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[BUG] Installation fails #118

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ecod3r opened this issue Mar 14, 2022 · 9 comments
Closed

[BUG] Installation fails #118

ecod3r opened this issue Mar 14, 2022 · 9 comments
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bug Something isn't working

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@ecod3r
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ecod3r commented Mar 14, 2022

Describe the bug
After installing from conda in a Python 3.9 environment, installation fails with the following

julia.core.JuliaError: Exception 'ReadOnlyMemoryError()' occurred while calling julia code Pkg.add(spec, io=stderr)

Version (please complete the following information):

  • OS: Ubuntu
  • Version 20.04.2 LTS (Focal Fossa)
  • Does the bug appear with the latest version of PySR? Yes

Configuration

  • What are your PySR settings? None. The installed version is 0.7.9 (pyh6c4a22f_0 from conda-forge)
  • What dataset are you running on? None

Error message

To silence this warning, you can run pysr.silence_julia_warning() after importing pysr.
  warnings.warn(
  Activating new environment at `~/.julia/environments/pysr-0.7.9/Project.toml`
     Cloning git-repo `https://github.com/MilesCranmer/SymbolicRegression.jl`
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home//anaconda3/envs/stable/lib/python3.9/site-packages/pysr/sr.py", line 46, in install
    _add_sr_to_julia_project(Main, io_arg)
  File "/home//anaconda3/envs/stable/lib/python3.9/site-packages/pysr/sr.py", line 343, in _add_sr_to_julia_project
    Main.eval(f"Pkg.add(spec, {io_arg})")
  File "/home//anaconda3/envs/stable/lib/python3.9/site-packages/julia/core.py", line 621, in eval
    ans = self._call(src)
  File "/home/em/anaconda3/envs/stable/lib/python3.9/site-packages/julia/core.py", line 549, in _call
    self.check_exception(src)
  File "/home/em/anaconda3/envs/stable/lib/python3.9/site-packages/julia/core.py", line 603, in check_exception
    raise JuliaError(u'Exception \'{}\' occurred while calling julia code:\n{}'
julia.core.JuliaError: Exception 'ReadOnlyMemoryError()' occurred while calling julia code:
Pkg.add(spec, io=stderr)

Additional context
@ecod3r ecod3r added the bug Something isn't working label Mar 14, 2022
@MilesCranmer
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Where is your anaconda3 folder located? The error trace back seems to reference two different folders: /home/anaconda3 and /home/em/anaconda3 - maybe do you have two conflicting installations?

@ecod3r
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ecod3r commented Mar 14, 2022

Strange, as I copy-pasted the trace back. No, I've only got one anaconda installation, just multiple envs. But just ran again (same env and everything) and now the paths look right. Alas, the error persists.

Environment:
  CONDA_BACKUP_FFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/em/anaconda3/include
  CONDA_BACKUP_LDFLAGS = -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/em/anaconda3/lib -Wl,-rpath-link,/home/em/anaconda3/lib -L/home/em/anaconda3/lib
  JAVA_HOME = /usr/lib/jvm/java-11-openjdk-amd64
  CONDA_BACKUP_DEBUG_CFLAGS = -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/em/anaconda3/include
  CONDA_BACKUP_DEBUG_CPPFLAGS = -D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /home/em/anaconda3/include
  CONDA_BACKUP_DEBUG_CXXFLAGS = -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/em/anaconda3/include
  CONDA_BACKUP_DEBUG_FORTRANFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/em/anaconda3/include
  HOME = /home/em
  CONDA_BACKUP_CFLAGS = -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/em/anaconda3/include
  CONDA_BACKUP_CXXFLAGS = -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/em/anaconda3/include
  TERM = xterm-256color
  CONDA_BACKUP_CMAKE_PREFIX_PATH = /home/em/anaconda3:/home/em/anaconda3/x86_64-conda-linux-gnu/sysroot/usr
  CONDA_BACKUP_CPPFLAGS = -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/em/anaconda3/include
  CONDA_BACKUP_DEBUG_FFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/em/anaconda3/include
  PATH = /home/em/anaconda3/envs/stable/bin:/home/em/anaconda3/condabin:/home/em/.local/bin:/home/em/google-cloud-sdk/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
  CONDA_BACKUP_FORTRANFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/em/anaconda3/include
[ Info: Julia executable: /home/em/anaconda3/envs/stable/bin/julia
[ Info: Trying to import PyCall...
┌ Info: PyCall is already installed and compatible with Python executable.
│ 
│ PyCall:
│     python: /home/em/anaconda3/envs/stable/bin/python
│     libpython: /home/em/anaconda3/envs/stable/lib/libpython3.9.so.1.0
│ Python:
│     python: /home/em/anaconda3/envs/stable/bin/python
└     libpython: 
/home/em/anaconda3/envs/stable/lib/python3.9/site-packages/pysr/sr.py:318: UserWarning: 
Your Python version is statically linked to libpython. For example, this could be the python included with conda, or maybe your system's built-in python.
This will still work, but the precompilation cache for Julia will be turned off, which may result in slower startup times on the initial pysr() call.

