Problems and Technical Issues with Rosetta@home

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Peter Hucker of the Scottish Boinc Team
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Message 104343 - Posted: 20 Jan 2022, 19:33:14 UTC - in response to Message 104341.  
Last modified: 20 Jan 2022, 19:33:48 UTC

Ignore that big fancy number on the front page.
That is what they have in queue for both the AI and RAH of which 99% are AI tasks.
But the point is that was spotted dropping suddenly, so they must have removed some, presumably due to problems. I wish other projects had that number. All we get to see is the little front end buffer on most projects.
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Peter Hucker of the Scottish Boinc Team
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Message 104344 - Posted: 20 Jan 2022, 19:35:13 UTC - in response to Message 104342.  

Check this out from a 4.2 task today

File: C:cygwin64homeboinc4.17Rosettamainsourcesrccore/pack/dunbrack/SingleResidueDunbrackLibrary.hh:306
chi angle must be between -180 and 180: -nan(ind)

Gees...really?!?!?
Looks rather like something tried to use the 4th dimension. Does your processor not support that function?
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Message 104345 - Posted: 20 Jan 2022, 19:48:38 UTC - in response to Message 104344.  

Check this out from a 4.2 task today

File: C:cygwin64homeboinc4.17Rosettamainsourcesrccore/pack/dunbrack/SingleResidueDunbrackLibrary.hh:306
chi angle must be between -180 and 180: -nan(ind)

Gees...really?!?!?
Looks rather like something tried to use the 4th dimension. Does your processor not support that function?

I have no graphics on my CPU.
Besides, the program is supposed to take care of any graphics or whatever.
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Message 104346 - Posted: 20 Jan 2022, 19:51:40 UTC - in response to Message 104343.  

Ignore that big fancy number on the front page.
That is what they have in queue for both the AI and RAH of which 99% are AI tasks.
But the point is that was spotted dropping suddenly, so they must have removed some, presumably due to problems. I wish other projects had that number. All we get to see is the little front end buffer on most projects.



But again, that number is mute to this aspect of the project.
It has no bearing on what we do.

Just watch the numbers I quoted. That is all you need to be concerned about. Because that is the work WE get, not the machine.
It just looks cool to say..oh we have 2 million tasks queued up, but when you dig deeper on Robetta, then you see, AI, AI, AI,AI.....Rosetta,AI,AI,AI,AI maybe a Rosetta.
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Peter Hucker of the Scottish Boinc Team
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Message 104347 - Posted: 20 Jan 2022, 19:55:34 UTC - in response to Message 104345.  

I have no graphics on my CPU.
Besides, the program is supposed to take care of any graphics or whatever.
I was trying to make a joke. It said the angle wasn't within the normal 360 degrees.
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Peter Hucker of the Scottish Boinc Team
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Message 104348 - Posted: 20 Jan 2022, 19:57:44 UTC - in response to Message 104346.  

Ignore that big fancy number on the front page.
That is what they have in queue for both the AI and RAH of which 99% are AI tasks.
But the point is that was spotted dropping suddenly, so they must have removed some, presumably due to problems. I wish other projects had that number. All we get to see is the little front end buffer on most projects.



But again, that number is mute to this aspect of the project.
Actually the word is moot, not that I ever use that strange sounding word. I also have an aversion to the word dupe.

It has no bearing on what we do.

Just watch the numbers I quoted. That is all you need to be concerned about. Because that is the work WE get, not the machine.
It just looks cool to say..oh we have 2 million tasks queued up, but when you dig deeper on Robetta, then you see, AI, AI, AI,AI.....Rosetta,AI,AI,AI,AI maybe a Rosetta.
Admittedly it doesn't tell you which of the two apps it is, but it's more meaningful than the tiny number, which is just the first bunch in their RAM buffer or whatever. The main number is what we always used to look at to see how much work was left. You could see there was a month's supply etc.
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Message 104351 - Posted: 20 Jan 2022, 23:33:40 UTC

Ah ha! Well sorry for the misspelling. Quick typing and no thinking after work.
4th dimension does exist...but anyway...again after work..not thinking. Missed the pun.

Now...if you go here: https://robetta.bakerlab.org/queue.php?id=&target=&username=&seq=&page=2 and look at the active tasks at random, you will see that the majority are queued for RoseTTAFold which is the AI.

You can read about it here:
https://www.ipd.uw.edu/2021/07/rosettafold-accurate-protein-structure-prediction-accessible-to-all/

Now bed...
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Message 104352 - Posted: 20 Jan 2022, 23:46:03 UTC - in response to Message 104351.  

Ah ha! Well sorry for the misspelling. Quick typing and no thinking after work.
4th dimension does exist...but anyway...again after work..not thinking. Missed the pun.

