using PyPlot hangs/kills julia 1.8.5 or 1.9.0 on MacOS

using PyPlot hangs or kills julia 1.8.5 or 1.9.0 on MacOS

Synopsis

using PyPlot hangs julia. No progress for >10 hours. No error message. User ^C exits julia with Killed: 9.

With repeated testing, behavior has evolved to crash immediately with Killed: 9, where it had hung.

Demonstration

Carefully recursively force-removed the conda directory $HOME/.julia/conda, which seems to be shared between julia 1.8 and 1.9.

Start julia, making sure dynamic dependencies are consistent with the conda python installation.

LD_LIBRARY_PATH="$HOME/.julia/conda/3/lib" /Applications/Julia-1.8.app/Contents/Resources/julia/bin/julia

or

LD_LIBRARY_PATH="$HOME/.julia/conda/3/lib" /Applications/Julia-1.9.app/Contents/Resources/julia/bin/julia

Make sure julia is using the conda python distribution and build PyCall.

ENV["PYTHON"]=""
]build PyCall
    Building Conda ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/e32a90da027ca45d84678b826fffd3110bb3fc90/build.log`
    Building PyCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/62f417f6ad727987c755549e9cd88c46578da562/build.log`
...

Quit and restart julia, then run

using PyPlot

Since we started by wiping ~/.julia/conda, matplotlib is not installed. Conda is automatically deployed to install it:

[ Info: Installing matplotlib via the Conda matplotlib package...
[ Info: Running `conda install -y matplotlib` in root environment
...
Executing transaction: done

It hangs there.

Kill julia with ^C -> Killed: 9.

Try again now that matplotlib is installed:

LD_LIBRARY_PATH="$HOME/.julia/conda/3/lib" /Applications/Julia-1.8.app/Contents/Resources/julia/bin/julia
ENV["PYTHON"]=""
using PyPlot

Result: It just hangs immediately. So, I think probably conda installs matplotlib (maybe OK?), but julia is unable to use it.

I have to kill julia with ^C -> Killed: 9.

Trying again.

LD_LIBRARY_PATH="$HOME/.julia/conda/3/lib" /Applications/Julia-1.8.app/Contents/Resources/julia/bin/julia
ENV["PYTHON"]=""
using Conda  # returns
using PyCall  # returns
using PyPlot  # crashes
Killed: 9

Crashes and exits.

Even wiping .julia/conda again, it just crashes now with Killed: 9

Background

PyPlot had previously been working for me.
The first sign of trouble was an MKL dylib conflict error message and crash when running using PyPlot.
Unfortunately after many ^Cs I can't find that error message.

I updated julia's conda after that. Then I got the behavior reported above.

Works for me… but I haven't updated my conda packages recently, maybe there is a problem with the latest anaconda release? You could try pinning numpy or matplotlib to an older version…

I recently installed mamba (outside julia), and it appears julia PyCall is using it:

using PyCall
os = pyimport("os")
os.environ
 ... , 'CONDA_PYTHON_EXE': '$HOME/mambaforge/bin/python'

I had installed anaconda on my system, but the conda environment became unsolvable, so I switched to mamba. I didn't expect this to affect julia. I had thought the conda in julia was a separate installation (I use ENV["PYTHON"]="" before building PyCall), but it appears mine got connected to mamba.

On Mac OS 14.0, using PyPlot leads to:

julia> using PyPlot
[1]    13395 killed     /Applications/Julia-1.9.app/Contents/Resources/julia/bin/julia

Saving session...completed.

[Opération terminée]

julia> versioninfo()
Julia Version 1.9.4
Commit 8e5136fa297 (2023-11-14 08:46 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: macOS (x86_64-apple-darwin22.4.0)
  CPU: 16 × Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, skylake)
  Threads: 1 on 16 virtual cores

Works fine for me on MacOS 14 and Julia 1.9.4 … maybe your Python installation is broken?

If you are using Python via Conda.jl (which is the default on MacOS), you could try removing conda (rm -rf ~/.julia/conda) and rebuilding PyCall and PyPlot.

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using PyPlot hangs/kills julia 1.8.5 or 1.9.0 on MacOS #567

using PyPlot hangs or kills julia 1.8.5 or 1.9.0 on MacOS

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using PyPlot hangs/kills julia 1.8.5 or 1.9.0 on MacOS #567

Description

using PyPlot hangs or kills julia 1.8.5 or 1.9.0 on MacOS

Synopsis

Demonstration

Background

Activity

stevengj commented on May 13, 2023

deszoeke commented on May 13, 2023

kevinpolisano commented on Nov 21, 2023

stevengj commented on Nov 23, 2023

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