Problems and Technical Issues with Rosetta@home

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Mr P Hucker
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Message 101188 - Posted: 9 Apr 2021, 17:03:34 UTC - in response to Message 101154.  
Last modified: 9 Apr 2021, 17:05:51 UTC

Hopefully it means something to someone somewhere.
Ah: divided by a common language… :-⁠)
Perfectly comprehensible this side of the pond.

tin o[f] fizzy stuff = can of soda
duff = defective
guff = nonsense

Also “septic tank” is occasionally used as rhyming slang for “Yank”, but I don’t think that’s what’s meant here.

Lol! Too much information.

Wrt whether that's what was meant, I didn't think it was wrt the slang. I thought it was wrt to the CGCCGGG stuff in the task names

Isn't that genetic code? I've assumed it was. Whether it is or not, it's only important it means something to them, not to us.

Unless they're too dumb to understand what they're naming means - far be it for me to exclude all possibilities...

I was going to say that, but what about the Y B and X?
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Message 101190 - Posted: 9 Apr 2021, 17:57:33 UTC - in response to Message 101173.  

same here, 10x C4s waiting for work due to the 6GB requirement.
Hopefully soon there will be a lot of tasks for the small computers available.
In the meanwhile i let them crunch WCG.
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Jim1348

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Message 101191 - Posted: 9 Apr 2021, 18:14:53 UTC - in response to Message 101190.  
Last modified: 9 Apr 2021, 18:16:45 UTC

I have never seen such easy Rosettas. They all under 500 MB on 50 Ryzen 3000 cores (Ubuntu 20.04.2).
But there is always WCG.

PS - Even less on Win10. Under 200 MB on 10 Ryzen3600 cores.
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Message 101194 - Posted: 9 Apr 2021, 23:38:49 UTC - in response to Message 101191.  

I have never seen such easy Rosettas. They all under 500 MB on 50 Ryzen 3000 cores (Ubuntu 20.04.2).
But there is always WCG.

PS - Even less on Win10. Under 200 MB on 10 Ryzen3600 cores.

Those may be taking advantage of a way that compilers often organize the compiled code. The read-write sections cannot be shared between tasks, but all the tasks running can share a read-only section.
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Sid Celery

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Message 101195 - Posted: 10 Apr 2021, 2:14:02 UTC - in response to Message 101183.  

I allocate 28Gb from 32Gb total
They don't need the RAM. If they run, they generally use 300Mb, not 5 or 6Gb each. It's more than a bit crackers.
Once you've started them, I wonder if Boinc adjusts to what they're actually using, or leaves the requested 6.5GB there just in case? You could see what happens if you try to run only Rosettas.

I've speculated that's the case too. Demand a maximum amount to start, then let the task decide once it's running.
I cleared all the problem tasks on my laptop before by setting NNT to Rosetta & WCG and only when all other tasks had completed did my problem task start.

That was a while ago.

Now I've got another one problem Rosetta task. I've suspended all unstarted Rosetta tasks, set NNT again, kept my last few WCG tasks so that as each of the 3 running Rosetta tasks finish, it switches to less-demanding WCG tasks to see if enough RAM is freed up.
If it isn't, let the WCG tasks complete as well until there's only the one problem Rosetta task.
If it runs, fine. If it doesn't, abort it.
What a performance...
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Sid Celery

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Message 101196 - Posted: 10 Apr 2021, 2:19:40 UTC - in response to Message 101188.  

Hopefully it means something to someone somewhere.
Ah: divided by a common language… :-⁠)
Perfectly comprehensible this side of the pond.

tin o[f] fizzy stuff = can of soda
duff = defective
guff = nonsense

Also “septic tank” is occasionally used as rhyming slang for “Yank”, but I don’t think that’s what’s meant here.

Lol! Too much information.

Wrt whether that's what was meant, I didn't think it was wrt the slang. I thought it was wrt to the CGCCGGG stuff in the task names

Isn't that genetic code? I've assumed it was. Whether it is or not, it's only important it means something to them, not to us.

Unless they're too dumb to understand what they're naming means - far be it for me to exclude all possibilities...

I was going to say that, but what about the Y B and X?

1) I don't know
2) It's none of my business and doesn't impinge on me or anyone else in any way
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Sid Celery

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Message 101197 - Posted: 10 Apr 2021, 2:20:57 UTC - in response to Message 101186.  

They have to be taught at some time. Which activity do you think they are allowed to do first? Or do you think that they can start both at the same time, with no tests of what the are doing works properly?

Christ...
What? It's a valid point. Why would you think a biologist knows about the code?

When you're in a hole, stop digging
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mrhastyrib

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Message 101199 - Posted: 10 Apr 2021, 6:26:51 UTC - in response to Message 101186.  

What? It's a valid point. Why would you think a biologist knows about the code?

All the cool kids who work on projects like this one, using proprietary software, know how to code, grandpa. Like just about everything else in life, some are better at it than others. Some are experienced and others are not.

SiDock@home is chugging along merrily on most of my boxes. I'm getting the memory appetite notice on the boxes with less than 8gb of RAM. One box scooped up some projects for Rosetta@home, so the comment that they are squeezing out a few every so often seems to be correct.
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Bryn Mawr

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Message 101205 - Posted: 10 Apr 2021, 16:17:29 UTC

Over the course of this afternoon I’ve had 6 segv errors, all on files starting miniprotien.

Anyone else? Or do I start checking my hardware?
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Jim1348

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Message 101206 - Posted: 10 Apr 2021, 16:26:02 UTC - in response to Message 101205.  

Over the course of this afternoon I’ve had 6 segv errors, all on files starting miniprotien.

Anyone else? Or do I start checking my hardware?

