[Bioperl-l] reducing time

Chris Dagdigian dag at sonsorol.org
Wed Jan 28 11:18:33 EST 2004

Interestingly enough there is a thread on the bioclusters list today 
about dealing with filesystems and directories of large files.

  Here it is in the archives:

  Tim Cutts also proposed an intersting perl hashing method that should
  handle up to "64 million files or so" -- this could be an option for 
people stuck with ext2 filesystems:


Andreas Bernauer wrote:

> Heikki Lehvaslaiho wrote:
>>I could not find anything wrong in your code. 95 seconds per file (you mean 
>>per sequence?) is really slow. The problem according my tests is your local 
>>system. Maybe you have too many files per directory? 
> I had this problem with too many files per directory.  When I use more
> than about 2000 files or so in single directory, the access to a file
> slows down noticeably.  There is nothing you can do about it on ext2
> or ext3 file systems except of not using so many files in a single
> directory (as far as I know).
> Andreas.
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Chris Dagdigian, <dag at sonsorol.org>
Independent life science IT & informatics consulting
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