COVID-19

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COVID-19

Postby sekramer10 » Mon May 25, 2020 10:00 pm

I just installed FAH and it's running "Project 13824. This project simulates several myosins found in the human body."

Even though I selected COVID-19.

Is there a reason why you can't select COVID-19 as the project? WTF? Not cool, people. I'd like to know why. Please tell me otherwise I'm going to look around for another program that WILL run COVID -19 solutions. Actually I'm going to do that anyway.

Thanks.
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Re: COVID-19

Postby Joe_H » Mon May 25, 2020 10:11 pm

A. it is a preference, if COVID-19 WUs are available for your system's configuration one will be assigned to it.

B. it also depends when you set the preference in the interface, the WU may have been downloaded and started before you got that far.
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Re: COVID-19

Postby bruce » Mon May 25, 2020 10:15 pm

The preference setting is exactly that: A preference. The scientists run FAH, not the Donors. FAH has studied many, many diseasers other than COVID and will continue to although we've put a priority on COVID. The other projects will resume when COVID projects are not available, whether that's a minute or a day or when a vaccine has been distributed to the world.

All projects have a start and a finish and they're generally assigned from a specific work server. Research begins with the scientist deciding what will be studied and proceeds through a number of steps before a protein model is ready to be introduce to early testing.

The scientists are mostly volunteers, and they do have lives and sometimes they take holidays. They don't release projects that aren't meaningful and they do their best not to waste your time running a duplicate of something that has already been analyzed by someone else. If you happened to request an assignment when the servers were out of COVID projects, you'll get something else. If a server happens to be down, you'll get something else.

I'm sure you'll find something to your liking elsewhere. If not, you'll be welcome to come back if you decide to.
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Re: COVID-19

Postby sekramer10 » Mon May 25, 2020 10:18 pm

Can you recommend a better program that will work on COVID-19 solutions like it should be doing instead of FAH which sucks?
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Re: COVID-19

Postby uyaem » Mon May 25, 2020 11:08 pm

format c: is great :]
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Re: COVID-19

Postby kiore » Mon May 25, 2020 11:11 pm

You have been told that your work is contributing to science and that when there is a COVID-19 project suitable for your hardware you will be assigned it, most currently work is on COVID-19 projects so you were perhaps unlucky on your initial assignment but that not the fault of anyone here and you opinion that the project sucks because you didn't get exactly what you wanted when you wanted it doesn't reflect so well on you.
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Re: COVID-19

Postby MeeLee » Mon May 25, 2020 11:22 pm

sekramer10 wrote:Can you recommend a better program that will work on COVID-19 solutions like it should be doing instead of FAH which sucks?

Most other programs (like World Community Grid, GPUGrid, and Rosetta) all use the same format.
COVID19 WUs are assigned upon availability, in between other WUs.
World Community Grid, being the only one allowing you to run COVID19 batches only, but even with the other projects, I'm only getting sporadic WUs from them.
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Re: COVID-19

Postby JimboPalmer » Mon May 25, 2020 11:37 pm

It is wildly unlikely that you selected COVID-19 before ever starting the program, so the first Work Unit will be random. Assuming you have now selected COVID-19, then if any Work Unit for that is available, you will get one.

However, if no COVID-19 work exists at that moment, you will NOT quit folding, you will fold a Work Unit for another Disease.

In my opinion, the worst that can happen is that you inadvertently help to cure a cancer, etc. Not actually much of a downside.

There are other Distrubuted Computing Projects working at COVID-19, one that comes up here a great deal is Rosetta@Home. I have never used it.

https://boinc.bakerlab.org/rosetta/

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Re: COVID-19

Postby Curt3g » Tue May 26, 2020 5:52 am

Hi sekramer10,

I would offer up one newb's experience/perspective. I discovered Rosetta@home about the same time as Folding@home and have ended up supporting both. I have my GPU working on FaH WU's and a percentage of my CPU cores supporting Rosetta. Before the ability to select a COVID-19 preference was added, the majority of my GPU's WU's were already COVID-related. Now with that preference selected, it's relatively rare that I get anything else.

Also, in doing a bit of reading I discovered the following. For me, the last sentence was particularly insightful.

https://en.wikipedia.org/wiki/Folding@home

“Rosetta@home is a distributed computing project aimed at protein structure prediction and is one of the most accurate tertiary structure predictors. The conformational states from Rosetta's software can be used to initialize a Markov state model as starting points for Folding@home simulations. Conversely, structure prediction algorithms can be improved from thermodynamic and kinetic models and the sampling aspects of protein folding simulations. As Rosetta only tries to predict the final folded state, and not how folding proceeds, Rosetta@home and Folding@home are complementary and address very different molecular questions.”

Hope you find what works for you. Cheers.
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Re: COVID-19

Postby RDDyer » Sun Jun 14, 2020 8:49 pm

Some users may misconstrue this post as a complaint, but it's truly a legit question.

