Various installation issues #262

TheLemonPig · 2023-02-06T20:30:08Z

TheLemonPig
Feb 6, 2023

I had been struggling to get PySR working in most environments but was successful in running the Google Colab tutorial. I was hoping to migrate the functionality of the first block of code out of Google Colab into a python or .pytoml file in order to run PySR outside of the Google Colab environment. However I have been struggling understand what the block of code does to make PySR work.

!echo "Runtime started."

%%shell
set -e

#---------------------------------------------------#
JULIA_VERSION="1.7.2"
JULIA_NUM_THREADS=4
export JULIA_PKG_PRECOMPILE_AUTO=0
#---------------------------------------------------#

if [ -z `which julia` ]; then
  # Install Julia
  JULIA_VER=`cut -d '.' -f -2 <<< "$JULIA_VERSION"`
  echo "Installing Julia $JULIA_VERSION on the current Colab Runtime..."
  BASE_URL="https://julialang-s3.julialang.org/bin/linux/x64"
  URL="$BASE_URL/$JULIA_VER/julia-$JULIA_VERSION-linux-x86_64.tar.gz"
  wget -nv $URL -O /tmp/julia.tar.gz # -nv means "not verbose"
  tar -x -f /tmp/julia.tar.gz -C /usr/local --strip-components 1
  rm /tmp/julia.tar.gz

  echo "Installing PyCall.jl..."
  julia -e 'using Pkg; Pkg.add("PyCall"); Pkg.build("PyCall")'
  julia -e 'println("Success")'

fi

Doing this Google Colab specific task was also necessary:
" Use fallback runtime. Run the above cell (!echo "Runtime started.") to start the runtime. Now, open the command pallette (bottom left -> second icon from the bottom), and search for "use fallback runtime", and hit enter. "

MilesCranmer · 2023-02-06T20:42:04Z

MilesCranmer
Feb 6, 2023
Maintainer

This block of code is colab-specific. It installs Julia within Google Colab, because their VM (based on Ubuntu) doesn't include Julia by default. Note that Google Colab runs in the cloud, rather than on your local machine – so even if Julia is installed locally, it still needs to be installed on the colab VM.

Doing this Google Colab specific task was also necessary:
" Use fallback runtime. Run the above cell (!echo "Runtime started.") to start the runtime. Now, open the command pallette (bottom left -> second icon from the bottom), and search for "use fallback runtime", and hit enter. "

This actually changed only 2 hours ago! See googlecolab/colabtools#3385. I need to update the colab notebook to remove that part, as you have noted 🙂

I had been struggling to get PySR working in most environments but was successful in running the Google Colab tutorial.

Please share where you are struggling and I can try to help

Edit: updated the notebook.

13 replies

TheLemonPig Feb 17, 2023
Author

Building PyCall → ~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/62f417f6ad727987c755549e9cd88c46578da562/build.log
ERROR: LoadError: Couldn't find libpython; check your PYTHON environment variable.

The python executable we tried was /Users/joshuahewson/Developer/venvs/pysrvenv/bin/python (= version 3.10).
Re-building with
ENV["PYCALL_DEBUG_BUILD"] = "yes"
may provide extra information for why it failed.

Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] find_libpython(python::String; _dlopen::typeof(Base.Libc.Libdl.dlopen))
@ Main ~/.julia/packages/PyCall/twYvK/deps/buildutils.jl:72
[3] find_libpython(python::String)
@ Main ~/.julia/packages/PyCall/twYvK/deps/buildutils.jl:40
[4] top-level scope
@ ~/.julia/packages/PyCall/twYvK/deps/build.jl:82
[5] include(fname::String)
@ Base.MainInclude ./client.jl:476
[6] top-level scope
@ none:5
in expression starting at /Users/joshuahewson/.julia/packages/PyCall/twYvK/deps/build.jl:43
ERROR: LoadError: Error building PyCall:

