good start. No matter what you grow, you’ll need to basics of spinning up a Folding@Home rig, which is something we can help with, of course.

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.

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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)

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