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Problems installing Oceananigans on a new server #4176

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francispoulin opened this issue Mar 6, 2025 · 9 comments
Open

Problems installing Oceananigans on a new server #4176

francispoulin opened this issue Mar 6, 2025 · 9 comments
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@francispoulin
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I had to delete my .julia folder on a server and then tried installing Oceananigans using Julia 1.10.0. It failed.

At this stage I have nothing else installed but it balks because of KernelAbstractions not found. This seems very strange to me. It could be that the server has a problem as I have not had this problem on any other computer.

Any suggestions what I could try doing to fix this?

    Updating `~/.julia/environments/v1.10/Project.toml`
ERROR: KeyError: key "KernelAbstractions" not found
Stacktrace:
  [1] getindex
    @ Base ./dict.jl:498 [inlined]
  [2] status_ext_info(pkg::Pkg.Types.PackageSpec, env::Pkg.Types.EnvCache)
    @ Pkg.Operations /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:2213
  [3] print_status(env::Pkg.Types.EnvCache, old_env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, header::Symbol, uuids::Vector{Base.UUID}, names::Vector{String}; manifest::Bool, diff::Bool, ignore_indent::Bool, outdated::Bool, extensions::Bool, io::Base.TTY, mode::Pkg.Types.PackageMode, hidden_upgrades_info::Bool, show_usagetips::Bool)
    @ Pkg.Operations /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:2298
  [4] print_status
    @ Pkg.Operations /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:2240 [inlined]
  [5] status(env::Pkg.Types.EnvCache, registries::Vector{Pkg.Registry.RegistryInstance}, pkgs::Vector{Pkg.Types.PackageSpec}; header::Symbol, mode::Pkg.Types.PackageMode, git_diff::Bool, env_diff::Pkg.Types.EnvCache, ignore_indent::Bool, io::Base.TTY, outdated::Bool, extensions::Bool, hidden_upgrades_info::Bool, show_usagetips::Bool)
    @ Pkg.Operations /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:2471
  [6] status (repeats 2 times)
    @ Pkg.Operations /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:2442 [inlined]
  [7] #show_update#167
    @ Pkg.Operations /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:2438 [inlined]
  [8] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Set{Base.UUID}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform)
    @ Pkg.Operations /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1397
  [9] add
    @ Pkg.Operations /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1376 [inlined]
 [10] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::@Kwargs{io::Base.TTY})
    @ Pkg.API /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/API.jl:278
 [11] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::@Kwargs{})
    @ Pkg.API /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/API.jl:159
 [12] add(pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.API /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/API.jl:148
 [13] do_cmd!(command::Pkg.REPLMode.Command, repl::REPL.LineEditREPL)
    @ Pkg.REPLMode /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/REPLMode/REPLMode.jl:412
 [14] do_cmd(repl::REPL.LineEditREPL, input::String; do_rethrow::Bool)
    @ Pkg.REPLMode /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/REPLMode/REPLMode.jl:390
 [15] do_cmd
    @ Pkg.REPLMode /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/REPLMode/REPLMode.jl:380 [inlined]
 [16] (::Pkg.REPLMode.var"#24#27"{REPL.LineEditREPL, REPL.LineEdit.Prompt})(s::REPL.LineEdit.MIState, buf::IOBuffer, ok::Bool)
    @ Pkg.REPLMode /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/Pkg/src/REPLMode/REPLMode.jl:557
 [17] #invokelatest#2
    @ Base ./essentials.jl:887 [inlined]
 [18] invokelatest
    @ Base ./essentials.jl:884 [inlined]
 [19] run_interface(terminal::REPL.Terminals.TextTerminal, m::REPL.LineEdit.ModalInterface, s::REPL.LineEdit.MIState)
    @ REPL.LineEdit /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/REPL/src/LineEdit.jl:2656
 [20] run_frontend(repl::REPL.LineEditREPL, backend::REPL.REPLBackendRef)
    @ REPL /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/REPL/src/REPL.jl:1312
 [21] (::REPL.var"#62#68"{REPL.LineEditREPL, REPL.REPLBackendRef})()
    @ REPL /cvmfs/soft.computecanada.ca/easybuild/software/2023/x86-64-v3/Compiler/gcccore/julia/1.10.0/share/julia/stdlib/v1.10/REPL/src/REPL.jl:386
@simone-silvestri
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Hmmm, I think this is a problem with previous versions of julia 1.10
If you try with julia 1.10.8 in theory there should be no issues

@francispoulin
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Thanks @simone-silvestri .

