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Drachta opened this issue Mar 1, 2022 · 8 comments
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unable to precompile JLD2 (Windows 7 - Julia 1.6.5) #383

Drachta opened this issue Mar 1, 2022 · 8 comments

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@Drachta
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Drachta commented Mar 1, 2022

Hello,

I'm having trouble using JLD2. It seems to complain about a permission on a temp file during precompile, but running Julia command prompt as admin didn't solve the issue.

I'm not sure what else I can try to solve this issue.

julia> using JLD2
[ Info: Precompiling JLD2 [033835bb-8acc-5ee8-8aae-3f567f8a3819]
┌ Error: mktemp cleanup
│   exception =
│    IOError: unlink("C:\\Users\\Etudiant\\AppData\\Local\\Temp\\jl_2605.tmp"): resource busy or locked (EBUSY)
│    Stacktrace:
│      [1] uv_error
│        @ .\libuv.jl:97 [inlined]
│      [2] unlink(p::String)
│        @ Base.Filesystem .\file.jl:934
│      [3] rm(path::String; force::Bool, recursive::Bool)
│        @ Base.Filesystem .\file.jl:272
│      [4] rm
│        @ .\file.jl:263 [inlined]
│      [5] mktemp(fn::JLD2.var"#81#85", parent::String)
│        @ Base.Filesystem .\file.jl:707
│      [6] mktemp(fn::Function)
│        @ Base.Filesystem .\file.jl:701
│      [7] top-level scope
│        @ C:\Users\Etudiant\.julia\packages\JLD2\MXv8x\src\precompile.jl:2
│      [8] include(mod::Module, _path::String)
│        @ Base .\Base.jl:384
│      [9] include
│        @ C:\Users\Etudiant\.julia\packages\JLD2\MXv8x\src\JLD2.jl:1 [inlined]
│     [10] top-level scope
│        @ C:\Users\Etudiant\.julia\packages\JLD2\MXv8x\src\JLD2.jl:539
│     [11] include
│        @ .\Base.jl:384 [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:1235
│     [13] top-level scope
│        @ none:1
│     [14] eval
│        @ .\boot.jl:360 [inlined]
│     [15] eval(x::Expr)
│        @ Base.MainInclude .\client.jl:446
│     [16] top-level scope
│        @ none:1
│     [17] eval
│        @ .\boot.jl:360 [inlined]
│     [18] exec_options(opts::Base.JLOptions)
│        @ Base .\client.jl:261
│     [19] _start()
│        @ Base .\client.jl:485
└ @ Base.Filesystem file.jl:709
ERROR: LoadError: LoadError: IOError: realpath("C:\\Users\\Etudiant\\AppData\\Local\\Temp\\jl_2605.tmp"): resource busy or locked (EBUSY)
Stacktrace:
  [1] uv_error
    @ .\libuv.jl:97 [inlined]
  [2] realpath(path::String)
    @ Base.Filesystem .\path.jl:448
  [3] jldopen(fname::String, wr::Bool, create::Bool, truncate::Bool, iotype::Type{JLD2.MmapIO}; fallback::Type{IOStream}, compress::Bool, mmaparrays::Bool, typemap::Dict{String, Any})
    @ JLD2 C:\Users\Etudiant\.julia\packages\JLD2\MXv8x\src\JLD2.jl:292
  [4] jldopen(fname::String, mode::String; iotype::Type, kwargs::Base.Iterators.Pairs{Symbol, Bool, Tuple{Symbol}, NamedTuple{(:compress,), Tuple{Bool}}})
    @ JLD2 C:\Users\Etudiant\.julia\packages\JLD2\MXv8x\src\JLD2.jl:356
  [5] jldopen(::Function, ::String, ::Vararg{String, N} where N; kws::Base.Iterators.Pairs{Symbol, Any, Tuple{Symbol, Symbol}, NamedTuple{(:compress, :iotype), Tuple{Bool, DataType}}})
    @ JLD2 C:\Users\Etudiant\.julia\packages\JLD2\MXv8x\src\loadsave.jl:2
  [6] #jldsave#49
    @ C:\Users\Etudiant\.julia\packages\JLD2\MXv8x\src\loadsave.jl:243 [inlined]
  [7] (::JLD2.var"#81#85")(path::String, #unused#::IOStream)
    @ JLD2 C:\Users\Etudiant\.julia\packages\JLD2\MXv8x\src\precompile.jl:14
  [8] mktemp(fn::JLD2.var"#81#85", parent::String)
    @ Base.Filesystem .\file.jl:703
  [9] mktemp(fn::Function)
    @ Base.Filesystem .\file.jl:701
 [10] top-level scope
    @ C:\Users\Etudiant\.julia\packages\JLD2\MXv8x\src\precompile.jl:2
