Problems and Technical Issues with Rosetta@home

Message boards : Number crunching : Problems and Technical Issues with Rosetta@home

To post messages, you must log in.

Previous · 1 . . . 204 · 205 · 206 · 207 · 208 · 209 · 210 . . . 280 · Next

AuthorMessage
Mr P Hucker
Avatar

Send message
Joined: 12 Aug 06
Posts: 1600
Credit: 9,781,664
RAC: 5,728
Message 106023 - Posted: 24 Apr 2022, 23:21:07 UTC - in response to Message 106021.  

And then we get to have fun with the buggy stuff.

This IS the buggy stuff. That is one reason I am concerned we may not get more.
They did not bother to fix it, so it may be good enough for what they need it for.
I'm not concerned. If all future tasks are made with 4.2, things will work properly again. Python is a shit programming language and Oracle is a shit virtual machine.
ID: 106023 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Jean-David Beyer

Send message
Joined: 2 Nov 05
Posts: 178
Credit: 5,705,004
RAC: 3,451
Message 106024 - Posted: 25 Apr 2022, 2:16:31 UTC - in response to Message 106011.  

I do not know how slow my spinning disks are. True, these 7200 rpm SATA hard drives are not as fast as the 10,000 rpm SCSI/320 LVD hard drives on a former machine, but Boinc does not do all that much disk IO as to slow me down much. All my BOINC stuff is on one of those spinning hard drives. I note that Boinc homework assignments are severely compute-limited, so disk IO is just a small part of the work load. I use half my cores on Boinc stuff that runs mainly at nice level 19. Since the machine is doing little else at the moment, not that the machine is running about 50% computing, about 50% idle, and no time waiting for IO. More subjectively, the disk IO light blinks a very very short blink with about a 5-second interval; i.e., hardly any disk IO. The machine is running 5 rosetta and 3 universe jobs at the moment.
top - 22:01:25 up 4 days, 13:20,  1 user,  load average: 8.00, 8.13, 8.31
Tasks: 454 total,   9 running, 444 sleeping,   0 stopped,   1 zombie
%Cpu(s):  0.4 us,  0.1 sy, 49.7 ni, 49.7 id,  0.0 wa,  0.1 hi,  0.0 si,  0.0 st
MiB Mem :  63902.1 total,   2784.7 free,   6276.7 used,  54840.8 buff/cache
MiB Swap:  15992.0 total,  15987.0 free,      5.0 used.  56835.9 avail Mem

ID: 106024 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 16 Jun 08
Posts: 1225
Credit: 13,906,158
RAC: 4,068
Message 106025 - Posted: 25 Apr 2022, 2:24:16 UTC - in response to Message 106022.  

I prefer both to the situation at Predictor@Home. They lost the two members of their project team who knew how the create useful new workunits (probably because they graduated). For several months, they kept the project running by repeatedly raising the number of times a workunit could fail before no more tasks would be sent out for it. Some of the remaining workunits failed over 30 times before the professor in charge decided it was not worthwhile to let the project continue, and it shut down.
ROFL, Wikipedia says "Though it was quite successful, a "disagreement" between the project administration and the user base caused a mass exodus of participating users"

I'd expect a user base to disagree a lot and start exiting once every task started failing.

What I wrote came from the professor in charge.
ID: 106025 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Grant (SSSF)

Send message
Joined: 28 Mar 20
Posts: 1506
Credit: 14,892,191
RAC: 20,872
Message 106026 - Posted: 25 Apr 2022, 3:07:36 UTC - in response to Message 106024.  

but Boinc does not do all that much disk IO as to slow me down much.
It depends on the application.
In the case of Rosetta, the Rosetta 4.20 Tasks don't require much disk I/O, however the Python Tasks require massive amounts of disk I/O when starting up & ending. And apparently they also require quite a bit during processing. The more cores & threads a system has & uses, then the higher the disk I/O requirements will be.
Grant
Darwin NT
ID: 106026 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Sid Celery

Send message
Joined: 11 Feb 08
Posts: 2003
Credit: 38,765,297
RAC: 21,892
Message 106027 - Posted: 25 Apr 2022, 5:53:00 UTC - in response to Message 106009.  

