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vtraag / leidenalg

Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.
GNU General Public License v3.0
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python Segmentation fault: 11 when running the partition function of leidenalg #154

Closed Shuang-Plum closed 6 months ago

Shuang-Plum commented 11 months ago

I just installed the latest version of leidenalg and python-igraph. When I try to run this code: partition = leidenalg.find_partition(ig_graph,leidenalg.RBERVertexPartition,weights='weight'), my python quit (Segmentation fault: 11) with the following error message. But when I downgrade both packages: python-igraph 0.10.4 and leidenalg 0.9.1, it worked. I was wondering what is causing the error in leidenalg 0.10.1? Thanks!

Process: Python [60748] Path: /Library/Frameworks/Python.framework/Versions/3.9/Resources/Python.app/Contents/MacOS/Python Identifier: Python Version: 3.9.12 (3.9.12) Code Type: X86-64 (Native) Parent Process: bash [54087] Responsible: Terminal [5970] User ID: 501

Date/Time: 2023-10-24 10:16:45.205 -0400 OS Version: Mac OS X 10.15.7 (19H2026) Report Version: 12

Time Awake Since Boot: 670000 seconds

System Integrity Protection: enabled

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000013 Exception Note: EXC_CORPSE_NOTIFY

Termination Signal: Segmentation fault: 11 Termination Reason: Namespace SIGNAL, Code 0xb Terminating Process: exc handler [60748]

VM Regions Near 0x13: --> __TEXT 000000010406b000-000000010406f000 [ 16K] r-x/r-x SM=COW /Library/Frameworks/Python.framework/Versions/3.9/Resources/Python.app/Contents/MacOS/Python

Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 _c_louvain.cpython-39-darwin.so 0x0000000116922d23 MutableVertexPartition::cache_neigh_communities(unsigned long, igraph_neimode_t) + 147 1 _c_louvain.cpython-39-darwin.so 0x0000000116922c69 MutableVertexPartition::weight_to_comm(unsigned long, unsigned long) + 41 2 liblibleidenalg.0.11.0.dylib 0x0000000116bdd3a9 RBERVertexPartition::diff_move(unsigned long, unsigned long) + 89 3 liblibleidenalg.0.11.0.dylib 0x0000000116bb9fc3 Optimiser::move_nodes(std::1::vector<MutableVertexPartition*, std::1::allocator<MutableVertexPartition> >, std::1::vector<double, std::1::allocator >, std::1::vector<bool, std::1::allocator > const&, int, int, bool, unsigned long) + 4195 4 liblibleidenalg.0.11.0.dylib 0x0000000116bb794f Optimiser::optimise_partition(std::__1::vector<MutableVertexPartition, std::1::allocator<MutableVertexPartition*> >, std::1::vector<double, std::1::allocator >, std::1::vector<bool, std::1::allocator > const&, unsigned long) + 1311 5 liblibleidenalg.0.11.0.dylib 0x0000000116bb7324 Optimiser::optimise_partition(MutableVertexPartition, std::1::vector<bool, std::1::allocator > const&, unsigned long) + 212 6 liblibleidenalg.0.11.0.dylib 0x0000000116bb7249 Optimiser::optimise_partition(MutableVertexPartition, std::1::vector<bool, std::__1::allocator > const&) + 41 7 _c_leiden.abi3.so 0x0000000116b8ee71 _Optimiser_optimise_partition + 465 8 org.python.python 0x000000010410cad5 cfunction_call + 69 9 org.python.python 0x00000001040c8d78 _PyObject_MakeTpCall + 376 10 org.python.python 0x00000001041b6812 call_function + 626 11 org.python.python 0x00000001041b3b82 _PyEval_EvalFrameDefault + 29074 12 org.python.python 0x00000001041b7676 _PyEval_EvalCode + 2950 ....... leiden_error_10_24_23.txt

vtraag commented 9 months ago

It is unclear to me what might be the problem. Perhaps you had installed conflicting versions of igraph somehow? What combination of versions of python-igraph and leidenalg gave this problem? Apparently you didn't experience a problem for the combination python-igraph==0.10.4 + leidenalg==0.9.1. But what is the python-igraph version that gives a problem for leidenalg==0.10.1? Also, how did you install the libraries?

GLking123 commented 6 months ago

The same issue occurs with igraph=0.9.9 and leidenalg=0.10.2.
Is my igraph version too low?

szhorvat commented 6 months ago

Yes.

vtraag commented 6 months ago

Indeed, as specified in pyproject.toml the dependency requirements are igraph >= 0.10.0,< 0.12 for leidenalg=0.10.2. Normally, you should then not be able to install igraph=0.9.9 while also installing leidenalg=0.10.2. I'm not sure how this happened, but if you upgrade igraph, it should all be fine.