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Python 3.8 with Julia 1.3 #752

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darrencl opened this issue Mar 5, 2020 · 10 comments · Fixed by #753
Closed

Python 3.8 with Julia 1.3 #752

darrencl opened this issue Mar 5, 2020 · 10 comments · Fixed by #753

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@darrencl
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darrencl commented Mar 5, 2020

I couldn't build PyCall with Python 3.8.0 and Julia 1.3.0. This happens with PyCall v1.91.4

julia> Pkg.build("PyCall")
  Building Conda ─→ `~/.julia/packages/Conda/3rPhK/deps/build.log`
  Building PyCall → `~/.julia/packages/PyCall/zqDXB/deps/build.log`
┌ Error: Error building `PyCall`: 
│ ERROR: LoadError: Couldn't find libpython; check your PYTHON environment variable.
│ 
│ The python executable we tried was /home/darren/miniconda3/bin/python3.8 (= version 3.7).
│ Re-building with
│     ENV["PYCALL_DEBUG_BUILD"] = "yes"
│ may provide extra information for why it failed.
│ 
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] #find_libpython#3(::typeof(Libdl.dlopen), ::typeof(find_libpython), ::String) at /home/darren/.julia/packages/PyCall/zqDXB/deps/buildutils.jl:72
│  [3] find_libpython(::String) at /home/darren/.julia/packages/PyCall/zqDXB/deps/buildutils.jl:41
│  [4] top-level scope at /home/darren/.julia/packages/PyCall/zqDXB/deps/build.jl:87
│  [5] include at ./boot.jl:328 [inlined]
│  [6] include_relative(::Module, ::String) at ./loading.jl:1105
│  [7] include(::Module, ::String) at ./Base.jl:31
│  [8] include(::String) at ./client.jl:424
│  [9] top-level scope at none:5
│ in expression starting at /home/darren/.julia/packages/PyCall/zqDXB/deps/build.jl:43
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/backwards_compatible_isolation.jl:649
false

Can confirm the Python path is correct:

(base) darren@darren-GK5CN5Z-APEX-15:~$ /home/darren/miniconda3/bin/python3.8
Python 3.8.0 (default, Oct 24 2019, 15:04:43) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>

Saw this issue, so PyCall seems to support Python 3.8 already? If so, why am I getting this? Is there any workaround?

Thanks!
@tkf
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tkf commented Mar 6, 2020

I think this line indicates there was something wrong (python3.8 vs version 3.7):

The python executable we tried was /home/darren/miniconda3/bin/python3.8 (= version 3.7).

Did you try

│ Re-building with
│     ENV["PYCALL_DEBUG_BUILD"] = "yes"
│ may provide extra information for why it failed.

? What was in the build log? The path of the log file is printed as Building PyCall → `~/.julia/packages/PyCall/zqDXB/deps/build.log`.

@darrencl
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darrencl commented Mar 6, 2020 •
edited
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@tkf It seems looking for libpython

julia> Pkg.build("PyCall")
  Building Conda ─→ `~/.julia/packages/Conda/3rPhK/deps/build.log`
  Building PyCall → `~/.julia/packages/PyCall/zqDXB/deps/build.log`
┌ Error: Error building `PyCall`: 
│ DEBUG is_windows = False
│ DEBUG is_apple = False
│ DEBUG Candidate: None
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/lib/python3.7/config-3.7m-x86_64-linux-gnu/libpython3.7m.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/lib/python3.7/config-3.7m-x86_64-linux-gnu/libpython3.7.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/lib/python3.7/config-3.7m-x86_64-linux-gnu/libpython3.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/lib/python3.7/config-3.7m-x86_64-linux-gnu/libpython.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/lib/python3.8/config-3.8-x86_64-linux-gnu/libpython3.7m.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/lib/python3.8/config-3.8-x86_64-linux-gnu/libpython3.7.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/lib/python3.8/config-3.8-x86_64-linux-gnu/libpython3.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/lib/python3.8/config-3.8-x86_64-linux-gnu/libpython.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/lib/libpython3.7m.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/lib/libpython3.7.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/lib/libpython3.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/lib/libpython.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/libpython3.7m.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/libpython3.7.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/libpython3.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/libpython.so
│ DEBUG Not found.
│ DEBUG Candidate: libpython3.7m.so.1.0
│ DEBUG Not found.
│ dlopen(libpython3.7m) ==> ErrorException("could not load library \"libpython3.7m\"\nlibpython3.7m.so: cannot open shared object file: No such file or directory")
│ dlopen(libpython3.7) ==> ErrorException("could not load library \"libpython3.7\"\nlibpython3.7.so: cannot open shared object file: No such file or directory")
│ dlopen(libpython3) ==> ErrorException("could not load library \"libpython3\"\nlibpython3.so: cannot open shared object file: No such file or directory")
│ dlopen(libpython) ==> ErrorException("could not load library \"libpython\"\nlibpython.so: cannot open shared object file: No such file or directory")
│ ERROR: LoadError: Couldn't find libpython; check your PYTHON environment variable.
│ 
│ The python executable we tried was /home/darren/miniconda3/bin/python3.8 (= version 3.7).
│ Re-building with
│     ENV["PYCALL_DEBUG_BUILD"] = "yes"
│ may provide extra information for why it failed.
│ 
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] #find_libpython#3(::typeof(Libdl.dlopen), ::typeof(find_libpython), ::String) at /home/darren/.julia/packages/PyCall/zqDXB/deps/buildutils.jl:72
│  [3] find_libpython(::String) at /home/darren/.julia/packages/PyCall/zqDXB/deps/buildutils.jl:41
│  [4] top-level scope at /home/darren/.julia/packages/PyCall/zqDXB/deps/build.jl:87
│  [5] include at ./boot.jl:328 [inlined]
│  [6] include_relative(::Module, ::String) at ./loading.jl:1105
│  [7] include(::Module, ::String) at ./Base.jl:31
│  [8] include(::String) at ./client.jl:424
│  [9] top-level scope at none:5
│ in expression starting at /home/darren/.julia/packages/PyCall/zqDXB/deps/build.jl:43
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/backwards_compatible_isolation.jl:649
false

