СmDock "long" and "short" tasks applications

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3man001

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Message 1848 - Posted: 17 Jan 2023, 15:43:44 UTC

After I started receiving long assignments, I began to encounter assignments that cross the deadline by several days, as their processing time has already taken several days, although usually it is about 20 hours.
Do I need to do something about these issues?
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hoarfrost
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Message 1856 - Posted: 17 Jan 2023, 21:42:06 UTC - in response to Message 1848.  

After I started receiving long assignments, I began to encounter assignments that cross the deadline by several days, as their processing time has already taken several days, although usually it is about 20 hours.
Do I need to do something about these issues?

Some task can be hung. You can check this. Now I try to reproduce this with one of workunits.
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JohnB

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Message 1861 - Posted: 18 Jan 2023, 1:54:36 UTC - in response to Message 1845.  

New version of BOINC did not help -- likely because I was already using the latest?

Where would I find the CA-Bundle.crt file?
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JohnB

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Message 1863 - Posted: 18 Jan 2023, 1:57:19 UTC - in response to Message 1861.  

Oooops... The CA-Bundle.crt file was right in front of me... Now to replace it as suggested.
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JohnB

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Message 1864 - Posted: 18 Jan 2023, 2:17:24 UTC - in response to Message 1863.  

THAT fixed it (replacing CA-Bundle.crt).

Thanks to all for your assistance!
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Mad_Max

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Message 1866 - Posted: 18 Jan 2023, 2:59:01 UTC
Last modified: 18 Jan 2023, 3:08:21 UTC

This new app looses CPU/elapsed time stats if restarted (full restarts,without leaving in memory). And so loose points/credits as well.
At the same time, actual progress is NOT lost. That is, checkpoints are working. After restarting the app (BOINC restart or BOINC manager just switch to another project without active option "leave in memory while suspended" ), calculations continue from the last checkpoint as intended, but all the stats counters reported to BOINC of elapsed time, CPU time and time elapsed from the last checkpoint are resets to zero.
Examples of such tasks:
https://www.sidock.si/sidock/result.php?resultid=77568221 13,613.24/13,521.96 sec of elapsed/CPU time

https://www.sidock.si/sidock/result.php?resultid=77568222 13,731.34/13,642.55 sec of elapsed/CPU time and 543.41 credits

https://www.sidock.si/sidock/result.php?resultid=77568208 - 1,302/1,280 sec of elapsed/CPU time and 50.30 credits

https://www.sidock.si/sidock/result.php?resultid=77568215 - 11,880/11,686 sec of elapsed/CPU time and 431.07 credits

While actual run times was about 40 000 - 60 000 sec for all of these tasks (~100 sec per 1 ligand on average in docking_out.log and there are 500 of them in each tasks)
I just restarted computer few times during it computation. And after each restarts tasks continues from checkpoint successfully but all time counters resets to zero each time.

Probably the problem that users have recently complained about in other topics (about a very small amount of credits granted for some of the tasks ) is related to this as well - if the task was restarted often during the calculation process, then only the calculation time since the last restart will be taken into account and evaluated. As it look like credits calculations are based on CPU time used by task and reported by BOINC.

P.S.
BOINC progress bar (% of task completed) also resets to zero after each restart. But it restore to correct values after some time (usually few mins). But time counters does not restore.
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marmot

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Message 1868 - Posted: 18 Jan 2023, 3:18:12 UTC - in response to Message 1866.  
Last modified: 18 Jan 2023, 3:19:15 UTC

This new app looses CPU/elapsed time stats if restarted (full restarts,without leaving in memory). And so loose points/credits as well.
At the same time, actual progress is NOT lost. That is, checkpoints are working. After restarting the app (BOINC restart or BOINC manager just switch to another project without active option "leave in memory while suspended" ), calculations continue from the last checkpoint as intended, but all the stats counters reported to BOINC of elapsed time, CPU time and time elapsed from the last checkpoint are resets to zero.

BOINC progress bar (% of task completed) also resets to zero after each restart. But it restore to correct values after some time (usually few mins). But time counters does not restore.


So we ae in a catch 22.
Hoar Frost says we need to restart the stuck tasks to get them to work but if we do we lose all the earned credit so far.

