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Category: Completed Research
Forum: FightAIDS@Home
Thread: Possible BUG in Autodock |
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Thread Status: Active Total posts in this thread: 19
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Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3315 Status: Offline Project Badges: 
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Hi all.I think it may be a bug and if it is, it is quite significant.
----------------------------------------Look at the stderr file from a FAAH task: Failed to get VersionInfo size: 1812 INFO:[14:21:35] Start AutoGrid... autogrid: autogrid4: Successful Completion. INFO:[14:29:13] End AutoGrid... Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 0) _maxGenSeenSoFar changed: 2500 _maxGenSeenSoFar changed: 2626 _maxGenSeenSoFar changed: 2758 _maxGenSeenSoFar changed: 2896 _maxGenSeenSoFar changed: 3041 _maxGenSeenSoFar changed: 3194 _maxGenSeenSoFar changed: 3354 _maxGenSeenSoFar changed: 3522 _maxGenSeenSoFar changed: 3699 _maxGenSeenSoFar changed: 3885 _maxGenSeenSoFar changed: 4080 _maxGenSeenSoFar changed: 4285 _maxGenSeenSoFar changed: 4500 _maxGenSeenSoFar changed: 4726 _maxGenSeenSoFar changed: 4963 _maxGenSeenSoFar changed: 5212 _maxGenSeenSoFar changed: 5473 _maxGenSeenSoFar changed: 5747 _maxGenSeenSoFar changed: 6035 _maxGenSeenSoFar changed: 6337 _maxGenSeenSoFar changed: 6654 _maxGenSeenSoFar changed: 6987 _maxGenSeenSoFar changed: 7337 _maxGenSeenSoFar changed: 7704 _maxGenSeenSoFar changed: 8090 _maxGenSeenSoFar changed: 8495 _maxGenSeenSoFar changed: 8920 _maxGenSeenSoFar changed: 9367 _maxGenSeenSoFar changed: 9836 _maxGenSeenSoFar changed: 10328 Updating Best Energy for WU: 0.00 Finished Docking number 0 Finished Docking number 1 Updating Best Energy for WU: -6.47 Before restarting Finished Docking number 2 Finished Docking number 3 Finished Docking number 4 Finished Docking number 5 Finished Docking number 6 Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.727420 maxGenSeen: 10328 After restarting AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 7) Finished Docking number 7 Finished Docking number 8 Finished Docking number 9 The log records the best energy after each docking if it was better than the previous energy as it is shown in bold. However after restarting windows, it shows a completely different energy as seen in red.This happened after restarting windows.This new energy wasn't record by the log file in any of the previous dockings.I restart Windows and the new energy replaced the old one(the one in bold). I may be missing something, but I have seen this in all my computers and even on wingmans logs. The computer where happened now is a Pentium 4 2.40 GHZ, BOINC 6.10.60, Windows XP SP3, 1.75 GB RAM and a partition for WCG only with 1.10GB. If it is a bug it very serious since the lower the energy, the better the compound.But if the docking results are unreliable then the scientists are wasting money and time and of course our computing time. Also on HFCC which also uses AutoDock, the difference between the energy recorded before the restart and the new is very small(like from 7.1289 to 7.1389).  - AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W - AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W - AMD Ryzen 7 7730U 8C/16T 3.0 GHz [Edit 4 times, last edit by Falconet at Apr 30, 2011 11:33:52 AM] |
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Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3315 Status: Offline Project Badges:
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Anyone?
----------------------------------------- AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W - AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W - AMD Ryzen 7 7730U 8C/16T 3.0 GHz |
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gb009761
Master Cruncher Scotland Joined: Apr 6, 2005 Post Count: 3010 Status: Offline Project Badges: 
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Falconet, considering its a weekend, I wouldn't at all be surprised to not see any authoritive response to your possible bug until the beginning of this next week.
----------------------------------------Scientists/WCG staff do deserve at least a couple of days off a week...  |
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Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3315 Status: Offline Project Badges:
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Falconet, considering its a weekend, I wouldn't at all be surprised to not see any authoritive response to your possible bug until the beginning of this next week. Scientists/WCG staff do deserve at least a couple of days off a week... They sure do. Thanks for your reply.I didn't remember it was Saturday.:D - AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W - AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W - AMD Ryzen 7 7730U 8C/16T 3.0 GHz |
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sk..
Master Cruncher http://s17.rimg.info/ccb5d62bd3e856cc0d1df9b0ee2f7f6a.gif Joined: Mar 22, 2007 Post Count: 2324 Status: Offline Project Badges: 
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It might not be a bug. If your system re-ran the same docking procedure that contains a random element then you would be highly unlikely to get the exact same result. The fact that it found a better energy is actually a confirmation of the previous run.
