Pluto.jl: Segmentation faults on Julia 1.7 M1

Edit from @fonsp

If you are also experiencing segmentation faults with Pluto on Julia 1.7, please post it here! Be sure to provide the following info:

  • a notebook file (the smaller, the better)
  • what did you do to produce the error? Is it consistent?
  • the output of running versioninfo()
  • the full output of your terminal, including the segmentation fault
  • Run the notebook as a julia script without Pluto, i.e. julia my_notebook.jl. Does it still error?

Original issue

The notebook MLJ-Ex6.jl.zip causes a segmentation fault (see full output and error message in ‘Details’) when using Pluto on Julia 1.7 (macOS Monterey 12.0.1, Apple M1).

The statement, where the error occurs after loading, is marked in the notebook.

It runs without problems on:

  • Julia 1.6.1 & Pluto
  • Julia 1.6.1 & REPL
  • Julia 1.7 & REPL

This may indicate that it is a Pluto problem. But as we have already seen in #1658 (and MLJ.jl#865) it might be also a problem of MLJ which is used in the notebook.

` 
  From worker 9:	[ Info: For silent loading, specify `verbosity=0`. 

  From worker 9:	import MLJLinearModels ✔
  From worker 9:	
  From worker 9:	signal (11): Segmentation fault: 11
  From worker 9:	in expression starting at none:1
  From worker 9:	ntuple at ./ntuple.jl:0
  From worker 9:	unknown function (ip: 0x1182de6cf)
  From worker 9:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	getindex at ./range.jl:373 [inlined]
  From worker 9:	check_supervised at /Users/roland/.julia/packages/MLJBase/QXObv/src/machines.jl:128
  From worker 9:	#check#92 at /Users/roland/.julia/packages/MLJBase/QXObv/src/machines.jl:185 [inlined]
  From worker 9:	check##kw at /Users/roland/.julia/packages/MLJBase/QXObv/src/machines.jl:185 [inlined]
  From worker 9:	#machine#100 at /Users/roland/.julia/packages/MLJBase/QXObv/src/machines.jl:311 [inlined]
  From worker 9:	machine at /Users/roland/.julia/packages/MLJBase/QXObv/src/machines.jl:310 [inlined]
  From worker 9:	##function_wrapped_cell#333 at /Users/roland/Desktop/MLJ-Ex6.jl#==#0798b952-eb9f-401e-8247-85326f72cfa7:1 [inlined]
  From worker 9:	##function_wrapped_cell#333 at ./none:0
  From worker 9:	unknown function (ip: 0x1182db60b)
  From worker 9:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	jl_f__call_latest at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	do_apply at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	#invokelatest#2 at ./essentials.jl:716
  From worker 9:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	do_apply at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	invokelatest at ./essentials.jl:714
  From worker 9:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	do_apply at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	compute at /Users/roland/.julia/packages/Pluto/7TMtD/src/runner/PlutoRunner.jl:380
  From worker 9:	#27 at /Users/roland/.julia/packages/Pluto/7TMtD/src/runner/PlutoRunner.jl:535
  From worker 9:	run_inside_trycatch at /Users/roland/.julia/packages/Pluto/7TMtD/src/runner/PlutoRunner.jl:420
  From worker 9:	#run_expression#25 at /Users/roland/.julia/packages/Pluto/7TMtD/src/runner/PlutoRunner.jl:535
  From worker 9:	run_expression##kw at /Users/roland/.julia/packages/Pluto/7TMtD/src/runner/PlutoRunner.jl:450
  From worker 9:	unknown function (ip: 0x11810fa97)
  From worker 9:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	do_call at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	eval_body at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	jl_interpret_toplevel_thunk at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	jl_toplevel_eval_flex at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	jl_toplevel_eval_in at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	eval at ./boot.jl:373
  From worker 9:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	do_apply at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	#103 at /Users/administrator/src/julia/usr/share/julia/stdlib/v1.7/Distributed/src/process_messages.jl:274
  From worker 9:	run_work_thunk at /Users/administrator/src/julia/usr/share/julia/stdlib/v1.7/Distributed/src/process_messages.jl:63
  From worker 9:	unknown function (ip: 0x11802c89b)
  From worker 9:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	run_work_thunk at /Users/administrator/src/julia/usr/share/julia/stdlib/v1.7/Distributed/src/process_messages.jl:72
  From worker 9:	#96 at ./task.jl:423
  From worker 9:	unknown function (ip: 0x11802c27f)
  From worker 9:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	start_task at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
  From worker 9:	Allocations: 159110384 (Pool: 159057943; Big: 52441); GC: 104

