search

JuliaPy / PyPlot.jl

Plotting for Julia based on matplotlib.pyplot
https://github.com/JuliaPy/PyPlot.jl
MIT License
469 stars 85 forks source link

Pyplot crash on window #575

Closed StephenVavasis closed 1 month ago

StephenVavasis commented 5 months ago

A short PyPlot program is crashing on my Windows 11 machine (i.e., the Julia REPL exits with no error message). I verified that it works correctly on Linux. This is Julia 1.9.3, PyPlot 2.11.2. The data file br1copy.txt [br1copy.txt](https://github.com/JuliaPy/PyPlot.jl/files/13823984/br1copy.txt) is attached.

module readbr1

using PyPlot

function readbr(filename, stepnum)
    ststepnum = string(stepnum)
    it = zeros(Int,0)
    res1 = zeros(0)
    res2 = zeros(0)
    open(filename, "r") do h
        while true
            p = readline(h)
            s = split(p)
            if length(s) < 12 || s[1] != "step" || s[3] != ststepnum
                if eof(h)
                    break
                else
                    continue
                end
            end
            itnum = parse(Int,s[6])
            push!(it, itnum)
            #println(itnum)
            push!(res1, parse(Float64, s[9]))
            push!(res2, parse(Float64, s[12]))
            if eof(h)
                break
            end
        end
    end
    return it, res1, res2
end

function makeplots(it, res1, res2)
    figure(1)
    clf()
    semilogy(it, res1)
    figure(2)
    clf()
    semilogy(it, res2)
    nothing
end

it, res1, res2 = readbr("br1copy.txt", 6)
makeplots(it, res1, res2)

end
StephenVavasis commented 5 months ago

This issue occurs on a particular Windows machine but not others, so it may be difficult to reproduce.

StephenVavasis commented 5 months ago

On the same Windows 11 box I created a new user test_julia, downloaded Julia 1.10.0 from scratch, installed PyPlot from scratch, and encountered the a crash as soon as I typed figure(1). There were a few warnings during the PyPlot installation and build (see below), but none of them appear serious.

Microsoft Windows [Version 10.0.22621.2861]
(c) Microsoft Corporation. All rights reserved.

C:\Users\test_julia>winget install julia -s msstore
The `msstore` source requires that you view the following agreements before using.
Terms of Transaction: https://aka.ms/microsoft-store-terms-of-transaction
The source requires the current machine's 2-letter geographic region to be sent to the backend service to function properly (ex. "US").

Do you agree to all the source agreements terms?
[Y] Yes  [N] No: y
Found Julia [9NJNWW8PVKMN] Version Unknown
This package is provided through Microsoft Store. winget may need to acquire the package from Microsoft Store on behalf of the current user.
Agreements for Julia [9NJNWW8PVKMN] Version Unknown
Version: Unknown
Publisher: Julia Computing, Inc.
Publisher Url: https://julialang.org/
Description: Julia is a high-level, high-performance, dynamic, open-source programming language.
License: ms-windows-store://pdp/?ProductId=9NJNWW8PVKMN
Privacy Url: https://juliacomputing.com/privacy/
Agreements:
Category: Developer tools
C:\Users\test_julia>julia
Installing Julia 1.10.0+0.x64.w64.mingw32
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.10.0 (2023-12-25)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