I got a signal 11, but nothing about a segv.
https://boinc.bakerlab.org/rosetta/result.php?resultid=1365882560
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Mr P Hucker
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Message 101207 - Posted: 10 Apr 2021, 17:17:23 UTC - in response to Message 101191.  

I have never seen such easy Rosettas. They all under 500 MB on 50 Ryzen 3000 cores (Ubuntu 20.04.2).
But there is always WCG.
WCG are not getting any tasks from me. Their admins are too arrogant.
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Mr P Hucker
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Message 101208 - Posted: 10 Apr 2021, 17:19:22 UTC - in response to Message 101195.  

I allocate 28Gb from 32Gb total
They don't need the RAM. If they run, they generally use 300Mb, not 5 or 6Gb each. It's more than a bit crackers.
Once you've started them, I wonder if Boinc adjusts to what they're actually using, or leaves the requested 6.5GB there just in case? You could see what happens if you try to run only Rosettas.

I've speculated that's the case too. Demand a maximum amount to start, then let the task decide once it's running.
I cleared all the problem tasks on my laptop before by setting NNT to Rosetta & WCG and only when all other tasks had completed did my problem task start.

That was a while ago.

Now I've got another one problem Rosetta task. I've suspended all unstarted Rosetta tasks, set NNT again, kept my last few WCG tasks so that as each of the 3 running Rosetta tasks finish, it switches to less-demanding WCG tasks to see if enough RAM is freed up.
If it isn't, let the WCG tasks complete as well until there's only the one problem Rosetta task.
If it runs, fine. If it doesn't, abort it.
What a performance...
If it's too big, I run it on a bigger machine. My PCs have 8, 8, 8, 16, 36, 36, and 64GB.
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Mr P Hucker
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Message 101209 - Posted: 10 Apr 2021, 17:20:51 UTC - in response to Message 101196.  

Hopefully it means something to someone somewhere.
Ah: divided by a common language… :-⁠)
Perfectly comprehensible this side of the pond.

tin o[f] fizzy stuff = can of soda
duff = defective
guff = nonsense

Also “septic tank” is occasionally used as rhyming slang for “Yank”, but I don’t think that’s what’s meant here.

Lol! Too much information.

Wrt whether that's what was meant, I didn't think it was wrt the slang. I thought it was wrt to the CGCCGGG stuff in the task names

Isn't that genetic code? I've assumed it was. Whether it is or not, it's only important it means something to them, not to us.

Unless they're too dumb to understand what they're naming means - far be it for me to exclude all possibilities...

I was going to say that, but what about the Y B and X?

1) I don't know
2) It's none of my business and doesn't impinge on me or anyone else in any way
Sometimes they're interesting. There's the drhicks ones. Some Universe tasks said "on_error" which is rather pessimistic. I wonder what Rosetta's "save all out" means?
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Message 101210 - Posted: 10 Apr 2021, 17:21:41 UTC - in response to Message 101197.  

They have to be taught at some time. Which activity do you think they are allowed to do first? Or do you think that they can start both at the same time, with no tests of what the are doing works properly?

Christ...
What? It's a valid point. Why would you think a biologist knows about the code?

When you're in a hole, stop digging
I'm not in a hole and I think you're confusing the two people you're replying to.
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Mr P Hucker
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Message 101211 - Posted: 10 Apr 2021, 17:22:46 UTC - in response to Message 101199.  

What? It's a valid point. Why would you think a biologist knows about the code?

All the cool kids who work on projects like this one, using proprietary software, know how to code, grandpa.
I disagree. I'm sure you can become a brilliant biologist without knowing the first thing about coding.
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Bryn Mawr

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Message 101212 - Posted: 10 Apr 2021, 17:56:18 UTC - in response to Message 101206.  

Over the course of this afternoon I’ve had 6 segv errors, all on files starting miniprotien.

Anyone else? Or do I start checking my hardware?

I got a signal 11, but nothing about a segv.
https://boinc.bakerlab.org/rosetta/result.php?resultid=1365882560


Yes, signal 11 is a segv fault.
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Message 101213 - Posted: 10 Apr 2021, 18:41:11 UTC - in response to Message 101211.  

All the cool kids who work on projects like this one, using proprietary software, know how to code, grandpa.

I disagree. I'm sure you can become a brilliant biologist without knowing the first thing about coding.

+1
They are not pure coders, they are biologists that use code.
They want results, not to create "beautiful" (and optimized) code.
And, in the past, Rsj5, analizing the rosetta sw said that is "fluffy code".
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Message 101215 - Posted: 10 Apr 2021, 20:08:19 UTC

I just suspended a task that has been running for 16:19:35 (stuck at 00:10:15 remaining). Any ideas how to get this one to finish and get credit for it?
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Message 101216 - Posted: 10 Apr 2021, 20:15:28 UTC - in response to Message 101215.  

I just suspended a task that has been running for 16:19:35 (stuck at 00:10:15 remaining). Any ideas how to get this one to finish and get credit for it?

It sometimes helps to shut down BOINC, then restart BOINC and then the task.

Progress seeming to freeze near the end of a task is often a sign that the task was created with a severe underestimate of how long the task would run.
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DizzyD

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Message 101217 - Posted: 10 Apr 2021, 20:57:45 UTC - in response to Message 101216.  

It sometimes helps to shut down BOINC, then restart BOINC and then the task.

Progress seeming to freeze near the end of a task is often a sign that the task was created with a severe underestimate of how long the task would run.


OK, thank you. I just tried that (rebooted in between as well), and it reset to ~16% complete... Maybe I just kill it if it's going to run forever?
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Message boards : Number crunching : Problems and Technical Issues with Rosetta@home



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