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

Stefano Forli forli at scripps.edu
Fri Aug 1 11:03:40 PDT 2014


Dave,

Vina does not have explicit options to not to write the output, but there's no need to 
edit the source code to redirect the output to stdout.
I'm not sure if it is what you are looking for, but this will write the docking output to 
stdout on POSIX systems (i.e. Linux) and redirect it to your script:

  vina --config docking.conf --out /dev/stdout | myscript -

  (note the last '-' to tell the script to read from stdin)

A more sophisticated alternative would be to create a small RAMdisk [1], e.g. 100 Mb, if 
more post-processing is required and temporary files need to be written.
In both cases, the final output could be compressed before being written, saving even more 
disk access time.

Hope this helps,

S



[1] https://www.google.com/search?q=linux+ramdisk



On 08/01/2014 08:08 AM, David M. Toth 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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-- 
  Stefano Forli, PhD

  Staff Scientist
  Molecular Graphics Laboratory
  Dept. of Integrative Structural
   and Computational Biology, MB-112F
  The Scripps Research Institute
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