Open arnold-c opened 2 years ago
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
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-1.7in 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 diedMy 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-1.7in 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.
I'm afraid that I keep getting an issue with my Julia kernel dying while trying to
previeworrendera.qmdfile to html. At some point through the process it'll returnERROR 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 errorThe notebook runs OK interactively, and so does the intermediate
.ipynbnotebook. I'm afraid it's unlikely to be a particularly reproducible error, as the.qmdnotebook 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.`] 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 [459566f4] DiffEqCallbacks v2.23.0 [c894b116] DiffEqJump v8.5.0 [77a26b50] DiffEqNoiseProcess v5.11.1 [163ba53b] DiffResults v1.0.3 [b552c78f] DiffRules v1.11.0 [0c46a032] DifferentialEquations v7.1.0 [b4f34e82] Distances v0.10.7 [31c24e10] Distributions v0.25.62 [ffbed154] DocStringExtensions v0.8.6 [5b8099bc] DomainSets v0.5.10 [fa6b7ba4] DualNumbers v0.6.8 [7c1d4256] DynamicPolynomials v0.4.5 [d4d017d3] ExponentialUtilities v1.17.1 [e2ba6199] ExprTools v0.1.8 [c87230d0] FFMPEG v0.4.1 [7a1cc6ca] FFTW v1.4.6 [7034ab61] FastBroadcast v0.1.17 [9aa1b823] FastClosures v0.3.2 [1a297f60] FillArrays v0.13.2 [6a86dc24] FiniteDiff v2.12.1 [53c48c17] FixedPointNumbers v0.8.4 [59287772] Formatting v0.4.2 [f6369f11] ForwardDiff v0.10.30 [069b7b12] FunctionWrappers v1.1.2 [0c68f7d7] GPUArrays v8.3.2 [28b8d3ca] GR v0.64.4 [c91e804a] Gadfly v1.3.4 [c145ed77] GenericSchur v0.5.3 [5c1252a2] GeometryBasics v0.4.2 [86223c79] Graphs v1.7.0 [42e2da0e] Grisu v1.0.2 [0b43b601] Groebner v0.2.7 [d5909c97] GroupsCore 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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 v1.3.4+4 [d091e8ba] Xorg_libXfixes_jll v5.0.3+4 [a51aa0fd] Xorg_libXi_jll v1.7.10+4 [d1454406] Xorg_libXinerama_jll v1.1.4+4 [ec84b674] Xorg_libXrandr_jll v1.5.2+4 [ea2f1a96] Xorg_libXrender_jll v0.9.10+4 [14d82f49] Xorg_libpthread_stubs_jll v0.1.0+3 [c7cfdc94] Xorg_libxcb_jll v1.13.0+3 [cc61e674] Xorg_libxkbfile_jll v1.1.0+4 [12413925] Xorg_xcb_util_image_jll v0.4.0+1 [2def613f] Xorg_xcb_util_jll v0.4.0+1 [975044d2] Xorg_xcb_util_keysyms_jll v0.4.0+1 [0d47668e] Xorg_xcb_util_renderutil_jll v0.3.9+1 [c22f9ab0] Xorg_xcb_util_wm_jll v0.4.1+1 [35661453] Xorg_xkbcomp_jll v1.4.2+4 [33bec58e] Xorg_xkeyboard_config_jll v2.27.0+4 [c5fb5394] Xorg_xtrans_jll v1.4.0+3 [3161d3a3] Zstd_jll v1.5.2+0 [0ac62f75] libass_jll v0.15.1+0 [f638f0a6] libfdk_aac_jll v2.0.2+0 [b53b4c65] libpng_jll v1.6.38+0 [f27f6e37] libvorbis_jll v1.3.7+1 [1270edf5] x264_jll v2021.5.5+0 [dfaa095f] x265_jll v3.5.0+0 [d8fb68d0] xkbcommon_jll v0.9.1+5 [0dad84c5] ArgTools [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [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 ```