The server only has 1.10.0, 1.9.3 and 1.11.3 installed. I can install 1.10.8 or try 1.11.3. Do you think 1.11.3 should be stable?

@simone-silvestri
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1.11.3 does not have this problem, however Oceananigans is not tested on julia 1.11 so there might be some unstable behavior (see #3836)

@francispoulin
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Thanks. Maybe I'll install 1.10.8 then, since that avoids this problem and is more stable than 1.11.

@glwagner
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glwagner commented Mar 6, 2025

yes, install julia yourself

@glwagner
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glwagner commented Mar 6, 2025

remember to close this issuse if that resolves it!

@francispoulin
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I tried it with 10.8 and still got an error, but a different error.

    Updating `~/.julia/environments/v1.10/Project.toml`
  [9e8cae18] + Oceananigans v0.95.19
    Updating `~/.julia/environments/v1.10/Manifest.toml`
   [621f4979] + AbstractFFTs v1.5.0
   [79e6a3ab] + Adapt v4.2.0
   [a9b6321e] + Atomix v1.1.1
   [ab4f0b2a] + BFloat16s v0.5.0
   [fa961155] + CEnum v0.5.0
   [179af706] + CFTime v0.1.4
   [052768ef] + CUDA v5.6.1
   [1af6417a] + CUDA_Runtime_Discovery v0.3.5
   [3da002f7] + ColorTypes v0.12.0
   [5ae59095] + Colors v0.13.0
   [1fbeeb36] + CommonDataModel v0.3.7
   [34da2185] + Compat v4.16.0
   [a216cea6] + CompoundPeriods v0.5.4
   [187b0558] + ConstructionBase v1.5.8
   [a8cc5b0e] + Crayons v4.1.1
   [7445602f] + CubedSphere v0.3.1
   [9a962f9c] + DataAPI v1.16.0
   [a93c6f00] + DataFrames v1.7.0
   [864edb3b] + DataStructures v0.18.20
   [e2d170a0] + DataValueInterfaces v1.0.0
   [3c3547ce] + DiskArrays v0.4.11
   [b4f34e82] + Distances v0.10.12
   [ffbed154] + DocStringExtensions v0.9.3
   [e2ba6199] + ExprTools v0.1.10
   [7a1cc6ca] + FFTW v1.8.1
   [5789e2e9] + FileIO v1.17.0
   [53c48c17] + FixedPointNumbers v0.8.5
   [0c68f7d7] + GPUArrays v11.2.2
   [46192b85] + GPUArraysCore v0.2.0
   [61eb1bfa] + GPUCompiler v1.2.0
   [c27321d9] + Glob v1.3.1
   [076d061b] + HashArrayMappedTries v0.2.0
   [40713840] + IncompleteLU v0.2.1
   [842dd82b] + InlineStrings v1.4.3
   [41ab1584] + InvertedIndices v1.3.1
   [42fd0dbc] + IterativeSolvers v0.9.4
   [82899510] + IteratorInterfaceExtensions v1.0.0
   [033835bb] + JLD2 v0.5.11
   [692b3bcd] + JLLWrappers v1.7.0
   [63c18a36] + KernelAbstractions v0.9.34
   [929cbde3] + LLVM v9.2.0
   [8b046642] + LLVMLoopInfo v1.0.0
   [8ac3fa9e] + LRUCache v1.6.1
   [b964fa9f] + LaTeXStrings v1.4.0
   [da04e1cc] + MPI v0.20.22
   [3da0fdf6] + MPIPreferences v0.1.11
   [1914dd2f] + MacroTools v0.5.15
   [e1d29d7a] + Missings v1.2.0
   [78c3b35d] + Mocking v0.8.1
   [85f8d34a] + NCDatasets v0.14.6
 ⌅ [5da4648a] + NVTX v0.3.5
   [9e8cae18] + Oceananigans v0.95.19
   [6fe1bfb0] + OffsetArrays v1.15.0
   [bac558e1] + OrderedCollections v1.8.0
   [eebad327] + PkgVersion v0.3.3
   [2dfb63ee] + PooledArrays v1.4.3
   [aea7be01] + PrecompileTools v1.2.1
   [21216c6a] + Preferences v1.4.3
   [08abe8d2] + PrettyTables v2.4.0
   [94ee1d12] + Quaternions v0.7.6
   [74087812] + Random123 v1.7.0
   [e6cf234a] + RandomNumbers v1.6.0
   [c1ae055f] + RealDot v0.1.0
   [3cdcf5f2] + RecipesBase v1.3.4
   [189a3867] + Reexport v1.2.2
