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Release CmDock v 0.1.2
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Author | Message |
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Send message Joined: 9 Oct 20 Posts: 185 Credit: 2,753,056 RAC: 4,023 |
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! |
Send message Joined: 28 Jan 21 Posts: 6 Credit: 561,720 RAC: 0 |
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 |
Send message Joined: 11 Oct 20 Posts: 332 Credit: 25,125,685 RAC: 12,896 |
Hello! Thank you! We temporary disable new version for Linux. |
Send message Joined: 11 Oct 20 Posts: 332 Credit: 25,125,685 RAC: 12,896 |
Hello! New version 2.03 of application for Linux available. Works on my PC with Ubuntu. |
Send message Joined: 28 Jan 21 Posts: 6 Credit: 561,720 RAC: 0 |
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> ]]> |
Send message Joined: 7 Jan 21 Posts: 4 Credit: 10,065,484 RAC: 0 |
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). 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. |
Send message Joined: 7 Jan 21 Posts: 4 Credit: 10,065,484 RAC: 0 |
Hello! 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. |
Send message Joined: 11 Oct 20 Posts: 332 Credit: 25,125,685 RAC: 12,896 |
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? |
Send message Joined: 7 Jan 21 Posts: 4 Credit: 10,065,484 RAC: 0 |
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 |
Send message Joined: 28 Jan 21 Posts: 6 Credit: 561,720 RAC: 0 |
I've just tried detaching/reattaching and still get the same error. My permissions of those files are identical to biodoc's. |
Send message Joined: 11 Oct 20 Posts: 332 Credit: 25,125,685 RAC: 12,896 |
We found a bug that doesn't always show up and disable this version. |
Send message Joined: 11 Oct 20 Posts: 332 Credit: 25,125,685 RAC: 12,896 |
New version for Linux - 2.4 released. :) |
Send message Joined: 7 Jan 21 Posts: 4 Credit: 10,065,484 RAC: 0 |
No issues so far. :) |
Send message Joined: 26 Oct 20 Posts: 53 Credit: 2,520,836 RAC: 0 |
Natalia wrote: We are glad to announce the new app version with checkpoints, CmDock v 0.1.2I'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. |
Send message Joined: 10 Jan 21 Posts: 8 Credit: 1,984,643 RAC: 0 |
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. :-/ |
Send message Joined: 11 Oct 20 Posts: 332 Credit: 25,125,685 RAC: 12,896 |
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. :) |
Send message Joined: 10 Jan 21 Posts: 8 Credit: 1,984,643 RAC: 0 |
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? |
Send message Joined: 11 Oct 20 Posts: 332 Credit: 25,125,685 RAC: 12,896 |
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. :) |
Send message Joined: 10 Jan 21 Posts: 8 Credit: 1,984,643 RAC: 0 |
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. |
Send message Joined: 11 Oct 20 Posts: 332 Credit: 25,125,685 RAC: 12,896 |
Verification not so simple. :) |
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