Posts by Crystal Pellet

1) Questions and Answers : Windows : Project communication failed: attempting access to reference site (Message 1394)
Posted 16 Dec 2021 by Crystal Pellet
Post:
There was a problem with certificates.

Probably you are not running the newest BOINC version on your problem laptop.
2) Message boards : Number crunching : w/u run time (Message 1387)
Posted 12 Dec 2021 by Crystal Pellet
Post:
https://www.sidock.si/sidock/forum_thread.php?id=163&postid=1385
3) Message boards : Number crunching : number of w/u for each machine (Message 1374)
Posted 28 Nov 2021 by Crystal Pellet
Post:
You get as many tasks as two times the number of available threads.
4) Message boards : Number crunching : Peer certificate cannot be authenticated with given CA certificates (Message 1255)
Posted 1 Oct 2021 by Crystal Pellet
Post:
One of the given CA certificates in BOINC's client certificate bundle stored in the file ca-bundle.crt is "DST Root CA X3"
The valid period of that certificate ended 30 September 2021 and that CA in ca_bundle.crt should be updated/removed by BOINC.
The file is stored locally on the client side in BOINC's Program folder, so no server issue.
5) Message boards : Number crunching : Peer certificate cannot be authenticated with given CA certificates (Message 1235)
Posted 30 Sep 2021 by Crystal Pellet
Post:
SiDock@home 30 Sep 14:03:19 UTC Scheduler request failed: Peer certificate cannot be authenticated with given CA certificates

Certificates outdated?
6) Message boards : News : Release CmDock v 0.1.3 (Message 1029)
Posted 7 Jun 2021 by Crystal Pellet
Post:
OK here is MORE PROOF that checkpoints are NOT working.
It seems not to work for you.
On my win64-systems checkpointing is working ok. I can suspend (LAIM off), restart BOINC, reboot.
Tasks resume from the latest checkpoint with only a few minutes loss at its most.

Application CurieMarieDock on BOINC + zipped input, checkpoints and progress bar 1.00 
Name corona_Eprot_v1_run_2_nb3di_018135_4
State Running
Received 07/06/2021 07:01:32
Report deadline 13/06/2021 07:01:33
Estimated computation size 50,000 GFLOPs
CPU time 06:33:34
CPU time since checkpoint 00:01:37
Elapsed time 06:45:57
Estimated time remaining 01:32:52
Fraction done 77.154%
Virtual memory size 149.04 MB
Working set size 151.33 MB
Directory slots/2
Process ID 1952
Progress rate 11.520% per hour
Executable cmdock-boinc-zcp_wrapper_1.0_windows_x86_64.exe

12-04-2021  13:50               740 target.prm
12-04-2021  13:50           307,542 target.mol2
12-04-2021  13:50         3,260,572 target.as
29-04-2021  02:55         1,543,794 ligands.sdf
06-06-2021  08:19               651 job.xml
06-06-2021  08:19               162 htvs.ptc
07-06-2021  07:01               108 cmdock-boinc-zcp_wrapper_1.0_windows_x86_64.exe
07-06-2021  07:01                 0 boinc_lockfile
07-06-2021  07:01               212 stderr.txt
07-06-2021  07:01                 8 docking_out.sd
07-06-2021  09:32             8,641 init_data.xml
07-06-2021  13:01                12 docking_out.progress
07-06-2021  13:08                22 docking_out.chk
07-06-2021  13:40            49,251 docking_log
07-06-2021  13:47            97,386 docking_out.log
07-06-2021  13:47                29 wrapper_checkpoint.txt
07-06-2021  13:47               512 boinc_task_state.xml
7) Message boards : News : Release CmDock v 0.1.3 (Message 1000)
Posted 31 May 2021 by Crystal Pellet
Post:
We are unable to reproduce the error at our side, but will be aware. Could it be a lack of disc space?
max allowed disk usage: 107.32 GB.
This happened the first time, so no great worry, but strange was, that for BOINC the task was finished and reported, but cmdock.exe was still running locking some files in a slot-folder.

I had errors on that machine a few days ago, because Windows Antimalware Service Executable (MsMpEng.exe) ate all memory when using 1.5 core.
It seems to happen only when cmdock.exe's are running. It makes no differnce when I exclude BOINC's folders or exclude MsMpEng.exe itself.
8) Message boards : News : Release CmDock v 0.1.3 (Message 995)
Posted 31 May 2021 by Crystal Pellet
Post:
Strange error on suspended task with a progress of ~13%: exp_eve_corona_Eprot_v1_run_2_nb3di_388288_4 ===> https://www.sidock.si/sidock/result.php?resultid=13391095

SiDock@home 31 May 09:04:50 task exp_eve_corona_Eprot_v1_run_2_nb3di_388288_4_eve_0 suspended by user
SiDock@home 31 May 09:06:38 [error] Can't rename output file slots/3/docking_out.log to projects/www.sidock.si_sidock/exp_eve_corona_Eprot_v1_run_2_nb3di_388288_4_eve_0_r1610030515_1: Error 32
SiDock@home 31 May 09:06:43 Computation for task exp_eve_corona_Eprot_v1_run_2_nb3di_388288_4_eve_0 finished
SiDock@home 31 May 09:06:43 Output file exp_eve_corona_Eprot_v1_run_2_nb3di_388288_4_eve_0_r1610030515_1 for task exp_eve_corona_Eprot_v1_run_2_nb3di_388288_4_eve_0 absent
SiDock@home 31 May 09:06:46 Started upload of exp_eve_corona_Eprot_v1_run_2_nb3di_388288_4_eve_0_r1610030515_0
SiDock@home 31 May 09:06:47 Finished upload of exp_eve_corona_Eprot_v1_run_2_nb3di_388288_4_eve_0_r1610030515_0
9) Message boards : News : Release CmDock v 0.1.3 (Message 994)
Posted 31 May 2021 by Crystal Pellet
Post:
Still seeing PROBLEMS with CHEKPOINTS on the new CurieMarieDock on BOINC + zipped input, checkpoints and progress bar v1.00
windows_x86_64 tasks.
No problems here with Windows 64.
The only problem is that progress jumping several times during a task to 100% and backwards and the 'write to disk every ... seconds' is ignored.
Checkpointing is after every job out of the 500 during a task.

