Problems and Technical Issues with Rosetta@home

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Mr P Hucker
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Message 108095 - Posted: 20 Feb 2023, 4:04:52 UTC - in response to Message 108094.  

Startallback, 3rd party software, makes it look like 7 or any version you want.
47% of Windows worldwide isn't paid for.
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srettie
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Message 108109 - Posted: 20 Feb 2023, 6:03:43 UTC - in response to Message 108090.  


And the word is "Decoys" for some strange reason only known to rosetta staff .


I can hopefully clear that up a little. When predicting protein structures we generate possible structures for a given sequence of amino acids and score them using the Rosetta energy function. These structures can be any chemically reasonable structure and can vary wildly from the correct one. If we have enough sampling and diversity in these decoys of the real structure we can obtain a complete (or at least close to complete) energy landscape for a given sequence, with an energy minimum at the correct structure.
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Jesse Viviano

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Message 108110 - Posted: 20 Feb 2023, 7:26:47 UTC

I have a task that has been stuck waiting for validation at https://boinc.bakerlab.org/rosetta/result.php?resultid=1498325740. Please diagnose why my task never validated.
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Mario W.

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Message 108111 - Posted: 20 Feb 2023, 9:10:02 UTC

Okay, just to reply on that. I complete uninstalled BOINC, deleted the "Program Data" Folder with the Projects complete and afterwards reinstalled the Client and suprisingly it gets (at the Moment 26 Tasks running) heck knows what causes it or maybe was the Issue. I leave it running for a bit and see what happens. Thanks for Reply and Help, much apprechiated.
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.clair.

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Message 108112 - Posted: 20 Feb 2023, 13:15:19 UTC - in response to Message 108109.  


And the word is "Decoys" for some strange reason only known to rosetta staff .


I can hopefully clear that up a little. When predicting protein structures we generate possible structures for a given sequence of amino acids and score them using the Rosetta energy function. These structures can be any chemically reasonable structure and can vary wildly from the correct one. If we have enough sampling and diversity in these decoys of the real structure we can obtain a complete (or at least close to complete) energy landscape for a given sequence, with an energy minimum at the correct structure.

Thankyou srettie that answers it ,
though I think my ear wax is melting :-)
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Mr P Hucker
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Message 108115 - Posted: 23 Feb 2023, 2:30:21 UTC - in response to Message 108109.  

I can hopefully clear that up a little. When predicting protein structures we generate possible structures for a given sequence of amino acids and score them using the Rosetta energy function. These structures can be any chemically reasonable structure and can vary wildly from the correct one. If we have enough sampling and diversity in these decoys of the real structure we can obtain a complete (or at least close to complete) energy landscape for a given sequence, with an energy minimum at the correct structure.
How come your tasks are 3 hours and the usual is 8 hours?
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kotenok2000
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Message 108116 - Posted: 23 Feb 2023, 2:35:14 UTC - in response to Message 108115.  

Probably because they have set Target CPU run time in https://boinc.bakerlab.org/rosetta/prefs.php?subset=project to 3
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Mr P Hucker
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Message 108117 - Posted: 23 Feb 2023, 3:07:22 UTC - in response to Message 108116.  

Probably because they have set Target CPU run time in https://boinc.bakerlab.org/rosetta/prefs.php?subset=project to 3
I meant the new batch are set at the server to be 3 hours. I was wondering why. When I said "your", I was replying to the scientist who created them.
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Profile [VENETO] boboviz

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Message 108126 - Posted: 2 Mar 2023, 14:55:50 UTC - in response to Message 106996.  

There are plans for more python tasks, but we are still working on creating the new disk image for the VM.
This image will likely be larger in size since we hope to run some of the latest deep-learning based methods for protein design and validation.

Computing resources are still very much in high demand within the Baker Lab and IPD so Rosetta@home will definitely help once we can get the latest software set up and running.

Also, the standard rosetta application is currently being worked on for an update.
The IPD has hired a software developer specifically to help expedite this.

I am not sure about timelines at the moment but hopefully there should be updates to both projects/apps within the next month or so.

David Kim


Still waiting...
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Mr P Hucker
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Message 108127 - Posted: 2 Mar 2023, 15:27:32 UTC - in response to Message 108126.  

There are plans for more python tasks, but we are still working on creating the new disk image for the VM.
This image will likely be larger in size since we hope to run some of the latest deep-learning based methods for protein design and validation.

Computing resources are still very much in high demand within the Baker Lab and IPD so Rosetta@home will definitely help once we can get the latest software set up and running.

