python Segmentation fault: 11 when running the partition function of leidenalg
Shuang-Plum opened this issue · 4 comments
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
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?
The same issue occurs with igraph=0.9.9 and leidenalg=0.10.2.
Is my igraph version too low?
Yes.
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.