   [ae029012] + Requires v1.3.1
   [6038ab10] + Rotations v1.7.1
   [7e506255] + ScopedValues v1.3.0
   [6c6a2e73] + Scratch v1.2.1
   [d496a93d] + SeawaterPolynomials v0.3.5
   [91c51154] + SentinelArrays v1.4.8
   [a2af1166] + SortingAlgorithms v1.2.1
   [90137ffa] + StaticArrays v1.9.13
   [1e83bf80] + StaticArraysCore v1.4.3
   [82ae8749] + StatsAPI v1.7.0
   [892a3eda] + StringManipulation v0.4.1
   [09ab397b] + StructArrays v0.7.0
   [dc5dba14] + TZJData v1.4.0+2025a
   [3783bdb8] + TableTraits v1.0.1
   [bd369af6] + Tables v1.12.0
   [6aa5eb33] + TaylorSeries v0.18.3
   [f269a46b] + TimeZones v1.21.3
   [a759f4b9] + TimerOutputs v0.5.28
   [bdfc003b] + TimesDates v0.3.1
   [3bb67fe8] + TranscodingStreams v0.11.3
   [013be700] + UnsafeAtomics v0.3.0
   [0b7ba130] + Blosc_jll v1.21.6+2
   [6e34b625] + Bzip2_jll v1.0.9+0
 ⌅ [4ee394cb] + CUDA_Driver_jll v0.10.4+0
→⌅ [76a88914] + CUDA_Runtime_jll v0.15.5+0
   [f5851436] + FFTW_jll v3.3.10+3
 ⌅ [0234f1f7] + HDF5_jll v1.14.2+1
   [e33a78d0] + Hwloc_jll v2.12.0+0
   [1d5cc7b8] + IntelOpenMP_jll v2025.0.4+0
   [9c1d0b0a] + JuliaNVTXCallbacks_jll v0.2.1+0
   [dad2f222] + LLVMExtra_jll v0.0.35+0
   [1d63c593] + LLVMOpenMP_jll v18.1.7+0
   [94ce4f54] + Libiconv_jll v1.18.0+0
   [5ced341a] + Lz4_jll v1.10.1+0
   [856f044c] + MKL_jll v2025.0.1+1
   [7cb0a576] + MPICH_jll v4.3.0+1
   [f1f71cc9] + MPItrampoline_jll v5.5.3+0
   [9237b28f] + MicrosoftMPI_jll v10.1.4+3
   [e98f9f5b] + NVTX_jll v3.1.1+0
 ⌃ [7243133f] + NetCDF_jll v400.902.209+0
   [fe0851c0] + OpenMPI_jll v5.0.7+0
   [458c3c95] + OpenSSL_jll v3.0.16+0
   [02c8fc9c] + XML2_jll v2.13.6+1
   [ffd25f8a] + XZ_jll v5.6.4+1
   [3161d3a3] + Zstd_jll v1.5.7+1
   [1e29f10c] + demumble_jll v1.3.0+0
   [477f73a3] + libaec_jll v1.1.3+0
   [337d8026] + libzip_jll v1.11.3+0
   [1317d2d5] + oneTBB_jll v2022.0.0+0
   [0dad84c5] + ArgTools v1.1.1
   [56f22d72] + Artifacts
   [2a0f44e3] + Base64
   [ade2ca70] + Dates
   [8ba89e20] + Distributed
   [f43a241f] + Downloads v1.6.0
   [7b1f6079] + FileWatching
   [9fa8497b] + Future
   [b77e0a4c] + InteractiveUtils
   [4af54fe1] + LazyArtifacts
   [b27032c2] + LibCURL v0.6.4
   [76f85450] + LibGit2
   [37e2e46d] + LinearAlgebra
   [56ddb016] + Logging
   [d6f4376e] + Markdown
   [a63ad114] + Mmap
   [ca575930] + NetworkOptions v1.2.0
   [44cfe95a] + Pkg v1.10.0
   [de0858da] + Printf
   [3fa0cd96] + REPL
   [9a3f8284] + Random
   [ea8e919c] + SHA v0.7.0
   [9e88b42a] + Serialization
   [6462fe0b] + Sockets
   [2f01184e] + SparseArrays v1.10.0
   [10745b16] + Statistics v1.10.0
   [fa267f1f] + TOML v1.0.3
   [a4e569a6] + Tar v1.10.0
   [8dfed614] + Test
   [cf7118a7] + UUIDs
   [4ec0a83e] + Unicode
   [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0
   [deac9b47] + LibCURL_jll v8.4.0+0
   [e37daf67] + LibGit2_jll v1.6.4+0
   [29816b5a] + LibSSH2_jll v1.11.0+1
   [c8ffd9c3] + MbedTLS_jll v2.28.2+1
   [14a3606d] + MozillaCACerts_jll v2023.1.10
   [4536629a] + OpenBLAS_jll v0.3.23+4
   [bea87d4a] + SuiteSparse_jll v7.2.1+1
   [83775a58] + Zlib_jll v1.2.13+1
   [8e850b90] + libblastrampoline_jll v5.11.0+0
   [8e850ede] + nghttp2_jll v1.52.0+1
   [3f19e933] + p7zip_jll v17.4.0+2
        Info Packages marked with → are not downloaded, use `instantiate` to download
        Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`
  Downloaded artifact: CUDA_Runtime