 [11] include(mod::Module, _path::String)
    @ Base .\Base.jl:384
 [12] include
    @ C:\Users\Etudiant\.julia\packages\JLD2\MXv8x\src\JLD2.jl:1 [inlined]
 [13] top-level scope
    @ C:\Users\Etudiant\.julia\packages\JLD2\MXv8x\src\JLD2.jl:539
 [14] include
    @ .\Base.jl:384 [inlined]
 [15] 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:1235
 [16] top-level scope
    @ none:1
 [17] eval
    @ .\boot.jl:360 [inlined]
 [18] eval(x::Expr)
    @ Base.MainInclude .\client.jl:446
 [19] top-level scope
    @ none:1
in expression starting at C:\Users\Etudiant\.julia\packages\JLD2\MXv8x\src\precompile.jl:1
in expression starting at C:\Users\Etudiant\.julia\packages\JLD2\MXv8x\src\JLD2.jl:1
┌ Warning: temp cleanup
│   exception =
│    IOError: unlink("C:\\Users\\Etudiant\\AppData\\Local\\Temp\\jl_2605.tmp"): permission denied (EACCES)
│    Stacktrace:
│     [1] uv_error
│       @ .\libuv.jl:97 [inlined]
│     [2] unlink(p::String)
│       @ Base.Filesystem .\file.jl:934
│     [3] rm(path::String; force::Bool, recursive::Bool)
│       @ Base.Filesystem .\file.jl:272
│     [4] temp_cleanup_purge(; force::Bool)
│       @ Base.Filesystem .\file.jl:518
│     [5] (::Base.var"#786#787")()
│       @ Base .\initdefs.jl:322
│     [6] _atexit()
│       @ Base .\initdefs.jl:343
│     [7] exit
│       @ .\initdefs.jl:28 [inlined]
│     [8] _start()
│       @ Base .\client.jl:488
└ @ Base.Filesystem file.jl:522
ERROR: Failed to precompile JLD2 [033835bb-8acc-5ee8-8aae-3f567f8a3819] to C:\Users\Etudiant\.julia\compiled\v1.6\JLD2\jl_187E.tmp.
Stacktrace:
  [1] error(s::String)
    @ Base .\error.jl:33
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::Base.TTY, internal_stdout::Base.TTY, ignore_loaded_modules::Bool)
    @ Base .\loading.jl:1385
  [3] compilecache(pkg::Base.PkgId, path::String)
    @ Base .\loading.jl:1329
  [4] _require(pkg::Base.PkgId)
    @ Base .\loading.jl:1043
  [5] require(uuidkey::Base.PkgId)
    @ Base .\loading.jl:936
  [6] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:923
  [7] eval
    @ .\boot.jl:360 [inlined]
  [8] eval
    @ .\Base.jl:39 [inlined]
  [9] repleval(m::Module, code::Expr, #unused#::String)
    @ VSCodeServer c:\Users\Etudiant\.vscode\extensions\julialang.language-julia-1.5.11\scripts\packages\VSCodeServer\src\repl.jl:157
 [10] (::VSCodeServer.var"#69#71"{Module, Expr, REPL.LineEditREPL, REPL.LineEdit.Prompt})()
    @ VSCodeServer c:\Users\Etudiant\.vscode\extensions\julialang.language-julia-1.5.11\scripts\packages\VSCodeServer\src\repl.jl:123
 [11] with_logstate(f::Function, logstate::Any)
    @ Base.CoreLogging .\logging.jl:491
 [12] with_logger
    @ .\logging.jl:603 [inlined]
 [13] (::VSCodeServer.var"#68#70"{Module, Expr, REPL.LineEditREPL, REPL.LineEdit.Prompt})()
    @ VSCodeServer c:\Users\Etudiant\.vscode\extensions\julialang.language-julia-1.5.11\scripts\packages\VSCodeServer\src\repl.jl:124
 [14] #invokelatest#2
    @ .\essentials.jl:708 [inlined]
 [15] invokelatest(::Any)
    @ Base .\essentials.jl:706
 [16] macro expansion
    @ c:\Users\Etudiant\.vscode\extensions\julialang.language-julia-1.5.11\scripts\packages\VSCodeServer\src\eval.jl:34 [inlined]
 [17] (::VSCodeServer.var"#53#54")()
    @ VSCodeServer .\task.jl:411
@JonasIsensee
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Hi @Drachta,
thanks for reporting this.
Does this happen every time?

It looks very similar to this: JuliaLang/julia#39457

@Drachta
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Drachta commented Mar 1, 2022 •
edited
Loading

Yes, it happens every time. I tried to restart my computer just in case, but it still happens.
It seems I also have the same problem with version 1.7.2 of Julia.

