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Segfault with package, but not with identical module #554

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kescobo opened this issue Sep 10, 2024 · 2 comments
Closed

Segfault with package, but not with identical module #554

kescobo opened this issue Sep 10, 2024 · 2 comments
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bug Something isn't working

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@kescobo
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kescobo commented Sep 10, 2024

Affects: PythonCall

Describe the bug

I am attempting to build julia package that uses the python package girder_client. When trying to call a python function from within the package, I get a segfault. But when I run the code by itself, or define the same module in the REPL, I don't get the error.

Bare code - works

julia> using PythonCall

julia> girder_client = pyimport("girder_client")
Python: <module 'girder_client' from '/home/kevin/Repos/DigitalSlideArchive.jl/.CondaPkg/env/lib/python3.12/site-packages/girder_client/__init__.py'>

julia> gc = girder_client.GirderClient(; apiUrl=ENV["DSA_API_URL"])
Python: <girder_client.GirderClient object at 0x7f956b5e7b60>

REPL-defined (and include()) - works

julia> module Foo

       using PythonCall
       const girder_client = pyimport("girder_client")

       end
Main.Foo

julia> gc = Foo.girder_client.GirderClient(; apiUrl=ENV["DSA_API_URL"])
Python: <girder_client.GirderClient object at 0x7f72737c4200>
shell> cat src/DigitalSlideArchive.jl
module DigitalSlideArchive

using PythonCall
const girder_client = pyimport("girder_client")

end

julia> include("src/DigitalSlideArchive.jl")
Main.DigitalSlideArchive

julia> gc = DigitalSlideArchive.girder_client.GirderClient(ENV["DSA_API_URL"])
Python: <girder_client.GirderClient object at 0x7f8e1cbc41a0>

Package version (doesn't work):

julia> using DigitalSlideArchive

julia> gc = DigitalSlideArchive.girder_client.GirderClient(ENV["DSA_API_URL"])

[265486] signal 11 (1): Segmentation fault
julia> versioninfo()
Julia Version 1.11.0-rc3
Commit 616e45539db (2024-08-26 15:46 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 16 × AMD Ryzen 9 7940HS w/ Radeon 780M Graphics
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, znver4)
Threads: 1 default, 0 interactive, 1 GC (on 16 virtual cores)
Environment:
  JULIA_PROJECT = /home/kevin/Repos/DigitalSlideArchive.jl
  JULIA_EDITOR = nvim

(DigitalSlideArchive) pkg> st
Project DigitalSlideArchive v0.1.0
Status `~/Repos/DigitalSlideArchive.jl/Project.toml`
  [992eb4ea] CondaPkg v0.2.23
  [6099a3de] PythonCall v0.9.23

(DigitalSlideArchive) pkg> conda st
CondaPkg Status /home/kevin/Repos/DigitalSlideArchive.jl/CondaPkg.toml
Environment
  /home/kevin/Repos/DigitalSlideArchive.jl/.CondaPkg/env
Pip packages
  girder-client v3.2.3
full segfault 

julia> gc = DigitalSlideArchive.girder_client.GirderClient(ENV["DSA_API_URL"])

[265486] signal 11 (1): Segmentation fault
in expression starting at REPL[2]:1
Py_TYPE at /usr/local/src/conda/python-3.12.5/Include/object.h:220 [inlined]
PyObject_GetAttr at /usr/local/src/conda/python-3.12.5/Objects/object.c:1034
PyObject_GetAttr at /home/kevin/.julia/packages/PythonCall/Nr75f/src/C/pointers.jl:303 [inlined]
macro expansion at /home/kevin/.julia/packages/PythonCall/Nr75f/src/Core/Py.jl:132 [inlined]
pygetattr at /home/kevin/.julia/packages/PythonCall/Nr75f/src/Core/builtins.jl:62
getproperty at /home/kevin/.julia/packages/PythonCall/Nr75f/src/Core/Py.jl:273
unknown function (ip: 0x7f0341939f86)
jl_apply at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
do_call at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/interpreter.c:126
eval_value at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/interpreter.c:223
eval_stmt_value at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/interpreter.c:174 [inlined]
eval_body at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/interpreter.c:663
jl_interpret_toplevel_thunk at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/interpreter.c:821
jl_toplevel_eval_flex at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/toplevel.c:943
jl_toplevel_eval_flex at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/toplevel.c:886
jl_toplevel_eval_flex at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/toplevel.c:886
jl_toplevel_eval_flex at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/toplevel.c:886
ijl_toplevel_eval_in at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/toplevel.c:994
eval at ./boot.jl:430 [inlined]
eval_user_input at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:226
repl_backend_loop at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:323
#start_repl_backend#59 at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:308
start_repl_backend at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:305
#run_repl#72 at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:464
run_repl at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/usr/share/julia/stdlib/v1.11/REPL/src/REPL.jl:450
jfptr_run_repl_11642 at /home/kevin/Dotfiles/.julia/juliaup/julia-1.11.0-rc3+0.x64.linux.gnu/share/julia/compiled/v1.11/REPL/u0gqU_5pcrL.so (unknown line)
#1137 at ./client.jl:441
jfptr_YY.1137_16382 at /home/kevin/Dotfiles/.julia/juliaup/julia-1.11.0-rc3+0.x64.linux.gnu/share/julia/compiled/v1.11/REPL/u0gqU_5pcrL.so (unknown line)
jl_apply at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
jl_f__call_latest at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/builtins.c:875
#invokelatest#2 at ./essentials.jl:1054 [inlined]
invokelatest at ./essentials.jl:1051 [inlined]
run_main_repl at ./client.jl:425
repl_main at ./client.jl:562 [inlined]
_start at ./client.jl:536
jfptr__start_71892.1 at /home/kevin/Dotfiles/.julia/juliaup/julia-1.11.0-rc3+0.x64.linux.gnu/lib/julia/sys.so (unknown line)
jl_apply at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/julia.h:2157 [inlined]
true_main at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/jlapi.c:900
jl_repl_entrypoint at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/src/jlapi.c:1059
main at /cache/build/tester-amdci5-12/julialang/julia-release-1-dot-11/cli/loader_exe.c:58
__libc_start_call_main at /lib64/libc.so.6 (unknown line)
__libc_start_main at /lib64/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 2719857 (Pool: 2719703; Big: 154); GC: 4
fish: Job 1, 'julia -q' terminated by signal SIGSEGV (Address boundary error)
```

</p>
</details>
@kescobo kescobo added the bug Something isn't working label Sep 10, 2024
@cjdoris
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cjdoris commented Sep 10, 2024

See here: https://juliapy.github.io/PythonCall.jl/stable/pythoncall/#Precompilation

@kescobo
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kescobo commented Sep 10, 2024

Ahh, that's very clear. Sorry I missed that!

@kescobo kescobo closed this as completed Sep 10, 2024
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