(@v1.10) pkg> add PyPlot
  Installing known registries into `C:\Users\test_julia\.julia`
    Updating registry at `C:\Users\test_julia\.julia\registries\General.toml`
   Resolving package versions...
   Installed PrecompileTools ─── v1.2.0
   Installed Conda ───────────── v1.10.0
   Installed FixedPointNumbers ─ v0.8.4
   Installed VersionParsing ──── v1.3.0
   Installed Parsers ─────────── v2.8.1
   Installed ColorTypes ──────── v0.11.4
   Installed Preferences ─────── v1.4.1
   Installed PyCall ──────────── v1.96.4
   Installed PyPlot ──────────── v2.11.2
   Installed LaTeXStrings ────── v1.3.1
   Installed MacroTools ──────── v0.5.12
   Installed Colors ──────────── v0.12.10
   Installed JSON ────────────── v0.21.4
   Installed Reexport ────────── v1.2.2
    Updating `C:\Users\test_julia\.julia\environments\v1.10\Project.toml`
  [d330b81b] + PyPlot v2.11.2
    Updating `C:\Users\test_julia\.julia\environments\v1.10\Manifest.toml`
  [3da002f7] + ColorTypes v0.11.4
  [5ae59095] + Colors v0.12.10
  [8f4d0f93] + Conda v1.10.0
  [53c48c17] + FixedPointNumbers v0.8.4
  [682c06a0] + JSON v0.21.4
  [b964fa9f] + LaTeXStrings v1.3.1
  [1914dd2f] + MacroTools v0.5.12
  [69de0a69] + Parsers v2.8.1
  [aea7be01] + PrecompileTools v1.2.0
  [21216c6a] + Preferences v1.4.1
  [438e738f] + PyCall v1.96.4
  [d330b81b] + PyPlot v2.11.2
  [189a3867] + Reexport v1.2.2
  [81def892] + VersionParsing v1.3.0
  [0dad84c5] + ArgTools v1.1.1
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [ade2ca70] + Dates
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching
  [b27032c2] + LibCURL v0.6.4
  [37e2e46d] + LinearAlgebra
  [56ddb016] + Logging
  [d6f4376e] + Markdown
  [a63ad114] + Mmap
  [ca575930] + NetworkOptions v1.2.0
  [de0858da] + Printf
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [6462fe0b] + Sockets
  [2f01184e] + SparseArrays v1.10.0
  [10745b16] + Statistics v1.10.0
  [fa267f1f] + TOML v1.0.3
  [8dfed614] + Test
  [cf7118a7] + UUIDs
  [4ec0a83e] + Unicode
  [e66e0078] + CompilerSupportLibraries_jll v1.0.5+1
  [deac9b47] + LibCURL_jll v8.4.0+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.2+1
  [14a3606d] + MozillaCACerts_jll v2023.1.10
  [4536629a] + OpenBLAS_jll v0.3.23+2
  [bea87d4a] + SuiteSparse_jll v7.2.1+1
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.8.0+1
  [8e850ede] + nghttp2_jll v1.52.0+1
    Building Conda ─→ `C:\Users\test_julia\.julia\scratchspaces\44cfe95a-1eb2-52ea-b672-e2afdf69b78f\51cab8e982c5b598eea9c8ceaced4b58d9dd37c9\build.log`
    Building PyCall → `C:\Users\test_julia\.julia\scratchspaces\44cfe95a-1eb2-52ea-b672-e2afdf69b78f\9816a3826b0ebf49ab4926e2b18842ad8b5c8f04\build.log`
Precompiling project...
  16 dependencies successfully precompiled in 18 seconds. 4 already precompiled.

julia> using PyPlot
[ Info: Installing matplotlib via the Conda matplotlib package...
[ Info: Running `conda install -y matplotlib` in root environment
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

==> WARNING: A newer version of conda exists. <==
  current version: 23.3.1
  latest version: 23.11.0

