News Rosetta's role in fighting coronavirus

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Assimilator1

Elite Member
Nov 4, 1999
23,438
192
106
Whose Mr 10? Oh, you mean Tony, right lol.

Am I right in thinking that (in part at least), the credit you get is partially dependant on the time it's crunched?
My main rig has just finished its last SETI WU *sniff*, so I'll switch it to R@H, I'll be the guinea pig for trying out 24hr task time!
 

StefanR5R

Diamond Member
Dec 10, 2016
3,433
3,674
106
Am I right in thinking that (in part at least), the credit you get is partially dependant on the time it's crunched?
Yes, you are. See the quote in post #58.

In a 24h task, the client uses 6 times as much time, but completes 6 times as many models, as in a 4h task. Credit is given for completed models, according to the quote. Therefore it doesn't matter for credit whether you run 1x24h or 6x4h --- if the simulated protein is the same. But credit will vary between tasks with different proteins.
 
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Assimilator1

Elite Member
Nov 4, 1999
23,438
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Thanks :), that was the one I was thinking of.
Well, it's rather academic atm as I can't get any R@H task for my main rig :(, so I've allowed LHC to get new tasks for it for now.
My 2nd rig had already grabbed enough WUs to keep 10 threads busy, so it's ok for now.
 

Markfw

CPU Moderator, VC&G Moderator, Elite Member
Super Moderator
May 16, 2002
20,242
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I still have several hundred Rosetta tasks...
 

Markfw

CPU Moderator, VC&G Moderator, Elite Member
Super Moderator
May 16, 2002
20,242
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136
Cool, been able to pick any up today?
I just looked, the number crunching is getting WAY log, so, I would have to say no.

Edit: I was wrong... They moved from high priority to running or vice-versa
 

Assimilator1

Elite Member
Nov 4, 1999
23,438
192
106
Well apparently R@H hasn't bothered to try to get WUs on my main rig since LHC was running!:rolleyes: (13+hrs ago).
Even though I set LHC to no new tasks a few minutes after starting it.
Has now I hit 'update', why the hell didn't it get some of it's own accord??o_O
 

Markfw

CPU Moderator, VC&G Moderator, Elite Member
Super Moderator
May 16, 2002
20,242
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I got a notice from BOINC (message) that I needed more disk space, and I think it was on my dual 7601, but I have plenty of space available, and I have all but one gig allowed in the config.

Ideas ?
 

Markfw

CPU Moderator, VC&G Moderator, Elite Member
Super Moderator
May 16, 2002
20,242
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Check your BOINC preferences. Along with MEMORY usage you will find DISK usage percentages.
I did that, thats the problem. Plenty available, and plenty specified.....
 

StefanR5R

Diamond Member
Dec 10, 2016
3,433
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There is also a summary of what the client thinks is used & available, in the last tab of boincmgr.
 

Markfw

CPU Moderator, VC&G Moderator, Elite Member
Super Moderator
May 16, 2002
20,242
7,887
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There is also a summary of what the client thinks is used & available, in the last tab of boincmgr.
well, system monitor and the boinc tab both are around 500gb free. I can't find the message now. Odd.....
 

Daishiki

Golden Member
Nov 9, 2001
1,941
36
91
Haven't seen any tasks in days. I just heard my fans spin up while in a meeting. I check F@H. Nope. I switch to Boinc. Finally.
 

Howdy

Senior member
Nov 12, 2017
563
458
106
Haven't seen any tasks in days. I just heard my fans spin up while in a meeting. I check F@H. Nope. I switch to Boinc. Finally.
My machine that had dried up needed a kick start (update) on Rosetta to get it to grab some work.
 

Endgame124

Senior member
Feb 11, 2008
288
182
116
I’ve been using Rosetta as my backup when there is no folding work. Is grid(correctly project name?) the next one to fall back to if Rosetta runs out of WU?
 

Assimilator1

Elite Member
Nov 4, 1999
23,438
192
106
(Sorry, I'm not familiar with that one)
Re R@H , so I have my task time set to 1day (it can go higher!).
These are the task credits etc for my i7 (see sig). (woah! It goes in as a whole table now! :))
Not sure if/how that can be compared to other rigs?

