Release CmDock v 0.1.2

Message boards : News : Release CmDock v 0.1.2
Message board moderation

To post messages, you must log in.

AuthorMessage
Profile Natalia
Project administrator
Project developer

Send message
Joined: 9 Oct 20
Posts: 125
Credit: 507,516
RAC: 3,025
Message 928 - Posted: 20 May 2021, 17:00:11 UTC

Hello everyone,

We are glad to announce the new app version with checkpoints, CmDock v 0.1.2 (cmdock-boinc-zip 2.0 in the BOINC project). Currently it is implemented for Windows 64bit, Linux 64bit and Raspberry Pi (for RPi, please check this thread if you need instructions on configuring the client).

The new release has been tested, but not on every existing computer. In case of any problems, please report.

Thank you all for participation!
ID: 928 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
cpalmer

Send message
Joined: 28 Jan 21
Posts: 6
Credit: 442,894
RAC: 502
Message 929 - Posted: 20 May 2021, 20:41:53 UTC - in response to Message 928.  

That's great to see checkpointing added. Unfortunately when I grabbed a bunch they all failed with

application /var/lib/boinc/slots/11/build/cmdock missing
ID: 929 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
hoarfrost
Project administrator
Project developer

Send message
Joined: 11 Oct 20
Posts: 91
Credit: 6,765,569
RAC: 45,848
Message 930 - Posted: 20 May 2021, 21:32:19 UTC

Hello! Thank you! We temporary disable new version for Linux.
ID: 930 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
hoarfrost
Project administrator
Project developer

Send message
Joined: 11 Oct 20
Posts: 91
Credit: 6,765,569
RAC: 45,848
Message 933 - Posted: 21 May 2021, 10:59:03 UTC

Hello!

New version 2.03 of application for Linux available. Works on my PC with Ubuntu.
ID: 933 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
cpalmer

Send message
Joined: 28 Jan 21
Posts: 6
Credit: 442,894
RAC: 502
Message 934 - Posted: 21 May 2021, 12:01:15 UTC - in response to Message 933.  

I've seen a few versions come and go this morning, each with different errors. However I just tried 2.03 on Fedora 33 and it fails as below. (Version 1 works fine).

<core_client_version>7.16.11</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
12:52:59 (71949): wrapper (7.17.26016): starting
12:52:59 (71949): wrapper (7.17.26016): starting
12:52:59 (71949): wrapper: running cmdock (-c -r target.prm -p "/var/lib/boinc/slots/1/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out)
execv() failed: : Permission denied
12:53:00 (71949): cmdock exited; CPU time 0.000275
12:53:00 (71949): app exit status: 0x6c
12:53:00 (71949): called boinc_finish(195)

</stderr_txt>
]]>
ID: 934 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
biodoc

Send message
Joined: 7 Jan 21
Posts: 4
Credit: 5,145,967
RAC: 6,699
Message 935 - Posted: 21 May 2021, 13:43:28 UTC - in response to Message 934.  

I've seen a few versions come and go this morning, each with different errors. However I just tried 2.03 on Fedora 33 and it fails as below. (Version 1 works fine).

<core_client_version>7.16.11</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
12:52:59 (71949): wrapper (7.17.26016): starting
12:52:59 (71949): wrapper (7.17.26016): starting
12:52:59 (71949): wrapper: running cmdock (-c -r target.prm -p "/var/lib/boinc/slots/1/data/scripts/dock.prm" -f htvs.ptc -i ligands.sdf -o docking_out)
execv() failed: : Permission denied
12:53:00 (71949): cmdock exited; CPU time 0.000275
12:53:00 (71949): app exit status: 0x6c
12:53:00 (71949): called boinc_finish(195)

</stderr_txt>
]]>


I'm seeing the same error with version 2.03 on Linux Mint 20.1 [5.4.0-73-generic|libc 2.31 (Ubuntu GLIBC 2.31-0ubuntu9.2)]. Version 1 works fine.
ID: 935 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
biodoc

Send message
Joined: 7 Jan 21
Posts: 4
Credit: 5,145,967
RAC: 6,699
Message 936 - Posted: 21 May 2021, 16:22:14 UTC - in response to Message 933.  
Last modified: 21 May 2021, 16:46:02 UTC

Hello!

New version 2.03 of application for Linux available. Works on my PC with Ubuntu.


Do you have any specific instructions on how you were able to get it to work? All 2.03 tasks are failing on my linux mint 20.1 computers.

