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JuliaPy / PyCall.jl

Package to call Python functions from the Julia language
MIT License
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MKL Fatal Error: Can't load libmkl_intel_thread.1.dylib #921

Closed ghost closed 3 years ago

ghost commented 3 years ago

Hi, I am new to julia. Recently I want to use PyCall to import some python packages such as scipy. But when I tried to use it on my macbook pro, I faced some problems.

using PyCall
py"""
import scipy
"""

But then I face a problem 

INTEL MKL ERROR: dlopen(/Users/xxx/.julia/conda/3/lib/libmkl_intel_thread.1.dylib, 9): Library not loaded: @rpath/libiomp5.dylib
  Referenced from: /Users/xxx/.julia/conda/3/lib/libmkl_intel_thread.1.dylib
  Reason: image not found.
Intel MKL FATAL ERROR: Cannot load libmkl_intel_thread.1.dylib.

I tried 

ENV["PYTHON"] =""
using Pkg
Pkg.build("PyCall")

But this does not work. I also tried method in this issue https://github.com/JuliaPy/PyCall.jl/issues/443 to set use_BLAS =0 (I downloaded julia 1.7 and used MKL.jl as suggested but I still have this problem). Anyone knows how to fix this problem?

By the way, I tried to use PyCall to import scipy on my windows computer and it works. Don't know why.

ghost commented 3 years ago

Ok, I just find one method which seems to work for julia 1.7 beta or 1.6.2. https://github.com/JuliaPy/PyPlot.jl/issues/315. As @tlienart suggested, this problem can be fixed by 

using Conda
Conda.rm("mkl")
Conda.add("nomkl")

Then I can use 

using PyCall
py"""
import numpy
import scipy
"""

as my windows computer. But one thing is that I need to re-download the packages like numpy and scipy by Conda.add() after I remove mkl and add nomkl. Not sure why this happens.

ghost commented 3 years ago

Well, even after I fix this issue and I can use numpy/scipy, another question shows up when I try to import a python package called quspin. I guess rm mkl and add nomkl may lead to some problem and we need to be careful about this.

tlienart commented 3 years ago

I think the MKL stuff is reasonably known after https://github.com/JuliaPy/PyPlot.jl/issues/315 but maybe post here the full error message you're getting with quspin, it'll help people try to fix this.

I'd find it surprising that quspin does not work because of the mkl trick.

ghost commented 3 years ago

This is the full error I face when I try to import the package quspin https://weinbe58.github.io/QuSpin/ via pycall. It is too long sorry for the inconvenience. I don't have this problem when I import numpy or scipy.

julia> py"""
       import quspin
       """