PLEASE submit a bug report to https://github.com/llvm/llvm-project/issues/ and include the crash backtrace.
Stack dump:
0.◓ TaylProgram arguments: /home/fpoulin/software/julia-1.10.8/libexec/julia/lld -flavor gnu  -shared -o /home/fpoulin/.julia/compiled/v1.10/Quaternions/jl_hjrXDO --whole-archive /home/fpoulin/.julia/compiled/v1.10/Quaternions/jl_LNSCyK --no-whole-archive -L/home/fpoulin/software/julia-1.10.8/lib/julia -L/home/fpoulin/software/julia-1.10.8/lib -ljulia -ljulia-internal
Stack dump without symbol names (ensure you have llvm-symbolizer in your PATH or set the environment var `LLVM_SYMBOLIZER_PATH` to point to it):◐ CUDA_Runtime_Discovery
/home/fpoulin/software/julia-1.10.8/lib/julia/libLLVM-15jl.so(+0xa3d44f)[0x7fad6ae0a44f]
/home/fpoulin/software/julia-1.10.8/lib/julia/libLLVM-15jl.so(+0xa3adfc)[0x7fad6ae07dfc]
/lib64/libc.so.6(+0x54db0)[0x7fad69e62db0]
/home/fpoulin/software/julia-1.10.8/libexec/julia/lld(_ZN3lld3elf9writeEhdrIN4llvm6object7ELFTypeILNS2_7support10endiannessE1ELb1EEEEEvPhRNS0_9PartitionE+0xc)[0x63988c]
/home/fpoulin/software/julia-1.10.8/libexec/julia/lld(_ZN3lld3elf11writeResultIN4llvm6object7ELFTypeILNS2_7support10endiannessE1ELb1EEEEEvv+0x585)[0x69fe75]appedTries
/home/fpoulin/software/julia-1.10.8/libexec/julia/lld(_ZN3lld3elf12LinkerDriver4linkERN4llvm3opt12InputArgListE+0x2a3a)[0x56654a]
/home/fpoulin/software/julia-1.10.8/libexec/julia/lld(_ZN3lld3elf12LinkerDriver10linkerMainEN4llvm8ArrayRefIPKcEE+0x10af)[0x56829f]
/home/fpoulin/software/julia-1.10.8/libexec/julia/lld(_ZN3lld3elf4linkEN4llvm8ArrayRefIPKcEERNS1_11raw_ostreamES7_bb+0x105c)[0x5696cc]
/home/fpoulin/software/julia-1.10.8/libexec/julia/lld[0x484d11]
/home/fpoulin/software/julia-1.10.8/libexec/julia/lld(main+0x215)[0x482ab5]
/lib64/libc.so.6(+0x3feb0)[0x7fad69e4deb0]
/lib64/libc.so.6(__libc_start_main+0x80)[0x7fad69e4df60]
/home/fpoulin/software/julia-1.10.8/libexec/julia/lld[0x483d53]
lld: error: failed to write to the output file: No such file or directory1
Precompiling packages  [===========>                             ]  38/141
  ◑ FileIO
  ◐ TaylorSeries
  ◓ MacroTools
  ◓ IncompleteLU
  ◓ Quaternions
  ◓ IteratorInterfaceExtensions
  ◓ UnsafeAtomics
  ◒ CompilerSupportLibraries_jll
  ◐ PkgVersion
  ◐ PooledArrays
  ◒ Scratch
  ◓ Missings
  ◑ Random123
  ◓ Adapt → AdaptSparseArraysExt
  ◒ GPUArraysCore
  ◐ TZJData
  ◒ ScopedValues
  ◐ DataStructures
  ◓ Mocking
  ◐ Distances
  ◑ FixedPointNumbers
  ◐ Preferences
  ◒ SortingAlgorithms
  ◒ CommonDataModel
  ◒ OffsetArrays → OffsetArraysAdaptExt
  ◐ DiskArrays
  ◐ Distances → DistancesSparseArraysExt
  ◒ ColorTypes
  ◓ MPIPreferences
  ◐ PrecompileTools
  ◑ JLLWrappers
  ◓ TaylorSeries
  ◑ MacroTools
  ◑ Quaternions
  ◑ IteratorInterfaceExtensions
  ◑ UnsafeAtomics
  ◐ CompilerSupportLibraries_jll
  ◓ PkgVersion
  ◓ PooledArrays
  ◐ Scratch
  ◑ Missings
  ◒ Random123
  ◑ Adapt → AdaptSparseArraysExt
  ◐ GPUArraysCore
  ◓ TZJData
  ◐ ScopedValues
  ◓ DataStructures
  ◑ Mocking
  ◓ Distances
  ◒ FixedPointNumbers
  ◓ Preferences
  ◐ SortingAlgorithms
  ◐ CommonDataModel
  ◐ OffsetArrays → OffsetArraysAdaptExt
  ◓ DiskArrays
  ◓ Distances → DistancesSparseArraysExt
  ◐ ColorTypes
  ◑ MPIPreferences
  ◓ PrecompileTools
  ◒ JLLWrappers
  ◐ Colors
  ◐ StaticArrays
  ◒ RecipesBase
  ◐ StringManipulation
  ◐ OpenSSL_jll
  ◒ NVTX_jll
