[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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