I have to pause my BOINC from 6-8am and 6-8pm every weekday because the electric company charges 9x normal rates during those periods.
The SIDock WU have been removed from RAM 2x per day. Have had 15 WU fail and 7 not validate of 113 total: 19.5% failure rate.

This WU are not ready for prime time... Too many unresolved issues. Use the Sidock test server for this and let the issues get worked out by people who know it's a beta test.
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marmot

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Message 1873 - Posted: 18 Jan 2023, 5:06:16 UTC
Last modified: 18 Jan 2023, 5:32:30 UTC

Look at this, this machine ran the hottest temperature LLR SRBase WU's for weeks without a single failure.

77561448 49614522 44886 15 Jan 2023, 18:16:18 UTC 18 Jan 2023, 2:09:25 UTC Error while computing 95,553.32 85,968.58 --- CurieMarieDock 0.2.0 long tasks v2.00
windows_x86_64
77558574 49611655 44886 15 Jan 2023, 16:39:03 UTC 17 Jan 2023, 14:04:34 UTC Error while computing 91,007.37 80,447.98 --- CurieMarieDock 0.2.0 long tasks v2.00
windows_x86_64

That's an entire wasted day for each of those cores.

Some of these WU are going to run 2-3 days ending in errors without any hardware cause?

This is not acceptable.

And the results are being purged way too quickly so we can not evaluate the run results and find the issues.

6 tasks all report less than 5% complete, been running for 12-15 hours and somehow they are going to complete in under 3 days (according to BOINC which is using past WU run time data)?
15 hours for 5% calculates to 12.5 more days to completion and the one is at 1.67% after 13 hours time to complete would be 33 days.
And the failure rate was 19% per day on my 5 machines.

Maybe this is the results of the percentages not being accurate from a BOINC restart as Mad Max found; but Mad Max reported the percentages displayed corrected themselves from checkpointing.

I'm concerned.
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hoarfrost
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Message 1874 - Posted: 18 Jan 2023, 7:15:21 UTC
Last modified: 19 Jan 2023, 14:51:07 UTC

After restart time counts from last successful checkpoint (as for any other project). Peoples that faced problem with credit says that problem was inconsistency of time and credit. For example: long time and low credit. Time is saved, but credit is low. This problem has other roots.
If computing in separate slot hung and checkpoint doesn't performs - time lost can be big.
Can time not be recorded in some cases? I think yes, it can be, need investigation.
Errors 0xc2, 0xc3 - looks intresting, thank you for report.

Just for fun. I made a simple chain of bash commands for viewing last modification time of docking_out.log in each slot directory.
BOINC_SLOTS=~/Computing/BOINC/slots ; for directory in $(ls -1 $BOINC_SLOTS) ; do ls -g --no-group $BOINC_SLOTS/$directory | grep docking_out.log; done

That save much time. :D For Windows, i think, can be make similar.
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Mad_Max

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Message 1875 - Posted: 18 Jan 2023, 8:06:23 UTC - in response to Message 1874.  
Last modified: 18 Jan 2023, 8:47:59 UTC

After restart time counts from last successful checkpoint (as for any other project).

Yes, it works this way for any OTHER projects, but not for SiDock - for sidoc it resets to zero afters restart!
May be it due to use of 2 level wrapped app (app launched by BOINC is not an actual app but just wrapper app which launch actual app which do all actual work/computations) - i do not run any other projects with wrapped apps used to compare.

Just reproduced it again. There were 4 SiDock WUs running, and few WUs from other project (from WCG this time, but also work OK with Rosetta@Home and Einstein@Home and MilkyWay@Home).
I restarted BOINC
For WCG WUs CPU/elapsed time counters and progress bar were immediately restored to values close to prior restart (from latest checkpoint i guess).
But for all SiDock WUs all time counters and progress bars were reset to zero.
After 5-7 minutes of computation progress bar recovered to near pre-restart values. But CPU/elapsed times still counting from moment of restart.

Suspending/resume WUs (with "leave in RAM" option turned off) also kills time counters but save progress bar % of BOINC manager is not restarted.
....
Oh, look like i just have found problem (or at least part of it) - BOINC do not see a checkpoints from SiDock at all:
CPU time
01:05:37
CPU time since checkpoint
01:05:34
Elapsed time
01:05:46

SiDock use own implementation of checkpoints ? Or do not report to BOINC properly after checkpoint saved? I know they actually works fine. But BOINC does not see/know about it.
Any way - BOINC thinks there are no any checkpoint made for WU and that's why it reset CPU/elapsed time counters.