  ◐ CUDA_Driver_jll
  ◒ JuliaNVTXCallbacks_jll
  ◑ MicrosoftMPI_jll
  ◓ XZ_jll
  ◐ oneTBB_jll
  ◓ LLVMExtra_jll
  ◒ Zstd_jll
  ◓ Hwloc_jll
  ◓ Libiconv_jll
  ◑ IntelOpenMP_jll
  ◓ LLVMOpenMP_jll
  ◒ Bzip2_jll
  ◓ Lz4_jll
  ◓ demumble_jll
  ◒ FFTW_jll
  ◓ libaec_jll
  ◒ NVTX
  ◐ StaticArrays → StaticArraysStatisticsExt
  ◐ ConstructionBase → ConstructionBaseStaticArraysExt
  ◑ Adapt → AdaptStaticArraysExt
  ◑ IterativeSolvers
  ◐ CUDA_Runtime_jll
  ◓ LLVM
  ◓ XML2_jll
  ◑ MKL_jll
  ◓ libzip_jll
  ◒ Blosc_jll
  ◒ FFTW
  ◒ LLVM → BFloat16sExt
Unhandled Task ERROR: failed process: Process(setenv(`/home/fpoulin/software/julia-1.10.8/libexec/julia/lld -flavor gnu '' -shared -o /home/fpoulin/.julia/compiled/v1.10/Quaternions/jl_hjrXDO --whole-archive /home/fpoulin/.julia/compiled/v1.10/Quaternions/jl_LNSCyK --no-whole-archive -L/home/fpoulin/software/julia-1.10.8/lib/julia -L/home/fpoulin/software/julia-1.10.8/lib -ljulia -ljulia-internal`,["EBROOTCUDA=/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.1.1", "LMOD_ROOT=/cvmfs/soft.computecanada.ca/custom/software/lmod", "LD_LIBRARY_PATH=/home/fpoulin/software/julia-1.10.8/lib/julia:/home/fpoulin/software/julia-1.10.8/lib:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.1.1/lib64:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.1.1/lib64:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.1.1/lib64:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.1.1/lib64::", "_ModuleTable019_=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", "EBVERSIONOPENMPI=4.0.3", "EBROOTCUDACORE=/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/cudacore/11.1.1", "SQUEUE_SORT=-t,e,S", "DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/3000519/bus", "MODULEPATH=/opt/software/modulefiles:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/avx2/CUDA/intel2020/cuda11.1:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/avx2/CUDA/cuda11.1:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/CUDA/cuda11.1:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/avx2/MPI/intel2020/openmpi4:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/avx2/Compiler/intel2020:/home/fpoulin/.local/easybuild/modules/2020/avx2/Core:/home/fpoulin/.local/easybuild/modules/2020/Core:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/avx2/Core:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/Core:/cvmfs/soft.computecanada.ca/custom/modules", "_ModuleTable_Sz_=19"  …  "_ModuleTable013_=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", "EASYBUILD_BUILDPATH=/tmp/fpoulin", "CC_RESTRICTED=true", "EBDEVELLIBFABRIC=/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/libfabric/1.10.1/easybuild/avx2-Core-libfabric-1.10.1-easybuild-devel", "EBDEVELCUDA=/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/cuda/11.1.1/easybuild/avx2-Compiler-intel2020-cuda-11.1.1-easybuild-devel", "__SCRATCH_PURGE_REPORTED=1", "EBVERSIONIMKL=2020.1.217", "_ModuleTable014_=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", "EPREFIX=/cvmfs/soft.computecanada.ca/gentoo/2020", "LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.webp=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.m4a=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.oga=01;36:*.opus=01;36:*.spx=01;36:*.xspf=01;36::su=00:sg=00:ca=00:ow=00:st=00:tw=00:ex=00:or=00::"]), ProcessExited(1)) [1]

