Problems and Technical Issues with Rosetta@home

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Jean-David Beyer

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Message 106270 - Posted: 25 May 2022, 1:54:56 UTC - in response to Message 106269.  

Looks like Rosetta 4.2 just got a batch of `miniprotein in , grab them while they iz hot
front page job que went up by millions .


I just got 25 4.2 work units and five are currently running.
Mine are regular work units, not Rosetta mini work units. But the tasks look like this:

Tue 24 May 2022 09:35:07 PM EDT | Rosetta@home | Starting task miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_5yb7eb8g_2914917_13_0
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Mr P Hucker
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Message 106272 - Posted: 25 May 2022, 9:18:03 UTC - in response to Message 106266.  

It may be a task that ran much longer than expected, without anything going wrong. If so, just letting it run enough longer would have let it finish.
I always leave them running unless the CPU is not actually being used. In that one, "CPU time 1d 02:32:21" I assume refers to real calculations, and "Elapsed time 1d 01:32:50" refers to actual time taken. I'm not familiar with wherever that came from, I use Boinctasks. So I think that one was calculating on a whole CPU core.
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Mr P Hucker
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Message 106273 - Posted: 25 May 2022, 9:20:08 UTC - in response to Message 106270.  

I just got 25 4.2 work units and five are currently running.
Mine are regular work units, not Rosetta mini work units. But the tasks look like this:

Tue 24 May 2022 09:35:07 PM EDT | Rosetta@home | Starting task miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_5yb7eb8g_2914917_13_0
Same here, I have about 80, some are rb (I think I got those by chance just before the onslaught) some are miniprotein, all labelled Rosetta 4.2 as the application though. So a small protein but not a small work unit?
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Profile robertmiles

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Message 106274 - Posted: 25 May 2022, 13:11:16 UTC - in response to Message 106272.  
Last modified: 25 May 2022, 13:13:17 UTC

It may be a task that ran much longer than expected, without anything going wrong. If so, just letting it run enough longer would have let it finish.
I always leave them running unless the CPU is not actually being used. In that one, "CPU time 1d 02:32:21" I assume refers to real calculations, and "Elapsed time 1d 01:32:50" refers to actual time taken. I'm not familiar with wherever that came from, I use Boinctasks. So I think that one was calculating on a whole CPU core.

CPU time is probably time used according to the small operating system inside the vbox64 emulation, which is usually close but not identical to the elapsed time,, or actual time used.

That task would be calculating on a whole or physical core if nothing else was trying to use the other virtual core for that physical core.

Multiple small proteins at once could give a long workunit.
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Mr P Hucker
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Message 106275 - Posted: 25 May 2022, 15:27:28 UTC

Every single one I've had failed has had bugger all CPU time compared to wall time. I usually notice 27 seconds of work has been done in 5 hours and cancel it. Everything else has run to completion. I wonder if there's an automated way to detect suss CPU time ratios?
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Message 106278 - Posted: 26 May 2022, 15:04:04 UTC
Last modified: 26 May 2022, 15:04:25 UTC

Ah, this is the problem. The Python book has only one use:

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.clair.

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Message 106281 - Posted: 26 May 2022, 18:28:24 UTC

My quick analysis of desktop items in the photo , I see with python tasks they realy are comparing oranges with almonds . . . .
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Mr P Hucker
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Message 106284 - Posted: 26 May 2022, 19:29:08 UTC - in response to Message 106281.  

What surprises me is they couldn't afford a monitor with adjustable height.
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Mr P Hucker
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Message 106285 - Posted: 26 May 2022, 20:19:05 UTC

I also like the way the width of the monitors is of no use. Bring back 4:3! 16:9 is for TVs!
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.clair.

