Installation error with python 3.9

[michaeldeistler]

The following installation fails, but it works with python 3.8. My julia version is 1.5.2.

conda create -n multicompartment python=3.9
cd diffeqtorch
pip install -e ".[dev]"
export JULIA_SYSIMAGE_DIFFEQTORCH="$HOME/.julia_sysimage_diffeqtorch.so"
python -c "from diffeqtorch.install import install_and_test; install_and_test()"

Traceback:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/michael/Documents/diffeqtorch/diffeqtorch/install.py", line 19, in install_and_test
    test_pyjulia()
  File "/home/michael/Documents/diffeqtorch/diffeqtorch/install.py", line 64, in test_pyjulia
    julia = Julia(compiled_modules=False, debug=True)
  File "/home/michael/anaconda3/envs/multicompartment/lib/python3.9/site-packages/julia/core.py", line 503, in __init__
    self._call(IMPORT_PYCALL)
  File "/home/michael/anaconda3/envs/multicompartment/lib/python3.9/site-packages/julia/core.py", line 538, in _call
    self.check_exception(src)
  File "/home/michael/anaconda3/envs/multicompartment/lib/python3.9/site-packages/julia/core.py", line 587, in check_exception
    raise JuliaError(u'Exception \'{}\' occurred while calling julia code:\n{}'
julia.core.JuliaError: Exception 'LoadError' occurred while calling julia code:
const PyCall = Base.require(Base.PkgId(Base.UUID("438e738f-606a-5dbb-bf0a-cddfbfd45ab0"), "PyCall"))

[michaeldeistler]

Full installation log:

Install PyJulia
[ Info: Julia version info
Julia Version 1.5.2
Commit 539f3ce943 (2020-09-23 23:17 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
      Ubuntu 19.10
  uname: Linux 5.3.0-64-generic #58-Ubuntu SMP Fri Jul 10 19:33:51 UTC 2020 x86_64 x86_64
  CPU: AMD Ryzen Threadripper 1920X 12-Core Processor: 
                 speed         user         nice          sys         idle          irq
       #1-24  1887 MHz  846670441 s    1808393 s   30214693 s  7014585225 s          0 s
       
  Memory: 62.736881256103516 GB (11923.42578125 MB free)
  Uptime: 3.293332e6 sec
  Load Avg:  1.41845703125  1.18359375  1.12255859375
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-9.0.1 (ORCJIT, znver1)
Environment:
  JULIA_SYSIMAGE_DIFFEQTORCH = /home/michael/.julia_sysimage_diffeqtorch.so
  JULIA_PROJECT = /home/michael/Documents/diffeqtorch/diffeqtorch/julia
  HOME = /home/michael
  TERM = xterm-256color
  PATH = /home/michael/.local/bin:/home/michael/anaconda3/envs/multicompartment/bin:/home/michael/anaconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
[ Info: Julia executable: /opt/julia-1.5.2/bin/julia
[ Info: Trying to import PyCall...
┌ Warning: PyCall is already installed.  However, you may have trouble using
│ this Python executable because it is statically linked to libpython.
│ 
│ For more information, see:
│     https://pyjulia.readthedocs.io/en/latest/troubleshooting.html
│ 
│ Python executable:
│     /home/michael/anaconda3/envs/multicompartment/bin/python
│ Julia executable:
│     /opt/julia-1.5.2/bin/julia
└ @ Main ~/anaconda3/envs/multicompartment/lib/python3.9/site-packages/julia/install.jl:90
Test PyJulia
DEBUG (28888) 
DEBUG (28888) Debug-level logging is enabled for PyJulia.
DEBUG (28888) PyJulia version: 0.5.6
DEBUG (28888) 
DEBUG (28888) pyprogramname = /home/michael/anaconda3/envs/diff_stats/bin/python
DEBUG (28888) sys.executable = /home/michael/anaconda3/envs/multicompartment/bin/python
DEBUG (28888) bindir = /opt/julia-1.5.2/bin
DEBUG (28888) libjulia_path = /opt/julia-1.5.2/bin/../lib/libjulia.so.1
DEBUG (28888) py_libpython = None
DEBUG (28888) jl_libpython = /home/michael/anaconda3/envs/diff_stats/lib/libpython3.9.so.1.0
DEBUG (28888) is_compatible_python = False
DEBUG (28888) compiled_modules = 'no'
DEBUG (28888) argv_list = [b'/home/michael/anaconda3/envs/multicompartment/bin/python', b'--compiled-modules', b'no']
DEBUG (28888) argc = c_int(3)
DEBUG (28888) jl_parse_opts called
DEBUG (28888) argc = c_int(0)
DEBUG (28888) calling jl_init_with_image(/opt/julia-1.5.2/bin, /opt/julia-1.5.2/lib/julia/sys.so)
DEBUG (28888) seems to work...
DEBUG (28888) exception occured? 140191496175344
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/michael/Documents/diffeqtorch/diffeqtorch/install.py", line 19, in install_and_test
    test_pyjulia()
  File "/home/michael/Documents/diffeqtorch/diffeqtorch/install.py", line 64, in test_pyjulia
    julia = Julia(compiled_modules=False, debug=True)
  File "/home/michael/anaconda3/envs/multicompartment/lib/python3.9/site-packages/julia/core.py", line 503, in __init__
    self._call(IMPORT_PYCALL)
  File "/home/michael/anaconda3/envs/multicompartment/lib/python3.9/site-packages/julia/core.py", line 538, in _call
    self.check_exception(src)
  File "/home/michael/anaconda3/envs/multicompartment/lib/python3.9/site-packages/julia/core.py", line 587, in check_exception
    raise JuliaError(u'Exception \'{}\' occurred while calling julia code:\n{}'
julia.core.JuliaError: Exception 'LoadError' occurred while calling julia code:
const PyCall = Base.require(Base.PkgId(Base.UUID("438e738f-606a-5dbb-bf0a-cddfbfd45ab0"), "PyCall"))

[jan-matthis]

Thanks for reporting this. I suspect that this has to do with PyJulia in combination with Python 3.9 but not 100% sure of it yet. As a temporary solution I'm thinking of restricting Python to < 3.9 as done in #2.

For a moment, I thought that the issue might perhaps be fixed by using Julia v1.6.0, but currently there is still this: JuliaPy/pyjulia#437

Edit: The temporary fix is implemented in version 1.0.1