I can delete the temporary file from within windows explorer without any popup saying that the file is used somewhere.

Is there any folder / files I can remove so I can start from a fresh envirronement ? Or reinstalling Julia is enough ?

EDIT: after reinstalling Julia and deleting the folder: C:\Users\Etudiant\.julia, the issue persists. Other packages seem to work fine. JLD2 is installed as a dependency and its target version is 0.4.21

@JonasIsensee
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The error sadly has little to do with JLD2 - only that JLD2 uses mktempdir during precompilation.
This was introduced in JLD2 v0.4.20 for better performance. 0.4.19 shouldn't have this issue.

@Drachta
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Drachta commented Mar 4, 2022

@JonasIsensee Thank you very much! It works with version 0.4.19.

@Drachta Drachta closed this as completed Mar 4, 2022
@kagalenko-m-b
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This issue prevents me from installing the latest version on Windows7

julia> versioninfo()
Julia Version 1.9.2
Commit e4ee485e90 (2023-07-05 09:39 UTC)
Platform Info:
OS: Windows (x86_64-w64-mingw32)
CPU: 4 × Intel(R) Core(TM) i5-3230M CPU @ 2.60GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-14.0.6 (ORCJIT, ivybridge)
Threads: 1 on 4 virtual cores
Environment:
JULIA_IMAGE_THREADS = 1

