I would like to attach to some project that study SARS-CoV-2 on GPU.

If you find one please share with us.

Sure.
It seems WCG in process of making project for that, but will it CPU only or not - time will tell. Signed up for news for now.

Their Open Pandemics project will be CPU to start with as they want the project up & running & from the 2 threads on that, it seems they are considering GPU once that is done.

Created team forum. Suggestions welcome.

Created team forum. Suggestions welcome.

Joined, but will ask no work for now from WCG.

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SETI apps news
We're not gonna fight them. We're gonna transcend them.

Please correct me if I'm wrong in Rosetta operation understanding.

It sends data to compute as many possible protein configurations/docking configurations as length of CPU run allows.
Default is 8h. And user can change it. So, if user allows more hours to run, already downloaded database and particular protein data will be used more fully. If time is short, some another user gets same data to continue modeling. Hence, if deadline allows better to use longer run times.
And if deadline miss occurs user can shorten allowable task computation time to avoid deadline miss (but project will need to resend data somewhere else to get full results).
Is it correct?

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SETI apps news
We're not gonna fight them. We're gonna transcend them.

It sends data to compute as many possible protein configurations/docking configurations as length of CPU run allows.
Default is 8h. And user can change it. So, if user allows more hours to run, already downloaded database and particular protein data will be used more fully. (...) Hence, if deadline allows better to use longer run times.

Yes, the downloaded files will be used for more work. This is good to decrease the load on the servers, even I can't recall issues over there like we know from SETI. Also you are not loosing so much time for starting the tasks. OTOH if a task errors out later, more work is lost. Must see how stable your computers are running Rosetta, that's different for every computer and nobody really knows why.

If time is short, some another user gets same data to continue modeling.

Well, many users will get same data anyway, they generate (hundreds of?) thousands of models from the same data.

And if deadline miss occurs user can shorten allowable task computation time to avoid deadline miss (but project will need to resend data somewhere else to get full results).

The user can even decrease the runtime after the WU has started if he might miss the deadline (or increase if he wants to, for example when server out of WUs, did that once myself and doubled my cache that way), just change it on the website, force scheduler request and restart BOINC, the task will start with new target CPU runtime or if you don't restart BOINC, all following tasks will start with it.
It is however not so critical if you miss the deadline a bit, a new task will be send out, but your accepted and validated, IIRC even if you return it after the other host. The starting points are generated randomly on the host before the actual crunching, so both results will be different and useful for the project, you just need to return the result before it's purged from the database. That's also the reason, why Rosetta uses a quorum of 1, no two results are the same anyway.

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All users are welcome.

Come help us "Seti Orhpans" fight Covad19 at Rosetta

Stay safe .

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Dave

Please correct me if I'm wrong in Rosetta operation understanding.

It sends data to compute as many possible protein configurations/docking configurations as length of CPU run allows.
Default is 8h. And user can change it. So, if user allows more hours to run, already downloaded database and particular protein data will be used more fully. If time is short, some another user gets same data to continue modeling. Hence, if deadline allows better to use longer run times.
And if deadline miss occurs user can shorten allowable task computation time to avoid deadline miss (but project will need to resend data somewhere else to get full results).
Is it correct?

Yes, You can adjust"Target Runtime" here https://boinc.bakerlab.org/rosetta/prefs.php?subset=project The default is 8 hours, you can select anything from 2 to 36 hours.

There is a fair amount of discussion on some old Rosetta threads if you search.

I used contribute to the RALPH project https://ralph.bakerlab.org/ as well as Rosetta.
RALPH is Rosetta Alpha.
RALPH message boards also have more discussion about the fine tuning of Rosetta.

Please correct me if I'm wrong in Rosetta operation understanding.

It sends data to compute as many possible protein configurations/docking configurations as length of CPU run allows.
Default is 8h.

And with generally 4 day deadlines (although apparently some Tasks do have longer deadlines), which is why a very small cache is best, i've found 1 & 0.02 work pretty well for Rosetta only. For those with multiple projects, a smaller cache would be even better.
Even though the Runtimes are fixed, the Estimated completion time for new types of Tasks can be way more, or way less, than the actual processing time. So often people with larger caches get more work than they can handle when a new type of Task (or a new Application with no APR history) is released.

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Grant
Darwin NT

Please correct me if I'm wrong in Rosetta operation understanding.

It sends data to compute as many possible protein configurations/docking configurations as length of CPU run allows.
Default is 8h. And user can change it. So, if user allows more hours to run, already downloaded database and particular protein data will be used more fully. If time is short, some another user gets same data to continue modeling. Hence, if deadline allows better to use longer run times.
And if deadline miss occurs user can shorten allowable task computation time to avoid deadline miss (but project will need to resend data somewhere else to get full results).
Is it correct?

If you move the allowed task computation time while the cache has tasks you can end up with a lot of "runs longer than it should" tasks. My understanding is the "Watch Dog" timer will kick if the task runs more than 4 hours past the "current" allowed task computation.

So if you shorten up your allowed task computation time you will probably get more watch dog cancels till the cache is full of the "new" allowed processing time.

I think if you go from small the larger it doesn't cause as much trouble. I think.

Tom M

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A proud member of the OFA (Old Farts Association).

Well, I'm out. Barring any rare resends at this point.
It's been a good twenty years.
Be looking forward to any news after the final processing of all that we have done.

Meow meow meow!

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"Time is simply the mechanism that keeps everything from happening all at once."

Congrats Mark you got your billion, with a little help, now show us a picture of your toaster.

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Congratulations Mark. It has been a good run.

You could come over to Rosetta and join us.

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Dave

Don't know about the others but, Rosetta has work.,

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Dave

If you move the allowed task computation time while the cache has tasks you can end up with a lot of "runs longer than it should" tasks. My understanding is the "Watch Dog" timer will kick if the task runs more than 4 hours past the "current" allowed task computation.

Nope, the "watch dog" gets the info about the new target runtime, did that myself, no issues at all.

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Thank you all a lot for answers, they definitely improved my understanding of Rosetta workflow. Will be usefull for other "refugees " too IMHO.

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SETI apps news
We're not gonna fight them. We're gonna transcend them.

yes thanks for the Rosetta help posts. I've shortened my tasks from 8 to 4 hours because pausing them when I get seti tasks was causing errors. With only 4 hours per task I can let the Rosetta ones finish before starting seti tasks (not that I get many- but I like prioritizing them).

I'm also asking for Rosetta in small batches (1 day) and then NNT the project. It is working and gives me something to play with while I'm stuck at home.

So.... look what can happen in a mere 1 week 4 days. I went from Zero to 11th place at Einstein, https://einsteinathome.org/community/stats/users.
Of course, things are still changing, and yesterday's numbers show an output of over 7 Million, so, it will probably go a little higher...especially if I get some of that Helicopter money from D.C.

So.... look what can happen in a mere 1 week 4 days. I went from Zero to 11th place at Einstein, https://einsteinathome.org/community/stats/users.
Of course, things are still changing, and yesterday's numbers show an output of over 7 Million, so, it will probably go a little higher...especially if I get some of that Helicopter money from D.C.

And 18th place for a system.

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Grant
Darwin NT

We have 2 new members of Seti Orphans at Rosetta

Boiler Paul and BettyA

Welcome

Come on guys, let's make it BIG.

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Dave

We have 2 new members of Seti Orphans at Rosetta

Boiler Paul and BettyA

Welcome

Come on guys, let's make it BIG.

+1

If I wasn't already in the GPU Usersgroup I would join. Sorry.

Tom

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A proud member of the OFA (Old Farts Association).