This is part of the log for one task I ran: Updating Best Energy for WU: 0.00 Finished Docking number 0 Updating Best Energy for WU: -7.57 Finished Docking number 1 Finished Docking number 2 Finished Docking number 3 Finished Docking number 4 Failed to get VersionInfo size: 2 Failed to get VersionInfo size: 2 Restoring grahics. bestEnergy: -9.605040 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 5) Finished Docking number 5 Finished Docking number 6 Finished Docking number 7 Finished Docking number 8 Finished Docking number 9 Updating Best Energy for WU: -9.61 Finished Docking number 10 As you can see,at some stage the Best Energy was improved by -9.61, so your value is not that uncommon. Some of the messages are also similar, so you can assume these are not errors. Eg., WARNING: Unrecognized keyword in docking parameter file. |
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Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3315 Status: Offline Project Badges:
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It might not be a bug. If your system re-ran the same docking procedure that contains a random element then you would be highly unlikely to get the exact same result. The fact that it found a better energy is actually a confirmation of the previous run. This is part of the log for one task I ran: Updating Best Energy for WU: 0.00 Finished Docking number 0 Updating Best Energy for WU: -7.57 Finished Docking number 1 Finished Docking number 2 Finished Docking number 3 Finished Docking number 4 Failed to get VersionInfo size: 2 Failed to get VersionInfo size: 2 Restoring grahics. bestEnergy: -9.605040 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 5) Finished Docking number 5 Finished Docking number 6 Finished Docking number 7 Finished Docking number 8 Finished Docking number 9 Updating Best Energy for WU: -9.61 Finished Docking number 10 As you can see,at some stage the Best Energy was improved by -9.61, so your value is not that uncommon. Some of the messages are also similar, so you can assume these are not errors. Eg., WARNING: Unrecognized keyword in docking parameter file. Yes, but what's bothering me is that it had one energy.Then I restarted and it had a different energy and since it didn't logged the "Updating Best Energy for WU:" thing thought it could be a bug. That's all. - AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W - AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W - AMD Ryzen 7 7730U 8C/16T 3.0 GHz [Edit 1 times, last edit by Falconet at Apr 30, 2011 5:55:51 PM] |
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Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3315 Status: Offline Project Badges:
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Can a tech enlighten me?
----------------------------------------- AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W - AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W - AMD Ryzen 7 7730U 8C/16T 3.0 GHz |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Falconet,
The initial log posted appears to be incomplete, the one posted after displaying that at the end of the run the Energy was bested in the end. Maybe you could post the whole where it ends into . About to enter main loop...(dockings already 32 Finished Docking number 33 Finished Docking number 34 Finished Docking number 35 ________________________________________________________________________________ autodock4: Successful Completion on "World Community Grid device" ________________________________________________________________________________ WARNING: No benchmark data to run! called boinc_finish </stderr_txt> ]]> though I've no doubt, that there was no equal or better energy recorded in your instance. This program is used by thousands outside of FA@H and this version at WCG has been running for years (sometime this year going to the VINA version), thus it's very hard to see a bug of this nature would have been overlooked that long or having an material impact on the findings... compounds escaping highlight... the researchers get these logs too, so I'd be patient until a scientist checks in to clarify. (all forum posts are read and when warranted, the scientists are polled). cheers and thanks for crunching at WCG. |
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Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3315 Status: Offline Project Badges:
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Falconet, The initial log posted appears to be incomplete, the one posted after displaying that at the end of the run the Energy was bested in the end. Maybe you could post the whole where it ends into . About to enter main loop...(dockings already 32 Finished Docking number 33 Finished Docking number 34 Finished Docking number 35 ________________________________________________________________________________ autodock4: Successful Completion on "World Community Grid device" ________________________________________________________________________________ WARNING: No benchmark data to run! called boinc_finish </stderr_txt> ]]> though I've no doubt, that there was no equal or better energy recorded in your instance. This program is used by thousands outside of FA@H and this version at WCG has been running for years (sometime this year going to the VINA version), thus it's very hard to see a bug of this nature would have been overlooked that long or having an material impact on the findings... compounds escaping highlight... the researchers get these logs too, so I'd be patient until a scientist checks in to clarify. (all forum posts are read and when warranted, the scientists are polled). cheers and thanks for crunching at WCG. Hi.Yes, the log is incomplete.When I posted this part of the log, the task was at 40%. In the meantime, the task complete successfully, but has been purged from the database so it doesn't show on the "results status" page anymore.But I know it was marked as valid.Sorry I can't help anymore. Thanks for all replies! - AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W - AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W - AMD Ryzen 7 7730U 8C/16T 3.0 GHz |
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Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3315 Status: Offline Project Badges:
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I went through my result status page and found one task I had aborted.
