Issue with OverlapBlockState and Overlapping SBM in graph_tool

Good morning everyone,

I hope this message finds you well.

I’m currently using the OverlapBlockState feature in graph_tool to detect overlapping communities in networks. While the algorithm works perfectly for some datasets, I’ve been encountering significant issues with others, even those of relatively small size. Here’s an example code snippet to demonstrate the workflow:

python

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import graph_tool.all as gt

# Load the dataset
g = gt.collection.data["polbooks"]

# Apply overlapping SBM
state = gt.minimize_blockmodel_dl(g, state=gt.OverlapBlockState)

# Draw the results
state.draw(pos=g.vp["pos"], output="polbooks_overlap_blocks_mdl.svg")

This works perfectly on datasets such as:

  • "polbooks": 105 nodes, 441 edges
  • "karate": 34 nodes, 78 edges
  • "football": 115 nodes, 615 edges
  • "power": 4,941 nodes, 6,594 edges

However, I face crashes and kernel deaths when working with other datasets, such as:

  • "celegansneural": 297 nodes, 2,359 edges
  • "polblogs": 1,490 nodes, 19,090 edges
  • Jazz dataset

On my local machine, the Jupyter kernel dies or the process crashes. Thinking it might be a memory issue, I tried running the same code on a server with 300 GiB of RAM and 16 CPUs, but I still encounter segmentation faults or crashes.

Given that the problem persists on the server, I’m unsure whether it’s a memory issue or something else, such as the structure of the datasets or a limitation of the algorithm for certain network characteristics.

Has anyone experienced something similar or have any insights into why this might be happening? Any suggestions or workarounds would be greatly appreciated.

Thank you in advance for your help!

Thanks for the bug report! Could you please open an issue at https://git.skewed.de/count0/graph-tool/-/issues, containing the description and example above? I will fix this ASAP.

FYI, this issue has been fixed in version 2.88.

1 Like

Good morning Professor Tiago,

Please I’m not able to open an issue at Issues · Tiago Peixoto / graph-tool · GitLab,

I’m very sorry for that.
Thank you

Good morning Professor Tiago,

Thank you very much for the answer,
Please this mean if I download the version 2.88 of graph_tool right now, I will not have the same issue?

Thank you very much by adavance.

Yes, that’s exactly what I mean.

Thank you very much once more !