quarto-dev / quarto-julia

Julia interface to quarto-cli
GNU General Public License v2.0
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Kernel Died #3

Open arnold-c opened 2 years ago

arnold-c commented 2 years ago

I'm afraid that I keep getting an issue with my Julia kernel dying while trying to preview or render a .qmd file to html. At some point through the process it'll return ERROR kernel died, and then will not be able to start again. I just upgraded Julia to the latest stable version (1.7.3), and am now getting the error

ERROR: 

Kernel died before replying to kernel_info

The notebook runs OK interactively, and so does the intermediate .ipynb notebook. I'm afraid it's unlikely to be a particularly reproducible error, as the .qmd notebook was rendering/previewing fine yesterday, and suddenly stopped working today with no new packages installed, or updates to VSCode. A complete restart of my computer didn't solve the issue.

julia> versioninfo()
Julia Version 1.7.3
Commit 742b9abb4d (2022-05-06 12:58 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin21.4.0)
  CPU: Apple M1
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-12.0.1 (ORCJIT, westmere)
Environment:
  JULIA_EDITOR = code
  JULIA_NUM_THREADS = 
`] st -m` ``` julia> ] st -m Status `~/Documents/Repos/project/Manifest.toml` [c3fe647b] AbstractAlgebra v0.26.0 [621f4979] AbstractFFTs v1.1.0 [1520ce14] AbstractTrees v0.3.4 [79e6a3ab] Adapt v3.3.3 [dce04be8] ArgCheck v2.3.0 [ec485272] ArnoldiMethod v0.2.0 [4fba245c] ArrayInterface v5.0.8 [30b0a656] ArrayInterfaceCore v0.1.10 [4c555306] ArrayLayouts v0.8.6 [69666777] Arrow v2.3.0 [31f734f8] ArrowTypes v1.2.1 [15f4f7f2] AutoHashEquals v0.2.0 [13072b0f] AxisAlgorithms v1.0.1 [aae01518] BandedMatrices v0.17.0 [198e06fe] BangBang v0.3.36 [9718e550] Baselet v0.1.1 [6e4b80f9] BenchmarkTools v1.3.1 [e2ed5e7c] Bijections v0.1.4 [c3b6d118] BitIntegers v0.2.6 [62783981] BitTwiddlingConvenienceFunctions v0.1.3 [764a87c0] BoundaryValueDiffEq v2.8.0 [fa961155] CEnum v0.4.2 [2a0fbf3d] CPUSummary v0.1.22 [00ebfdb7] CSTParser v3.3.3 [49dc2e85] Calculus v0.5.1 [324d7699] CategoricalArrays v0.10.6 [8be319e6] Chain v0.4.10 [d360d2e6] ChainRulesCore v1.15.0 [9e997f8a] ChangesOfVariables v0.1.3 [fb6a15b2] CloseOpenIntervals v0.1.8 [da1fd8a2] CodeTracking v1.0.9 [5ba52731] CodecLz4 v0.4.0 [6b39b394] CodecZstd v0.7.2 [a2cac450] ColorBrewer v0.4.0 [35d6a980] ColorSchemes v3.18.0 [3da002f7] ColorTypes v0.11.3 [c3611d14] ColorVectorSpace v0.9.9 [5ae59095] Colors v0.12.8 [861a8166] Combinatorics v1.0.2 [a80b9123] CommonMark v0.8.6 [38540f10] CommonSolve v0.2.1 [bbf7d656] CommonSubexpressions v0.3.0 [34da2185] Compat v3.45.0 [a81c6b42] Compose v0.9.3 [b152e2b5] CompositeTypes v0.1.2 [a33af91c] CompositionsBase v0.1.1 [187b0558] ConstructionBase v1.3.0 [d38c429a] Contour v0.5.7 [7ad07ef1] CoupledFields v0.2.0 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.1.1 [754358af] DEDataArrays v0.2.4 [9a962f9c] DataAPI v1.10.0 [a93c6f00] DataFrames v1.3.4 [1313f7d8] DataFramesMeta v0.11.0 [864edb3b] DataStructures v0.18.13 [e2d170a0] DataValueInterfaces v1.0.0 [244e2a9f] DefineSingletons v0.1.2 [bcd4f6db] DelayDiffEq v5.37.0 [b429d917] DensityInterface v0.4.0 [2b5f629d] DiffEqBase v6.84.0 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GroupsCore v0.4.0 [cd3eb016] HTTP v0.9.17 [a1b4810d] Hexagons v0.2.0 [3e5b6fbb] HostCPUFeatures v0.1.7 [34004b35] HypergeometricFunctions v0.3.10 [615f187c] IfElse v0.1.1 [9b13fd28] IndirectArrays v1.0.0 [d25df0c9] Inflate v0.1.2 [83e8ac13] IniFile v0.5.1 [22cec73e] InitialValues v0.3.1 [842dd82b] InlineStrings v1.1.2 [18e54dd8] IntegerMathUtils v0.1.0 [a98d9a8b] Interpolations v0.13.6 [8197267c] IntervalSets v0.6.2 [3587e190] InverseFunctions v0.1.7 [41ab1584] InvertedIndices v1.1.0 [92d709cd] IrrationalConstants v0.1.1 [c8e1da08] IterTools v1.4.0 [42fd0dbc] IterativeSolvers v0.9.2 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.4.1 [682c06a0] JSON v0.21.3 [98e50ef6] JuliaFormatter v1.0.2 [aa1ae85d] JuliaInterpreter v0.9.13 [e5e0dc1b] Juno v0.8.4 [ef3ab10e] KLU v0.3.0 [5ab0869b] KernelDensity v0.6.3 [ba0b0d4f] Krylov v0.8.1 [0b1a1467] KrylovKit v0.5.4 [929cbde3] LLVM v4.14.0 [b964fa9f] LaTeXStrings v1.3.0 [2ee39098] LabelledArrays v1.9.0 [23fbe1c1] Latexify 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SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.32 [0bca4576] SciMLBase v1.39.0 [6c6a2e73] Scratch v1.1.0 [91c51154] SentinelArrays v1.3.13 [efcf1570] Setfield v0.8.2 [992d4aef] Showoff v1.0.3 [699a6c99] SimpleTraits v0.9.4 [a2af1166] SortingAlgorithms v1.0.1 [47a9eef4] SparseDiffTools v1.21.0 [276daf66] SpecialFunctions v2.1.6 [171d559e] SplittablesBase v0.1.14 [aedffcd0] Static v0.6.6 [90137ffa] StaticArrays v1.4.7 [82ae8749] StatsAPI v1.4.0 [2913bbd2] StatsBase v0.33.16 [4c63d2b9] StatsFuns v1.0.1 [9672c7b4] SteadyStateDiffEq v1.8.0 [789caeaf] StochasticDiffEq v6.49.1 [7792a7ef] StrideArraysCore v0.3.9 [09ab397b] StructArrays v0.6.8 [c3572dad] Sundials v4.9.4 [d1185830] SymbolicUtils v0.19.9 [0c5d862f] Symbolics v4.6.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.7.0 [62fd8b95] TensorCore v0.1.1 [8ea1fca8] TermInterface v0.2.3 [8290d209] ThreadingUtilities v0.5.0 [ac1d9e8a] ThreadsX v0.1.10 [f269a46b] TimeZones v1.7.3 [a759f4b9] TimerOutputs v0.5.20 [0796e94c] Tokenize v0.5.24 [3bb67fe8] TranscodingStreams v0.9.6 [28d57a85] Transducers v0.4.73 [a2a6695c] TreeViews v0.3.0 [d5829a12] TriangularSolve v0.1.11 [5c2747f8] URIs v1.3.0 [3a884ed6] UnPack v1.0.2 [1cfade01] UnicodeFun v0.4.1 [1986cc42] Unitful v1.11.0 [41fe7b60] Unzip v0.1.2 [3d5dd08c] VectorizationBase v0.21.33 [19fa3120] VertexSafeGraphs v0.2.0 [efce3f68] WoodburyMatrices v0.5.5 [700de1a5] ZygoteRules v0.2.2 [6e34b625] Bzip2_jll v1.0.8+0 [83423d85] Cairo_jll v1.16.1+1 [5ae413db] EarCut_jll v2.2.3+0 [2e619515] Expat_jll v2.4.8+0 [b22a6f82] FFMPEG_jll v4.4.0+0 [f5851436] FFTW_jll v3.3.10+0 [a3f928ae] Fontconfig_jll v2.13.93+0 [d7e528f0] FreeType2_jll v2.10.4+0 [559328eb] FriBidi_jll v1.0.10+0 [0656b61e] GLFW_jll v3.3.6+0 [d2c73de3] GR_jll v0.64.4+0 [78b55507] Gettext_jll v0.21.0+0 [7746bdde] Glib_jll v2.68.3+2 [3b182d85] Graphite2_jll v1.3.14+0 [2e76f6c2] HarfBuzz_jll v2.8.1+1 [1d5cc7b8] IntelOpenMP_jll v2018.0.3+2 [aacddb02] JpegTurbo_jll v2.1.2+0 [c1c5ebd0] LAME_jll v3.100.1+0 [88015f11] LERC_jll v3.0.0+1 [dad2f222] LLVMExtra_jll v0.0.16+0 [dd4b983a] LZO_jll v2.10.1+0 [e9f186c6] Libffi_jll v3.2.2+1 [d4300ac3] Libgcrypt_jll v1.8.7+0 [7e76a0d4] Libglvnd_jll v1.3.0+3 [7add5ba3] Libgpg_error_jll v1.42.0+0 [94ce4f54] Libiconv_jll v1.16.1+1 [4b2f31a3] Libmount_jll v2.35.0+0 [89763e89] Libtiff_jll v4.4.0+0 [38a345b3] Libuuid_jll v2.36.0+0 [5ced341a] Lz4_jll v1.9.3+0 [856f044c] MKL_jll v2022.0.0+0 [e7412a2a] Ogg_jll v1.3.5+1 [458c3c95] OpenSSL_jll v1.1.14+0 [efe28fd5] OpenSpecFun_jll v0.5.5+0 [91d4177d] Opus_jll v1.3.2+0 [2f80f16e] PCRE_jll v8.44.0+0 [30392449] Pixman_jll v0.40.1+0 [ea2cea3b] Qt5Base_jll v5.15.3+1 [f50d1b31] Rmath_jll v0.3.0+0 [fb77eaff] Sundials_jll v5.2.1+0 [a2964d1f] Wayland_jll v1.19.0+0 [2381bf8a] Wayland_protocols_jll v1.25.0+0 [02c8fc9c] XML2_jll v2.9.14+0 [aed1982a] XSLT_jll v1.1.34+0 [4f6342f7] Xorg_libX11_jll v1.6.9+4 [0c0b7dd1] Xorg_libXau_jll v1.0.9+4 [935fb764] Xorg_libXcursor_jll v1.2.0+4 [a3789734] Xorg_libXdmcp_jll v1.1.3+4 [1082639a] Xorg_libXext_jll 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[8bb1440f] DelimitedFiles [8ba89e20] Distributed [f43a241f] Downloads [7b1f6079] FileWatching [9fa8497b] Future [b77e0a4c] InteractiveUtils [4af54fe1] LazyArtifacts [b27032c2] LibCURL [76f85450] LibGit2 [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [a63ad114] Mmap [ca575930] NetworkOptions [44cfe95a] Pkg [de0858da] Printf [9abbd945] Profile [3fa0cd96] REPL [9a3f8284] Random [ea8e919c] SHA [9e88b42a] Serialization [1a1011a3] SharedArrays [6462fe0b] Sockets [2f01184e] SparseArrays [10745b16] Statistics [4607b0f0] SuiteSparse [fa267f1f] TOML [a4e569a6] Tar [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll [deac9b47] LibCURL_jll [29816b5a] LibSSH2_jll [c8ffd9c3] MbedTLS_jll [14a3606d] MozillaCACerts_jll [4536629a] OpenBLAS_jll [05823500] OpenLibm_jll [bea87d4a] SuiteSparse_jll [83775a58] Zlib_jll [8e850b90] libblastrampoline_jll [8e850ede] nghttp2_jll [3f19e933] p7zip_jll ```
arnold-c commented 2 years ago

