Pluto intermittently needs to be restarted on Julia-1.7-RC3 (arm version, MacOS Monterey 16" M1) when attempting to plot. #1686

goedman · 2021-11-25T15:00:35Z

goedman
Nov 25, 2021

Hi,

First question is if there are other users working with above configuration.

If so, I've seen many issues over the last 2 weeks and have been trying to create a MWE to show the issues. Below one case.
Unfortunately it is not a "minimum" MWE. The file pluto_test.jl.txt needs to be renamed to pluto_test.jl.

Both files need to be in a single directory and it uses (in addition to Pluto.jl):

using Pkg

begin
    using CSV, DelimitedFiles, Unicode
    using DataFrames
    using Statistics
    using StatsPlots
   using Plots.PlotMeasures
end

As I state in the notebook:

This MWE works in the Julia-1.7-RC3 REPL. In Pluto it requires:

`import Pluto; Pluto.run(workspace_use_distributed=false)`"

At least for this MWE. I have also seen cases where disabling distribution does not suffice and simply hangs, e.g. in CSV.read but these have been harder to pin down in a MWE. All cases work fine in the REPL.

With distribution enabled the notebook hangs and wants to be restarted (mostly, I've also seen Julia terminated and task errors).

Some of these issues I've also seen on my Intel MacBook. I'll dig into that more today.

pluto_test.jl.txt
electric.csv

Answered by goedman

Feb 1, 2022

This week, after building Julia 1.8-DEV from sources I have not seen this issue anymore, neither with Plots/GR nor Make/GLMakie.
I consider the discussion as closed and answered now.

View full answer

goedman · 2021-11-25T19:48:47Z

goedman
Nov 25, 2021
Author

Digging into what was going on using an Intel based machine I noticed my export JULIA_NUM_THREADS=-1 was incorrect. It doesn't by default take all available cores. Changing it to export JULIA_NUM_THREADS=8 fixed it.

So I went back to the M1 machine and noticed there I had used export JULIA_NUM_THREADS=8 and I decided to go back to export JULIA_NUM_THREADS=5 which seems way more stable and the RESTART option often works. Not rock solid, but at least an ok workaround. I'll also set export JULIA_NUM_THREADS=4.

The problem always seems to be related to working with Plots/StatsPlots.

0 replies

goedman · 2021-11-25T20:09:31Z

goedman
Nov 25, 2021
Author

Just for completeness, I will try Make/AlgebraOfGraphics/CairoMakie as well, the problem always shows up as:

Press Ctrl+C in this terminal to stop Pluto

┌ Warning: FYI, running unbundled (dev) frontend
└ @ Pluto ~/.julia/packages/Pluto/7TMtD/src/webserver/WebServer.jl:264
    Updating registry at `~/.julia/registries/General.toml`
      From worker 3:	
      From worker 3:	signal (11): Segmentation fault: 11
      From worker 3:	in expression starting at none:1
      From worker 3:	^ at ./math.jl:0 [inlined]
      From worker 3:	bounding_order_of_magnitude at /Users/rob/.julia/packages/PlotUtils/VgXdq/src/ticks.jl:14
      From worker 3:	unknown function (ip: 0x10c6fb6f7)
      From worker 3:	jl_apply_generic at /Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libjulia-internal.1.7.dylib (unknown line)

... <snipped>

Further lowering the number of Julia threads doesn't help a lot (but going from 5 to 4 is a small step).

0 replies

fonsp · 2021-11-27T14:31:34Z

fonsp
Nov 27, 2021
Maintainer

Hi! Thanks for the report. Just to make it easier to understand, could you edit your original message to make it really clear what the problem is. You say "Issues", but we don't know what they are.

This also makes it easier for other users to find this discussion and contribute.

0 replies

goedman · 2021-11-27T22:27:47Z

goedman
Nov 27, 2021
Author

Hi Fons, bedankt voor je reactie!

Here some more details what I meant by "With distribution enabled the notebook hangs". At the bottom a screenshot showing how the notebook looks after "hanging".

Since I set JULIA_NUM_THREADS=4 restart mostly works.

In the terminal, after a fresh Julia-1.7-RC3 restart, updating my project (ROS, just so the packages are available), I start Pluto and select pluto_test.jl. The notebook hangs in the plot cell at the end as shown in the screenshot.

