SpanningEdgeCentrality causing memory error #967
Description
Using SpanningEdgeCentrality with non-indexed graphs occassionally causes memory errors. This can be reproduced by running the notebook-tests (i.e. Centrality.ipynb), whereas example-code doesn't include indexing of the input graph.
Example:
> python3 notebooks/test_notebooks.py 'notebooks/'
...
Start /***/Centrality.ipynb
free(): invalid next size (fast)
/***/Centrality.ipynb test successfully completed.
...
Adding G.indexEdges() before initializing the algorithm does solve the problem:
G = nk.readGraph("../input/karate.graph", nk.Format.METIS)
G.indexEdges()
span = nk.centrality.SpanningEdgeCentrality(G, 1e-6)
span.run()
Depending on the Python version, nbconvert can also fail entirely to run the notebook. Example from the CI:
Start notebooks/Centrality.ipynb
Traceback (most recent call last):
File "/home/runner/work/networkit/networkit/pyenv/lib/python3.10/site-packages/nbclient/client.py", line 780, in _async_poll_for_reply
msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout))
File "/home/runner/work/networkit/networkit/pyenv/lib/python3.10/site-packages/nbclient/util.py", line 97, in ensure_async
result = await obj
File "/home/runner/work/networkit/networkit/pyenv/lib/python3.10/site-packages/jupyter_client/channels.py", line 224, in get_msg
ready = await self.socket.poll(timeout)
asyncio.exceptions.CancelledError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/runner/work/networkit/networkit/pyenv/lib/python3.10/site-packages/nbclient/client.py", line 1006, in async_execute_cell
exec_reply = await self.task_poll_for_reply
asyncio.exceptions.CancelledError
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/runner/work/networkit/networkit/notebooks/test_notebooks.py", line 49, in <module>
status += run_notebook(os.path.join(path, file))
File "/home/runner/work/networkit/networkit/notebooks/test_notebooks.py", line 27, in run_notebook
proc.preprocess(nb, {'metadata': {'path': dirname}})
File "/home/runner/work/networkit/networkit/pyenv/lib/python3.10/site-packages/nbconvert/preprocessors/execute.py", line 89, in preprocess
self.preprocess_cell(cell, resources, index)
File "/home/runner/work/networkit/networkit/pyenv/lib/python3.10/site-packages/nbconvert/preprocessors/execute.py", line 110, in preprocess_cell
cell = self.execute_cell(cell, index, store_history=True)
File "/home/runner/work/networkit/networkit/pyenv/lib/python3.10/site-packages/nbclient/util.py", line 85, in wrapped
return just_run(coro(*args, **kwargs))
File "/home/runner/work/networkit/networkit/pyenv/lib/python3.10/site-packages/nbclient/util.py", line 60, in just_run
return loop.run_until_complete(coro)
File "/opt/hostedtoolcache/Python/3.10.5/x64/lib/python3.10/asyncio/base_events.py", line 646, in run_until_complete
return future.result()
File "/home/runner/work/networkit/networkit/pyenv/lib/python3.10/site-packages/nbclient/client.py", line 1010, in async_execute_cell
raise DeadKernelError("Kernel died")
nbclient.exceptions.DeadKernelError: Kernel died
Since this error was introduced recently, it is likely caused by changes from #957.