Please update conda by running

    $ conda update -n base -c conda-forge conda

Or to minimize the number of packages updated during conda update use

     conda install conda=23.11.0

## Package Plan ##

  environment location: C:\Users\test_julia\.julia\conda\3\x86_64

  added / updated specs:
    - matplotlib

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    brotli-1.1.0               |       hcfcfb64_1          19 KB  conda-forge
    brotli-bin-1.1.0           |       hcfcfb64_1          20 KB  conda-forge
    contourpy-1.2.0            |  py310h232114e_0         186 KB  conda-forge
    cycler-0.12.1              |     pyhd8ed1ab_0          13 KB  conda-forge
    fonttools-4.47.0           |  py310h8d17308_0         1.8 MB  conda-forge
    freetype-2.12.1            |       hdaf720e_2         498 KB  conda-forge
    gettext-0.21.1             |       h5728263_0         5.3 MB  conda-forge
    glib-2.78.3                |       h12be248_0         495 KB  conda-forge
    glib-tools-2.78.3          |       h12be248_0         141 KB  conda-forge
    gst-plugins-base-1.22.8    |       h001b923_1         2.0 MB  conda-forge
    gstreamer-1.22.8           |       hb4038d2_1         1.8 MB  conda-forge
    icu-73.2                   |       h63175ca_0        12.8 MB  conda-forge
    kiwisolver-1.4.5           |  py310h232114e_1          54 KB  conda-forge
    lcms2-2.16                 |       h67d730c_0         496 KB  conda-forge
    lerc-4.0.0                 |       h63175ca_0         190 KB  conda-forge
    libbrotlicommon-1.1.0      |       hcfcfb64_1          69 KB  conda-forge
    libbrotlidec-1.1.0         |       hcfcfb64_1          32 KB  conda-forge
    libbrotlienc-1.1.0         |       hcfcfb64_1         241 KB  conda-forge
    libclang-15.0.7            |default_h77d9078_3         144 KB  conda-forge
    libclang13-15.0.7          |default_h77d9078_3        20.9 MB  conda-forge
    libdeflate-1.19            |       hcfcfb64_0         150 KB  conda-forge
    libglib-2.78.3             |       h16e383f_0         2.5 MB  conda-forge
    libjpeg-turbo-3.0.0        |       hcfcfb64_1         804 KB  conda-forge
    libogg-1.3.4               |       h8ffe710_1          34 KB  conda-forge
    libpng-1.6.39              |       h19919ed_0         336 KB  conda-forge
    libtiff-4.6.0              |       h6e2ebb7_2         769 KB  conda-forge
    libvorbis-1.3.7            |       h0e60522_0         267 KB  conda-forge
    libwebp-base-1.3.2         |       hcfcfb64_0         263 KB  conda-forge
    libxcb-1.15                |       hcd874cb_0         947 KB  conda-forge
    m2w64-gcc-libgfortran-5.3.0|                6         342 KB  conda-forge
    m2w64-gcc-libs-5.3.0       |                7         520 KB  conda-forge
    m2w64-gcc-libs-core-5.3.0  |                7         214 KB  conda-forge
    m2w64-gmp-6.1.0            |                2         726 KB  conda-forge
    m2w64-libwinpthread-git-5.0.0.4634.697f757|                2          31 KB  conda-forge
    matplotlib-3.8.2           |  py310h5588dad_0           9 KB  conda-forge
    matplotlib-base-3.8.2      |  py310hc9baf74_0         6.6 MB  conda-forge
    msys2-conda-epoch-20160418 |                1           3 KB  conda-forge
    munkres-1.1.4              |     pyh9f0ad1d_0          12 KB  conda-forge
    openjpeg-2.5.0             |       h3d672ee_3         231 KB  conda-forge
    pcre2-10.42                |       h17e33f8_0         860 KB  conda-forge
    pillow-10.2.0              |  py310h1e6a543_0        39.6 MB  conda-forge
    ply-3.11                   |             py_1          44 KB  conda-forge
    pthread-stubs-0.4          |    hcd874cb_1001           6 KB  conda-forge
    pyparsing-3.1.1            |     pyhd8ed1ab_0          87 KB  conda-forge
    pyqt-5.15.9                |  py310h1fd54f2_5         3.7 MB  conda-forge
    pyqt5-sip-12.12.2          |  py310h00ffb61_5          78 KB  conda-forge
    python-dateutil-2.8.2      |     pyhd8ed1ab_0         240 KB  conda-forge
    qt-main-5.15.8             |      h9e85ed6_18        58.0 MB  conda-forge
    sip-6.7.12                 |  py310h00ffb61_0         493 KB  conda-forge
    six-1.16.0                 |     pyh6c4a22f_0          14 KB  conda-forge
    toml-0.10.2                |     pyhd8ed1ab_0          18 KB  conda-forge
    tomli-2.0.1                |     pyhd8ed1ab_0          16 KB  conda-forge
    tornado-6.3.3              |  py310h8d17308_1         630 KB  conda-forge
    unicodedata2-15.1.0        |  py310h8d17308_0         361 KB  conda-forge
    xorg-libxau-1.0.11         |       hcd874cb_0          50 KB  conda-forge
    xorg-libxdmcp-1.1.3        |       hcd874cb_0          66 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       166.0 MB

