Posts by Crystal Pellet

41) Message boards : Number crunching : Windows 7 and V11.81 huge number of errors (Message 130) Posted 15 Nov 2020 by Crystal Pellet Post: The combination of OS Win 7 and version 11.81 of the application leads to a huge number of errors.
42) Questions and Answers : Unix/Linux : Used bc command in Linux Debian (Message 129) Posted 15 Nov 2020 by Crystal Pellet Post: The bc command that's used in get_fraction_done is not default installed in Linux Debian. Echo every 10 seconds to stderr: get_fraction_done: 1: get_fraction_done: bc: not found No influence on the task outcome, but probably in the progress bar of the task during crunching.
43) Message boards : Number crunching : EXIT_CHILD_FAILED (Message 126) Posted 15 Nov 2020 by Crystal Pellet Post: Since introducing version 11.08, I see more errors with exit status EXIT_CHILD_FAILED I suppose a file is (still) locked (maybe by the unzip) and not accessible by rbdock.exe. See errors https://fightcovid.boinc.ru/sidocktest/results.php?hostid=419&offset=0&show_names=0&state=6&appid= The process cannot access the file because it is being used by another process. The handle could not be opened during redirection of handle 0. 0 was unexpected at this time. Inserting "@TIMEOUT 5 > nul" before rbdock.exe starts could maybe avoid this.
44) Message boards : Number crunching : Restart of a task always ends into an error. (Message 125) Posted 14 Nov 2020 by Crystal Pellet Post: Crystal Pellet, thank you for notice! My pleasure! It could be done simpler by replacing the line MOVE target.mol2 %targetmol2% by one line IF NOT EXIST %targetmol2% MOVE target.mol2 %targetmol2% >NUL
45) Message boards : Number crunching : Restart of a task always ends into an error. (Message 121) Posted 13 Nov 2020 by Crystal Pellet Post: The error after BOINC's restart can be avoided. The problem is the MOVE-command. It tries to move a non-existing file. I solved this by replacing in rbdock-boinc_11.4_windows_x86_64.bat (in slot renamed in worker.bat) the line MOVE target.mol2 %targetmol2% with following lines IF NOT EXIST target.mol2 GOTO alreadymoved MOVE target.mol2 %targetmol2% :alreadymoved
46) Message boards : Science : Testing status (Message 119) Posted 12 Nov 2020 by Crystal Pellet Post: Technically we have 500 000 packets with 2000 compound each. In COVID.SI we are running in direction from 1 -> 25 000 and in SiDock@home from 500 000 -> 25 000 I discovered 2 tasks on one system of mine only differencing 1 figure: sidocktest corona_3CLpro_v3_nb3di_433178_4_0 sidocktest corona_3CLpro_v3_nb3di_433178_1_0 It seems you divided the packages into 4 for each BOINC-task. So every task is doing 500 compounds out of total 950,000,000 compounds ToDo for SiDock@home being 0.0000526315789473684% Calculating with the progress so far ( 12.493% ) we returned already 237,367 valid tasks ;-) for this target.
47) Message boards : Number crunching : Restart of a task always ends into an error. (Message 118) Posted 12 Nov 2020 by Crystal Pellet Post: Hello Crystal Pellet! Explain please - this error occurs after restart of BOINC only, not computer? At every restart of the task, the task starts from the very beginning, because no checkpoints of the job are written. As stated before that tasks errors out. A task will restart when BOINC-client restarts (thus also after a boot). When you suspend a task, the task will stay in memory and will run further from that point after a resume even without a checkpoint. A feature of BOINC is to keep a task in memory until the first checkpoint, even when you had set to not keep a suspended task in memory, cause it will never achieve the first checkpoint.
48) Message boards : Number crunching : Restart of a task always ends into an error. (Message 114) Posted 11 Nov 2020 by Crystal Pellet Post: Since there are no checkpoints (yet) for a running task, the task has to start from scratch after a BOINC client restart due to whatever reason. However such a restart always ends into an error. Part of the result of the initially start of a task: 09:20:23 (4300): wrapper (7.7.26016): starting 09:20:23 (4300): wrapper: running get_fraction_done.bat (ligands.sdf docking_log fraction_done.txt 500 TARGET_PRO_1.mol2) 09:20:23 (4300): wrapper: running worker.bat ( 500 TARGET_PRO_1.mol2) 1 file(s) moved. ECHO is off. Part of the result after a restart of a task: 11:47:45 (3140): wrapper (7.7.26016): starting 11:47:45 (3140): wrapper: running get_fraction_done.bat (ligands.sdf docking_log fraction_done.txt 500 TARGET_PRO_1.mol2) 11:47:46 (3140): wrapper: running worker.bat ( 500 TARGET_PRO_1.mol2) 1 file(s) moved. The requested operation cannot be performed on a file with a user-mapped section open. 11:47:52 (3140): worker.bat exited; CPU time 0.000000 11:47:52 (3140): app exit status: 0x1 11:47:52 (3140): called boinc_finish(195)
49) Message boards : Cafe : welcome (Message 79) Posted 7 Nov 2020 by Crystal Pellet Post: Thanks. Looking forward to learn more ... Have you seen this page ==> https://covid.si/en/ ?
50) Message boards : Science : Testing status (Message 77) Posted 7 Nov 2020 by Crystal Pellet Post: Thanks Natalia for responding. Nice that we are doing real work.
51) Message boards : Science : Testing status (Message 75) Posted 7 Nov 2020 by Crystal Pellet Post: What is the purpose of the test? On Stats - COVID.SI I see target corona_3CLpro_v3 and progress ~52% complete. Here at SiDock@home [test] I see 7.209% complete for the same target. Are we calculating the same packages here as a test to compare them?
52) Message boards : Number crunching : WU download error (Message 42) Posted 28 Oct 2020 by Crystal Pellet Post: Couldn't get input file nb3di_483714_1.sdf http://188.68.219.141/sidocktest/result.php?resultid=50752

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