After getting hooked on FAH several weeks ago, I built a new system purely for FAH to add to my two multi-tasking, 'daily-drivers'. The new one has a 12-core AMD processor with two RX5700XT GPUs. Lately, like many of you, I'm going through gaps when one or more of my GPUs are idle while waiting for a WU. (btw, I have selected "ANY disease".)

As Curt3g already noted, "The conformational states from Rosetta's software can be used...as starting points for Folding@home simulations. Rosetta@home and Folding@home are complementary and address very different molecular questions.”

Bottom line: If some of us moved to Rosetta, at least for a while, would it help to decrease FAH idle time by both 1) reducing the demand for WUs and 2) increasing the supply of new FAH WUs, thus helping the overall COVID-19 global effort?

Thanks for your attention!
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Re: COVID-19

Postby JohnChodera » Mon Jun 15, 2020 1:18 am

Hi folks! Just a quick perspective from the Folding@home folks:

The COVID-19 projects come in waves and often have a finite number of work units (WUs) that can run in parallel at once. When all COVID-19 WUs are being computed, you might find that you pick up WUs associated with some other disease for a little while.

This week, we'll be launching a few upcoming waves of both CPU and GPU projects to support the next phase of compound prioritization for the COVID Moonshot, which has already made ~600 compounds and tested ~500 experimentally to try to develop inhibitors of the SARS-CoV-2 main viral protease. You can find more information here: https://foldingathome.org/2020/05/28/the-covid-moonshot

If you could help support that next push, we'd be super grateful! We're also trying to see if we can better announce these pushes and put up some progress bars showing how much of each wave of compound prioritization Folding@home volunteers have made it through.

Thanks again for all of your help! We couldn't do any of this without you all!

~ John Chodera // MSKCC
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Re: COVID-19

Postby RDDyer » Mon Jun 15, 2020 10:32 am

This type of information is invaluable! Understanding the 'wave nature' of this work helps to make sense of times when WUs are scarce. More announcements of this kind, as you say, would be helpful. Maybe they have been there all along, and I just needed to go digging for them??

I know the researchers are your main 'customers', but I as a donor, (aka collaborator), am also a different class of customer. The 'product' you provide for me is the knowledge that my effort and concern for FAH are needed and appreciated. Keeping me in the loop is maybe the best way to keep me a satisfied customer.

Also, I sure don't mind working on other diseases, I just want to help as best I can. And as Jerry Maguire said, "Help me help you."
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Re: COVID-19

Postby Crunchtimer » Mon Jun 15, 2020 9:07 pm

First of all I just want to express my gratitude for having the opportunity to contribute to fighting Covid-19.
John, your write-up of the Moonshot is nothing short of brilliant and I can read it over and over again and still get all excited. I also really like how you reference Moonshot in F@H-projects, as it gets me even more motivated to making sure my rig is crunching 24/7 @ Max.

Your idea of having something similar to the Compound Tracker for F@H-project progress sounds great for motivation.

Thanks!
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Re: COVID-19

Postby Jonazz » Tue Jun 16, 2020 12:32 am

RDDyer wrote:
Bottom line: If some of us moved to Rosetta, at least for a while, would it help to decrease FAH idle time by both 1) reducing the demand for WUs and 2) increasing the supply of new FAH WUs, thus helping the overall COVID-19 global effort?

Thanks for your attention!


The answer to 2 is no. F@H and Rosetta are independent projects. There have been some collaborations in the past, but they're not tackling COVID-19 together as far as I know. I'm not part of the team so I might be wrong here.
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Re: COVID-19

Postby RDDyer » Tue Jun 16, 2020 7:20 am

Jonazz wrote:
RDDyer wrote:
Bottom line: If some of us moved to Rosetta, at least for a while, would it help to decrease FAH idle time by both 1) reducing the demand for WUs and 2) increasing the supply of new FAH WUs, thus helping the overall COVID-19 global effort?

Thanks for your attention!


The answer to 2 is no. F@H and Rosetta are independent projects. There have been some collaborations in the past, but they're not tackling COVID-19 together as far as I know. I'm not part of the team so I might be wrong here.


Hello Jonazz,

The following is from Wikipedia regarding the topic of Rosetta@home, sub-topic "Comparison to similar distributed computing projects":
"Some of Rosetta@home's results are used as the basis for some Folding@home projects. Rosetta provides the most likely structure, but it is not definite if that is the form the molecule takes or whether or not it is viable. Folding@home can then be used to verify Rosetta@home's results, and can provide added atomic-level information, and details of how the molecule changes shape."

While this doesn't say they are working together, they appear to be working cooperatively. Do you know if this is old information and no longer relevant? I too am not part of the team, and as a former colleague used to say, "I always reserve the right to be wrong."
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