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GLMakie segmentation fault #4373

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chriswaudby opened this issue Sep 17, 2024 · 13 comments
Open
3 tasks done

GLMakie segmentation fault #4373

chriswaudby opened this issue Sep 17, 2024 · 13 comments
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bug GLMakie This relates to GLMakie.jl, the OpenGL backend for Makie. Integration with other packages needs more info

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@chriswaudby
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  • what version of Makie are you running? GLMakie v0.10.11; Julia 1.10.5.
  • can you reproduce the bug with a fresh environment ? yes
  • What platform + GPU are you on? MacBook Air (13-inch, M3, 2024)

I'm creating a data analysis package using GLMakie. I have a toggle switch to turn on data fitting. This normally works fine. However, if I resize the figure window before pressing the switch, I get a segmentation fault:

[67224] signal (11.2): Segmentation fault: 11
in expression starting at none:0
gleRunVertexSubmitImmediate at /System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine (unknown line)
Allocations: 52378689 (Pool: 52327128; Big: 51561); GC: 57
[1]    67224 segmentation fault  Julia

No other error messages are displayed. I'm unsure how to even begin to debug this - any advice would be welcome.
@EdsterG
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EdsterG commented Sep 18, 2024

Would you please post a MWE?

@jebej
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jebej commented Sep 26, 2024

I have also been getting segfaults when interacting/zooming with figures with GLMakie on my M1 MacBook pro. This doesn't happen on Windows. Not much of a MWE, just plot something (maybe it happens more regularly with heatmaps?), interact a bunch with it, and it ends up crashing.

@chriswaudby
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I don't really have a MWE - it's an app I've been building up to view some datasets that are currently private. I'm working to get it towards a workable state along with example data but in the meantime if there's any advice on how to diagnose the problem I'm happy to take a look locally.

@ffreyer ffreyer added GLMakie This relates to GLMakie.jl, the OpenGL backend for Makie. Integration with other packages needs more info labels Sep 30, 2024
@chriswaudby
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Hi,

I've now released a version of the package - which is still giving problems with segmentation faults. The package is NMRAnalysis (v0.2.0). The interface needs some data to run, I've uploaded a small dataset here:

https://github.com/chriswaudby/NMRAnalysis-bug-data/blob/main/data.tgz

This contains a single directory, 21. The MWE is then (run from the directory containing the test data):

using NMRAnalysis
hetnoe2d(["21/pdata/231","21/pdata/232"],[false,true])

On my system (M3 MacBook), I occasionally get a segfault when the window opens, or upon my first interaction with it - clicking a button, pressing a key, or trying to resize the window. On my student's computer (M1 MacBook) there's a segfault 100% of the time immediately. On a linux cluster, I don't seem to have any issues.

My versioninfo:

Julia Version 1.11.3
Commit d63adeda50d (2025-01-21 19:42 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: macOS (arm64-apple-darwin24.0.0)
  CPU: 8 × Apple M3
  WORD_SIZE: 64
  LLVM: libLLVM-16.0.6 (ORCJIT, apple-m2)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

(@v1.11) pkg> st
Status `~/.julia/environments/v1.11/Project.toml`
  [13f3f980] CairoMakie v0.13.1
  [e9467ef8] GLMakie v0.11.2
  [2fda8390] LsqFit v0.15.0
  [eff96d63] Measurements v2.12.0
  [2774e3e8] NLsolve v4.5.1
  [e8f11e50] NMRAnalysis v0.2.0
  [e6af4f88] NMRScreen v0.0.4
  [c2839fe3] NMRTools v0.1.11
  [14b8a8f1] PkgTemplates v0.7.53
  [91a5bcdd] Plots v1.40.9
  [295af30f] Revise v3.7.2

@SimonDanisch
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Is it the same as: #4771 (comment) ?
Did this start happening at some point and was working fine before?

