BUG: Core dump and Segfault when calculating Network.nsi_betweenness() centrality
#142
Comments
- Single-source Cython/C type definitions: `core._ext.types`
- Introduce semantic type aliases: ADJ, NODE, DEGREE, WEIGHT, FIELD, etc.
- Remove deprecated type aliases: `np.{int|float}`
- Replace C type aliases by Numpy type aliases
- Add missing Numpy type casts before Python/Cython boundary
- Disambiguate `timeseries._ext.numerics._twin_surrogates_{s|r}`
(blame: 098489b & 2f6a5b9)
- Fix some broken output pointers
- Reduce redundant copying
- Vectorize some simple Python loops
- Eliminate some dead code
- Potentially related issues: #128, #141, #142, #145
fkuehlein
changed the title
Network.nsi_betweenness() centrality
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Could not reproduce this, Assuming this has been resolved by @ntfrgl's recent fixes in the Cython/C modules, and hence closing the issue. |
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@fkuehlein, I don't think that you have provided sufficient reason for closing this issue: The work you mentioned on the Cython/C method signatures wouldn't concern an indexing error deeply inside a Cython function, and you could in principle, say, spin up a moderately sized Amazon Elastic Compute Cloud instance to obtain enough RAM for reproducing the issue. Nonetheless, I agree with closing the issue for now. My commit above removes some obvious slowdowns in the method, after which I successfully tested it on a random network with slightly higher node and edge counts than the bug report: from pyunicorn import Network
net = Network.Model("ErdosRenyi", n_nodes=26000, link_probability=.2)
btw = net.nsi_betweenness(parallelize=True)The explanation suggested by the issue author is unfortunately incorrect: As is now explicitly asserted, the array In contrast, the error message above appears to have |
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Right, I was a bit too quick to conclude there.. All the more thanks for your speedup work and for providing good reference and documentation! |
I am currently trying to calculate the nsi_betweenness of my directed graph. printing my network object gives me
Network: undirected, 25600 nodes, 61761383 links, link density 0.188.I tried to find the error with gdb and it seems to happen because of indexerrors in the cython function _nsi_betweenness.
I think that the problem lies in the indexing via the degree.
Some arrays in the function are of size [0,E] with E being the number of edges/links and indexing is done via the sum of degrees, which can be of size [0,2*E]. that results in a segmentation error.
running gdp python on the core dump file lead to this:
running gdb python again with the _nsi_betweenness function now pythonized lead to this:
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