[Bioperl-l] reducing time

[Andreas Bernauer]

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.