Worker 9 terminated.

Unhandled Task ERROR: IOError: read: connection reset by peer (ECONNRESET)
Stacktrace:
[1] wait_readnb(x::Sockets.TCPSocket, nb::Int64)
@ Base ./stream.jl:408
[2] (::Base.var"#wait_locked#645")(s::Sockets.TCPSocket, buf::IOBuffer, nb::Int64)
@ Base ./stream.jl:894
[3] unsafe_read(s::Sockets.TCPSocket, p::Ptr{UInt8}, nb::UInt64)
@ Base ./stream.jl:900
[4] unsafe_read
@ ./io.jl:724 [inlined]
[5] unsafe_read(s::Sockets.TCPSocket, p::Base.RefValue{NTuple{4, Int64}}, n::Int64)
@ Base ./io.jl:723
[6] read!
@ ./io.jl:725 [inlined]
[7] deserialize_hdr_raw
@ /Applications/Julia-    1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Distributed/src/messages.jl:167 [inlined]
[8] message_handler_loop(r_stream::Sockets.TCPSocket, w_stream::Sockets.TCPSocket, incoming::Bool)
@ Distributed /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Distributed/src/process_messages.jl:165
[9] process_tcp_streams(r_stream::Sockets.TCPSocket, w_stream::Sockets.TCPSocket, incoming::Bool)
@ Distributed /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Distributed/src/process_messages.jl:126
[10] (::Distributed.var"#99#100"{Sockets.TCPSocket, Sockets.TCPSocket, Bool})()
@ Distributed ./task.jl:423

About this issue

  • Original URL
  • State: closed
  • Created 3 years ago
  • Comments: 15 (5 by maintainers)

Commits related to this issue

Most upvoted comments

Awesome! In that case, it looks like this will be fixed by Julia 1.8, which will be released in a couple of months. Until then, we recommend using Julia x86! The M1 build is still too experimental.

Thanks for opening the issue and for the useful testing!! Let us know if something comes up again!

About the new issue, always open a new issue! (And check for existing ones)

+2
fonsp on Jan 28, 2022

I think our goal is to try to create a MWE to send to the Julia developers. The main differences between running the notebook in Pluto and running it as a standalone script with julia notebook.jl are:

  • We evaluate code on a Distributed process
  • We evaluate code inside a module, not inside Main

You can emulate this environment without Pluto like so:

using Distributed
ps = Distributed.addprocs(1)

Distributed.remotecall_eval(Main, ps, quote
module Test
include("mynotebook.jl")
end
end)
+1
fonsp on Dec 12, 2021

The notebook 02-worldmap-AoG.jl.zip, which doesn’t use MLJ at all, causes the segmentation fault mentioned above too. So the problem isn’t related to MLJ.

The notebook reads Shapefiles, describing the outline of all countries, and plots them using Makie/AlgebraOfGraphics. The segmentation fault occurs on the last cell, when the plot is rendered (using draw).

The circumstances when the problem occurs are a bit strange again. In a first version of the notebook I used CairoMakie instead of GLMakie (–> using statement in the first cell). That version worked without problems. After changing CairoMakie to GLMakie the segmentation fault occurred. But it remained even after changing back to CairoMakie.

Further observations:

  • The notebook runs without problems using the REPL.
  • The notebook crashes when running within the REPL using VSCode (the REPL-window disappears so fast that I cannot see the error message).