signal (11): Segmentation fault: 11
in expression starting at REPL[3]:1
_ZN4llvm17PMTopLevelManager16addImmutablePassEPNS_13ImmutablePassE at /Users/xiaozhoufeng/.julia/conda/3/lib/libLLVM-10.dylib (unknown line)
_ZN4llvm17PMTopLevelManager12schedulePassEPNS_4PassE at /Users/xiaozhoufeng/.julia/conda/3/lib/libLLVM-10.dylib (unknown line)
_ZN4llvm17PMTopLevelManager12schedulePassEPNS_4PassE at /Users/xiaozhoufeng/.julia/conda/3/lib/libLLVM-10.dylib (unknown line)
_ZN4llvm18PassManagerBuilder25populateModulePassManagerERNS_6legacy15PassManagerBaseE at /Users/xiaozhoufeng/.julia/conda/3/lib/libLLVM-10.dylib (unknown line)
LLVMPY_PassManagerBuilderPopulateModulePassManager at /Users/xiaozhoufeng/.julia/conda/3/lib/python3.9/site-packages/llvmlite/binding/libllvmlite.dylib (unknown line)
ffi_call_unix64 at /Users/xiaozhoufeng/.julia/conda/3/lib/libffi.7.dylib (unknown line)
ffi_call_int at /Users/xiaozhoufeng/.julia/conda/3/lib/libffi.7.dylib (unknown line)
_ctypes_callproc at /Users/xiaozhoufeng/.julia/conda/3/lib/python3.9/lib-dynload/_ctypes.cpython-39-darwin.so (unknown line)
PyCFuncPtr_call at /Users/xiaozhoufeng/.julia/conda/3/lib/python3.9/lib-dynload/_ctypes.cpython-39-darwin.so (unknown line)
_PyObject_Call at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_FastCallDictTstate at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
slot_tp_call at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_MakeTpCall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
method_vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_FastCallDictTstate at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
slot_tp_init at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
type_call at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_MakeTpCall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_FastCallDictTstate at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
slot_tp_init at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
type_call at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_MakeTpCall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
object_vacall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
PyObject_CallFunctionObjArgs at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_GenericGetAttrWithDict at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
property_descr_get at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_GenericGetAttrWithDict at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_FastCallDictTstate at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
slot_tp_init at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
type_call at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_Call at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
PyVectorcall_Call at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
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_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
builtin_exec at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
cfunction_vectorcall_FASTCALL at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
object_vacall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_CallMethodIdObjArgs at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
PyImport_ImportModuleLevelObject at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
builtin_exec at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
cfunction_vectorcall_FASTCALL at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
object_vacall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_CallMethodIdObjArgs at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
PyImport_ImportModuleLevelObject at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
builtin_exec at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
cfunction_vectorcall_FASTCALL at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
object_vacall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_CallMethodIdObjArgs at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
PyImport_ImportModuleLevelObject at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
builtin_exec at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
cfunction_vectorcall_FASTCALL at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
object_vacall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_CallMethodIdObjArgs at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
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object_vacall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
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object_vacall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
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PyImport_ImportModuleLevelObject at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
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builtin_exec at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
cfunction_vectorcall_FASTCALL at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
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call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
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call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
call_function at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyFunction_Vectorcall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
object_vacall at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyObject_CallMethodIdObjArgs at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
PyImport_ImportModuleLevelObject at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalFrameDefault at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
_PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
PyEval_EvalCode at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
macro expansion at /Users/xiaozhoufeng/.julia/packages/PyCall/BD546/src/exception.jl:95 [inlined]
#117 at /Users/xiaozhoufeng/.julia/packages/PyCall/BD546/src/pyeval.jl:38 [inlined]
disable_sigint at ./c.jl:458 [inlined]
pyeval_ at /Users/xiaozhoufeng/.julia/packages/PyCall/BD546/src/pyeval.jl:37
unknown function (ip: 0x1202eb588)
jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
do_call at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
eval_body at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_interpret_toplevel_thunk at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_toplevel_eval_flex at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_toplevel_eval_flex at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_toplevel_eval_in at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
eval at ./boot.jl:373 [inlined]
eval_user_input at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:150
repl_backend_loop at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:241
start_repl_backend at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:226
#run_repl#47 at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:359
run_repl at /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:346
jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
#919 at ./client.jl:394
jfptr_YY.919_38471.clone_1 at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_f__call_latest at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
#invokelatest#2 at ./essentials.jl:716 [inlined]
invokelatest at ./essentials.jl:714 [inlined]
run_main_repl at ./client.jl:379
exec_options at ./client.jl:309
_start at ./client.jl:495
jfptr__start_22991.clone_1 at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
true_main at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_repl_entrypoint at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
Allocations: 3220529 (Pool: 3219582; Big: 947); GC: 4

signal (11): Segmentation fault: 11
in expression starting at REPL[3]:1
tupledealloc at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
code_dealloc at /Users/xiaozhoufeng/.julia/conda/3/lib/libpython3.9.dylib (unknown line)
pydecref_ at /Users/xiaozhoufeng/.julia/packages/PyCall/BD546/src/PyCall.jl:118 [inlined]
pydecref at /Users/xiaozhoufeng/.julia/packages/PyCall/BD546/src/PyCall.jl:123
jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
run_finalizer at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_gc_run_finalizers_in_list at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_gc_run_pending_finalizers at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_generate_fptr at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_compile_method_internal at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
_atexit at ./initdefs.jl:350
jfptr__atexit_31697.clone_1 at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/sys.dylib (unknown line)
jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_atexit_hook at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_exit at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
jl_exit_thread0_cb at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
Allocations: 4059643 (Pool: 4058427; Big: 1216); GC: 5

[Process completed]
tlienart commented 3 years ago

Hmm QuSpin is a CPython lib with lots of dependencies... this is out of my depth, not sure how PyCall generally handles this.

ghost commented 3 years ago

Anyway, thanks @tlienart. I think I can use quspin in python and import the results into julia for further calculation. So right now, this problem does not bother me too much. Thank you a lot for the patience.