364860 jobs reacn 100% and continue for hours
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Message boards : Number crunching : 364860 jobs reacn 100% and continue for hours

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keputnam
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Message 2194 - Posted: 1 Apr 2015, 18:02:24 UTC

I've had two jobs in the 364860 series continue for more than 6 hours after reaching 100% (with a 12 minute estimate!!)

Combined with the refusal of VINA to respect suspend commands, and it's refusal to respect CPU percentages I'm afraid I'll have to stop supporting this worthy project

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Message 2201 - Posted: 2 Apr 2015, 10:42:24 UTC - in response to Message 2194.

:(

Thank you for helping us.

(I'm going to update Vina with the API but I have to much work. Lab work is time consuming ^^ )

keputnam
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Message 2220 - Posted: 5 Apr 2015, 5:47:25 UTC - in response to Message 2201.

I'll check back from time to time

If you ever get Vina to play nice, I'll start throwing cpu cycles your way again

Larry
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Message 2221 - Posted: 5 Apr 2015, 10:33:53 UTC

Just FYI:

I don't know what version of Vina is being used by this project. But, Vina 7.32 utilized by the FightAIDS@Home project (administrated by World Community Grid) does not exhibit the lack of adherence to CPU utilization and application suspend command functions controlled/specified within the BOINC Manager client environment that is being exhibited by the Vina application used for FiND@Home.

Perhaps a Vina upgrade is worth investigation when time allows.

Ananas
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Message 2222 - Posted: 5 Apr 2015, 11:14:18 UTC - in response to Message 2221.
Last modified: 5 Apr 2015, 11:14:50 UTC

.. But, Vina 7.32 utilized by the FightAIDS@Home project (administrated by World Community Grid) ...

Are you sure that those are the same programs? My WCG project folder contains a file that identifies as Autodock but doesn't mention Vina, it has totally different parameters too.

Arthur J. Olsen is one of the developers of both programs and both have been developed at Scripps but they seem not to be two versions of the same program.

Larry
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Message 2237 - Posted: 6 Apr 2015, 9:38:53 UTC

It is my understanding that the FightAIDS@Home project, in fact, uses both applications. (I'm pretty sure I run both. I haven't double-checked myself, but my memory is pretty good.) As I recall, each is individually selectable for processing on the "volunteer" client because one or the other (Autodock?) is considerably more "time-consuming."

But, I am sure what the application description was within my BOINC Manager for the WCG FightAIDS@Home task that prompted me to submit the previous post: Vina 7.32.

Ananas
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Message 2238 - Posted: 6 Apr 2015, 10:22:07 UTC - in response to Message 2237.
Last modified: 6 Apr 2015, 10:27:40 UTC

Version and splash screen here :

AutoDock Vina 1.1.2 (May 11, 2011) ################################################################# # If you used AutoDock Vina in your work, please cite: # # # # O. Trott, A. J. Olson, # # AutoDock Vina: improving the speed and accuracy of docking # # with a new scoring function, efficient optimization and # # multithreading, Journal of Computational Chemistry 31 (2010) # # 455-461 # # # # DOI 10.1002/jcc.21334 # # # # Please see http://vina.scripps.edu for more information. # #################################################################

and you're right, WCG does refer to Vina (on the web site) as "the new tool", so maybe my project folder is somewhat outdated :
This new tool, called Vina, is more accurate and significantly faster than the original tool, called AutoDock

Ananas
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Message 2284 - Posted: 14 Apr 2015, 17:34:09 UTC - in response to Message 2237.
Last modified: 14 Apr 2015, 18:13:51 UTC

I checked tha current WCG FAAH Win x64 binary and it actually is a VC++ compiled vina. It is missing the rligand and rreceptor parameters that the vina program here has, so it cannot be used just by adding app_info.xml. Their progress bar seems to work, so they probably have identified the main loop.

p.s.: and it is 1.1.2 too, same version string as here.

Message boards : Number crunching : 364860 jobs reacn 100% and continue for hours


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