Ok, I've just used Windows Disk cleanup and ensured storage sense is enabled and freed up a few Gb, but that's on a PC that isn't running VBox
I'll give that a go when I get back to my main PC tomorrow evening
I run the Windows disk cleanup (including system files) then run treesize which shows me what folders are using the most, so I can manually remove stuff I don't want anymore. Last time I reduced the stuff on my disk by a third.

I only bother doing this when the line changes from blue to red in windows explorer.

Looking at this message was a reminder to do all this.
No new .tmp files, freed up a few Gb here too, grabbed Treeview but it's not telling me anything I expect to find useful so removed again.
I've got BoincTasks but hadn't set it up to run at startup, which I've now done. Yes, very useful in finding tasks that are very far behind in CPU time compared to Elapsed time.
More useful when running VBox tasks compared to running plain Rosetta tasks - I'll keep this going now.
All good, ta
ID: 106027 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Paddles

Send message
Joined: 15 Mar 15
Posts: 11
Credit: 5,005,167
RAC: 3,946
Message 106028 - Posted: 25 Apr 2022, 12:22:52 UTC - in response to Message 106007.  

Update: The first task to be postponed reached the end of its one day postponement, and now appears to be computing successfully (in VBox 6.1.34). Haven't tried reverting to previous version to see what happens, but whatever the problem was it seems to have resolved.


I may have spoken too soon. The tasks were running for exceptionally long times (18-26 hours) - although unlike the normal "not doing anything" vbox tasks, they were showing significant CPU time utilised (rather than the tasks that "run" for 18 hours but have only consumed 10-20 seconds of CPU). I shut down BOINC, rolled VBox back to version 6.1.12 (BOINC recommended version, not 6.1.32 which I had been running), restarted, and all the vbox tasks came up with computation errors.

Oh well, will see what happens with the next tasks to run.
ID: 106028 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mr P Hucker
Avatar

Send message
Joined: 12 Aug 06
Posts: 1600
Credit: 9,781,664
RAC: 5,728
Message 106029 - Posted: 25 Apr 2022, 16:37:56 UTC - in response to Message 106024.  

I do not know how slow my spinning disks are. True, these 7200 rpm SATA hard drives are not as fast as the 10,000 rpm SCSI/320 LVD hard drives on a former machine, but Boinc does not do all that much disk IO as to slow me down much. All my BOINC stuff is on one of those spinning hard drives. I note that Boinc homework assignments are severely compute-limited, so disk IO is just a small part of the work load. I use half my cores on Boinc stuff that runs mainly at nice level 19. Since the machine is doing little else at the moment, not that the machine is running about 50% computing, about 50% idle, and no time waiting for IO. More subjectively, the disk IO light blinks a very very short blink with about a 5-second interval; i.e., hardly any disk IO. The machine is running 5 rosetta and 3 universe jobs at the moment.
Try 24 cores running virtualbox. 2GB disk read and 2GB disk write to start each one, followed by many checkpoints.
ID: 106029 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mr P Hucker
Avatar

Send message
Joined: 12 Aug 06
Posts: 1600
Credit: 9,781,664
RAC: 5,728
Message 106030 - Posted: 25 Apr 2022, 16:39:01 UTC - in response to Message 106025.  