julia> using JLD2
[ Info: Precompiling JLD2 [033835bb-8acc-5ee8-8aae-3f567f8a3819]
┌ Error: mktemp cleanup
│ exception =
│ IOError: unlink("C:\Users\kmb\AppData\Local\Temp\jl_2127.tmp"): resou
rce busy or locked (EBUSY)
│ Stacktrace:
│ [1] uv_error
│ @ .\libuv.jl:100 [inlined]
│ [2] unlink(p::String)
│ @ Base.Filesystem .\file.jl:972
│ [3] rm(path::String; force::Bool, recursive::Bool)
│ @ Base.Filesystem .\file.jl:283
│ [4] rm
│ @ .\file.jl:273 [inlined]
│ [5] mktemp(fn::JLD2.var"#121#125", parent::String)
│ @ Base.Filesystem .\file.jl:736
│ [6] mktemp(fn::Function)
│ @ Base.Filesystem .\file.jl:730
│ [7] top-level scope
│ @ C:\Users\kmb.julia\packages\JLD2\cHcDY\src\precompile.jl:2
│ [8] include(mod::Module, _path::String)
│ @ Base .\Base.jl:457
│ [9] include
│ @ C:\Users\kmb.julia\packages\JLD2\cHcDY\src\JLD2.jl:1 [inlined]
│ [10] top-level scope
│ @ C:\Users\kmb.julia\packages\JLD2\cHcDY\src\JLD2.jl:616
│ [11] include
│ @ .\Base.jl:457 [inlined]
│ [12] include_package_for_output(pkg::Base.PkgId, input::String, depot_path
::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concr
ete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
│ @ Base .\loading.jl:2049
│ [13] top-level scope
│ @ stdin:3
│ [14] eval
│ @ .\boot.jl:370 [inlined]
│ [15] include_string(mapexpr::typeof(identity), mod::Module, code::String,
filename::String)
│ @ Base .\loading.jl:1903
│ [16] include_string
│ @ .\loading.jl:1913 [inlined]
│ [17] exec_options(opts::Base.JLOptions)
│ @ Base .\client.jl:305
│ [18] _start()
│ @ Base .\client.jl:522
└ @ Base.Filesystem file.jl:738
ERROR: LoadError: IOError: realpath("C:\Users\kmb\AppData\Local\Temp\jl_21
27.tmp"): resource busy or locked (EBUSY)
Stacktrace:
[1] uv_error
@ .\libuv.jl:100 [inlined]
[2] realpath(path::String)
@ Base.Filesystem .\path.jl:487
[3] jldopen(fname::String, wr::Bool, create::Bool, truncate::Bool, iotype::Typ
e{JLD2.MmapIO}; fallback::Type{IOStream}, compress::Bool, mmaparrays::Bool, type
map::Dict{String, Any}, parallel_read::Bool)
@ JLD2 C:\Users\kmb.julia\packages\JLD2\cHcDY\src\JLD2.jl:357
[4] jldopen(fname::String, mode::String; iotype::Type, kwargs::Base.Pairs{Symb
ol, Bool, Tuple{Symbol}, NamedTuple{(:compress,), Tuple{Bool}}})
@ JLD2 C:\Users\kmb.julia\packages\JLD2\cHcDY\src\JLD2.jl:439
[5] jldopen(::Function, ::String, ::Vararg{String}; kws::Base.Pairs{Symbol, An
y, Tuple{Symbol, Symbol}, NamedTuple{(:compress, :iotype), Tuple{Bool, DataType}
}})
@ JLD2 C:\Users\kmb.julia\packages\JLD2\cHcDY\src\loadsave.jl:2
[6] jldopen
@ C:\Users\kmb.julia\packages\JLD2\cHcDY\src\loadsave.jl:1 [inlined]
[7] #jldsave#81
@ C:\Users\kmb.julia\packages\JLD2\cHcDY\src\loadsave.jl:243 [inlined]
[8] jldsave (repeats 2 times)
@ C:\Users\kmb.julia\packages\JLD2\cHcDY\src\loadsave.jl:240 [inlined]
[9] (::JLD2.var"#121#125")(path::String, #unused#::IOStream)
@ JLD2 C:\Users\kmb.julia\packages\JLD2\cHcDY\src\precompile.jl:14
[10] mktemp(fn::JLD2.var"#121#125", parent::String)
@ Base.Filesystem .\file.jl:732
[11] mktemp(fn::Function)
@ Base.Filesystem .\file.jl:730
[12] top-level scope
@ C:\Users\kmb.julia\packages\JLD2\cHcDY\src\precompile.jl:2
[13] include(mod::Module, _path::String)
@ Base .\Base.jl:457
[14] include
@ C:\Users\kmb.julia\packages\JLD2\cHcDY\src\JLD2.jl:1 [inlined]
[15] top-level scope
@ C:\Users\kmb.julia\packages\JLD2\cHcDY\src\JLD2.jl:616
[16] include
@ .\Base.jl:457 [inlined]
[17] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vec
tor{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_d
eps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
@ Base .\loading.jl:2049
[18] top-level scope
@ stdin:3
in expression starting at C:\Users\kmb.julia\packages\JLD2\cHcDY\src\precompile
.jl:1
in expression starting at C:\Users\kmb.julia\packages\JLD2\cHcDY\src\JLD2.jl:1
in expression starting at stdin:3
┌ Warning: temp cleanup
│ exception =
│ IOError: unlink("C:\Users\kmb\AppData\Local\Temp\jl_2127.tmp"): permi
ssion denied (EACCES)
│ Stacktrace:
│ [1] uv_error
│ @ .\libuv.jl:100 [inlined]
│ [2] unlink(p::String)
│ @ Base.Filesystem .\file.jl:972
│ [3] rm(path::String; force::Bool, recursive::Bool)
│ @ Base.Filesystem .\file.jl:283
│ [4] rm
│ @ .\file.jl:273 [inlined]
│ [5] temp_cleanup_purge(; force::Bool)
│ @ Base.Filesystem .\file.jl:543
│ [6] temp_cleanup_purge
│ @ .\file.jl:535 [inlined]
│ [7] (::Base.var"#930#931")()
│ @ Base .\initdefs.jl:354
│ [8] _atexit(exitcode::Int32)
│ @ Base .\initdefs.jl:416
│ [9] exit
│ @ .\initdefs.jl:28 [inlined]
│ [10] exec_options(opts::Base.JLOptions)
│ @ Base .\client.jl:312
│ [11] _start()
│ @ Base .\client.jl:522
└ @ Base.Filesystem file.jl:547
ERROR: Failed to precompile JLD2 [033835bb-8acc-5ee8-8aae-3f567f8a3819] to "C:\
Users\kmb\.julia\compiled\v1.9\JLD2\jl_F81D.tmp".
Stacktrace:
[1] error(s::String)
@ Base .\error.jl:35
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_s
tdout::IO, keep_loaded_modules::Bool)
@ Base .\loading.jl:2300
[3] compilecache
@ .\loading.jl:2167 [inlined]
[4] _require(pkg::Base.PkgId, env::String)
@ Base .\loading.jl:1805
[5] _require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base .\loading.jl:1660
[6] macro expansion
@ .\loading.jl:1648 [inlined]
[7] macro expansion
@ .\lock.jl:267 [inlined]
[8] require(into::Module, mod::Symbol)
@ Base .\loading.jl:1611

@kagalenko-m-b kagalenko-m-b mentioned this issue Aug 16, 2023
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@mkitti
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mkitti commented Nov 25, 2023

See JuliaLang/julia#47730 (comment)

@kagalenko-m-b kagalenko-m-b mentioned this issue Nov 28, 2023
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@HongBinYu-hub
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Hello, this problem may be caused by the jldopen() function under win7 being unable to write. Under win7, iotype = IOStream is required to write. It is likely that this problem causes the precompilation to fail under win7.

@mkitti
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mkitti commented Dec 7, 2023

Both users here are showing problems with unlink. That is Julia is unable to remove the temporary files.

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@mkitti @kagalenko-m-b @JonasIsensee @HongBinYu-hub @Drachta