[Numpy-discussion] Efficient square distance computation

Henry Gomersall heng at cantab.net
Tue Oct 8 05:56:52 EDT 2013


On 08/10/13 09:49, Matthew Brett wrote:
> On Tue, Oct 8, 2013 at 1:06 AM, Ke Sun<sunk.cs at gmail.com>  wrote:
>> >Dear all,
>> >
>> >I have written the following function to compute the square distances of a large
>> >matrix (each sample a row). It compute row by row and print the overall progress.
>> >The progress output is important and I didn't use matrix multiplication.
>> >
>> >I give as input a 70,000x800 matrix. The output should be a 70,000x70,000
>> >matrix. The program runs really slow (16 hours for 1/3 progress). And it eats
>> >36G memory (fortunately I have enough).
> That is very slow.
>
> As a matter of interest - why didn't you use matrix multiplication?
> On a machine I had access to it took about 20 minutes.

Out of interest, how did you do this with matrix multiplication?

Henry



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