It seems to me that the whole issue is related to https://github.com/JuliaLang/julia/issues/41440.

Versioninfo:

Julia Version 1.7.0 Commit 3bf9d17731 (2021-11-30 12:12 UTC) Platform Info: OS: macOS (arm64-apple-darwin21.1.0) CPU: Apple M1 Pro WORD_SIZE: 64 LIBM: libopenlibm LLVM: libLLVM-12.0.1 (ORCJIT, cyclone)

Complete error message: 
    From worker 3:	signal (11): Segmentation fault: 11
      From worker 3:	in expression starting at none:1
      From worker 3:	ntuple at ./ntuple.jl:0 [inlined]
      From worker 3:	argument_names at 

/Users/roland/.julia/packages/MakieCore/S8PkO/src/recipes.jl:49
      From worker 3:	getindex at /Users/roland/.julia/packages/MakieCore/S8PkO/src/attributes.jl:189
      From worker 3:	getproperty at /Users/roland/.julia/packages/MakieCore/S8PkO/src/attributes.jl:83 [inlined]
      From worker 3:	plot! at /Users/roland/.julia/packages/Makie/gQOQF/src/basic_recipes/poly.jl:116
      From worker 3:	plot! at /Users/roland/.julia/packages/Makie/gQOQF/src/interfaces.jl:428
      From worker 3:	unknown function (ip: 0x10c161713)
      From worker 3:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	#plot!#159 at /Users/roland/.julia/packages/Makie/gQOQF/src/interfaces.jl:339
      From worker 3:	unknown function (ip: 0x10c15cd3b)
      From worker 3:	plot! at /Users/roland/.julia/packages/Makie/gQOQF/src/interfaces.jl:308
      From worker 3:	unknown function (ip: 0x10c15c54f)
      From worker 3:	#plot!#331 at /Users/roland/.julia/packages/Makie/gQOQF/src/makielayout/layoutables/axis.jl:658
      From worker 3:	plot! at /Users/roland/.julia/packages/Makie/gQOQF/src/makielayout/layoutables/axis.jl:653 [inlined]
      From worker 3:	#plot!#332 at /Users/roland/.julia/packages/Makie/gQOQF/src/makielayout/layoutables/axis.jl:670 [inlined]
      From worker 3:	plot!##kw at /Users/roland/.julia/packages/Makie/gQOQF/src/makielayout/layoutables/axis.jl:669
      From worker 3:	unknown function (ip: 0x10c15890f)
      From worker 3:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	do_apply at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	plot! at /Users/roland/.julia/packages/AlgebraOfGraphics/uTcZk/src/entries.jl:117
      From worker 3:	foreach at ./abstractarray.jl:2694
      From worker 3:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	#plot!#112 at /Users/roland/.julia/packages/AlgebraOfGraphics/uTcZk/src/algebra/layers.jl:151
      From worker 3:	plot!##kw at /Users/roland/.julia/packages/AlgebraOfGraphics/uTcZk/src/algebra/layers.jl:150 [inlined]
      From worker 3:	#plot#113 at /Users/roland/.julia/packages/AlgebraOfGraphics/uTcZk/src/algebra/layers.jl:158
      From worker 3:	plot##kw at /Users/roland/.julia/packages/AlgebraOfGraphics/uTcZk/src/algebra/layers.jl:157 [inlined]
      From worker 3:	#draw#114 at /Users/roland/.julia/packages/AlgebraOfGraphics/uTcZk/src/algebra/layers.jl:174
      From worker 3:	draw##kw at /Users/roland/.julia/packages/AlgebraOfGraphics/uTcZk/src/algebra/layers.jl:174
      From worker 3:	unknown function (ip: 0x10bfa8837)
      From worker 3:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	##function_wrapped_cell#289 at /Users/roland/OneDrive - adviion GmbH/__Projekte/Julia/PlutoNB/CompThinkFa20/02-worldmap-AoG.jl#==#daa9d82d-9847-40ae-b9c9-c787afbcfcd8:1 [inlined]
      From worker 3:	##function_wrapped_cell#289 at ./none:0
      From worker 3:	unknown function (ip: 0x10bf843df)
      From worker 3:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	jl_f__call_latest at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	do_apply at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	#invokelatest#2 at ./essentials.jl:716