Now...if you go here: https://robetta.bakerlab.org/queue.php?id=&target=&username=&seq=&page=2 and look at the active tasks at random, you will see that the majority are queued for RoseTTAFold which is the AI.

You can read about it here:
https://www.ipd.uw.edu/2021/07/rosettafold-accurate-protein-structure-prediction-accessible-to-all/

Now bed...



Since these Robetta jobs aren't run at Rosetta@home, it doesn't make sense that they would get queued at Rosetta@home.
They seem to be directly sent from Robetta to the Baker Lab cluster and to the HHMI's Janelia Research Campus.

My bet is the 2.6 million tasks on the Rosetta@home queue are all Pythons.
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Peter Hucker of the Scottish Boinc Team
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Message 104353 - Posted: 21 Jan 2022, 0:27:08 UTC - in response to Message 104351.  

Now...if you go here: https://robetta.bakerlab.org/queue.php?id=&target=&username=&seq=&page=2 and look at the active tasks at random, you will see that the majority are queued for RoseTTAFold which is the AI.
The first thing I spotted when looking at the "user input" page was the word KILL somewhere in the sequence. Either I'm a homicidal maniac, or it's because I'm playing fallout 4 on a Ryzen 3900XT that should be folding.
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Peter Hucker of the Scottish Boinc Team
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Message 104354 - Posted: 21 Jan 2022, 1:23:20 UTC - in response to Message 104352.  
Last modified: 21 Jan 2022, 1:23:33 UTC

https://robetta.bakerlab.org/queue.php?id=&target=&username=&seq=&page=2
Since these Robetta jobs aren't run at Rosetta@home, it doesn't make sense that they would get queued at Rosetta@home.
They seem to be directly sent from Robetta to the Baker Lab cluster and to the HHMI's Janelia Research Campus.

My bet is the 2.6 million tasks on the Rosetta@home queue are all Pythons.
So how come there are so many usernames, it certainly looks like Boinc.
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Message 104355 - Posted: 21 Jan 2022, 7:18:41 UTC - in response to Message 104354.  
Last modified: 21 Jan 2022, 7:34:58 UTC

https://robetta.bakerlab.org/queue.php?id=&target=&username=&seq=&page=2
Since these Robetta jobs aren't run at Rosetta@home, it doesn't make sense that they would get queued at Rosetta@home.
They seem to be directly sent from Robetta to the Baker Lab cluster and to the HHMI's Janelia Research Campus.

My bet is the 2.6 million tasks on the Rosetta@home queue are all Pythons.
So how come there are so many usernames, it certainly looks like Boinc.



That's not users related to us. That's the person who submitted the protein.
Again...if its Robetta, its not us. That's all there is to it.


I'll have to dig around some more.
I have always known from other sources that Robetta server supplied Rosetta servers.
That Robetta was where everything is stored.
That may not be the case, but it's something that will take some digging around.
The group is not that transparent on how their setup works.
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Message 104357 - Posted: 21 Jan 2022, 10:18:38 UTC - in response to Message 104355.  

Robetta, as far as I can tell, is separate from Rosetta@home and is used mostly by researchers outside of the Baker Lab/IPD. It's an interface for users who wish to get computing power for their jobs.
Jobs that require the use of Rosetta 4.20 that are submitted to Robetta get sent to Rosetta@home but the rest goes to the other servers that they set up when they launched RoseTTAFold.
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Message 104360 - Posted: 21 Jan 2022, 14:06:18 UTC - in response to Message 104355.  

https://robetta.bakerlab.org/queue.php?id=&target=&username=&seq=&page=2
Since these Robetta jobs aren't run at Rosetta@home, it doesn't make sense that they would get queued at Rosetta@home.
They seem to be directly sent from Robetta to the Baker Lab cluster and to the HHMI's Janelia Research Campus.

My bet is the 2.6 million tasks on the Rosetta@home queue are all Pythons.
So how come there are so many usernames, it certainly looks like Boinc.



That's not users related to us. That's the person who submitted the protein.
Again...if its Robetta, its not us. That's all there is to it.


I'll have to dig around some more.
I have always known from other sources that Robetta server supplied Rosetta servers.
That Robetta was where everything is stored.
That may not be the case, but it's something that will take some digging around.
The group is not that transparent on how their setup works.


Hi, regular Boinc user here, first time posting.

I don't know why, but I've never had issues with python projects tasks. I haven't done anything special apart from downloading VirtualBox alongside Boinc. I assume many people did, unless there's some controversy around VirtualBox that I'm unaware of.
I've seen that I can't have more than 2 python tasks at a time, whatever the reason is, but it's not a limitation for me, as I mostly run tasks for Numberfields@home.