As a follow up - uninstalling and re-installing ] add IJulia seemed to get it running again. I'm going to close this for now, but as the original error happened sporadically a number of times before I don't think this is a long-term fix, so will re-open if it happens again

korsbo commented 2 years ago

I hit this one too. Removing and re-adding IJulia did not fix the problem but

using IJulia
installkernel("julia_test")

and then specifying

jupyter: julia_test-1.7

in the quarto yaml header made it work again. Just posting in case someone else googles their way here just like I did.

slwu89 commented 1 year ago

I have the same problem. After setting quarto to give verbose error messages I get:

Starting julia-1.8 kernel...Done

signal (6): Aborted
in expression starting at In[1]:32
unknown function (ip: 0x7fd67a091184)
raise at /usr/lib/x86_64-linux-gnu/libc.so.6 (unknown line)
abort at /usr/lib/x86_64-linux-gnu/libc.so.6 (unknown line)
jl_reinit_item at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/dump.c:2834
jl_finalize_deserializer at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/dump.c:2854 [inlined]
_jl_restore_incremental at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/dump.c:3379
ijl_restore_incremental at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/dump.c:3436
_include_from_serialized at ./loading.jl:807
_require_search_from_serialized at ./loading.jl:1039
_require at ./loading.jl:1315
_require_prelocked at ./loading.jl:1200
macro expansion at ./loading.jl:1180 [inlined]
macro expansion at ./lock.jl:223 [inlined]
require at ./loading.jl:1144
unknown function (ip: 0x7fd674119de6)
_jl_invoke at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/gf.c:2377 [inlined]
ijl_apply_generic at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/gf.c:2559
jl_apply at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/julia.h:1843 [inlined]
call_require at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/toplevel.c:462 [inlined]
eval_import_path at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/toplevel.c:499
jl_toplevel_eval_flex at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/toplevel.c:778
eval_body at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/interpreter.c:560
eval_body at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/interpreter.c:522
jl_interpret_toplevel_thunk at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/interpreter.c:750
jl_toplevel_eval_flex at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/toplevel.c:906
jl_toplevel_eval_flex at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/toplevel.c:850
ijl_toplevel_eval_in at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/toplevel.c:965
eval at ./boot.jl:368 [inlined]
include_string at ./loading.jl:1428
softscope_include_string at /home/slwu89/.julia/packages/SoftGlobalScope/u4UzH/src/SoftGlobalScope.jl:65
_jl_invoke at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/gf.c:2377 [inlined]
ijl_apply_generic at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/gf.c:2559
execute_request at /home/slwu89/.julia/packages/IJulia/6TIq1/src/execute_request.jl:67
unknown function (ip: 0x7fd67414e296)
_jl_invoke at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/gf.c:2377 [inlined]
ijl_apply_generic at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/gf.c:2559
jl_apply at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/julia.h:1843 [inlined]
jl_f__call_latest at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/builtins.c:774
#invokelatest#2 at ./essentials.jl:729 [inlined]
invokelatest at ./essentials.jl:726 [inlined]
eventloop at /home/slwu89/.julia/packages/IJulia/6TIq1/src/eventloop.jl:8
#15 at ./task.jl:484
unknown function (ip: 0x7fd67413f0ff)
_jl_invoke at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/gf.c:2377 [inlined]
ijl_apply_generic at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/gf.c:2559
jl_apply at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/julia.h:1843 [inlined]
start_task at /cache/build/default-aws-shared0-3/julialang/julia-release-1-dot-8/src/task.c:931
Allocations: 16101868 (Pool: 16091194; Big: 10674); GC: 19
2022-12-29 15:39:19,267 - traitlets - ERROR - Kernel died while waiting for execute reply.

Kernel died

My version info is as below, and I installed Quarto, followed by IJulia as instructed on the official docs.

Julia Version 1.8.4
Commit 00177ebc4fc (2022-12-23 21:32 UTC)
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 32 × AMD Ryzen 9 5950X 16-Core Processor
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, znver3)
  Threads: 1 on 32 virtual cores
pdeffebach commented 1 year ago

I hit this one too. Removing and re-adding IJulia did not fix the problem but

using IJulia
installkernel("julia_test")

and then specifying

jupyter: julia_test-1.7

in the quarto yaml header made it work again. Just posting in case someone else googles their way here just like I did.

Neither this nor simply installing and uninstalling work for me. This is with and without modifying the kernel json file to use a project with IJulia.

henry2004y commented 1 year ago

Neither this nor simply installing and uninstalling work for me. This is with and without modifying the kernel json file to use a project with

Same here. However, I had this issue on Linux but not on Windows, as reported on Discourse

pdeffebach commented 1 year ago

@jjallaire Can we re-open this issue? There seem to still be problems with quarto on linux.

arnold-c commented 1 year ago

I'll reopen this as it seems like more people are running into the same issue with Linux. For what it's worth, I haven't had this issue since on Mac M1.

pdeffebach commented 1 year ago

For reference, here is my output with --execute-debug

quarto render test.qmd --to html --execute-debug
- Connecting to kernel

Starting julia_test-1.8 kernel...2023-01-10 11:15:00,637 - root - Level 25 - starting notebook server subprocess
2023-01-10 11:15:00,637 - root - Level 25 - starting notebook server subprocess
2023-01-10 11:15:00,829 - root - Level 25 - running notebook server subprocess
2023-01-10 11:15:00,829 - root - Level 25 - creating notebook server (tcp: /run/user/1000/jt/fdf7fc6f505f54b50223)
2023-01-10 11:15:00,829 - root - Level 25 - notebook server bound to port 37305
- Kernel connection successful
2023-01-10 11:15:00,979 - root - Level 25 - handling server request
- Sending execute command to kernel
- Execute command sent, reading response
2023-01-10 11:15:00,981 - root - Level 25 - executing notebook
2023-01-10 11:15:02,252 - traitlets - ERROR - Error occurred while starting new kernel client for kernel fe6518c3-811a-4cda-8b3f-4e569d9c4ea7: Kernel died before replying to kernel_info
- Error response received
ERROR: 

Kernel died before replying to kernel_info
gdkrmr commented 1 year ago

On Manjaro Linux I can only use julia-1.7 as a kernel, julia-1.8 and julia-1.9 fail with the same error as above.

gustavdelius commented 1 year ago

Uninstalling and reinstalling Quarto worked for me today.