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Message 106287 - Posted: 26 May 2022, 23:55:51 UTC
Last modified: 27 May 2022, 0:05:14 UTC

With some of the long work unit names rosetta has it gives a better chance to fit them on the screen , Save_aall_the_squishy_bIt5-and -puT_the_rest0uT_for_the_traj5.rAbid_raBit names

All this digital tecknology creating a paperless society . not
More and more bits of dead tree pulverized and squashed flat and skribled on to remind us WTF all that stuff on screen is about .
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Mr P Hucker
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Message 106288 - Posted: 27 May 2022, 0:43:31 UTC - in response to Message 106287.  
Last modified: 27 May 2022, 0:50:37 UTC

I once had a colleague with 30 post it notes all around her monitor with all the passwords she used.

Paper is a renewable resource (and isn't it trapping that "evil" carbon?). At my work they said to stop using so much paper. People were alledgedly printing at 14p a page in colour. The management produced colour photocopiers that could do it for 6p a page. I pointed out we were actually using Brother printers with fake ink at 1p a page. The paper cost more than the ink even for a full colour page. Then I found out the "survey" on cost was done by the company (Xerox) renting us the photocopiers, using the cost of HP printers with genuine rip off ink. Then the arguments started.
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Felicia

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Message 106292 - Posted: 27 May 2022, 9:27:07 UTC - in response to Message 106285.  

I also like the way the width of the monitors is of no use. Bring back 4:3! 16:9 is for TVs!

I love 16:9 on my 25 inch, it's better than 16:10 for running 2 programs side by side (or three when troubleshooting logs, webclient and server side) .

That said, I've got a weird scheduling issue with my client. I have jobs that need to report before x but those jobs are not always the ones that get initiated when another job finishes. This leads to jobs reporting past their due date and I'm not sure whether that invalidates them.

Screenshot (sorted by report before date): https://imgur.com/a/wbHnfzf
There's 2 jobs that need to report before 28-5 6 am, and 2 that need to report before 11:30 am but there are 4 jobs running that need to report before 28-5 3:30pm and later.
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Bryn Mawr

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Message 106294 - Posted: 27 May 2022, 14:18:53 UTC - in response to Message 106292.  

I also like the way the width of the monitors is of no use. Bring back 4:3! 16:9 is for TVs!

I love 16:9 on my 25 inch, it's better than 16:10 for running 2 programs side by side (or three when troubleshooting logs, webclient and server side) .

That said, I've got a weird scheduling issue with my client. I have jobs that need to report before x but those jobs are not always the ones that get initiated when another job finishes. This leads to jobs reporting past their due date and I'm not sure whether that invalidates them.

Screenshot (sorted by report before date): https://imgur.com/a/wbHnfzf
There's 2 jobs that need to report before 28-5 6 am, and 2 that need to report before 11:30 am but there are 4 jobs running that need to report before 28-5 3:30pm and later.


Have you actually had jobs miss deadlines?

Boinc will choose which job to run based on your preferred resource share until and unless there are jobs in danger of missing their deadline when it will switch to running the late jobs as high priority
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Bill Acree

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Message 106295 - Posted: 27 May 2022, 14:39:47 UTC - in response to Message 80621.  

I have a Rosetta@home task, rosetta python projects 1.03 (vbox64), that has been running for over four days. It is two days past its deadline. Today it is now showing 00:00:00 Remaining. The task is showing very little use of CPU time in Activity Monitor. Will this task ever end? It took over two days to go from 00:00:04 to 00:00:00 Remaining. Should I just abort the task?

TASK PROPERTIES:

Application
rosetta python projects 1.03 (vbox64)
Name
aagb-NMABU-mPHE-mACHC13T-mACPenC12T_pp_6_2667468_6
State
Running
Received
Sunday, May 22, 2022 at 08:49:12 AM
Report deadline
Wednesday, May 25, 2022 at 08:49:12 AM
Estimated computation size
80,000 GFLOPs
CPU time
00:33:11
CPU time since checkpoint
00:00:01
Elapsed time
4d 11:58:29
Estimated time remaining
00:00:00
Fraction done
100.000%
Virtual memory size
65.57 GB
Working set size
2.79 GB
Directory
slots/2
Process ID
16253
Progress rate
1.080% per hour
Executable
vboxwrapper_26199_x86_64-apple-darwin
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Felicia

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Message 106299 - Posted: 27 May 2022, 18:40:38 UTC - in response to Message 106294.  