      From worker 3:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	do_apply at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	invokelatest at ./essentials.jl:714
      From worker 3:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	do_apply at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	compute at /Users/roland/.julia/packages/Pluto/auhyB/src/runner/PlutoRunner.jl:380
      From worker 3:	#27 at /Users/roland/.julia/packages/Pluto/auhyB/src/runner/PlutoRunner.jl:535
      From worker 3:	run_inside_trycatch at /Users/roland/.julia/packages/Pluto/auhyB/src/runner/PlutoRunner.jl:420
      From worker 3:	#run_expression#25 at /Users/roland/.julia/packages/Pluto/auhyB/src/runner/PlutoRunner.jl:535
      From worker 3:	run_expression##kw at /Users/roland/.julia/packages/Pluto/auhyB/src/runner/PlutoRunner.jl:450
      From worker 3:	unknown function (ip: 0x10bf32a57)
      From worker 3:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	do_call at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	eval_body at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	jl_interpret_toplevel_thunk at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	jl_toplevel_eval_flex at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	jl_toplevel_eval_in at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	eval at ./boot.jl:373
      From worker 3:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	do_apply at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	#103 at /Users/administrator/src/julia/usr/share/julia/stdlib/v1.7/Distributed/src/process_messages.jl:274
      From worker 3:	run_work_thunk at /Users/administrator/src/julia/usr/share/julia/stdlib/v1.7/Distributed/src/process_messages.jl:63
      From worker 3:	unknown function (ip: 0x10beb88ab)
      From worker 3:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	run_work_thunk at /Users/administrator/src/julia/usr/share/julia/stdlib/v1.7/Distributed/src/process_messages.jl:72
      From worker 3:	#96 at ./task.jl:423
      From worker 3:	unknown function (ip: 0x10beb828f)
      From worker 3:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	start_task at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)
      From worker 3:	Allocations: 205624910 (Pool: 205580436; Big: 44474); GC: 119
Worker 3 terminated.
Unhandled Task ERROR: IOError: read: connection reset by peer (ECONNRESET)
Stacktrace:
  [1] wait_readnb(x::Sockets.TCPSocket, nb::Int64)
    @ Base ./stream.jl:408
  [2] (::Base.var"#wait_locked#645")(s::Sockets.TCPSocket, buf::IOBuffer, nb::Int64)
    @ Base ./stream.jl:894
  [3] unsafe_read(s::Sockets.TCPSocket, p::Ptr{UInt8}, nb::UInt64)
    @ Base ./stream.jl:900
  [4] unsafe_read
    @ ./io.jl:724 [inlined]
  [5] unsafe_read(s::Sockets.TCPSocket, p::Base.RefValue{NTuple{4, Int64}}, n::Int64)
    @ Base ./io.jl:723
  [6] read!
    @ ./io.jl:725 [inlined]
  [7] deserialize_hdr_raw
    @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Distributed/src/messages.jl:167 [inlined]
  [8] message_handler_loop(r_stream::Sockets.TCPSocket, w_stream::Sockets.TCPSocket, incoming::Bool)
    @ Distributed /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Distributed/src/process_messages.jl:165
  [9] process_tcp_streams(r_stream::Sockets.TCPSocket, w_stream::Sockets.TCPSocket, incoming::Bool)
    @ Distributed /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Distributed/src/process_messages.jl:126
 [10] (::Distributed.var"#99#100"{Sockets.TCPSocket, Sockets.TCPSocket, Bool})()
    @ Distributed ./task.jl:423
+1
roland-KA on Dec 11, 2021
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