Please let me know if this is not sufficient.
Thanks for your help,
Rob

Terminal output:


(ROS) pkg> up
    Updating registry at `~/.julia/registries/General.toml`
  No Changes to `~/.julia/dev/ROS/Project.toml`
  No Changes to `~/.julia/dev/ROS/Manifest.toml`

julia> cd("notebooks");import Pluto; Pluto.run()

Opening http://localhost:1234/?secret=bkrNCdgC in your default browser... ~ have fun!

Press Ctrl+C in this terminal to stop Pluto

┌ Warning: FYI, running unbundled (dev) frontend
└ @ Pluto ~/.julia/packages/Pluto/7TMtD/src/webserver/WebServer.jl:264
    Updating registry at `~/.julia/registries/General.toml`





      From worker 3:	
      From worker 3:	signal (11): Segmentation fault: 11
      From worker 3:	in expression starting at none:1
      From worker 3:	^ at ./math.jl:0 [inlined]
      From worker 3:	bounding_order_of_magnitude at /Users/rob/.julia/packages/PlotUtils/VgXdq/src/ticks.jl:14
      From worker 3:	unknown function (ip: 0x11231234f)
      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:	optimize_ticks_typed at /Users/rob/.julia/packages/PlotUtils/VgXdq/src/ticks.jl:161
      From worker 3:	#optimize_ticks#42 at /Users/rob/.julia/packages/PlotUtils/VgXdq/src/ticks.jl:139 [inlined]
      From worker 3:	optimize_ticks##kw at /Users/rob/.julia/packages/PlotUtils/VgXdq/src/ticks.jl:138
      From worker 3:	unknown function (ip: 0x11231211b)
      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:	optimal_ticks_and_labels at /Users/rob/.julia/packages/Plots/PomtQ/src/axes.jl:170
      From worker 3:	unknown function (ip: 0x11230da67)
      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:	get_ticks at /Users/rob/.julia/packages/Plots/PomtQ/src/axes.jl:320
      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:	#get_ticks#115 at /Users/rob/.julia/packages/Plots/PomtQ/src/axes.jl:241
      From worker 3:	get_ticks at /Users/rob/.julia/packages/Plots/PomtQ/src/axes.jl:224 [inlined]
      From worker 3:	_update_min_padding! at /Users/rob/.julia/packages/Plots/PomtQ/src/backends/gr.jl:888
      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:	iterate at ./generator.jl:47 [inlined]
      From worker 3:	_collect at ./array.jl:744
      From worker 3:	collect_similar at ./array.jl:653 [inlined]
      From worker 3:	map at ./abstractarray.jl:2849 [inlined]
      From worker 3:	_update_min_padding! at /Users/rob/.julia/packages/Plots/PomtQ/src/layouts.jl:287
      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:	prepare_output at /Users/rob/.julia/packages/Plots/PomtQ/src/plot.jl:224
      From worker 3:	show at /Users/rob/.julia/packages/Plots/PomtQ/src/output.jl:212
      From worker 3:	unknown function (ip: 0x1122f5953)
      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:	show_richest at /Users/rob/.julia/packages/Pluto/7TMtD/src/runner/PlutoRunner.jl:1001
      From worker 3:	unknown function (ip: 0x11221b2bf)
      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:	#sprint_withreturned#54 at /Users/rob/.julia/packages/Pluto/7TMtD/src/runner/PlutoRunner.jl:947
      From worker 3:	sprint_withreturned##kw at /Users/rob/.julia/packages/Pluto/7TMtD/src/runner/PlutoRunner.jl:946
      From worker 3:	unknown function (ip: 0x1122f2ed3)
      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:	format_output_default at /Users/rob/.julia/packages/Pluto/7TMtD/src/runner/PlutoRunner.jl:842
      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:	#format_output#42 at /Users/rob/.julia/packages/Pluto/7TMtD/src/runner/PlutoRunner.jl:859
      From worker 3:	format_output##kw at /Users/rob/.julia/packages/Pluto/7TMtD/src/runner/PlutoRunner.jl:859
      From worker 3:	unknown function (ip: 0x1122189ff)
      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:	formatted_result_of at /Users/rob/.julia/packages/Pluto/7TMtD/src/runner/PlutoRunner.jl:774
      From worker 3:	unknown function (ip: 0x11209af6b)
      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:	#106 at /Users/administrator/src/julia/usr/share/julia/stdlib/v1.7/Distributed/src/process_messages.jl:278
      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:	macro expansion at /Users/administrator/src/julia/usr/share/julia/stdlib/v1.7/Distributed/src/process_messages.jl:278 [inlined]
      From worker 3:	#105 at ./task.jl:423
      From worker 3:	unknown function (ip: 0x1120eecbf)
      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: 152318568 (Pool: 152267074; Big: 51494); GC: 91
Worker 3 terminated.
Unhandled Task ERROR: EOFError: read end of file
Stacktrace:
 [1] (::Base.var"#wait_locked#645")(s::Sockets.TCPSocket, buf::IOBuffer, nb::Int64)
   @ Base ./stream.jl:892
 [2] unsafe_read(s::Sockets.TCPSocket, p::Ptr{UInt8}, nb::UInt64)
   @ Base ./stream.jl:900
 [3] unsafe_read
   @ ./io.jl:724 [inlined]
 [4] unsafe_read(s::Sockets.TCPSocket, p::Base.RefValue{NTuple{4, Int64}}, n::Int64)
   @ Base ./io.jl:723
 [5] read!
   @ ./io.jl:725 [inlined]
 [6] deserialize_hdr_raw
   @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Distributed/src/messages.jl:167 [inlined]
 [7] 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
 [8] 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
 [9] (::Distributed.var"#99#100"{Sockets.TCPSocket, Sockets.TCPSocket, Bool})()
   @ Distributed ./task.jl:423

