Re: [Numpy-discussion] numpy blas running slow: how to check that it is properly linked

2011-09-06 Thread David Cournapeau
On Tue, Sep 6, 2011 at 5:12 PM, David Cottrell wrote: > Actually this link: http://www.scipy.org/PerformanceTips seems to > indicate that numpy.dot does use blas ... This not true (you can check by looking into numpy/core/setup.py, which explicitly checks for ATLAS for _dotblas). The idea is that

Re: [Numpy-discussion] numpy blas running slow: how to check that it is properly linked

2011-09-06 Thread David Cottrell
Actually this link: http://www.scipy.org/PerformanceTips seems to indicate that numpy.dot does use blas ... Is there some way of running ldd on the install to see what libraries are being pulled in? On Tue, Sep 6, 2011 at 4:13 PM, David Cottrell wrote: > Thanks, I didn't realize dot was not just

Re: [Numpy-discussion] gradient with memmap array bug (?)

2011-09-06 Thread Fred
Le 05/09/2011 18:41, Ralf Gommers a écrit : > That rings a bell. I can reproduce this with 1.5.1, and it's fixed in > master. Thanks! Cheers, -- Fred ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/

Re: [Numpy-discussion] numpy blas running slow: how to check that it is properly linked

2011-09-06 Thread David Cottrell
Thanks, I didn't realize dot was not just calling dgemm or some variant which I assume would be reasonably fast. I see dgemm appears in the numpy code in various places such as the lapack_lite module. I ran the svd test on the solaris setup and will check the OSX run when back at my laptop. 8.4 se

Re: [Numpy-discussion] numpy blas running slow: how to check that it is properly linked

2011-09-06 Thread David Cournapeau
On Tue, Sep 6, 2011 at 2:38 PM, David Cottrell wrote: > I posted on stackoverflow but then noticed this message board: > > http://stackoverflow.com/questions/7311869/python-numpy-on-solaris-blas-slow-or-not-linked > > I'm reposting the full post below: > > Matrix-Matrix multiplies are very slow on

[Numpy-discussion] numpy blas running slow: how to check that it is properly linked

2011-09-06 Thread David Cottrell
I posted on stackoverflow but then noticed this message board: http://stackoverflow.com/questions/7311869/python-numpy-on-solaris-blas-slow-or-not-linked I'm reposting the full post below: Matrix-Matrix multiplies are very slow on my Solaris install (running on a sparc server) compared to my OSX

[Numpy-discussion] Smoothing binary volumes

2011-09-06 Thread Thiago Franco Moraes
Hi all, I've been implementing the algorithm from this paper "Reducing Aliasing Artifacts in Iso-Surfaces of Binary Volumes" from Ross T. Whitaker. Because I develop a opensource software which works with segmentation of CT and MRI medical images, and the results of segmentation is a binary volume

Re: [Numpy-discussion] Efficient way to load a 1Gb file?

2011-09-06 Thread Derek Homeier
On 02.09.2011, at 1:47AM, Russell E. Owen wrote: >> I've made a pull request >> https://github.com/numpy/numpy/pull/144 >> implementing that option as a switch 'prescan'; could you review it in >> particular regarding the following: >> >> Is the option reasonably named and documented? >> >> In

Re: [Numpy-discussion] load from text files Pull Request Review

2011-09-06 Thread Christopher Jordan-Squire
On Tue, Sep 6, 2011 at 9:32 AM, Derek Homeier wrote: > On 02.09.2011, at 11:45PM, Christopher Jordan-Squire wrote: and unfortunately it's for 1D-arrays only). >>> >>> That's not bad for this use -- make a row a struct dtype, and you've got >>> a 1-d array anyway -- you can optionally con

Re: [Numpy-discussion] load from text files Pull Request Review

2011-09-06 Thread Derek Homeier
On 02.09.2011, at 11:45PM, Christopher Jordan-Squire wrote: >>> >>> and unfortunately it's for 1D-arrays only). >> >> That's not bad for this use -- make a row a struct dtype, and you've got >> a 1-d array anyway -- you can optionally convert to a 2-d array after >> the fact. >> >> I don't know