----------------------------------------And it looks exactly like the one I mention in my post. faah20644_ZINC13216061_xh2_xtal_02 <core_client_version>5.10.30</core_client_version> <![CDATA[ <stderr_txt> Failed to get VersionInfo size: 1812 INFO:[12:12:54] Start AutoGrid... autogrid: autogrid4: Successful Completion. INFO:[12:16:10] End AutoGrid... Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 0) _maxGenSeenSoFar changed: 2500 _maxGenSeenSoFar changed: 2626 _maxGenSeenSoFar changed: 2758 _maxGenSeenSoFar changed: 2896 _maxGenSeenSoFar changed: 3041 _maxGenSeenSoFar changed: 3194 _maxGenSeenSoFar changed: 3354 _maxGenSeenSoFar changed: 3522 _maxGenSeenSoFar changed: 3699 _maxGenSeenSoFar changed: 3885 _maxGenSeenSoFar changed: 4080 _maxGenSeenSoFar changed: 4285 _maxGenSeenSoFar changed: 4500 _maxGenSeenSoFar changed: 4726 _maxGenSeenSoFar changed: 4963 _maxGenSeenSoFar changed: 5212 _maxGenSeenSoFar changed: 5473 _maxGenSeenSoFar changed: 5747 _maxGenSeenSoFar changed: 6035 _maxGenSeenSoFar changed: 6337 _maxGenSeenSoFar changed: 6654 _maxGenSeenSoFar changed: 6987 _maxGenSeenSoFar changed: 7337 _maxGenSeenSoFar changed: 7704 _maxGenSeenSoFar changed: 8090 _maxGenSeenSoFar changed: 8495 _maxGenSeenSoFar changed: 8920 _maxGenSeenSoFar changed: 9367 _maxGenSeenSoFar changed: 9836 _maxGenSeenSoFar changed: 10328 Updating Best Energy for WU: 0.00 Finished Docking number 0 Updating Best Energy for WU: -6.49 Finished Docking number 1 Updating Best Energy for WU: -7.06 Finished Docking number 2 Updating Best Energy for WU: -7.58 Before restarting Finished Docking number 3 Finished Docking number 4 Finished Docking number 5 Failed to get VersionInfo size: 1812 After Restoring grahics. bestEnergy: -7.964490 maxGenSeen: 10328 After restarting AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 6) Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -7.964490 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 6) Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -7.964490 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 6) Updating Best Energy for WU: -7.96 Before restarting(i think because of several "Beginning Autodock" messages) Finished Docking number 6 <--Here it finishes a docking after restarting Finished Docking number 7 <--Here it finishes a docking after restarting Failed to get VersionInfo size: 1812 Here it restarts Restoring grahics. bestEnergy: -9.053500 maxGenSeen: 10328 wwith a new and different energy! AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 8) Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.053500 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 8) Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.053500 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 8) Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.053500 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 8) Finished Docking number 8 Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.053500 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 9) Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.053500 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.053500 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 9) Updating Best Energy for WU: -9.05 Finished Docking number 9 Finished Docking number 10 Finished Docking number 11 Finished Docking number 12 Finished Docking number 13 Finished Docking number 14 Finished Docking number 15 Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.128840 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 16) Finished Docking number 16 Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.128840 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 17) Finished Docking number 17 Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.128840 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 18) Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.128840 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 18) Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.128840 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 18) Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.128840 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 18) Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.128840 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 18) Finished Docking number 18 Finished Docking number 19 Finished Docking number 20 Failed to get VersionInfo size: 1812 Restoring grahics. bestEnergy: -9.128840 maxGenSeen: 10328 AG Check: Found receptor.A.map Beginning AutoDock... INFO: Setting num_generations: 10000 autodock4: WARNING: Unrecognized keyword in docking parameter file. About to enter main loop...(dockings already completed: 21) Finished Docking number 21 Finished Docking number 22 Finished Docking number 23 Finished Docking number 24 Finished Docking number 25 Finished Docking number 26 Finished Docking number 27 Finished Docking number 28 Finished Docking number 29 Finished Docking number 30 ________________________________________________________________________________ autodock4: Successful Completion on "World Community Grid device" ________________________________________________________________________________ INFO:[14:06:06] Start AutoGrid... autogrid: autogrid4: Successful Completion. INFO:[14:06:56] End AutoGrid... Beginning AutoDock... INFO: Setting num_generations: 27000 About to enter main loop...(dockings already completed: 31) Finished Docking number 0 ________________________________________________________________________________ autodock4: Successful Completion on "World Community Grid device" ________________________________________________________________________________ called boinc_finish </stderr_txt> ]]> - AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W - AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W - AMD Ryzen 7 7730U 8C/16T 3.0 GHz [Edit 2 times, last edit by Falconet at May 4, 2011 8:54:36 PM] |
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