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ChainComplex() runs 24 times slower than homology()

asked 2018-10-28 03:55:39 -0500

Leon gravatar image

I load a list of matrices bdrs representing a chain complex, their dimensions are {1, 21, 210, 1330, 5985, 20349, 54264, 116280, 203490, 293930, 352716, 352716, 293930, 203490, 116280, 54264, 20349, 5985, 1330, 210, 21, 1}, and the largest has density 3.91*10^-6. In total they take up 50MB of disk space. This finishes in 63sec.

When I run chcx=ChainComplex(bdrs,base_ring=GF(2)), it takes 7hrs20min, but chcx.homology() finishes in only 18min. Why does it take so long to just store a few matrices? At first I thought that ChainComplex() also does some simplifications/reductions, but [chcx.free_module_rank(i) for i in range(0,21)] shows the original dimensions of matrices :/.

Is there a faster way to compute the homology of a chain complex (over $\mathbb{Z}$ or $\mathbb{Z}_p$)?

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answered 2018-10-28 04:51:41 -0500

rburing gravatar image

According to the documentation of ChainComplex there is an optional argument

check – boolean (optional, default True). If True, check that each consecutive pair of differentials are composable and have composite equal to zero.

I can imagine this takes a while. How fast is it with check=False?

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Aaah, you're right, with check=False, it only takes 3sec. Sorry for not noticing this option in the documentation, and thank you for your help!

Leon gravatar imageLeon ( 2018-10-28 09:42:00 -0500 )edit

answered 2018-10-28 06:15:18 -0500

tmonteil gravatar image

Apparently (unfortunately), there is no way to specify/detect that your objects are sparse when defining the chain complex.

You could try to enforce that by giving as few choice as possible to the ChainComplex by defining bdrs to be sparse matrices explicitely defined over GF(2).

Please tell us if is works. Otherwise, could you please provide your code so that we can handle a concrete example and see what is going on ?

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Surely, ChainComplex() detects that these are sparse matrices, otherwise I wouldn't have enough RAM to store $10^6\times10^6=10^{12}$ entries... But still, thank you for your help!

Leon gravatar imageLeon ( 2018-10-28 09:45:02 -0500 )edit

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Asked: 2018-10-28 03:55:39 -0500

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Last updated: Oct 28 '18