11374569631024375112376966930 Mar 2020, 13:31:27 UTC3 Apr 2020, 12:58:23 UTCCompleted and validated
86,217.28​
86,239.71​
843.37​
Rosetta v4.07
windows_intelx86
11374571351024375115376966930 Mar 2020, 13:31:27 UTC3 Apr 2020, 12:58:23 UTCCompleted and validated
86,086.52​
86,045.77​
608.22​
Rosetta v4.07
windows_intelx86
11374568971024374980376966930 Mar 2020, 13:31:26 UTC3 Apr 2020, 12:56:26 UTCCompleted and validated
86,209.78​
86,285.60​
602.96​
Rosetta v4.07
windows_intelx86
11374569021024374990376966930 Mar 2020, 13:31:26 UTC3 Apr 2020, 12:58:23 UTCCompleted and validated
86,245.33​
86,304.15​
831.97​
Rosetta v4.07
windows_intelx86
11374569041024374994376966930 Mar 2020, 13:31:26 UTC3 Apr 2020, 12:50:44 UTCCompleted and validated
86,022.00​
86,098.68​
1,035.73​
Rosetta v4.07
windows_intelx86
11374569051024374996376966930 Mar 2020, 13:31:26 UTC3 Apr 2020, 12:56:26 UTCCompleted and validated
86,123.94​
86,180.65​
877.16​
Rosetta v4.07
windows_intelx86
11374569611024375108376966930 Mar 2020, 13:31:26 UTC3 Apr 2020, 13:01:13 UTCCompleted and validated
86,225.42​
86,190.21​
826.55​
Rosetta v4.07
windows_intelx86
11374569621024375110376966930 Mar 2020, 13:31:26 UTC3 Apr 2020, 20:50:43 UTCCompleted and validated
86,177.41​
86,146.76​
733.65​
Rosetta v4.07
windows_intelx86
11374571131024375089376966930 Mar 2020, 13:31:26 UTC3 Apr 2020, 12:56:26 UTCCompleted and validated
86,017.40​
85,993.21​
813.67​
Rosetta v4.07
windows_intelx86
11374571291024375109376966930 Mar 2020, 13:31:26 UTC3 Apr 2020, 12:59:16 UTCCompleted and validated
86,193.22​
86,208.12​
731.99​
 

StefanR5R

Diamond Member
Dec 10, 2016
3,433
3,674
106
Here is a glance at what Rosetta@home is currently on to, posted in a recent news thread of the R@h message board:
On April 3 Admin said:


The primary way proteins interact with each other is by sticking to one another. As you may have seen from the R@h graphics application, proteins come in all shapes and sizes. For this reason, most proteins do not stick randomly to each other, but rather stick very specifically to a handful of other proteins. For instance, the viral spike protein of COVID-19 sticks to the human ACE2 protein which is how the virus gains entry to the cell.

The IPD [Institute for Protein Design, University of Washington] has been working hard at improving the ability to design such binding interactions. This process starts by creating a set of scaffold proteins that do not have a purpose other than to fold precisely to an atomic structure. These scaffolds are then docked onto a target protein of interest and their surfaces designed to perfectly complement the target. Finally, the designs are scored, filtered, and tested for binding in the lab.

We will now be using R@h to do the surface design step. Docking and filtering are fast, but actually doing protein design is slow. We will be using the massive amounts of compute power available on R@h to sample every amino acid at every position at the interface. We will then pick the best combinations of amino acids using simulated annealing and Monte-Carlo. Sampling is key for this process and this is why we turn to R@h.

So, join us in the coming weeks as we make binders to COVID-19 and related proteins. We'll still be doing structure prediction and scaffold design as these are absolutely critical to protein science as well. But look out for the interface design cases, because someone might be designing the next COVID-19 cure.

And hopefully you'll stick around once the pandemic is over. We can only design binders like this because we've been working hard at the problem for years. There's still a long way to go, though. Improving the science takes time and computing, so we hope you'll join us on this exciting ride.

-- Brian Coventry
 

borandi

Member
Feb 27, 2011
133
104
116
My big dual 48-core rig had an issue and crashed, which caused about 190 R@H units to error out. Now it's not getting any new R@H work :(
 

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