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!

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

Hello! Thank you! We temporary disable new version for Linux.

Hello!

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

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'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.

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.

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?

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

I've just tried detaching/reattaching and still get the same error. My permissions of those files are identical to biodoc's.

We found a bug that doesn't always show up and disable this version.

New version for Linux - 2.4 released. :)

No issues so far. :)

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.

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. :-/

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. :)

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?

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. :)

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.

Verification not so simple. :)