Also SiDock does not report progress % to BOINC properly.
In working slot directory in boinc_task_state.xml files of all running SiDock WUs i see
<fraction_done>0.000000</fraction_done>
While in BOINC GUI i see correct values.

Probable it report it via API (app-to-app communication on the fly) but does not write same info to the state file as it should? It could explain strange progress bar behavior after restart: BOINC always reads files fist and see fraction_done = 0 and so revert progress bar in GUI to zero too. But later gets actual progress % some other way and corrects progress bar.

P.S.
I use latest BOINC(v7.20.2) on x64 windows. May be on *nix it works differently...
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Mad_Max

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Message 1881 - Posted: 18 Jan 2023, 9:17:31 UTC - in response to Message 1874.  


Errors 0xc2, 0xc3 - looks intresting, thank you for report.

This additional errors (all of them only on a computer with hostid 25851 or Cruiser-2 as name) you can ignore.
I know exact reason and it is not SiDock or BOINC related. This was 3rd party(non BOINC) buggy app running on same computer with nasty memory leak. It just ate up all the memory (including the virtual/swap file - about 24 GB total) yesterday and other programs started crashing due to out of RAM. After I noticed it and restarted it to free trashed RAM, all these errors stopped immediately.

But this has nothing to do with the problem of resets of time counters, progress bar and credit calculations which i see on all of my computers.
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hoarfrost
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Message 1886 - Posted: 19 Jan 2023, 8:40:30 UTC

At Linux and BOINC 7.4.22 time before checkpoint saved after BOINC restart. With more recent version of BOINC, should be working also, I think.
I waited until there were a couple of hours left before end of tasks for workunits 49617538 and 49617309 and restarted BOINC. After ~ 2 and 4 hours computations for this tasks completed and time saved:
77564558	4	15 Jan 2023, 20:42:57 UTC	19 Jan 2023, 0:55:57 UTC	Completed and validated	86,440.24	86,196.93	1,418.98	CurieMarieDock 0.2.0 long tasks v2.00 x86_64-pc-linux-gnu
77564279	4	15 Jan 2023, 20:33:39 UTC	19 Jan 2023, 2:52:41 UTC	Completed and validated	105,178.79	104,859.20	1,721.03	CurieMarieDock 0.2.0 long tasks v2.00 x86_64-pc-linux-gnu

I should try it under Windows. :)
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JohnB

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Message 1895 - Posted: 19 Jan 2023, 21:57:41 UTC

Now that I have SiDock working...

Some 32 instances of CurieMarieDock 0.2.0 LONG failed after ONE SECOND recently. Mose show as corona_sprot...

ONE task shows 15+ hours of elapsed time with 1d5h plus to go. This shows as corona_RdRp_v2_sample although three of these failed immediately as well.

This project is definitely not ready for prime time... The log is simply showing them as having been downloaded and then finished.

--------------

It appears that at least some (all?) of these are being blocked by PCMatic's Super Shield. (I forced an update to SiDock and watch PcMatic reject them.) I do not have this problem with any other project. (And I will NOT be bypassing PcMatic -- which works off a "white list" rather than a "black list" like most AV programs.)

For the moment I plan to block new updates and try again in a few days.

THOUGHTS?
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JohnB

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Message 1897 - Posted: 20 Jan 2023, 3:58:05 UTC - in response to Message 1895.  

An update to my post above...

While PC Matic is definitely preventing some tasks from running, others run fine. I am only seeing one running on my laptop, but my other computers are definitely running one or more SiDock tasks. They, too, are also rejecting some (many?).

This is also not unique to SiDock. The LHC project is also seeing some tasks blocked on a regular basis. On RARE occasions some WCG (World Community Grid) projects are being blocked as well, generally when something new runs.
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3man001

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Message 1898 - Posted: 20 Jan 2023, 13:15:22 UTC

At the moment, I have stopped processing the tasks of this project so as not to waste resources in vain.
I will continue after there is information that these problems have been fixed.
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marmot

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Message 1899 - Posted: 20 Jan 2023, 15:29:42 UTC

This has been a bad SiDock day for me.
31 tasks completed successfully across 9 computers.
27 WU of 32 on the daytime BOINC installation on the one server that is running dual BOINC (10 hours morning/ 10 Hours night for avoiding peak electric rate hours)
are increasing expectation time 3 seconds every second.
I paused them but they are set to NOT leave RAM because that loses credit.
They have 35+ hours or runtime already and looking at another 50+ hours (some said 5-9 days left) and can't beat their deadline so I aborted them.
The nighttime BOINC install appears to be working but another 5 appear unable to be able to meet the deadline.