Correction: 2 of my computers are processing the tasks successfully. I'll try detaching/attaching the project on the one that's giving errors.
ID: 936 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
hoarfrost
Project administrator
Project developer

Send message
Joined: 11 Oct 20
Posts: 91
Credit: 6,765,569
RAC: 45,848
Message 937 - Posted: 21 May 2021, 16:56:14 UTC

Could you check permissions on files

cmdock-boinc-zip_wrapper_2.3_x86_64-pc-linux-gnu
cmdock_v0.1.2_x86_64-pc-linux-gnu

in project directory?
ID: 937 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
biodoc

Send message
Joined: 7 Jan 21
Posts: 4
Credit: 5,145,967
RAC: 6,699
Message 938 - Posted: 21 May 2021, 17:32:29 UTC - in response to Message 937.  
Last modified: 21 May 2021, 17:35:52 UTC

The permissions look ok.
-rwxr-xr-x  1 boinc boinc  367288 May 21 13:27 cmdock_v0.1.2_x86_64-pc-linux-gnu
-rw-r--r--  1 boinc boinc  217675 May 21 13:27 CmDock_v0.1.2_x86_64-pc-linux-gnu.zip
-rwxr-xr-x  1 boinc boinc 4429872 May 21 13:27 cmdock-boinc-zip_wrapper_2.3_x86_64-pc-linux-gnu


EDIT: added the wrapper
ID: 938 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
cpalmer

Send message
Joined: 28 Jan 21
Posts: 6
Credit: 442,894
RAC: 502
Message 940 - Posted: 21 May 2021, 17:42:50 UTC - in response to Message 938.  

I've just tried detaching/reattaching and still get the same error. My permissions of those files are identical to biodoc's.
ID: 940 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
hoarfrost
Project administrator
Project developer

Send message
Joined: 11 Oct 20
Posts: 91
Credit: 6,765,569
RAC: 45,848
Message 941 - Posted: 21 May 2021, 17:47:44 UTC

We found a bug that doesn't always show up and disable this version.
ID: 941 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
hoarfrost
Project administrator
Project developer

Send message
Joined: 11 Oct 20
Posts: 91
Credit: 6,765,569
RAC: 45,848
Message 942 - Posted: 21 May 2021, 20:23:16 UTC
Last modified: 21 May 2021, 21:13:12 UTC

New version for Linux - 2.4 released. :)
ID: 942 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
biodoc

Send message
Joined: 7 Jan 21
Posts: 4
Credit: 5,145,967
RAC: 6,699
Message 945 - Posted: 22 May 2021, 0:06:11 UTC

No issues so far. :)
ID: 945 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
Crystal Pellet

Send message
Joined: 26 Oct 20
Posts: 47
Credit: 1,606,988
RAC: 1,517
Message 955 - Posted: 23 May 2021, 10:54:12 UTC - in response to Message 928.  
Last modified: 23 May 2021, 10:59:27 UTC

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.
ID: 955 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
floyd

Send message
Joined: 10 Jan 21
Posts: 8
Credit: 1,706,187
RAC: 10,480
Message 958 - Posted: 24 May 2021, 21:09:29 UTC - in response to Message 942.  

New version for Linux - 2.4 released. :)
I see many segfaults. AIUI the wrapper crashes when a task is stopped, not suspended. That doesn't seem to affect the result though, all my results are validated. I hope this is correct. :-/
ID: 958 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
hoarfrost
Project administrator
Project developer

Send message
Joined: 11 Oct 20
Posts: 91
Credit: 6,765,569
RAC: 45,848
Message 960 - Posted: 25 May 2021, 7:04:12 UTC - in response to Message 958.  

That doesn't seem to affect the result though, all my results are validated. I hope this is correct. :-/

Hello! If you see in docking_log file information of completion of all ligands - result is correct. :)
ID: 960 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
floyd

Send message
Joined: 10 Jan 21
Posts: 8
Credit: 1,706,187
RAC: 10,480
Message 961 - Posted: 25 May 2021, 8:33:28 UTC - in response to Message 960.  

Hello! If you see in docking_log file information of completion of all ligands - result is correct. :)
Thanks for the confirmation. The log files (?) look complete as long as I can see them - while the computation is still in progress. However out of curiosity I wanted to have a look at the actual result and I can't find any. Where is it stored and what should it look like?
ID: 961 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
hoarfrost
Project administrator
Project developer

Send message
Joined: 11 Oct 20
Posts: 91
Credit: 6,765,569
RAC: 45,848
Message 962 - Posted: 25 May 2021, 9:19:44 UTC - in response to Message 961.  

However out of curiosity I wanted to have a look at the actual result and I can't find any. Where is it stored and what should it look like?

Results of ligands docking modeling stored in file docking_out.sd. For current target most of results empty, if you see this - don't worry. :)
ID: 962 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
floyd

Send message
Joined: 10 Jan 21
Posts: 8
Credit: 1,706,187
RAC: 10,480
Message 972 - Posted: 26 May 2021, 8:40:44 UTC - in response to Message 962.  

Results of ligands docking modeling stored in file docking_out.sd. For current target most of results empty, if you see this - don't worry. :)
Now that does worry me somewhat. It seems to mean that the result of the computation is simplified to a yes / no answer, or rather yes / not yes, by the client, with no way for you to judge the validity. You completely rely on the wingman to give the same simple answer and after your comment we can even predict that answer. In my opinion you trust both the client and the person operating it too much.
ID: 972 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote
hoarfrost
Project administrator
Project developer

Send message
Joined: 11 Oct 20
Posts: 91
Credit: 6,765,569
RAC: 45,848
Message 974 - Posted: 26 May 2021, 18:45:41 UTC - in response to Message 972.  

Verification not so simple. :)
ID: 974 · Rating: 0 · rate: Rate + / Rate - Report as offensive     Reply Quote

Message boards : News : Release CmDock v 0.1.2

©2021 SiDock@home Team