I think this is same issue as #565, which means the libpython finder needs to be updated.

FYI, this is my libpython paths

(base) darren@darren-GK5CN5Z-APEX-15:~$ find /home/darren/miniconda3/ -type f -name "*libpython*"
/home/darren/miniconda3/pkgs/python-3.8.0-h0371630_0/lib/libpython3.8.so.1.0
/home/darren/miniconda3/pkgs/python-3.8.0-h0371630_0/lib/libpython3.8.a
/home/darren/miniconda3/pkgs/python-3.7.4-h265db76_1/lib/libpython3.7m.so.1.0
/home/darren/miniconda3/pkgs/python-3.7.4-h265db76_1/lib/libpython3.7m.a
/home/darren/miniconda3/lib/libpython3.8.so.1.0
/home/darren/miniconda3/lib/libpython3.8.a

@darrencl
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darrencl commented Mar 6, 2020

And of course, the hacky workaround for this is to create a symlink to one of those expected path, e.g.

sudo ln -s /home/darren/miniconda3/lib/libpython3.8.so /home/darren/miniconda3/libpython.so

@tkf
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tkf commented Mar 7, 2020

This is puzzling. It's trying to find libpython3.7m.so under lib/python3.8...:

│ DEBUG Candidate: /home/darren/miniconda3/lib/python3.8/config-3.8-x86_64-linux-gnu/libpython3.7m.so
│ DEBUG Not found.
│ DEBUG Candidate: /home/darren/miniconda3/lib/python3.8/config-3.8-x86_64-linux-gnu/libpython3.7.so
│ DEBUG Not found.

Did you use Python 3.7 before? Maybe there is a path to Python 3.7 in ~/.julia/prefs/PyCall?

@darrencl
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darrencl commented Mar 8, 2020

@tkf Never used Python 3.7 in this machine and there is also no path to Python 3.7.

(base) darren@darren-GK5CN5Z-APEX-15:~$ cat ~/.julia/prefs/PyCall 
/home/darren/miniconda3/bin/python3.8(base) darren@darren-GK5CN5Z-APEX-15:~$

@tkf
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tkf commented Mar 8, 2020

You have ~/miniconda3/pkgs/python-3.7.4-h265db76_1/ so miniconda definitely downloaded Python 3.7 in your machine. Though I don't know how PyCall's build script would be confused by it.

@darrencl
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darrencl commented Mar 9, 2020

@tkf You're right! Hmm, anything I can help to investigate this?

@tkf
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tkf commented Mar 9, 2020

This part of the build is just a Python script: https://github.com/JuliaPy/PyCall.jl/blob/master/deps/find_libpython.py

So if you want to debug it, you can run it with python find_libpython.py. See --help for what it does. Passing --verbose --list-all may print something useful.

@darrencl darrencl mentioned this issue Mar 9, 2020
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@darrencl
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darrencl commented Mar 9, 2020 •
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@tkf Found the issue, it seems that for some reason the python version in config var sysconfig.get_config_var("VERSION") is not updated (More info in the PR). This might happen to someone else too, so I think using config var only as last resort will fix this.

@PatrickStar10086
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how do you solve this problem? I use Julia 1.10 and python 3.11(anaconda), same problem as you!

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Improving find libpython darrencl/PyCall.jl
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@tkf @darrencl @PatrickStar10086