To install a Python version that is dynamically linked to libpython, pyenv is recommended (https://github.com/pyenv/pyenv). With pyenv, you can run: `PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.9.10` to install Python 3.9.10 with dynamic linking.

To silence this warning, you can run pysr.silence_julia_warning() after importing pysr.
  warnings.warn(
  Activating new environment at `~/.julia/environments/pysr-0.7.9/Project.toml`
     Cloning git-repo `https://github.com/MilesCranmer/SymbolicRegression.jl`
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/em/anaconda3/envs/stable/lib/python3.9/site-packages/pysr/sr.py", line 46, in install
    _add_sr_to_julia_project(Main, io_arg)
  File "/home/em/anaconda3/envs/stable/lib/python3.9/site-packages/pysr/sr.py", line 343, in _add_sr_to_julia_project
    Main.eval(f"Pkg.add(spec, {io_arg})")
  File "/home/em/anaconda3/envs/stable/lib/python3.9/site-packages/julia/core.py", line 621, in eval
    ans = self._call(src)
  File "/home/em/anaconda3/envs/stable/lib/python3.9/site-packages/julia/core.py", line 549, in _call
    self.check_exception(src)
  File "/home/em/anaconda3/envs/stable/lib/python3.9/site-packages/julia/core.py", line 603, in check_exception
    raise JuliaError(u'Exception \'{}\' occurred while calling julia code:\n{}'
julia.core.JuliaError: Exception 'ReadOnlyMemoryError()' occurred while calling julia code:
Pkg.add(spec, io=stderr)

@MilesCranmer
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Very strange. Any chance you installed conda with sudo? It looks like it’s unable to write because of permission issues.

@ecod3r
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ecod3r commented Mar 14, 2022

Strange indeed. Everything is in my home directory and I've never had to change permissions on anaconda's folders. Would you know what path is problematic? Also, I've checked, and ~/.julia/environments/pysr-0.7.9 does not exist.

@MilesCranmer
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This looks similar in some ways: JuliaLang/julia#39396

Maybe you are running out of RAM? How much RAM do you have?

@ecod3r
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ecod3r commented Mar 15, 2022

1 TB, half of which is available - can free up more, though I'd be very surprised if that mattered. Info, as printed by pysr.install()

Platform Info:
  OS: Linux (x86_64-conda-linux-gnu)
      Ubuntu 20.04.2 LTS
  uname: Linux 5.4.0-77-generic #86-Ubuntu SMP Thu Jun 17 02:35:03 UTC 2021 x86_64 x86_64
  CPU: AMD EPYC 7702P 64-Core Processor: 
                  speed         user         nice          sys         idle          irq
       #1-128  1499 MHz  1189067606 s      89796 s   73479266 s  8341110380 s          0 s
       
  Memory: 1003.5033874511719 GB (455850.2890625 MB free)

@MilesCranmer
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MilesCranmer commented Mar 15, 2022 •
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Yes, that's definitely enough RAM!! I was more wondering if it was like on a tiny virtual machine or something and running out of memory. This bug is really perplexing me.

Could you try each of the following potential solutions?

  1. Delete the Julia registry using rm ~/.julia/registries/* and then re-run pysr.install().
  2. Create a new conda environment just for PySR, with conda create -n pysr pysr, and see if it works in a fresh environment.

@MilesCranmer
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Also, make sure your conda is up to date (conda update -n base conda), but I'm not sure if that's relevant for this.

@MilesCranmer MilesCranmer removed their assignment Apr 20, 2023
@MilesCranmer MilesCranmer mentioned this issue Jul 2, 2023
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@MilesCranmer
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Presumably fixed by #535

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