ADL: Can I avoid writing the output file with AutoDock Vina

David M. Toth david.toth at centre.edu
Fri Aug 1 17:58:08 PDT 2014


Thanks for the suggestions, Oleg and Stefano.  I'll definitely try those out this weekend.  It turns out that redirecting stdout to /dev/null so it doesn't keep scrolling by on the screen speeds up things significantly (~727 compounds screened in 1 hour to ~3300 compounds screened in 1 hour on my system.  

I like the idea of filtering the data before writing the files as Stafano suggested.  That should definitely cut down on bandwidth, too.

Thanks again!

Dave



________________________________________
From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] on behalf of Oleg Trott [trott at scripps.edu]
Sent: Friday, August 01, 2014 6:58 PM
To: autodock at scripps.edu
Subject: Re: ADL: Can I avoid writing the output file with AutoDock Vina

David,

This doesn't seem plausible. The ratio of a HDD bandwidth to what Vina
docking using 64 cores would produce is about 10000:1

Oleg

On Fri, Aug 1, 2014 at 8:08 AM, David M. Toth <david.toth at centre.edu> wrote:
> Hi.  I am running AutoDock Vina on a 64-core system and the cores are completing the calculations and producing output files faster than my disk can write the output files, thus slowing down the process of screening lots of compounds.
>
> Is there a command line option to tell AutoDock Vina to NOT write the output file, or do I have to go edit the code by hand and comment out the part that writes the output file?  I can capture the tiny amount of output I need by just redirecting stdout and filtering it, thus minimizing the writes to the file system and hopefully speeding things up a lot.
>
> Thanks!
>
> Dave Toth
> ________________________________________________
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--
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com

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