The following NEW packages will be INSTALLED:

  brotli             conda-forge/win-64::brotli-1.1.0-hcfcfb64_1
  brotli-bin         conda-forge/win-64::brotli-bin-1.1.0-hcfcfb64_1
  contourpy          conda-forge/win-64::contourpy-1.2.0-py310h232114e_0
  cycler             conda-forge/noarch::cycler-0.12.1-pyhd8ed1ab_0
  fonttools          conda-forge/win-64::fonttools-4.47.0-py310h8d17308_0
  freetype           conda-forge/win-64::freetype-2.12.1-hdaf720e_2
  gettext            conda-forge/win-64::gettext-0.21.1-h5728263_0
  glib               conda-forge/win-64::glib-2.78.3-h12be248_0
  glib-tools         conda-forge/win-64::glib-tools-2.78.3-h12be248_0
  gst-plugins-base   conda-forge/win-64::gst-plugins-base-1.22.8-h001b923_1
  gstreamer          conda-forge/win-64::gstreamer-1.22.8-hb4038d2_1
  icu                conda-forge/win-64::icu-73.2-h63175ca_0
  kiwisolver         conda-forge/win-64::kiwisolver-1.4.5-py310h232114e_1
  lcms2              conda-forge/win-64::lcms2-2.16-h67d730c_0
  lerc               conda-forge/win-64::lerc-4.0.0-h63175ca_0
  libbrotlicommon    conda-forge/win-64::libbrotlicommon-1.1.0-hcfcfb64_1
  libbrotlidec       conda-forge/win-64::libbrotlidec-1.1.0-hcfcfb64_1
  libbrotlienc       conda-forge/win-64::libbrotlienc-1.1.0-hcfcfb64_1
  libclang           conda-forge/win-64::libclang-15.0.7-default_h77d9078_3
  libclang13         conda-forge/win-64::libclang13-15.0.7-default_h77d9078_3
  libdeflate         conda-forge/win-64::libdeflate-1.19-hcfcfb64_0
  libglib            conda-forge/win-64::libglib-2.78.3-h16e383f_0
  libjpeg-turbo      conda-forge/win-64::libjpeg-turbo-3.0.0-hcfcfb64_1
  libogg             conda-forge/win-64::libogg-1.3.4-h8ffe710_1
  libpng             conda-forge/win-64::libpng-1.6.39-h19919ed_0
  libtiff            conda-forge/win-64::libtiff-4.6.0-h6e2ebb7_2
  libvorbis          conda-forge/win-64::libvorbis-1.3.7-h0e60522_0
  libwebp-base       conda-forge/win-64::libwebp-base-1.3.2-hcfcfb64_0
  libxcb             conda-forge/win-64::libxcb-1.15-hcd874cb_0
  m2w64-gcc-libgfor~ conda-forge/win-64::m2w64-gcc-libgfortran-5.3.0-6
  m2w64-gcc-libs     conda-forge/win-64::m2w64-gcc-libs-5.3.0-7
  m2w64-gcc-libs-co~ conda-forge/win-64::m2w64-gcc-libs-core-5.3.0-7
  m2w64-gmp          conda-forge/win-64::m2w64-gmp-6.1.0-2
  m2w64-libwinpthre~ conda-forge/win-64::m2w64-libwinpthread-git-5.0.0.4634.697f757-2
  matplotlib         conda-forge/win-64::matplotlib-3.8.2-py310h5588dad_0
  matplotlib-base    conda-forge/win-64::matplotlib-base-3.8.2-py310hc9baf74_0
  msys2-conda-epoch  conda-forge/win-64::msys2-conda-epoch-20160418-1
  munkres            conda-forge/noarch::munkres-1.1.4-pyh9f0ad1d_0
  openjpeg           conda-forge/win-64::openjpeg-2.5.0-h3d672ee_3
  pcre2              conda-forge/win-64::pcre2-10.42-h17e33f8_0
  pillow             conda-forge/win-64::pillow-10.2.0-py310h1e6a543_0
  ply                conda-forge/noarch::ply-3.11-py_1
  pthread-stubs      conda-forge/win-64::pthread-stubs-0.4-hcd874cb_1001
  pyparsing          conda-forge/noarch::pyparsing-3.1.1-pyhd8ed1ab_0
  pyqt               conda-forge/win-64::pyqt-5.15.9-py310h1fd54f2_5
  pyqt5-sip          conda-forge/win-64::pyqt5-sip-12.12.2-py310h00ffb61_5
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
  qt-main            conda-forge/win-64::qt-main-5.15.8-h9e85ed6_18
  sip                conda-forge/win-64::sip-6.7.12-py310h00ffb61_0
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  toml               conda-forge/noarch::toml-0.10.2-pyhd8ed1ab_0
  tomli              conda-forge/noarch::tomli-2.0.1-pyhd8ed1ab_0
  tornado            conda-forge/win-64::tornado-6.3.3-py310h8d17308_1
  unicodedata2       conda-forge/win-64::unicodedata2-15.1.0-py310h8d17308_0
  xorg-libxau        conda-forge/win-64::xorg-libxau-1.0.11-hcd874cb_0
  xorg-libxdmcp      conda-forge/win-64::xorg-libxdmcp-1.1.3-hcd874cb_0

