[SciPy-user] Scipy/Numeric slow under Debian?

Robert Kern rkern at ucsd.edu
Fri Aug 19 02:17:46 CDT 2005

Greg Novak wrote:
> I recently had trouble getting Scipy to work under Fedora 4, and this 
> drove me to try Debian.  Now, apt-get python-scipy gets me going just 
> fine, but it seems rather... slow.  Code seems to run about a factor of 
> 10 slower than when I had Scipy running under Fedora 3.
> I'm using Debian stable on a dual Intel Xeon 2.8 Ghz.  The version of 
> scipy that I got when I installed through apt was 0.3.2.  The slow code 
> is heavy on Numeric calls like argsort and cumsum, without much linear 
> algebra.  It seems to me that the culprit could be:
> 1) Compiler optimization
> 2) instruction set (i386 vs. i686)
> 3) kernel version (2.4 vs 2.6)
> 4) Some obscure hardware problem, like Debian isn't using some fancy 
> memory-bandwidth enhancing feature that Fedora did (pure conjecture).
> All of the above seem unlikely to account for a factor of 10 speed 
> difference.  Any insight about what's going on would be much appreciated...

We won't have any until you give us some more information. I recommend 
writing some small targetted benchmarks testing individual operations 
under various conditions (like array size).

It's possible that rebuilding the relevant packages locally with tweaked 
compiler flags might help.

Robert Kern
rkern at ucsd.edu

"In the fields of hell where the grass grows high
  Are the graves of dreams allowed to die."
   -- Richard Harter

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