@chriswaudby
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chriswaudby commented Feb 12, 2025 via email

@SimonDanisch
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Hm, maybe it's related and just doesn't lead to a segfault as often on your system.
I think we found a fix for #4771, so maybe you can try that once it's online and see if that fixes it.

@ffreyer ffreyer mentioned this issue Feb 12, 2025
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@chriswaudby
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chriswaudby commented Feb 12, 2025 via email

@SimonDanisch
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PR is up: #4782

@chriswaudby
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I've just run Julia through lldb and attaching a backtrace below - maybe this is helpful?

* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x0)
    frame #0: 0x00000001e8be963c GLEngine`gleRunVertexSubmitImmediate + 3424
GLEngine`gleRunVertexSubmitImmediate:
->  0x1e8be963c <+3424>: ldr    s0, [x9]
    0x1e8be9640 <+3428>: str    s0, [sp, #0xc0]
    0x1e8be9644 <+3432>: b      0x1e8be964c    ; <+3440>
    0x1e8be9648 <+3436>: mov    w24, #0x0 ; =0 
Target 0: (julia) stopped.
(lldb) bt
* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x0)
  * frame #0: 0x00000001e8be963c GLEngine`gleRunVertexSubmitImmediate + 3424
    frame #1: 0x00000001e8b83a68 GLEngine`gleDrawArraysOrElements_ExecCore + 624
    frame #2: 0x00000001e8b7d894 GLEngine`glDrawElements_GL3Exec + 412
    frame #3: 0x0000000337214bd4 nfnZR_8pCiU.dylib`julia_render_59077 at functionloading.jl:73
    frame #4: 0x00000003373432b0 nfnZR_8pCiU.dylib`jfptr_render_59078 + 64
    frame #5: 0x0000000337263520 nfnZR_8pCiU.dylib`julia_StandardPostrender_63972 at GLRenderObject.jl:68
    frame #6: 0x0000000337391650 nfnZR_8pCiU.dylib`jfptr_StandardPostrender_63973 + 52
    frame #7: 0x00000003372fdaa0 nfnZR_8pCiU.dylib`julia_render_59046 at GLRender.jl:93
    frame #8: 0x00000003372fdd6c nfnZR_8pCiU.dylib`jfptr_render_59047 + 60
    frame #9: 0x0000000337234450 nfnZR_8pCiU.dylib`julia_render_59006 at GLRender.jl:71
    frame #10: 0x000000033723449c nfnZR_8pCiU.dylib`jfptr_render_59007 + 56
    frame #11: 0x0000000337196eec nfnZR_8pCiU.dylib`julia_render_59126 at rendering.jl:132
    frame #12: 0x000000033719976c nfnZR_8pCiU.dylib`julia_YY.render_frameYY.160_60662 at rendering.jl:78
    frame #13: 0x0000000337199ff0 nfnZR_8pCiU.dylib`julia_refreshwindowcb_60106 at rendering.jl:29
    frame #14: 0x000000033719a100 nfnZR_8pCiU.dylib`julia_YY.82_60113 at screen.jl:959
    frame #15: 0x00000003372c1f60 nfnZR_8pCiU.dylib`jfptr_YY.82_60114 + 64
    frame #16: 0x0000000351fe80b8
    frame #17: 0x0000000199ee0428 QuartzCore`CA::Layer::display_if_needed(CA::Transaction*) + 744
    frame #18: 0x000000019a0651a4 QuartzCore`CA::Context::commit_transaction(CA::Transaction*, double, double*) + 512
    frame #19: 0x0000000199ec2e4c QuartzCore`CA::Transaction::commit() + 648
    frame #20: 0x00000001956589d0 AppKit`__62+[CATransaction(NSCATransaction) NS_setFlushesWithDisplayLink]_block_invoke + 272
    frame #21: 0x0000000196018208 AppKit`___NSRunLoopObserverCreateWithHandler_block_invoke + 64
    frame #22: 0x0000000191cd187c CoreFoundation`__CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ + 36