*Why did 29 of 32 SiDock WU stop advancing on a machine that pauses 2x a day for 2 hours each period?*
I am switching to a single BOINC install but it will still need to pause 2x a day with a cron job boinccmd --set_run_mode never 7320
So I need assurances that these WU won't keep stalling out because they paused.

Also, still getting a few ending in error after very long runs.

So today I'm at 31 success and 23 failures.
42% failure rate is abominable!


77279883	49343723	44965	11 Jan 2023, 23:44:08 UTC	18 Jan 2023, 16:16:43 UTC	Aborted	493391.9	486944.8	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77337873	49399835	44888	12 Jan 2023, 19:26:44 UTC	16 Jan 2023, 17:47:08 UTC	Error while computing	13412.96	13299.98	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77337845	49399809	44888	12 Jan 2023, 19:26:44 UTC	16 Jan 2023, 17:16:13 UTC	Error while computing	11594.1	11437.84	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77398977	49459298	44888	13 Jan 2023, 15:36:16 UTC	16 Jan 2023, 16:29:53 UTC	Error while computing	8851.1	8775.33	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77398985	49459314	44888	13 Jan 2023, 15:36:16 UTC	16 Jan 2023, 16:53:02 UTC	Error while computing	10180.91	10069.2	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77399065	49459325	44888	13 Jan 2023, 15:38:10 UTC	16 Jan 2023, 17:00:55 UTC	Error while computing	10682.11	10552.55	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77440386	49499316	44898	14 Jan 2023, 3:44:08 UTC	19 Jan 2023, 2:10:12 UTC	Aborted	180865.64	161821.8	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77440796	49499732	44900	14 Jan 2023, 3:50:29 UTC	15 Jan 2023, 12:52:36 UTC	Error while computing	238.91	209.97	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77446164	49505088	44965	14 Jan 2023, 5:27:09 UTC	18 Jan 2023, 16:16:43 UTC	Aborted	331879.66	327318.9	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77557978	49611032	44887	15 Jan 2023, 16:19:56 UTC	20 Jan 2023, 13:30:06 UTC	Aborted	278329.64	268281.6	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77558574	49611655	44886	15 Jan 2023, 16:39:03 UTC	17 Jan 2023, 14:04:34 UTC	Error while computing	91007.37	80447.98	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77561448	49614522	44886	15 Jan 2023, 18:16:18 UTC	18 Jan 2023, 2:09:25 UTC	Error while computing	95553.32	85968.58	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77561513	49614582	44886	15 Jan 2023, 18:17:09 UTC	20 Jan 2023, 2:23:25 UTC	Aborted	140384.21	122982.7	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77575916	49628894	44888	16 Jan 2023, 14:00:54 UTC	20 Jan 2023, 14:54:31 UTC	Aborted	160172.45	70500.13	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77575917	49628899	44888	16 Jan 2023, 14:00:54 UTC	20 Jan 2023, 14:54:31 UTC	Aborted	164651.93	74874.86	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77575927	49628909	44888	16 Jan 2023, 14:00:55 UTC	17 Jan 2023, 18:37:29 UTC	Error while computing	4871.7	4784.16	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77575864	49628849	44888	16 Jan 2023, 14:01:56 UTC	20 Jan 2023, 14:46:51 UTC	Aborted	140432.11	35749.41	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77576808	49629786	44888	16 Jan 2023, 16:29:53 UTC	20 Jan 2023, 14:54:31 UTC	Aborted	142096.72	37286.89	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77576812	49629790	44888	16 Jan 2023, 16:29:53 UTC	20 Jan 2023, 14:54:31 UTC	Aborted	152900.31	73801.61	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77576971	49629949	44888	16 Jan 2023, 16:53:02 UTC	20 Jan 2023, 14:54:31 UTC	Aborted	151144.96	70712.69	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77576972	49629952	44888	16 Jan 2023, 16:53:02 UTC	20 Jan 2023, 14:46:51 UTC	Aborted	152046.29	71703.56	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77576991	49629969	44888	16 Jan 2023, 17:00:55 UTC	20 Jan 2023, 14:54:31 UTC	Aborted	148436.82	68058.72	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77576993	49629971	44888	16 Jan 2023, 17:00:55 UTC	20 Jan 2023, 14:46:51 UTC	Aborted	149894.3	45036	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77577026	