[Numpy-discussion] loadtxt slow

Michael Gilbert michael.s.gilbert@gmail....
Sun Mar 1 13:29:54 CST 2009


On Sun, 1 Mar 2009 16:12:14 -0500 Gideon Simpson wrote:

> So I have some data sets of about 160000 floating point numbers stored  
> in text files.  I find that loadtxt is rather slow.  Is this to be  
> expected?  Would it be faster if it were loading binary data?

i have run into this as well.  loadtxt uses a python list to allocate
memory for the data it reads in, so once you get to about 1/4th of your
available memory, it will start allocating the updated list (every
time it reads a new value from your data file) in swap instead of main
memory, which is rediculously slow (in fact it causes my system to be
quite unresponsive and a jumpy cursor). i have rewritten loadtxt to be
smarter about allocating memory, but it is slower overall and doesn't
support all of the original arguments/options (yet).  i have some
ideas to make it smarter/more efficient, but have not had the time
to work on it recently.

i will send the current version to the list tomorrow when i have access
to the system that it is on.

best wishes,
mike


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