I also like the way the width of the monitors is of no use. Bring back 4:3! 16:9 is for TVs!

I love 16:9 on my 25 inch, it's better than 16:10 for running 2 programs side by side (or three when troubleshooting logs, webclient and server side) .

That said, I've got a weird scheduling issue with my client. I have jobs that need to report before x but those jobs are not always the ones that get initiated when another job finishes. This leads to jobs reporting past their due date and I'm not sure whether that invalidates them.

Screenshot (sorted by report before date): https://imgur.com/a/wbHnfzf
There's 2 jobs that need to report before 28-5 6 am, and 2 that need to report before 11:30 am but there are 4 jobs running that need to report before 28-5 3:30pm and later.


Have you actually had jobs miss deadlines?

Boinc will choose which job to run based on your preferred resource share until and unless there are jobs in danger of missing their deadline when it will switch to running the late jobs as high priority

Yeah, but I cancelled a few of those to keep it going. I'm unsure whether the overdue jobs would actually be useful which is why I cancelled them.
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kotenok2000
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Message 106300 - Posted: 27 May 2022, 18:44:39 UTC - in response to Message 106299.  

I had one rosetta python job miss deadline, but it still was accepted when i reported it.
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Message 106301 - Posted: 27 May 2022, 18:48:44 UTC - in response to Message 106295.  

I have a Rosetta@home task, rosetta python projects 1.03 (vbox64), that has been running for over four days. It is two days past its deadline. Today it is now showing 00:00:00 Remaining. The task is showing very little use of CPU time in Activity Monitor. Will this task ever end? It took over two days to go from 00:00:04 to 00:00:00 Remaining. Should I just abort the task?

TASK PROPERTIES:

Application
rosetta python projects 1.03 (vbox64)
Name
aagb-NMABU-mPHE-mACHC13T-mACPenC12T_pp_6_2667468_6

Look at these two parts:

CPU time
00:33:11

Elapsed time
4d 11:58:29

When the elapsed time gets hours more than the CPU time, the task is no longer doing anything useful, so you might as well abort it,

Some difference between the two is normal, but not that much.
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Mr P Hucker
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Message 106302 - Posted: 27 May 2022, 23:23:02 UTC - in response to Message 106294.  

Boinc will choose which job to run based on your preferred resource share until and unless there are jobs in danger of missing their deadline when it will switch to running the late jobs as high priority
No, Boinc uses no common sense when deciding to run anything. For example, I have 100 4-core tasks queued on a 4-core machine, plus 3 1-core tasks. So it quite sensibly uses the 4-core tasks to keep the whole CPU busy. But at some point, those 3 1-core tasks have to be done. So what does it do? Runs them at the same time as a 4-core task, and at the very last minute, so they would just be done in time if the 4-core one wasn't there. Obviously, they end up being returned late.
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Mr P Hucker
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Message 106303 - Posted: 27 May 2022, 23:24:04 UTC - in response to Message 106292.  

I love 16:9 on my 25 inch, it's better than 16:10 for running 2 programs side by side (or three when troubleshooting logs, webclient and server side) .
So you're basically using it like two monitors. I prefer two monitors. Or an ultrawide which is effectively two 4:3s, it's 16:6.
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.clair.

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Message 106304 - Posted: 28 May 2022, 0:02:19 UTC

I have seen some of the ultra wide monitors/TV`s on the web , it must be like looking at the world through a letterbox .
nice , but expensive .
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Message boards : Number crunching : Problems and Technical Issues with Rosetta@home



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