Segmentation fault while importing nuSQuIDS in python

[greesman]

Hi! I have correctly installed all of the prerequisites for nuSQuIDS. However, when I try to use python bindings by importing nuSQuIDS, I get a segmentation fault.

 % python                 
Python 3.11.0 | packaged by conda-forge | (main, Jan 15 2023, 05:44:48) [Clang 14.0.6 ] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import nuSQuIDS
zsh: segmentation fault  python

No output or logs are generated.

All of the 18 tests in nuSQuIDS pass when I run make test. The following are the versions of the packages I am using:

python - 3.11.0
boost - 1.80.0
hdf5 - 1.12.2_2
squids - 1.3.0

I'd be happy to provide any more information that you might need.

[cnweaver]

Hi! That's unfortunate, and we would definitely like to fix it! Can you give us:

• Any details on which OS you're using (which version of Mac OS?)
• Any sort of stack trace of where the crash happens (Running python under lldb might work)

[greesman]

Sorry for the delayed response! I am using Ventura 13.0.1. Here is the output of running python under lldb:

(lldb) run
Process 19878 launched: '/Users/username/opt/anaconda3/envs/emcee/bin/python' (x86_64)
Process 19878 stopped
* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x10)
    frame #0: 0x0000000105e865d1 libpython3.11.dylib`PyImport_Import + 49
libpython3.11.dylib`PyImport_Import:
->  0x105e865d1 <+49>: movq   0x10(%rax), %rax
    0x105e865d5 <+53>: movl   0x11a0(%rax), %ecx
    0x105e865db <+59>: testl  %ecx, %ecx
    0x105e865dd <+61>: je     0x105e8683a               ; <+666>
Target 0: (python) stopped.
(lldb) 

[michelelucente]

Hi, I have the same issue. I am on Mac OS 13.2.1, here is the output of running python under lldb:

(lldb) run
Process 81648 launched: '/opt/anaconda3/bin/python' (x86_64)
Process 81648 stopped
* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x10)
    frame #0: 0x0000000104a48205 libpython3.10.dylib`PyImport_Import + 53
libpython3.10.dylib`PyImport_Import:
->  0x104a48205 <+53>: movq   0x10(%rax), %r15
    0x104a48209 <+57>: movq   0x161f48(%rip), %rbx      ; PyImport_Import.PyId___import__.1
    0x104a48210 <+64>: testq  %rbx, %rbx
    0x104a48213 <+67>: js     0x104a48650               ; <+1152>
Target 0: (python) stopped.

Thank you for your help!

[cnweaver]

Can you get a backtrace (thread backtrace) of how it got to that point? That would help us narrow it down.

[michelelucente]

(lldb) thread backtrace
* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x10)
  * frame #0: 0x0000000104a48205 libpython3.10.dylib`PyImport_Import + 53
    frame #1: 0x0000000104a48196 libpython3.10.dylib`PyImport_ImportModule + 54
    frame #2: 0x0000000103803130 nuSQuIDS.so`init_module_nuSQuIDS() + 32
    frame #3: 0x0000000102757065 libboost_python310.dylib`boost::python::handle_exception_impl(boost::function0<void>) + 69
    frame #4: 0x0000000102757bdb libboost_python310.dylib`boost::python::detail::init_module(PyModuleDef&, void (*)()) + 107
    frame #5: 0x00000001001e8364 python`_imp_create_dynamic + 868
    frame #6: 0x00000001000c7f37 python`cfunction_vectorcall_FASTCALL + 103
    frame #7: 0x000000010018d5c2 python`_PyEval_EvalFrameDefault + 59970
    frame #8: 0x00000001000699f6 python`_PyFunction_Vectorcall + 582
    frame #9: 0x000000010018ae79 python`_PyEval_EvalFrameDefault + 49913
    frame #10: 0x00000001000699f6 python`_PyFunction_Vectorcall + 582
    frame #11: 0x000000010018757f python`_PyEval_EvalFrameDefault + 35327
    frame #12: 0x00000001000699f6 python`_PyFunction_Vectorcall + 582
    frame #13: 0x00000001001af83b python`call_function + 187
    frame #14: 0x0000000100180fdf python`_PyEval_EvalFrameDefault + 9311
    frame #15: 0x00000001000699f6 python`_PyFunction_Vectorcall + 582
    frame #16: 0x00000001001af83b python`call_function + 187
    frame #17: 0x0000000100180fdf python`_PyEval_EvalFrameDefault + 9311
    frame #18: 0x00000001000699f6 python`_PyFunction_Vectorcall + 582
    frame #19: 0x00000001001af83b python`call_function + 187
    frame #20: 0x0000000100180fdf python`_PyEval_EvalFrameDefault + 9311
    frame #21: 0x00000001000699f6 python`_PyFunction_Vectorcall + 582
    frame #22: 0x0000000100067ef9 python`_PyObject_VectorcallTstate.728 + 73
    frame #23: 0x000000010006cc6a python`object_vacall + 410
    frame #24: 0x000000010006ce59 python`_PyObject_CallMethodIdObjArgs + 249
    frame #25: 0x00000001001e4ce1 python`PyImport_ImportModuleLevelObject + 3905
    frame #26: 0x0000000100185be1 python`_PyEval_EvalFrameDefault + 28769
    frame #27: 0x000000010017cde1 python`_PyEval_Vector + 545
    frame #28: 0x0000000100205440 python`run_mod + 240
    frame #29: 0x0000000100205205 python`pyrun_file + 133
    frame #30: 0x0000000100204d56 python`_PyRun_SimpleFileObject + 422
    frame #31: 0x000000010020467f python`_PyRun_AnyFileObject + 143
    frame #32: 0x0000000100229978 python`pymain_run_file_obj + 216
    frame #33: 0x0000000100229305 python`pymain_run_file + 85
    frame #34: 0x0000000100228b38 python`pymain_run_python + 376
    frame #35: 0x0000000100228975 python`Py_RunMain + 37
    frame #36: 0x00000001000017c8 python`main + 56
    frame #37: 0x00007ff80e3d0310 dyld`start + 2432