Also, the standard rosetta application is currently being worked on for an update.
The IPD has hired a software developer specifically to help expedite this.

I am not sure about timelines at the moment but hopefully there should be updates to both projects/apps within the next month or so.

David Kim


Still waiting...
There are 3 million normal tasks again (a batch last week too). Try kicking your computer.
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.clair.

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Message 108132 - Posted: 3 Mar 2023, 1:47:23 UTC - in response to Message 108127.  

Try kicking your computer.

I have done that kind of `reboot` wearing steel toecap boots [just for the hell of it]
though I knew I was sending the case off for scrap metal the next week :-)
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Mr P Hucker
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Message 108133 - Posted: 3 Mar 2023, 1:59:27 UTC - in response to Message 108132.  

I have done that kind of `reboot` wearing steel toecap boots [just for the hell of it]
though I knew I was sending the case off for scrap metal the next week :-)
As a boy we used to go to the skip and make old CRTs implode. My friend caused my dad's primus stove to explode. Apparently it was designed for paraffin not petrol.
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Profile [VENETO] boboviz

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Message 108134 - Posted: 3 Mar 2023, 14:47:17 UTC - in response to Message 108127.  

There are 3 million normal tasks again (a batch last week too). Try kicking your computer.


I'm already crunching.

By the way, Ralph@Home published a new Win64 app after almost 3 years from the last update...
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Mr P Hucker
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Message 108135 - Posted: 3 Mar 2023, 15:15:36 UTC - in response to Message 108134.  

There are 3 million normal tasks again (a batch last week too). Try kicking your computer.


I'm already crunching.
But you said "still waiting" when I was crunching. What was wrong?

By the way, Ralph@Home published a new Win64 app after almost 3 years from the last update...
I left that project as nothing ever happened. Any tasks?
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Profile [VENETO] boboviz

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Message 108136 - Posted: 3 Mar 2023, 16:49:57 UTC - in response to Message 108135.  

But you said "still waiting" when I was crunching. What was wrong?

I'm waiting the new app that David annunced months ago.
Meantime i'm crunching the "3-years-old" app. :-P

Ileft that project as nothing ever happened. Any tasks?

Up to now, no tasks with new app.
And we don't know if is only bugfix or has new protocols/optimizations/etc
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Mr P Hucker
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Message 108139 - Posted: 3 Mar 2023, 17:59:03 UTC - in response to Message 108136.  
Last modified: 3 Mar 2023, 18:02:54 UTC

I'm waiting the new app that David annunced months ago.
Meantime i'm crunching the "3-years-old" app. :-P
Steven changed something, I saw test tasks, now I see named tasks. I thought he'd changed the programming, or was it just the data sets?

Up to now, no tasks with new app.
And we don't know if is only bugfix or has new protocols/optimizations/etc
I'll shove it back on and see if anything happens.

Strangely I had to recreate my account.
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Profile [VENETO] boboviz

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Message 108147 - Posted: 5 Mar 2023, 8:14:44 UTC - in response to Message 108139.  
Last modified: 5 Mar 2023, 8:15:03 UTC

Steven changed something, I saw test tasks, now I see named tasks. I thought he'd changed the programming, or was it just the data sets?

From the apps page the executable is still the same.
Maybe they change the input files


Strangely I had to recreate my account.

Uh, that's stange.
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Mr P Hucker
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Message 108149 - Posted: 5 Mar 2023, 14:39:45 UTC - in response to Message 108147.  

Strangely I had to recreate my account.
Uh, that's stange.
Maybe I closed it, I wouldn't have thought so, but my memory isn't good enough to know what I did. I want to be one of those people who can actually remember with accuracy things they did months ago (do they exist?)
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.clair.

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Message 108150 - Posted: 5 Mar 2023, 22:30:35 UTC - in response to Message 108149.  

Strangely I had to recreate my account.
Uh, that's stange.
Maybe I closed it, I wouldn't have thought so, but my memory isn't good enough to know what I did. I want to be one of those people who can actually remember with accuracy things they did months ago (do they exist?)

Yes , and they end up with top jobs and earn loadzamoney , well maybe .
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kotenok2000
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Message 108151 - Posted: 5 Mar 2023, 22:33:39 UTC - in response to Message 108149.  

They work with british police.
https://en.wikipedia.org/wiki/Super_recogniser
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Message boards : Number crunching : Problems and Technical Issues with Rosetta@home



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