RecursionError

Hi, thanks for the great package.

I have a dataset which has 200000 rows and 15 columns. I tried to apply UMAP as following

embedding = umap.UMAP(n_neighbors=5, min_dist=0.3, metric='correlation').fit_transform(data)

After 10 seconds, I got following exceptions :

• RecursionError: maximum recursion depth exceeded while calling a Python object
• return make_angular_tree(data, indices, rng_state, leaf_size) SystemError: CPUDispatcher(<function angular_random_projection_split at 0x000001C8260D6378>) returned a result with an error set

I set the system recursion limit to 10000 as below and tried again but then python exited with a code like -143537645 meaning exited with error.

sys.setrecursionlimit(10000)

Is there any solution, workaround or anything I can do for this problem?

Thanks.

[scharron]

@lmcinnes I attached you a 5000x100 numpy array that always makes UMAP crashes. I’m reproducing the error with : umap = UMAP(metric="cosine", n_components=2, min_dist=0.3).fit_transform(data)

data.npy.zip

[lmcinnes]

I think some fixes to other issues may actually resolve this, so I’ll try to roll out a patch release in the next few days that will hopefully solve this.