Are you using BoincTasks for your info. Maybe the task has restarted somewhere in between.
When you look with BOINC Manager, you'll see last checkpoint mostly a few minutes ago.
10) Message boards : News : Release CmDock v 0.1.3 (Message 986)
Posted 29 May 2021 by Crystal Pellet
Post:
Check your project preferences . . .
11) Message boards : News : Release CmDock v 0.1.3 (Message 984)
Posted 29 May 2021 by Crystal Pellet
Post:
- There is a little bug in progress file generation. Apparently only the beginning of docking_out.progress is overwritten with a new number and a line feed, occasionally leaving a remnant of the previous number:
root@zaphod:/var/lib/boinc-client/slots/7# xxd docking_out.progress 
00000000: 302e 3235 0a36 3134 0a0a                 0.25.614..
root@zaphod:/var/lib/boinc-client/slots/7# xxd docking_out.progress 
00000000: 302e 3238 3138 0a31 0a0a                 0.2818.1..
The Manager then displays 100% progress until the next step.

I'm seeing similar for the Windows version.
Sometimes progress jumps to 100%. When that happens, there is a second line in docking_out.progress with an integer on that 2nd line.
I've seen
first line 0.168 second line 3
first line 0.052 second line 9
first line 0.118 second line 2
first line 0.16 second line 89
first line 0.056 second line 99

Edit: Not always an integer on the 2nd line.
Now I've seen:
1st line: 0.19
2nd line: [empty]
3rd line: 5
4th line: [empty]
5th line: [empty]
6th line: [empty]
12) Message boards : News : Release CmDock v 0.1.2 (Message 955)
Posted 23 May 2021 by Crystal Pellet
Post:
Natalia wrote:
We are glad to announce the new app version with checkpoints, CmDock v 0.1.2
I'm glad too. Thanks to the team for the good work.
Although the application is ignoring BOINC's setting 'write to disk at most .... seconds'.
That's the minor issue. Better too many checkpoints than no checkpoints at all.
13) Message boards : Number crunching : Deadline is too short (Message 906)
Posted 11 May 2021 by Crystal Pellet
Post:
This 2 day deadline causes all SD WUs to Run High Priority. This is very annoying since it interferes with any other BOINC project one wants to run. Sometimes it even prevents a GPU from having a CPU. Requires a lot of babysitting to constantly suspend some of the SD WUs so BOINC will behave a little better.
You just have set your cache buffer too high.
Set it low to e.g. ~1 hour = 0.04 in setting: "Store at least ... days of work" and
you may set "Store up to an additional .... days of work" much higher.
Normally you would get rid of 'High priority'.
14) Message boards : Number crunching : No checkpoints? (Message 722)
Posted 22 Mar 2021 by Crystal Pellet
Post:
hoarfrost wrote:
Of course, for many computers our application is uncomfortable, and we understand it. But at this stage of project life we cannot provide tasks event for 1% of BOINC Grid. Of course we think how to change it.
Hoarfrost, initially your tasks are 2000 compounds and for BOINC you divided that into 4 times 500 creating workunits *_1_, *_2_, *_3_ and *_4_.
For your fifth target with the E protein, you could consider to create from that 2000 compounds tasks with 'only'
100 or 200 compounds to reduce the run time duration as long as you don't have a solution for the (no) checkpoints issue.
15) Message boards : Number crunching : Never ending WU's ? (Message 720)
Posted 21 Mar 2021 by Crystal Pellet
Post:
My longest CPU time: 14 hours 30 min 28 sec
16) Message boards : News : Fourth target (corona_RdRp_v1) (Message 587)
Posted 11 Feb 2021 by Crystal Pellet
Post:
Yes, they are docked against the library of ~1 billion compounds. Now we have quorum 2, so about 2 billion WUs.

Sorry to correct you Natalia.

1 billion compounds make 2 million workunits of 500 compounds each times quorum 2 makes 4 milllion tasks.
17) Message boards : Number crunching : Something wrong with the validator? (Message 450)
Posted 23 Jan 2021 by Crystal Pellet
Post:
It seems that the validator is working again.

All tasks are validating now, except tasks that reached the maximum replication of 8.
Those finished tasks got the state 'Can't validate' :(
18) Message boards : Number crunching : Something wrong with the validator? (Message 437)
Posted 22 Jan 2021 by Crystal Pellet
Post:
My last task returned that got the status Valid was at 22 Jan 2021, 12:56:28 UTC.

All tasks thereafter got the status: Completed, validation inconclusive.

The highest number for initial replication, I could find so far is 6.
19) Message boards : Number crunching : Something wrong with the validator? (Message 434)
Posted 22 Jan 2021 by Crystal Pellet
Post:
Huge number of resends for the 3rd, 4th etc time.

The returned tasks are all ending into the status Completed, validation inconclusive
20) Message boards : Number crunching : All 8 tries of this WU failed (Message 407)
Posted 13 Jan 2021 by Crystal Pellet
Post:
Another workunit with max errors: https://www.sidock.si/sidock/workunit.php?wuid=1491199


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