Computation error after 10seconds of number crunching

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Profile Jari Kosonen
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Message 106277 - Posted: 26 May 2022, 14:06:34 UTC
Last modified: 26 May 2022, 14:07:49 UTC

The event log shows as:
Thu May 26 21:59:36 2022 | Rosetta@home | Sending scheduler request: To fetch work.
Thu May 26 21:59:36 2022 | Rosetta@home | Requesting new tasks for CPU
Thu May 26 21:59:43 2022 | Rosetta@home | Scheduler request completed: got 4 new tasks
Thu May 26 21:59:43 2022 | Rosetta@home | Project requested delay of 31 seconds
Thu May 26 21:59:45 2022 | Rosetta@home | Started download of fr_flags_bcov2
Thu May 26 21:59:45 2022 | Rosetta@home | Started download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xc7as6d.zip
Thu May 26 21:59:47 2022 | Rosetta@home | Finished download of fr_flags_bcov2
Thu May 26 21:59:47 2022 | Rosetta@home | Started download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xc7as6d.flags
Thu May 26 21:59:49 2022 | Rosetta@home | Finished download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xc7as6d.zip
Thu May 26 21:59:49 2022 | Rosetta@home | Finished download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xc7as6d.flags
Thu May 26 21:59:49 2022 | Rosetta@home | Started download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_0iv3mu6e.zip
Thu May 26 21:59:49 2022 | Rosetta@home | Started download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_0iv3mu6e.flags
Thu May 26 22:00:07 2022 | Rosetta@home | Starting task miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xc7as6d_2914917_121_0
Thu May 26 22:00:08 2022 | Rosetta@home | Finished download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_0iv3mu6e.flags
Thu May 26 22:00:08 2022 | Rosetta@home | Started download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xz6qe8w.zip
Thu May 26 22:00:09 2022 | Rosetta@home | Finished download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_0iv3mu6e.zip
Thu May 26 22:00:09 2022 | Rosetta@home | Finished download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xz6qe8w.zip
Thu May 26 22:00:09 2022 | Rosetta@home | Started download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xz6qe8w.flags
Thu May 26 22:00:09 2022 | Rosetta@home | Started download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2yx0fd4d.zip
Thu May 26 22:00:10 2022 | Rosetta@home | Finished download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xz6qe8w.flags
Thu May 26 22:00:10 2022 | Rosetta@home | Finished download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2yx0fd4d.zip
Thu May 26 22:00:10 2022 | Rosetta@home | Started download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2yx0fd4d.flags
Thu May 26 22:00:12 2022 | Rosetta@home | Finished download of miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2yx0fd4d.flags
Thu May 26 22:00:21 2022 | Rosetta@home | Computation for task miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xc7as6d_2914917_121_0 finished
Thu May 26 22:00:21 2022 | Rosetta@home | Output file miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xc7as6d_2914917_121_0_r1379842579_0 for task miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xc7as6d_2914917_121_0 absent
Thu May 26 22:00:35 2022 | Rosetta@home | Starting task miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2yx0fd4d_2914917_121_0
Thu May 26 22:00:49 2022 | Rosetta@home | Starting task miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_0iv3mu6e_2914917_121_0
Thu May 26 22:00:59 2022 | Rosetta@home | Computation for task miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2yx0fd4d_2914917_121_0 finished
Thu May 26 22:00:59 2022 | Rosetta@home | Output file miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2yx0fd4d_2914917_121_0_r1778569496_0 for task miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2yx0fd4d_2914917_121_0 absent
Thu May 26 22:01:13 2022 | Rosetta@home | Starting task miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xz6qe8w_2914917_121_0
Thu May 26 22:01:14 2022 | Rosetta@home | Computation for task miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_0iv3mu6e_2914917_121_0 finished
Thu May 26 22:01:14 2022 | Rosetta@home | Output file miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_0iv3mu6e_2914917_121_0_r1144441723_0 for task miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_0iv3mu6e_2914917_121_0 absent
Thu May 26 22:01:23 2022 | Rosetta@home | Computation for task miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xz6qe8w_2914917_121_0 finished
Thu May 26 22:01:23 2022 | Rosetta@home | Output file miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xz6qe8w_2914917_121_0_r1619180589_0 for task miniprotein_relax_v2_1_SAVE_ALL_OUT_IGNORE_THE_REST_2xz6qe8w_2914917_121_0 absent
And this looks like no clear error shown in the event log...

Then in the "Tasks", I can see message as "Computation Error" after 10 seconds elapsed.

The system info is as:
$ inxi -CG
CPU: Info: Quad Core model: Intel Core i7-8565U bits: 64 type: MT MCP cache: L2: 8 MiB
Speed: 1000 MHz min/max: 400/4600 MHz Core speeds (MHz): 1: 1000 2: 1000 3: 1000 4: 1000 5: 1000 6: 1000
7: 1000 8: 1000
Graphics: Device-1: Intel WhiskeyLake-U GT2 [UHD Graphics 620] driver: i915 v: kernel
Device-2: NVIDIA GP108M [GeForce MX250] driver: nvidia v: 510.47.03
Display: x11 server: X.Org 1.20.13 driver: loaded: modesetting,nvidia unloaded: fbdev,nouveau,vesa
resolution: 1: 1920x1080~60Hz 2: 1920x1080~60Hz
OpenGL: renderer: Mesa Intel UHD Graphics 620 (WHL GT2) v: 4.6 Mesa 21.2.5
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Profile Grant (SSSF)

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Message 106290 - Posted: 27 May 2022, 6:02:45 UTC

ERROR: Unable to open file: minirosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt
A over protective AV programme could be clobbering the files.
I'd suggest putting the BOINC data folder in the exemptions list- then Reset the project. It should then re-download all the files it needs, and be able to start processing again.
Grant
Darwin NT
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Profile Jari Kosonen
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Message 106331 - Posted: 30 May 2022, 12:23:56 UTC - in response to Message 106290.  
Last modified: 30 May 2022, 12:27:44 UTC

It looks as below:
drwxrwx--x. 3 jari jari 4096 May 30 20:15 boinc.bakerlab.org_rosetta
drwxrwx--x 2 jari jari 4096 May 30 08:38 boinc.thesonntags.com_collatz

And the "collatz" seemed to work without computation error...
The dot (for SELinux) then possibly is there, but not sure how it got there.

According to the Filesystem permissions wiki page, the dot indicates a SELinux context is present. Show activity on this post. + (plus) suffix indicates an access control list that can control additional permissions. . (dot) suffix indicates an SELinux context is present
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Profile Jari Kosonen
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Message 106338 - Posted: 1 Jun 2022, 6:47:24 UTC - in response to Message 106290.  

OK. that seems correct assumption and it was fixed by reinstalling the whole MX-linux (and changed from November2021 base to April2022 base).
And it looks the firewall came back and the Rosetta is running now as well.
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Profile Jari Kosonen
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Message 106339 - Posted: 1 Jun 2022, 16:24:04 UTC - in response to Message 106290.  
Last modified: 1 Jun 2022, 17:08:13 UTC

I think there is some issue, because the all the unfinished tasks were lost during the system reinstallation.
This case the tasks are stored into the /home/user/projects (what I think) and system installation case only the /-partition is formatted and rewritten by the linux installation.
It could be better if the boinc keeps all the files in the /home/user/projects directory, but some of the files were found also in the /home/user directory
and in the /var/lib/boinc-client directory.

The boinc directory as below:
--dir <path> use given dir as BOINC home
Could be set as default to /home/user/BOINC by the boinc installation...
To avoid making it too complicated.
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Message boards : Number crunching : Computation error after 10seconds of number crunching



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