I'd expect a user base to disagree a lot and start exiting once every task started failing.
I'm not that arrogant. I keep trying to help a project in difficulty.
ID: 106030 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mr P Hucker
Avatar

Send message
Joined: 12 Aug 06
Posts: 1600
Credit: 9,781,664
RAC: 5,728
Message 106031 - Posted: 25 Apr 2022, 16:39:39 UTC - in response to Message 106026.  

but Boinc does not do all that much disk IO as to slow me down much.
It depends on the application.
In the case of Rosetta, the Rosetta 4.20 Tasks don't require much disk I/O, however the Python Tasks require massive amounts of disk I/O when starting up & ending. And apparently they also require quite a bit during processing. The more cores & threads a system has & uses, then the higher the disk I/O requirements will be.
LHC aswell.
ID: 106031 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mr P Hucker
Avatar

Send message
Joined: 12 Aug 06
Posts: 1600
Credit: 9,781,664
RAC: 5,728
Message 106032 - Posted: 25 Apr 2022, 16:43:02 UTC - in response to Message 106027.  

Looking at this message was a reminder to do all this.
No new .tmp files, freed up a few Gb here too, grabbed Treeview but it's not telling me anything I expect to find useful so removed again.
I've got BoincTasks but hadn't set it up to run at startup, which I've now done. Yes, very useful in finding tasks that are very far behind in CPU time compared to Elapsed time.
More useful when running VBox tasks compared to running plain Rosetta tasks - I'll keep this going now.
All good, ta
I assume you used treeSIZE. That one is great, it's like a windows explorer tree, but with sizes. I removed a whole load of stuff *I* had put there that I didn't need. Games I no longer played, films that can be archived onto the rust spinner, etc.

No idea how people can manage with just the plain Boinc Manager, it's absolutely horrid, especially if you have a lot of tasks. No colour coding, no grouping of queued tasks, etc. And with me having 7 computers, I really need a central controller. At least Folding at Home supplies such a thing, but I don't think the Boinc Manager will look at many computers easily.
ID: 106032 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mr P Hucker
Avatar

Send message
Joined: 12 Aug 06
Posts: 1600
Credit: 9,781,664
RAC: 5,728
Message 106033 - Posted: 25 Apr 2022, 16:44:52 UTC - in response to Message 106028.  

Update: The first task to be postponed reached the end of its one day postponement, and now appears to be computing successfully (in VBox 6.1.34). Haven't tried reverting to previous version to see what happens, but whatever the problem was it seems to have resolved.


I may have spoken too soon. The tasks were running for exceptionally long times (18-26 hours) - although unlike the normal "not doing anything" vbox tasks, they were showing significant CPU time utilised (rather than the tasks that "run" for 18 hours but have only consumed 10-20 seconds of CPU). I shut down BOINC, rolled VBox back to version 6.1.12 (BOINC recommended version, not 6.1.32 which I had been running), restarted, and all the vbox tasks came up with computation errors.

Oh well, will see what happens with the next tasks to run.
I'm on VB version 5 (or Cosmology breaks completely) and it seems to run Rosetta Python just as well as 6. LHC is also happy with it. Kryptos at Home also hates 6. Seems like VB screwed up when they made the new one.
ID: 106033 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
kotenok2000
Avatar

Send message
Joined: 22 Feb 11
Posts: 234
Credit: 335,789
RAC: 1,205
Message 106034 - Posted: 25 Apr 2022, 16:46:50 UTC - in response to Message 106033.  

Does QuChempedia hate vbox 6 too?
ID: 106034 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mr P Hucker
Avatar

Send message
Joined: 12 Aug 06
Posts: 1600
Credit: 9,781,664
RAC: 5,728
Message 106035 - Posted: 25 Apr 2022, 17:02:34 UTC - in response to Message 106034.  

Does QuChempedia hate vbox 6 too?
Never heard of it, let alone used it. Can't test here as I have VB 5 on everything.
ID: 106035 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
kotenok2000
Avatar

Send message
Joined: 22 Feb 11
Posts: 234
Credit: 335,789
RAC: 1,205
Message 106036 - Posted: 25 Apr 2022, 17:05:05 UTC - in response to Message 106035.  

https://boinc.berkeley.edu/projects.php#:~:text=Details-,QuChemPedIA%40home,-%D0%A4%D0%B8%D0%B7%D0%B8%D0%BA%D0%B0
ID: 106036 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mr P Hucker
Avatar

Send message
Joined: 12 Aug 06
Posts: 1600
Credit: 9,781,664
RAC: 5,728
Message 106037 - Posted: 25 Apr 2022, 17:09:38 UTC - in response to Message 106034.  