Screen Shot 2021-11-27 at 15.12.12.pdf

0 replies

goedman · 2021-11-27T23:17:12Z

goedman
Nov 27, 2021
Author

My versions and loaded packages are:

julia> versioninfo()
Julia Version 1.7.0-rc3
Commit 3348de4ea6 (2021-11-15 08:22 UTC)
Platform Info:
  OS: macOS (arm64-apple-darwin21.1.0)
  CPU: Apple M1 Max
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-12.0.1 (ORCJIT, cyclone)
Environment:
  JULIA_NUM_THREADS = 4
  JULIA_EDITOR = subl
  JULIA_CMDSTAN_HOME = /Users/rob/Projects/StanSupport/cmdstan
  JULIA_SVG_BROWSER = Google Chrome.app
  JULIA_SPECIALFUNCTIONS_BUILD_SOURCE = true
  JULIA_MPI_PATH = /usr/local/Cellar/open-mpi/4.0.2
  JULIA_PKG3_PRECOMPILE = true
  JULIA_PKG_SERVER = pkg.julialang.org
  JULIA_SR_HOME = /Users/rob/.julia/dev/StatisticalRethinking/src
  JULIA_ROS_HOME = /Users/rob/Projects/R/ROS-Examples

(ROS) pkg> st
      Status `~/.julia/dev/ROS/Project.toml`
  [336ed68f] CSV v0.9.11
  [a93c6f00] DataFrames v1.2.2
  [31c24e10] Distributions v0.25.33
  [634d3b9d] DrWatson v2.7.5
  [38e38edf] GLM v1.5.1
  [91a5bcdd] Plots v1.24.2
  [c1514b29] StanSample v5.1.0
  [f3b207a7] StatsPlots v0.14.29
  [ade2ca70] Dates
  [8bb1440f] DelimitedFiles
  [10745b16] Statistics
  [4ec0a83e] Unicode

The ROS project is part of StanJulia.

0 replies

goedman · 2021-12-01T16:51:35Z

goedman
Dec 1, 2021
Author

I've seen 2 updates tp Plots and StatsPlots and haven't seen this issue since.

I'll leave this open for one more week and then mark this as an answer.

0 replies

goedman · 2021-12-04T14:33:45Z

goedman
Dec 4, 2021
Author

I wonder if this is related/similar as JuliaLang/julia#43285 (comment)

My experiences with native (arm) Julia--1.7 on Apple silicon and Pluto have been pretty good since above updates.

0 replies

goedman · 2022-02-01T14:58:20Z

goedman
Feb 1, 2022
Author

This week, after building Julia 1.8-DEV from sources I have not seen this issue anymore, neither with Plots/GR nor Make/GLMakie.
I consider the discussion as closed and answered now.

0 replies

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Pluto intermittently needs to be restarted on Julia-1.7-RC3 (arm version, MacOS Monterey 16" M1) when attempting to plot. #1686

goedman Nov 25, 2021

Replies: 8 comments

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