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

julia> figure(1)

C:\Users\test_julia>
Finnm commented 5 months ago

I'm experiencing the same issue, also on Windows 11. I have tried Julia v. 1.6.7 and v. 1.10.0, and reinstalled everything several times, but I get the same issue every time. Matplotlib works fine when called from Python. I also tried a different user on the same PC but got the same result. For me, this issue happened after I reinstalled Windows 11 (and Julia and Python); before that, everything was working perfectly.

Finnm commented 5 months ago

I got it to work for me. My best guess is that something goes wrong when PyPlot uses Conda to install Matplotlib. So here is what I did to make it work:

  1. Install Python (check the box to add it to PATH)
  2. Install Matplotlib as described here: https://matplotlib.org/stable/users/installing/index.html
  3. Check that Matplotlib works in Python
  4. Add an environment variable named "PYTHON" that links to the exe-file of the Python version from steps 1 through 3.
  5. Install Julia
  6. Check that ENV["PYTHON"] in Julia returns the path to the python exe-file from step 4.
  7. Add PyPlot in Julia

After that, when typing using PyPlot it should not start installing Matplotlib through Conda, but just return. Running figure() should open an empty figure without crashing.

ufechner7 commented 3 months ago

Did you try:

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

This installs a version of Python and Matplotlib for Julia only and thus avoids compatibility issues with versions installed outside of Julia.

StephenVavasis commented 1 month ago

I tried both of the solutions mentioned in the two previous posts (installing Python and Matplotlib "manually" and then installing the PyPlot package, followed by using PyPlot and figure(1)), and also not installing Python at all and building PyPlot, but neither worked. I am still getting a crash as soon as I type figure(1). Does anyone know if there is a log file written somewhere before Julia crashes? I should mention that I seem to see a figure window flash briefly on my screen before the crash, so PyPlot seems to be active. I'll add that Matplotlib invoked from Python seems to be working.

stevengj commented 1 month ago

Have you tried switching to a different Matplotlib backend? (e.g. set ENV["MPLBACKEND"]="TkAgg" or ="QtAgg" or ="GTK4Agg" before loading PyPlot).

Try using the same backend that you are using from Python, as printed by matplotlib.get_backend().

StephenVavasis commented 1 month ago

I retried the solution of manually installing Python and Matplotlib, setting the Windows environment variable PYTHON, and then reinstalling Julia and PyPlot. It didn't work yesterday, but it worked today. The difference between what I did yesterday versus today is: yesterday I partially cleaned out Julia and PyPlot; today I fully cleaned them out (uninstall julia and delete the entire .julia folder). So this problem is solved for me, and I will close the issue.