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Precompilation failure (InitError: failed process)

Open pedromxavier opened this issue 3 years ago • 7 comments

When precompiling Anneal.jl (docs branch) there seems to be some process lock problem with libmamba.

The complete shell session is here: (.CondaPkg is created but left empty)

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PS D:\gits\Anneal.jl> julia --project
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.    
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.7.0 (2021-11-30)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release  
|__/                   |

(Anneal) pkg> precompile
Precompiling project...
  ✗ Anneal
  0 dependencies successfully precompiled in 19 seconds (32 already precompiled)

ERROR: The following 1 direct dependency failed to precompile:

Anneal [e4d9eb7f-b088-426e-aeb5-1c0dae3d8abb]

Failed to precompile Anneal [e4d9eb7f-b088-426e-aeb5-1c0dae3d8abb] to C:\Users\pedroxavier\.julia\compiled\v1.7\Anneal\jl_E2.tmp.
    CondaPkg Found dependencies: D:\gits\Anneal.jl\CondaPkg.toml
    CondaPkg Found dependencies: C:\Users\pedroxavier\.julia\packages\PythonCall\4eoCM\CondaPkg.toml
    CondaPkg Resolving changes
             + dwave-neal (pip)
             + pip
             + python
    CondaPkg Installing packages
warning  libmamba Cannot lock 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache'
    Waiting for other mamba process to finish
error    libmamba Path already locked by the same PID: 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache'
warning  libmamba LockFile creation for path 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache' failed, continuing without it
error    libmamba Path already locked by the same PID: 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache'
warning  libmamba LockFile creation for path 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache' failed, continuing without it
error    libmamba Path already locked by the same PID: 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache'
warning  libmamba LockFile creation for path 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache' failed, continuing without it
error    libmamba Path already locked by the same PID: 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache'
ERROR: LoadError: InitError: failed process: Process(`'C:\Users\pedroxavier\.julia\artifacts\d628738c351341856bc6e8abe94cd6c8d8a7bf66\Library\bin\micromamba.exe' -r 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root' create -q -y -p 'D:\gits\Anneal.jl\.CondaPkg\env' --override-channels --no-channel-priority pip "python[version='>=3.7,<4']" -c anaconda -c conda-forge`, ProcessExited(3221226505)) [3221226505]

Stacktrace:
  [1] pipeline_error
    @ .\process.jl:531 [inlined]
  [2] run(::Cmd; wait::Bool)
    @ Base .\process.jl:446
  [3] run(::Cmd)
    @ Base .\process.jl:444
  [4] _run(io::IO, cmd::Cmd, args::Any; flags::Any)
    @ CondaPkg C:\Users\pedroxavier\.julia\packages\CondaPkg\Olo5Y\src\resolve.jl:283
  [5] _resolve_conda_install(io::Any, conda_env::Any, specs::Any, channels::Any; create::Any)
    @ CondaPkg C:\Users\pedroxavier\.julia\packages\CondaPkg\Olo5Y\src\resolve.jl:191
  [6] resolve(; force::Bool, io::IO, interactive::Bool, dry_run::Bool)
    @ CondaPkg C:\Users\pedroxavier\.julia\packages\CondaPkg\Olo5Y\src\resolve.jl:395
  [7] resolve()
    @ CondaPkg C:\Users\pedroxavier\.julia\packages\CondaPkg\Olo5Y\src\resolve.jl:288
  [8] envdir()
    @ CondaPkg C:\Users\pedroxavier\.julia\packages\CondaPkg\Olo5Y\src\env.jl:70
  [9] init_context()
    @ PythonCall.C C:\Users\pedroxavier\.julia\packages\PythonCall\4eoCM\src\cpython\context.jl:56
 [10] __init__()
    @ PythonCall.C C:\Users\pedroxavier\.julia\packages\PythonCall\4eoCM\src\cpython\CPython.jl:21
 [11] _include_from_serialized(path::String, depmods::Vector{Any})
    @ Base .\loading.jl:768
 [12] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
    @ Base .\loading.jl:854
 [13] _require(pkg::Base.PkgId)
    @ Base .\loading.jl:1097
 [14] require(uuidkey::Base.PkgId)
    @ Base .\loading.jl:1013
 [15] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:997
 [16] include(mod::Module, _path::String)
    @ Base .\Base.jl:418
 [17] include(x::String)
    @ Anneal D:\gits\Anneal.jl\src\Anneal.jl:1
 [18] top-level scope
    @ D:\gits\Anneal.jl\src\Anneal.jl:40
 [19] include
    @ .\Base.jl:418 [inlined]
 [20] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
    @ Base .\loading.jl:1318
 [21] top-level scope
    @ none:1
 [22] eval
    @ .\boot.jl:373 [inlined]
 [23] eval(x::Expr)
    @ Base.MainInclude .\client.jl:453
 [24] top-level scope
    @ none:1
during initialization of module C
in expression starting at D:\gits\Anneal.jl\src\annealers\simulated\simulated.jl:1
in expression starting at D:\gits\Anneal.jl\src\Anneal.jl:1

