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World Community Grid Forums
Category: Completed Research
Forum: FightAIDS@Home
Thread: Error running FAAH Vina WUs |
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Thread Status: Active Total posts in this thread: 5
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keithhenry
Ace Cruncher Senile old farts of the world ....uh.....uh..... nevermind Joined: Nov 18, 2004 Post Count: 18667 Status: Offline Project Badges: 
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I am seeing an error running the VINA FAAH WUs. Given the volumes I'm crunching, the errors are very rare but always the same. Here's the log from one with the error highlighted. Is this just an error in the build for a batch or something else?
----------------------------------------Result Name: FAHV_ 1000419_ 4xfx_ P2_ Rigid_ 11266_ 7-- <core_client_version>7.2.42</core_client_version> <![CDATA[ <message> process exited with code 1 (0x1, -255) </message> <stderr_txt> INFO: result number = 7 INFO: No state to restore. Start from the beginning. [08:31:11] Number of tasks = 6 [08:31:11] Running task 0,CPU time at start of task 0 was 0.000000 [08:31:11] ./ZINC000003866030.pdbqt size = 11 3 ../../projects/www.worldcommunitygrid.org/fahv.4xfx_P2_Rigid.pdbqt size = 2019 0 [08:32:09] Finished task #0 cpu time used 56.972402 [08:32:09] Running task 1,CPU time at start of task 1 was 56.972402 [08:32:09] ./ZINC000002548341.pdbqt size = 17 4 ../../projects/www.worldcommunitygrid.org/fahv.4xfx_P2_Rigid.pdbqt size = 2019 0 [08:33:31] Finished task #1 cpu time used 82.852978 [08:33:31] Running task 2,CPU time at start of task 2 was 139.825380 [08:33:31] ./ZINC000239402588.pdbqt size = 12 1 ../../projects/www.worldcommunitygrid.org/fahv.4xfx_P2_Rigid.pdbqt size = 2019 0 Parse error on line 15 in file "./ZINC000239402588.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive. VINA failed. rc = 1. Exiting </stderr_txt> ]]> |
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adriverhoef
Master Cruncher The Netherlands Joined: Apr 3, 2009 Post Count: 2346 Status: Offline Project Badges: 
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Scott L
Senior Cruncher United States Joined: Jun 24, 2013 Post Count: 183 Status: Offline Project Badges:
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in the mass number of results for FA@H, 20K+ in the last few days, i have only seen one error
----------------------------------------Result Name: FAHV_ 1000368_ 3j3y-3S-P2_ 15248_ 3-- <core_client_version>7.6.22</core_client_version> <![CDATA[ <message> Incorrect function. (0x1) - exit code 1 (0x1) </message> <stderr_txt> INFO: result number = 3 INFO: No state to restore. Start from the beginning. [18:53:29] Number of tasks = 4 [18:53:29] Running task 0,CPU time at start of task 0 was 0.000000 [18:53:29] ./ZINC000169811458.pdbqt size = 11 1 ../../projects/www.worldcommunitygrid.org/fahv.3j3y-3S-P2.pdbqt size = 2193 0 Parse error on line 14 in file ".\ZINC000169811458.pdbqt": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive. VINA failed. rc = 1. Exiting </stderr_txt> ]]> Edit: This machine is a win 10 64bit that runs 24/7 so no starting and stopping.  PowerEdge C6105 AMD Opteron 4332HE 3GHZ x8 64 GB Threadripper 1950x 3.4ghz OC 3.875ghz [Edit 2 times, last edit by Scott L at Jan 8, 2017 4:33:33 PM] |
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seippel
Former World Community Grid Tech Joined: Apr 16, 2009 Post Count: 392 Status: Offline Project Badges:
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I am seeing an error running the VINA FAAH WUs. Given the volumes I'm crunching, the errors are very rare but always the same. Here's the log from one with the error highlighted. Is this just an error in the build for a batch or something else? Each docking in Vina has a .pdbqt file for the target docking site and another candidate ligand. This error usually indicates a problem with the format of the .pdbqt file for the candidate ligand. Unfortunately, that candidate ligand will cause a work unit error for each target site it is attempted with. I'll contact the researchers to see if the ligand can be fixed so it doesn't cause errors with future targets. Seippel |
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seippel
Former World Community Grid Tech Joined: Apr 16, 2009 Post Count: 392 Status: Offline Project Badges:
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The ligand files that were causing the "ATOM syntax incorrect: "Si" is not a valid AutoDock type" error have been filter from batch inputs and the ones that have errored out completely have been fixed and are currently being re-run (some have already completed successfully). There may be a few resends of the bad ones lingering out there, but these should be effectively eliminated going forward.
Seippel |
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