On 24/02/14 16:11, Javier Martínez-López wrote:
> I am sorry Sturla but I am new in python and I cannot follow you on
> this... hopefully someone else will! I am now combining the R and the
> Python code and trying to scale up the process! Thank you very much
> and cheers, Javier
This would be
I am sorry Sturla but I am new in python and I cannot follow you on
this... hopefully someone else will! I am now combining the R and the
Python code and trying to scale up the process! Thank you very much
and cheers, Javier
On Mon, Feb 24, 2014 at 3:56 PM, Sturla Molden wrote:
> Sturla Molden
>
Sturla Molden
wrote:
> Just a tiny comment on this: It might be easier for the LAPACK library to
> use SIMD extensions (SSE2, SSE3, AVX) if we use DTRTRS. So we need to
> benchmark with relevant matrix sizes to see which strategy is the better.
> One is better for SIMD, the other is better for ca
Sturla Molden
wrote:
> Yes there is! We can make a very cache friendly loop by iterating over
> DTRSV instead of using DTRTRS as this example does. That also avoids
> temporary variables, and we can multithread the call to DTRSV.
Just a tiny comment on this: It might be easier for the LAPACK li
Javier Martínez-López
wrote:
> That is great, thanks! I do not have the mkl module (it isn't free,
> right?) but with your script the calculation is approx. 10 times
> faster than in R.
Great!
By the way, using OpenBLAS will be fast as well.
On Mac OS X Mavericks it seems Accelerate framewo
Thank you very much! Already working!
However, contrasting with the results obtained by Sturla, I get the
fastest result with cholesky, parallel method:
bash-4.1$ python mahalk.py
Similar result to scipy.spatial.distance.mahalanobis: true
Similar results with and without parallel execution: true
If you're affiliated with a university, Anaconda has free academic
licenses that include MKL and their optimized builds.
Vlad
On Mon Feb 24 09:22:07 2014, Javier Martínez-López wrote:
> That is great, thanks! I do not have the mkl module (it isn't free,
> right?) but with your script the calcula
That is great, thanks! I do not have the mkl module (it isn't free,
right?) but with your script the calculation is approx. 10 times
faster than in R. Is there a way to increase performance using Cython,
BLAS and LAPACK? Could you possibly show some examples of how to do
it?
Thank you very much ag
On 21/02/14 14:07, Javier Martínez-López wrote:
> Hello,
>
> I am quite new to python, so I am sorry if I am asking something too
> simple: I am trying to speed up a raster processing with python and I
> want to use the "sklearn.metrics.pairwise.pairwise_distances" module
> with the mahalanobis dis
