search

rivetTDA / rivet

RIVET is a tool for Topological Data Analysis, in particular two-parameter persistent homology.
GNU General Public License v3.0
73 stars 24 forks source link

Crash with H3N2 Data set (Fixed in Mike's Fork) #85

Closed mlesnick closed 6 years ago

mlesnick commented 7 years ago

[See comment below; this bug will presumably be addressed by the updates for multi-critical support, which are almost done, hence the "wontfix" label.]

Originally reported by: M L (GitHub: mlesnick)

[Not posting the file here, due to size.]

As explained in Otter's Roadmap paper, the H3N3 data set has 500 points, so we do not expect this to be a memory issue.

Details of bug: After Matthew's thresholding fix, I successfully computed H0 with 20x20 bins for this data set.

But now I am trying to compute H1 with 12x12 bins. Below is the end of the console output on Mac OS X Sierra, using -V 8.

STAGE PROGRESS 30 Building Vietoris-Rips bifiltration. x-grades: 12 y-grades: 12 Created SimplexTree( 1 , 8 ) Killed: 9

mlesnick commented 7 years ago

Original comment by M L (GitHub: mlesnick):

It may be worth waiting until Roy removes the simplex tree class before addressing this particular issue, since it seems to be related to construction of the bifiltration and the boundary matrices. The issue is likely to disappear with Roy's changes.

mlesnick commented 6 years ago

With the updated version of RIVET in my fork this is no longer an issue. Will be resolved once I do a pull request.

mlesnick commented 6 years ago

Contrary to what was said above, the H3N2 data set has 1000 points, not 500. I was getting two influenza data sets from the Rabadan lab confused. Thus, it's not clear to me that this was ever really a bug, rather than simply a memory issue with a large example.

I'm closing for now. If I see a problem with this data set in the future, I will open a new issue.