segfault after importing CSV and Images, PyPlot from a separate module

MaxandreJ commented 5 years ago

Hi,

I get the following segfault

signal (11): Segmentation fault: 11
in expression starting at /MyProjectDirectory/Test.jl:4
_platform_strcmp at /usr/lib/system/libsystem_platform.dylib (unknown line)

when I run /MyProjectDirectory/Test.jl which contains the code

push!(LOAD_PATH, "/MyProjectDirectory")
import CSV
using MyModule

that uses /MyProjectDirectory/MyModule.jl which contains the code

module MyModule
using Images
import PyPlot
end

I don't know if this is an issue to do with CSV, Images, PyPlot or Julia itself. This is a minimal working example. I'm using Julia 1.0.1 on MacOS Mojave. The segfault goes away if I don't load any one of these three packages. There is still a segault if I start Julia with --check-bounds=yes.

I hope this can be resolved soon! Segfaults are frightening...

These are the versions of the packages in question + important dependencies

Images v0.16.0
PyCall v1.18.5+ #Master (https://github.com/JuliaPy/PyCall.jl.git)
PyPlot v2.6.3
CSV v0.4.1

I have also posted this issue on the Images.jl github and the CSV.jl github.

Best, Max

tkf commented 5 years ago

I can't reproduce the issue:

$ cat MyModule.jl
module MyModule
using Images
import PyPlot
end

$ cat Test.jl
push!(LOAD_PATH, @__DIR__)
import CSV
using MyModule

$ julia-1.0.1 --startup-file=no
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.0.1 (2018-09-29)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> include("Test.jl")
[ Info: Recompiling stale cache file /home/takafumi/.julia/compiled/v1.0/CSV/HHBkp.ji for CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b]
WARNING: Method definition intern(Type{WeakRefStrings.WeakRefString{UInt8}}, Tuple{Ptr{UInt8}, Int64}) in module Parsers at /home/takafumi/.julia/packages/Parsers/kL0P9/src/strings.jl:17 overwritten in module CSV at /home/takafumi/.julia/packages/CSV/uLyo0/src/CSV.jl:5.
[ Info: Recompiling stale cache file /home/takafumi/.julia/compiled/v1.0/MyModule.ji for MyModule [top-level]

julia> MyModule
MyModule

julia> CSV
CSV

(v1.0) pkg> st
    Status `~/.julia/environments/v1.0/Project.toml`
  ...
  [336ed68f] CSV v0.4.1
  [916415d5] Images v0.16.1
  [438e738f] PyCall v1.18.5+ [`~/.julia/dev/PyCall`]
  [d330b81b] PyPlot v2.6.3

FYI, There is a documentation on how to analyze segfaults: https://docs.julialang.org/en/latest/devdocs/backtraces/#Segfaults-when-running-a-script-1

(But I just noticed that julia-debug is missing from Linux binary distribution. If it's not in your installation, you need to compile Julia from scratch, which is not so bad)

MaxandreJ commented 5 years ago

Thanks for trying @tkf ! I tried to build julia from source but after an evening of trying and running into multiple errors (MacOS Mojave) I'm done. So I won't be able to give the segfault analysis.

tkf commented 5 years ago

Yeah, it looks like Mac users have some trouble building Julia now... https://github.com/JuliaLang/julia/issues/29433

tkf commented 5 years ago

https://github.com/JuliaLang/julia/issues/29734

MaxandreJ commented 5 years ago

Too bad!

johnnychen94 commented 3 years ago

FWIW, I no longer see this by trying https://github.com/JuliaPy/PyPlot.jl/issues/402#issuecomment-431214656 in Julia 1.6.0 with macOS BigSur

julia> versioninfo()
Julia Version 1.6.0
Commit f9720dc2eb (2021-03-24 12:55 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin19.6.0)
  CPU: Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-11.0.1 (ORCJIT, skylake)

JuliaPy / PyPlot.jl

segfault after importing CSV and Images, PyPlot from a separate module #402