Message boards : Number crunching : Problems and Technical Issues with Rosetta@home
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Mr P Hucker Send message Joined: 12 Aug 06 Posts: 1600 Credit: 11,717,270 RAC: 10,117 |
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.And then we get to have fun with the buggy stuff. |
Jean-David Beyer Send message Joined: 2 Nov 05 Posts: 187 Credit: 6,380,354 RAC: 5,710 |
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 |
robertmiles Send message Joined: 16 Jun 08 Posts: 1232 Credit: 14,269,631 RAC: 2,123 |
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. |
Grant (SSSF) Send message Joined: 28 Mar 20 Posts: 1673 Credit: 17,643,156 RAC: 22,340 |
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 |
Sid Celery Send message Joined: 11 Feb 08 Posts: 2117 Credit: 41,162,648 RAC: 14,990 |
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 VBoxI 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. 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 |
Paddles Send message Joined: 15 Mar 15 Posts: 11 Credit: 5,337,832 RAC: 2,215 |
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. |
Mr P Hucker Send message Joined: 12 Aug 06 Posts: 1600 Credit: 11,717,270 RAC: 10,117 |
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. |
Mr P Hucker Send message Joined: 12 Aug 06 Posts: 1600 Credit: 11,717,270 RAC: 10,117 |
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. |
Mr P Hucker Send message Joined: 12 Aug 06 Posts: 1600 Credit: 11,717,270 RAC: 10,117 |
LHC aswell.but Boinc does not do all that much disk IO as to slow me down much.It depends on the application. |
Mr P Hucker Send message Joined: 12 Aug 06 Posts: 1600 Credit: 11,717,270 RAC: 10,117 |
Looking at this message was a reminder to do all this.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. |
Mr P Hucker Send message Joined: 12 Aug 06 Posts: 1600 Credit: 11,717,270 RAC: 10,117 |
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.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. |
kotenok2000 Send message Joined: 22 Feb 11 Posts: 258 Credit: 483,503 RAC: 109 |
Does QuChempedia hate vbox 6 too? |
Mr P Hucker Send message Joined: 12 Aug 06 Posts: 1600 Credit: 11,717,270 RAC: 10,117 |
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. |
kotenok2000 Send message Joined: 22 Feb 11 Posts: 258 Credit: 483,503 RAC: 109 |
https://boinc.berkeley.edu/projects.php#:~:text=Details-,QuChemPedIA%40home,-%D0%A4%D0%B8%D0%B7%D0%B8%D0%BA%D0%B0 |
Mr P Hucker Send message Joined: 12 Aug 06 Posts: 1600 Credit: 11,717,270 RAC: 10,117 |
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. |
Greg_BE Send message Joined: 30 May 06 Posts: 5691 Credit: 5,859,226 RAC: 0 |
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. |
Mr P Hucker Send message Joined: 12 Aug 06 Posts: 1600 Credit: 11,717,270 RAC: 10,117 |
https://boinc.berkeley.edu/projects.php#:~:text=Details-,QuChemPedIA%40home,-%D0%A4%D0%B8%D0%B7%D0%B8%D0%BA%D0%B0I think I hadn't looked through that list since I set up Boinc originally. |
Mr P Hucker Send message Joined: 12 Aug 06 Posts: 1600 Credit: 11,717,270 RAC: 10,117 |
We were discussing VB version 6 messing things up. It breaks Cosmology, I have to use 5.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. |
Greg_BE Send message Joined: 30 May 06 Posts: 5691 Credit: 5,859,226 RAC: 0 |
We were discussing VB version 6 messing things up. It breaks Cosmology, I have to use 5.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. 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. |
Greg_BE Send message Joined: 30 May 06 Posts: 5691 Credit: 5,859,226 RAC: 0 |
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. |
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Number crunching :
Problems and Technical Issues with Rosetta@home
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