I'm just posting to tell you that users like me exist, although we may be rare (I assume I'm not the only one). I'm not saying that there aren't users related to the running team among the ~1000 users running python tasks right now, I can just tell that I'm not one of them and that it's possible to run python tasks through Boinc and VB. I guess I'm just lucky it works on my laptop.
I can give you more info if you want but I haven't really followed the discussion and I'm not an expert with computers, so try to give instructions if you want technical details.
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Message 104361 - Posted: 21 Jan 2022, 15:19:49 UTC
Last modified: 21 Jan 2022, 15:59:59 UTC

I have posted this many times before. They should make it a sticky if there were any moderator around to do it.

If you are running VirtualBox 6.1.x, you will get the "Vm job unmanageable" problem with the pythons. That is true whether you are running Windows or Linux.
The difference is that it can be fixed with Windows. You go back to VirtualBox 5.2.44
https://www.virtualbox.org/wiki/Download_Old_Builds_5_2

Unfortunately, that does not work on Linux, at least Ubuntu. Firstly, Ubuntu 20.04.3 works only with VBox 6.1.x.
Secondly, even going back to Ubuntu 18.04.6, which allows you to install VBox 5.2.44, still has the problem.

They need to fix it at the project end, by compiling a new Vbox wrapper. They did it on LHC, and it works there. (It has to do with the COM interface, in case you are interested.)

NB: If you reboot frequently, you may not see the problem. It usually occurs after the pythons have been running 12 hours or so, but I have seen it even after a reboot on Ubuntu.
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Peter Hucker of the Scottish Boinc Team
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Message 104363 - Posted: 21 Jan 2022, 18:12:33 UTC - in response to Message 104361.  

That's only one of the problems, I can't get python to work on 6 of 7 Windows PCs no matter which version of VB I use. One of them fails validation at the server end, the rest just sit with almost 0 CPU time.

Pythons for 12 hours? They average 2 hours here.

As for only being able to run a couple at a time, you need a lot of RAM. I can run 5 but it won't do 6 in 16GB.
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Message 104364 - Posted: 21 Jan 2022, 18:31:15 UTC - in response to Message 104363.  

Pythons for 12 hours? They average 2 hours here.

As for only being able to run a couple at a time, you need a lot of RAM. I can run 5 but it won't do 6 in 16GB.

No, not an individual run for 12 hours. After running a series of them continually.
I didn't say anything about running only two. I usually run at least eight, and am presently running twenty on a Ryzen 3900X with 80 GB of memory.
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Peter Hucker of the Scottish Boinc Team
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Message 104365 - Posted: 21 Jan 2022, 18:33:59 UTC - in response to Message 104364.  
Last modified: 21 Jan 2022, 18:34:14 UTC

Pythons for 12 hours? They average 2 hours here.

As for only being able to run a couple at a time, you need a lot of RAM. I can run 5 but it won't do 6 in 16GB.

No, not an individual run for 12 hours. After running a series of them continually.
I didn't say anything about running only two. I usually run at least eight, and am presently running twenty on a Ryzen 3900X with 80 GB of memory.
The two was the post before yours. Sorry, I was too lazy to quote who I was talking to in which bit. I'm giving a dodgy machine another go on the old VB, but I think I've tried this. It just doesn't use the CPU at all.
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Message 104366 - Posted: 21 Jan 2022, 18:36:18 UTC - in response to Message 104365.  

I'm giving a dodgy machine another go on the old VB, but I think I've tried this. It just doesn't use the CPU at all.

I wish I had a fix, but you have tried a lot. Good luck.
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Message 104368 - Posted: 21 Jan 2022, 19:09:29 UTC - in response to Message 104357.  

Robetta, as far as I can tell, is separate from Rosetta@home and is used mostly by researchers outside of the Baker Lab/IPD. It's an interface for users who wish to get computing power for their jobs.
Jobs that require the use of Rosetta 4.20 that are submitted to Robetta get sent to Rosetta@home but the rest goes to the other servers that they set up when they launched RoseTTAFold.



Ok..so then where do they get the million something tasks in queue?
But yet there appears to be only a few thousand released?
There has always been a million something in queue, even back when it was just 4.2 alone.
So something doesn't add up.
And that you can't see what is next in line....but yet you can see Robetta?
Plus someone kept quoting Robetta information some time ago as if that was where RAH gets its work.
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Message 104369 - Posted: 21 Jan 2022, 19:12:32 UTC - in response to Message 104364.  

Pythons for 12 hours? They average 2 hours here.

As for only being able to run a couple at a time, you need a lot of RAM. I can run 5 but it won't do 6 in 16GB.

No, not an individual run for 12 hours. After running a series of them continually.
I didn't say anything about running only two. I usually run at least eight, and am presently running twenty on a Ryzen 3900X with 80 GB of memory.



Holy cow! 80 gigs?!?! That's more than my budget can afford!
It hurt enough to put in 32 on top of the 16 I put in about 4 years ago.

I just can't see investing much more for being a volunteer.
At best another 1080 or better, but that's it.
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