Does QuChempedia hate vbox 6 too?
Thanks for telling me about that one, I was looking for a chemistry project! If you use windows you have to turn on beta tests, as only linux is non-beta.
ID: 106037 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Greg_BE
Avatar

Send message
Joined: 30 May 06
Posts: 5664
Credit: 5,711,666
RAC: 931
Message 106038 - Posted: 25 Apr 2022, 17:10:25 UTC - in response to Message 106035.  
Last modified: 25 Apr 2022, 17:29:45 UTC

Does QuChempedia hate vbox 6 too?
Never heard of it, let alone used it. Can't test here as I have VB 5 on everything.


Vbox per project is not relevant.
It is a matter of does the project run their tasks with Vbox
In this case yes it does use Vbox
| QuChemPedIA@home | Finished download of vboxwrapper_26200_windows_x86_64.exe
You can also check this page [url]https://boinc.berkeley.edu/projects.php [/url] to see if your project choice uses Vbox or not. The blue box symbol at the end of the icon list is for Vbox.


Have to try QuChem again, last time it was not stable enough to run on my system with other projects.
ID: 106038 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mr P Hucker
Avatar

Send message
Joined: 12 Aug 06
Posts: 1600
Credit: 9,781,664
RAC: 5,728
Message 106039 - Posted: 25 Apr 2022, 17:10:44 UTC - in response to Message 106036.  

https://boinc.berkeley.edu/projects.php#:~:text=Details-,QuChemPedIA%40home,-%D0%A4%D0%B8%D0%B7%D0%B8%D0%BA%D0%B0
I think I hadn't looked through that list since I set up Boinc originally.
ID: 106039 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mr P Hucker
Avatar

Send message
Joined: 12 Aug 06
Posts: 1600
Credit: 9,781,664
RAC: 5,728
Message 106040 - Posted: 25 Apr 2022, 17:11:38 UTC - in response to Message 106038.  

Does QuChempedia hate vbox 6 too?
Never heard of it, let alone used it. Can't test here as I have VB 5 on everything.


Vbox per project is not relevant.
We were discussing VB version 6 messing things up. It breaks Cosmology, I have to use 5.
ID: 106040 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Greg_BE
Avatar

Send message
Joined: 30 May 06
Posts: 5664
Credit: 5,711,666
RAC: 931
Message 106041 - Posted: 25 Apr 2022, 17:31:31 UTC - in response to Message 106040.  

Does QuChempedia hate vbox 6 too?
Never heard of it, let alone used it. Can't test here as I have VB 5 on everything.


Vbox per project is not relevant.
We were discussing VB version 6 messing things up. It breaks Cosmology, I have to use 5.


That's strange. How vbox processes tasks is above my head.
Computermeze or whatever his name is knows more about that kind of stuff.
Have you asked in Cosmo forum at all if anyone knows why 6 does not work?
Maybe post in Github and see what the experts say.
ID: 106041 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Greg_BE
Avatar

Send message
Joined: 30 May 06
Posts: 5664
Credit: 5,711,666
RAC: 931
Message 106042 - Posted: 25 Apr 2022, 17:38:48 UTC

Vbox projects listed:

BOINC@TACC (not worth the time, its leftovers)
Cosmology (as you already know)
LHC@home
QuChemPedIA@home
RNA World (also leftovers or stuff that can not run on the supercomputer they have) so 0 tasks available.
Here at Rosetta

And that's all that is on the list.
ID: 106042 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Previous · 1 . . . 204 · 205 · 206 · 207 · 208 · 209 · 210 . . . 280 · Next

Message boards : Number crunching : Problems and Technical Issues with Rosetta@home



©2024 University of Washington
https://www.bakerlab.org