julia> versioninfo()
Julia Version 1.7.0
Commit 3bf9d17731 (2021-11-30 12:12 UTC)
Platform Info:
  OS: Windows (x86_64-w64-mingw32)
  CPU: Intel(R) Core(TM) i7-7500U CPU @ 2.70GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-12.0.1 (ORCJIT, skylake)

julia> using Pkg; Pkg.status()
     Project Anneal v0.1.0
      Status `D:\gits\Anneal.jl\Project.toml`
  [992eb4ea] CondaPkg v0.2.10
  [b8f27783] MathOptInterface v1.2.0
  [6099a3de] PythonCall v0.9.0
  [9a3f8284] Random

julia> using CondaPkg; CondaPkg.status()
CondaPkg Status D:\gits\Anneal.jl\CondaPkg.toml
Not Resolved (resolve first for more information)
Packages
  python (>=3.7,<4)
Channels
  anaconda
  conda-forge
Pip packages
  dwave-neal (>=0.5.6)

julia> CondaPkg.re
read_deps read_meta  resolve
julia> CondaPkg.resolve()
    CondaPkg Found dependencies: D:\gits\Anneal.jl\CondaPkg.toml
    CondaPkg Found dependencies: C:\Users\pedroxavier\.julia\packages\PythonCall\4eoCM\CondaPkg.toml
    CondaPkg Resolving changes
             + dwave-neal (pip)
             + pip
             + python
    CondaPkg Installing packages
warning  libmamba Cannot lock 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache'
    Waiting for other mamba process to finish
error    libmamba Path already locked by the same PID: 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache'
warning  libmamba LockFile creation for path 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache' failed, continuing without it
error    libmamba Path already locked by the same PID: 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache'
warning  libmamba LockFile creation for path 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache' failed, continuing without it
error    libmamba Path already locked by the same PID: 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache'
warning  libmamba LockFile creation for path 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache' failed, continuing without it
error    libmamba Path already locked by the same PID: 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root\pkgs\cache'
ERROR: failed process: Process(`'C:\Users\pedroxavier\.julia\artifacts\d628738c351341856bc6e8abe94cd6c8d8a7bf66\Library\bin\micromamba.exe' -r 'C:\Users\pedroxavier\.julia\scratchspaces\0b3b1443-0f03-428d-bdfb-f27f9c1191ea\root' create -q -y -p 'D:\gits\Anneal.jl\.CondaPkg\env' --override-channels --no-channel-priority pip "python[version='>=3.7,<4']" -c anaconda -c conda-forge`, ProcessExited(3221226505)) [3221226505]

Stacktrace:
 [1] pipeline_error
   @ .\process.jl:531 [inlined]
 [2] run(::Cmd; wait::Bool)
   @ Base .\process.jl:446
 [3] run(::Cmd)
   @ Base .\process.jl:444
 [4] _run(io::IO, cmd::Cmd, args::Any; flags::Any)
   @ CondaPkg C:\Users\pedroxavier\.julia\packages\CondaPkg\Olo5Y\src\resolve.jl:283
 [5] _resolve_conda_install(io::Any, conda_env::Any, specs::Any, channels::Any; create::Any)
   @ CondaPkg C:\Users\pedroxavier\.julia\packages\CondaPkg\Olo5Y\src\resolve.jl:191
 [6] resolve(; force::Bool, io::IO, interactive::Bool, dry_run::Bool)
   @ CondaPkg C:\Users\pedroxavier\.julia\packages\CondaPkg\Olo5Y\src\resolve.jl:395
 [7] resolve()
   @ CondaPkg C:\Users\pedroxavier\.julia\packages\CondaPkg\Olo5Y\src\resolve.jl:288
 [8] top-level scope
   @ REPL[5]:1

julia>

PS: I have some experience with the Python C API . If you could provide some insights about your thought process on this topic, so I can learn more about the package, I'd be happy to make pull requests for PythonCall in the future!

pedromxavier avatar May 27 '22 14:05 pedromxavier

I'm totally stumped, I cannot reproduce this issue on Windows with the same package versions as you. I tried deleting ~/.julia/compiled and .CondaPkg. I also tried working in an entirely new Julia Depot, making a fresh clone of your repo and precompiling that.

