[SciPy-Dev] scipy.io.loadmat and matvec multiply

[Jonathan Taylor]

Hmm... I am running scipy 0.19.1 (added that line to gist to be sure). When
it loaded as aligned was the timing comparable to `Xnp`?

Just to be sure, I  created a new conda ipython environment and installed
scipy -- version is 0.19.1. Flags are still the same.

The docs for scipy.io.loadmat don't seem to have an aligned option -- will
ping Matthew Brett....


On Mon, Aug 28, 2017 at 10:35 AM, CJ Carey <perimosocordiae at gmail.com>
wrote:

> I tried reproducing the results from your gist using scipy 0.19.0, and I
> found that Xmat is aligned after loadmat:
>
> In [3]: Xmat = sio.loadmat('data.mat')['X']
>
> In [4]: Xmat.flags
> Out[4]:
>   C_CONTIGUOUS : False
>   F_CONTIGUOUS : True
>   OWNDATA : False
>   WRITEABLE : True
>   ALIGNED : True
>   UPDATEIFCOPY : False
>
> On Mon, Aug 28, 2017 at 1:26 PM, Robert Kern <robert.kern at gmail.com>
> wrote:
>
>> On Mon, Aug 28, 2017 at 10:13 AM, Jonathan Taylor <
>> jonathan.taylor at stanford.edu> wrote:
>> >
>> > Thanks for all the help.
>> >
>> > That said, I'm not sure it is an issue of the strides. I can easily
>> recreate the slowdown as in the above gist (
>> https://gist.github.com/da7b2ef6ef109511af06a9cebbfc8ed1 ). Also,
>> modifying the flags of a user-created ndarray so they agree with the loaded
>> one is still noticably faster than using the array from `scipy.io.loadmat`
>>
>> Ah yeah, if the data is aligned, then that might end up faster. Your
>> optimized BLAS will be able to use certain CPU instructions that require
>> aligned data. Setting the ALIGNED flag to false won't actually make the
>> data unaligned; your BLAS checks the data itself, not the numpy flag.
>>
>> > For my purposes, a copy is just fine, but I think this might be an
>> issue that could be looked into. Perhaps I should file an issue on github?
>>
>> It might be worth checking if scipy.io.loadmat() can be made to ensure
>> that it always creates aligned arrays. There isn't anything to be done
>> about .dot(), though.
>>
>> --
>> Robert Kern
>>
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>
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-- 
Jonathan Taylor
Dept. of Statistics
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390 Serra Mall
Stanford, CA 94305
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Fax:   650.725.8977
Web: http://www-stat.stanford.edu/~jtaylo
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