    frame #23: 0x0000000191cd1768 CoreFoundation`__CFRunLoopDoObservers + 536
    frame #24: 0x0000000191cd0d94 CoreFoundation`__CFRunLoopRun + 776
    frame #25: 0x0000000191cd0434 CoreFoundation`CFRunLoopRunSpecific + 608
    frame #26: 0x000000019c47419c HIToolbox`RunCurrentEventLoopInMode + 292
    frame #27: 0x000000019c473e2c HIToolbox`ReceiveNextEventCommon + 220
    frame #28: 0x000000019c473d30 HIToolbox`_BlockUntilNextEventMatchingListInModeWithFilter + 76
    frame #29: 0x000000019552fd68 AppKit`_DPSNextEvent + 660
    frame #30: 0x0000000195d25808 AppKit`-[NSApplication(NSEventRouting) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 700
    frame #31: 0x000000019580cfdc AppKit`-[NSWindow(NSWindowResizing) _resizeWithEvent:] + 612
    frame #32: 0x000000019572c2e4 AppKit`-[NSTitledFrame attemptResizeWithEvent:] + 156
    frame #33: 0x000000019572c0fc AppKit`-[NSThemeFrame handleMouseDown:] + 196
    frame #34: 0x00000001957a2894 AppKit`-[NSThemeFrame mouseDown:] + 32
    frame #35: 0x00000001956d0dcc AppKit`-[NSWindow(NSEventRouting) _handleMouseDownEvent:isDelayedEvent:] + 3472
    frame #36: 0x000000019565c40c AppKit`-[NSWindow(NSEventRouting) _reallySendEvent:isDelayedEvent:] + 288
    frame #37: 0x000000019565c118 AppKit`-[NSWindow(NSEventRouting) sendEvent:] + 284
    frame #38: 0x0000000195d24828 AppKit`-[NSApplication(NSEventRouting) sendEvent:] + 1604
    frame #39: 0x0000000172bc0980 libglfw.3.4.dylib`_glfwPollEventsCocoa + 144
    frame #40: 0x000000033718474c nfnZR_8pCiU.dylib`julia_pollevents_59997 at glfw3.jl:702
    frame #41: 0x00000003372ac2b8 nfnZR_8pCiU.dylib`julia_on_demand_renderloop_60150 at screen.jl:1027
    frame #42: 0x000000033728a420 nfnZR_8pCiU.dylib`julia_renderloop_59760 at screen.jl:1055
    frame #43: 0x0000000337161898 nfnZR_8pCiU.dylib`jfptr_renderloop_59761 + 56
    frame #44: 0x000000033717e180 nfnZR_8pCiU.dylib`julia_YY.79_60101 at screen.jl:916
    frame #45: 0x00000003372a4aac nfnZR_8pCiU.dylib`jfptr_YY.79_60102 + 52
    frame #46: 0x0000000100a6e2ac libjulia-internal.1.11.3.dylib`start_task [inlined] jl_apply(args=0x0000000344cd3ba0, nargs=1) at julia.h:2157:12 [opt]
    frame #47: 0x0000000100a6e2a0 libjulia-internal.1.11.3.dylib`start_task at task.c:1202:19 [opt]

@SimonDanisch SimonDanisch mentioned this issue Feb 12, 2025
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@SimonDanisch
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Interesting that it happens in refreshwindowcb.. That gets triggert from the OS e.g. when the window gets focussed/uncovered.
It maybe, that the context is not active, or it gets called from e.g. a thread.
I'm not convinced this helps, but could you try this: #4785 ?
Also, you should set ENV["MODERNGL_DEBUGGING"] = "true", before loading any package.

@chriswaudby
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chriswaudby commented Feb 12, 2025 via email

@chriswaudby
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chriswaudby commented Feb 12, 2025 via email

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bug GLMakie This relates to GLMakie.jl, the OpenGL backend for Makie. Integration with other packages needs more info
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@SimonDanisch @EdsterG @ffreyer @jebej @chriswaudby