Are you able to reliably reproduce the problem? That is, is there a sequence of steps that you can run which always/usually gets to this problem? If not, I'm not sure I can help.

I have just released a new version of MicroMamba.jl with a newer version of micromamba (0.24.0 instead of 0.22.0). Maybe that helps?

cjdoris avatar Jun 04 '22 18:06 cjdoris

I have just tried and failed to reproduce the issue in a Julia 1.7.0 Docker container too.

Given the error message is about lock files, maybe reproducing the problem in a clean environment won't work, we probably need some stale lock files lying around.

cjdoris avatar Jun 04 '22 19:06 cjdoris

I've just deleted ~/.julia and installed 1.7.3 (Windows) and 1.7.0 (WSL). It works fine now on both with PythonCall 0.9 + MicroMamba 0.24. I've updateded the packages before reinstall but only complete julia reset made the error disappear. I think you can close this issue, but there should be some check to erase old files/artifacts/locks under updates or package cleanups after ]rm. I'm not sure if it is possible or it is something for Pkg to figure out. Thanks for your help!

pedromxavier avatar Jun 04 '22 23:06 pedromxavier

I'll leave it open for now. If it happens again, please make a copy of the pkgs/cache directory that is mentioned in the logs. Also please record the modification times on all the files in there (e.g. the output of dir).

I suspect the problem occurs if you interrupt MicroMamba while resolving dependencies, leaving lock files lying around. It may be possible to get CondaPkg to manually remove them.

cjdoris avatar Jun 05 '22 10:06 cjdoris

Happens to me on M1 Mac as well from Rossetta, I'm not sure if this is a M1 issue or not

julia> using Bloqade
[ Info: Precompiling Bloqade [bd27d05e-4ce1-5e79-84dd-c5d7d508bbe1]
┌ Warning: Python library "/Users/roger/Code/Julia/Bloqade/build/2.adiabatic/.CondaPkg/env/lib/libpython3.10.dylib" could not be opened.
└ @ PythonCall.C ~/.julia/packages/PythonCall/XgP8G/src/cpython/context.jl:109
ERROR: LoadError: InitError: ArgumentError: NULL library handle
Stacktrace:
  [1] #dlsym#1
    @ ./libdl.jl:57 [inlined]
  [2] dlsym
    @ ./libdl.jl:57 [inlined]
  [3] init_pointers(p::PythonCall.C.CAPIPointers, lib::Ptr{Nothing}) (repeats 2 times)
    @ PythonCall.C ~/.julia/packages/PythonCall/XgP8G/src/cpython/pointers.jl:283
  [4] init_context()
    @ PythonCall.C ~/.julia/packages/PythonCall/XgP8G/src/cpython/context.jl:129
  [5] __init__()
    @ PythonCall.C ~/.julia/packages/PythonCall/XgP8G/src/cpython/CPython.jl:21
  [6] _include_from_serialized(path::String, depmods::Vector{Any})
    @ Base ./loading.jl:768
  [7] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
    @ Base ./loading.jl:854
  [8] _require(pkg::Base.PkgId)
    @ Base ./loading.jl:1097
  [9] require(uuidkey::Base.PkgId)
    @ Base ./loading.jl:1013
 [10] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:997
 [11] include
    @ ./Base.jl:418 [inlined]
 [12] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
    @ Base ./loading.jl:1318
 [13] top-level scope
    @ none:1
 [14] eval
    @ ./boot.jl:373 [inlined]
 [15] eval(x::Expr)
    @ Base.MainInclude ./client.jl:453
 [16] top-level scope
    @ none:1
during initialization of module C
in expression starting at /Users/roger/.julia/packages/Bloqade/c5pbN/src/Bloqade.jl:1
ERROR: Failed to precompile Bloqade [bd27d05e-4ce1-5e79-84dd-c5d7d508bbe1] to /Users/roger/.julia/compiled/v1.7/Bloqade/jl_UrbrnH.
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:33
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
   @ Base ./loading.jl:1466
 [3] compilecache(pkg::Base.PkgId, path::String)
   @ Base ./loading.jl:1410
 [4] _require(pkg::Base.PkgId)
   @ Base ./loading.jl:1120
 [5] require(uuidkey::Base.PkgId)
   @ Base ./loading.jl:1013
 [6] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:997

Roger-luo avatar Jul 07 '22 16:07 Roger-luo

This issue has been marked as stale because it has been open for 30 days with no activity. If the issue is still relevant then please leave a comment, or else it will be closed in 7 days.

github-actions[bot] avatar Sep 09 '23 01:09 github-actions[bot]

This issue has been closed because it has been stale for 7 days. If it is still relevant, please re-open it.

github-actions[bot] avatar Sep 16 '23 01:09 github-actions[bot]