Stacktrace:
[1] pkgerror(msg::String)
@ Pkg.Types ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Types.jl:67
[2] (::Pkg.Operations.var"#66#73"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String})()
@ Pkg.Operations ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1060
[3] withenv(::Pkg.Operations.var"#66#73"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, ::Pair{String, String}, ::Vararg{Pair{String}})
@ Base ./env.jl:172
[4] (::Pkg.Operations.var"#107#112"{String, Bool, Bool, Bool, Pkg.Operations.var"#66#73"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.PackageSpec})()
@ Pkg.Operations ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1619
[5] with_temp_env(fn::Pkg.Operations.var"#107#112"{String, Bool, Bool, Bool, Pkg.Operations.var"#66#73"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.PackageSpec}, temp_env::String)
@ Pkg.Operations ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1493
[6] (::Pkg.Operations.var"#105#110"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#66#73"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, Pkg.Types.Project, String})(tmp::String)
@ Pkg.Operations ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1582
[7] mktempdir(fn::Pkg.Operations.var"#105#110"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#66#73"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec, String}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, Pkg.Types.Project, String}, parent::String; prefix::String)
@ Base.Filesystem ./file.jl:764
[8] mktempdir(fn::Function, parent::String) (repeats 2 times)
@ Base.Filesystem ./file.jl:760
[9] sandbox(fn::Function, ctx::Pkg.Types.Context, target::Pkg.Types.PackageSpec, target_path::String, sandbox_path::String, sandbox_project_override::Pkg.Types.Project; preferences::Dict{String, Any}, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool)
@ Pkg.Operations ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1540
[10] build_versions(ctx::Pkg.Types.Context, uuids::Set{Base.UUID}; verbose::Bool)
@ Pkg.Operations ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:1041
[11] build(ctx::Pkg.Types.Context, uuids::Set{Base.UUID}, verbose::Bool)
@ Pkg.Operations ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/Operations.jl:898
[12] build(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; verbose::Bool, kwargs::Base.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
@ Pkg.API ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/API.jl:1029
[13] build(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Pairs{Symbol, Bool, Tuple{Symbol}, NamedTuple{(:verbose,), Tuple{Bool}}})
@ Pkg.API ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/API.jl:156
[14] #build#99
@ ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/API.jl:144 [inlined]
[15] #build#98
@ ~/.julia/juliaup/julia-1.8.5+0.x64.apple.darwin14/share/julia/stdlib/v1.8/Pkg/src/API.jl:143 [inlined]
[16] build_pycall()
@ Main ~/Developer/venvs/pysrvenv/lib/python3.10/site-packages/julia/install.jl:54
[17] top-level scope
@ ~/Developer/venvs/pysrvenv/lib/python3.10/site-packages/julia/install.jl:115
in expression starting at /Users/joshuahewson/Developer/venvs/pysrvenv/lib/python3.10/site-packages/julia/install.jl:73
Traceback (most recent call last):
File "", line 1, in
File "/Users/joshuahewson/Developer/venvs/pysrvenv/lib/python3.10/site-packages/pysr/julia_helpers.py", line 84, in install
julia.install(quiet=quiet)
File "/Users/joshuahewson/Developer/venvs/pysrvenv/lib/python3.10/site-packages/julia/tools.py", line 118, in install
raise PyCallInstallError("Installing", output)
julia.tools.PyCallInstallError: Installing PyCall failed.

** Important information from Julia may be printed before Python's Traceback **

Some useful information may also be stored in the build log file
~/.julia/packages/PyCall/*/deps/build.log.

MilesCranmer Feb 17, 2023
Maintainer

Very strange...

Can you try to delete your entire ~/.julia and then re-run the installation?

TheLemonPig Feb 17, 2023
Author

Same output unfortunately

MilesCranmer Feb 17, 2023
Maintainer

It looks like the error:

 ERROR: LoadError: Couldn't find libpython; check your PYTHON environment variable.

relates to it not being able to find libpython.dylib or libpython.so. Can you check if you have one of those?

TheLemonPig Feb 21, 2023
Author

I don't seem to have either one of those in my entire computer. Definitely not within the virtual environment I am working :/

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Various installation issues #262

{{title}}

{{editor}}'s edit

{{editor}}'s edit

Replies: 1 comment 13 replies

{{title}}

{{editor}}'s edit

{{editor}}'s edit

{{title}}

{{title}}

{{title}}

{{title}}

{{title}}

Select a reply

Various installation issues #262

TheLemonPig Feb 6, 2023

Replies: 1 comment · 13 replies

MilesCranmer Feb 6, 2023 Maintainer

TheLemonPig Feb 17, 2023 Author

MilesCranmer Feb 17, 2023 Maintainer

TheLemonPig Feb 17, 2023 Author

MilesCranmer Feb 17, 2023 Maintainer

TheLemonPig Feb 21, 2023 Author

TheLemonPig
Feb 6, 2023

Replies: 1 comment 13 replies

MilesCranmer
Feb 6, 2023
Maintainer

TheLemonPig Feb 17, 2023
Author

MilesCranmer Feb 17, 2023
Maintainer

TheLemonPig Feb 17, 2023
Author

MilesCranmer Feb 17, 2023
Maintainer

TheLemonPig Feb 21, 2023
Author