49630004	44888	16 Jan 2023, 17:16:13 UTC	20 Jan 2023, 14:54:31 UTC	Aborted	146550.13	66754.64	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77577052	49630030	44888	16 Jan 2023, 17:16:13 UTC	20 Jan 2023, 14:54:31 UTC	Aborted	144242.85	65149.5	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77577165	49630145	44888	16 Jan 2023, 17:39:47 UTC	20 Jan 2023, 14:54:31 UTC	Aborted	146132.22	65806.09	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77577227	49630209	44888	16 Jan 2023, 17:47:08 UTC	20 Jan 2023, 14:54:31 UTC	Aborted	145234.13	64319.44	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77577289	49630271	44888	16 Jan 2023, 17:55:21 UTC	20 Jan 2023, 14:55:11 UTC	Aborted	144869.21	64534.8	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77577296	49630270	44888	16 Jan 2023, 17:55:21 UTC	20 Jan 2023, 14:55:11 UTC	Aborted	144408.69	63322.3	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77577308	49630289	44888	16 Jan 2023, 17:58:26 UTC	20 Jan 2023, 14:54:31 UTC	Aborted	144100.1	62643.67	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77577263	49630238	44888	16 Jan 2023, 17:59:20 UTC	20 Jan 2023, 14:54:31 UTC	Aborted	144041.11	63361.22	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77577321	49630296	44888	16 Jan 2023, 18:00:14 UTC	20 Jan 2023, 14:54:31 UTC	Aborted	143210.83	63137.41	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77585195	49638144	13277	17 Jan 2023, 17:47:15 UTC	19 Jan 2023, 2:09:39 UTC	Aborted	10668.42	10534.66	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77585527	49638492	44888	17 Jan 2023, 18:37:29 UTC	20 Jan 2023, 14:54:31 UTC	Aborted	142162.91	52501.22	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77580116	49633069	44893	17 Jan 2023, 3:07:02 UTC	20 Jan 2023, 14:29:05 UTC	Aborted	192815.89	179682.8	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77580105	49633104	44895	17 Jan 2023, 3:09:24 UTC	20 Jan 2023, 14:29:18 UTC	Aborted	185638.03	180320.3	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77581948	49634901	13277	17 Jan 2023, 8:53:04 UTC	19 Jan 2023, 2:09:39 UTC	Aborted	28511.6	26879.02	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
77588447	49641410	44886	18 Jan 2023, 4:06:39 UTC	20 Jan 2023, 4:28:35 UTC	Error while computing	128506.93	112809.9	---	CurieMarieDock 0.2.0 long tasks v2.00 windows_x86_64
 
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marmot

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Message 1900 - Posted: 20 Jan 2023, 15:34:00 UTC
Last modified: 20 Jan 2023, 15:48:03 UTC

You all could make management of these huge jobs easier if you multi-threaded the problem and set run limits.

Look at Amicable Numbers user settings.
We get to choose number of threads and run time length.

I've spent about 12 hours over the last 3 days baby sitting these WU's.
And I foresee more management hours to come.
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Message 1908 - Posted: 20 Jan 2023, 20:30:57 UTC - in response to Message 1900.  

You have been very vocal in your disappointment as seen over a number of different threads.

I suggest you move on to a different project (like I and others) or simply stop until the issues are resolved. It's not worth getting bent out of shape over.
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Profile vaughan

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Message 1909 - Posted: 21 Jan 2023, 1:56:37 UTC - in response to Message 1908.  

Yes, I did that. The long tasks are too long.
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Crissy

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Joined: 18 Oct 22
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Message 1910 - Posted: 21 Jan 2023, 10:05:18 UTC

Dear Admins / Software Developers,

Please address the reported issues asap.
I already watch top contributors leaving this project and I will shortly follow when there is no improvement.

Take care.

Chris
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Message boards : News : СmDock "long" and "short" tasks applications

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