Stacktrace:
  [1] pipeline_error
    @ ./process.jl:565 [inlined]
  [2] run(::Cmd, ::Base.DevNull, ::Vararg{Any}; wait::Bool)
    @ Base ./process.jl:480
  [3] run
    @ ./process.jl:477 [inlined]
  [4] link_image (repeats 2 times)
    @ ./linking.jl:166 [inlined]
  [5] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:2450
  [6] (::Pkg.API.Precompilation.var"#28#68"{Pipe, Dict{Base.PkgId, Base.PkgId}, Dict{Base.PkgId, Vector{Base.PkgId}}, String, Base.PkgId})()
    @ Pkg.API.Precompilation ~/software/julia-1.10.8/share/julia/stdlib/v1.10/Pkg/src/precompilation.jl:871
  [7] with_logstate(f::Function, logstate::Any)
    @ Base.CoreLogging ./logging.jl:515
  [8] with_logger
    @ ./logging.jl:627 [inlined]
  [9] #27
    @ ~/software/julia-1.10.8/share/julia/stdlib/v1.10/Pkg/src/precompilation.jl:865 [inlined]
 [10] mkpidlock(f::Pkg.API.Precompilation.var"#27#67"{Pipe, Dict{Base.PkgId, Base.PkgId}, Dict{Base.PkgId, Vector{Base.PkgId}}, String, Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/software/julia-1.10.8/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:93
 [11] #mkpidlock#6
    @ ~/software/julia-1.10.8/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:88 [inlined]
 [12] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/software/julia-1.10.8/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:111
 [13] trymkpidlock
    @ ~/software/julia-1.10.8/share/julia/stdlib/v1.10/FileWatching/src/pidfile.jl:109 [inlined]
 [14] precompile_pkgs_maybe_cachefile_lock(f::Pkg.API.Precompilation.var"#27#67"{Pipe, Dict{Base.PkgId, Base.PkgId}, Dict{Base.PkgId, Vector{Base.PkgId}}, String, Base.PkgId}, io::IOContext{IO}, print_lock::ReentrantLock, fancyprint::Bool, pkg_config::Tuple{Base.PkgId, Pair{Cmd, Base.CacheFlags}}, pkgspidlocked::Dict{Tuple{Base.PkgId, Pair{Cmd, Base.CacheFlags}}, String}, hascolor::Bool)
    @ Pkg.API.Precompilation ~/software/julia-1.10.8/share/julia/stdlib/v1.10/Pkg/src/precompilation.jl:1055
 [15] macro expansion
    @ ./timing.jl:395 [inlined]
 [16] (::Pkg.API.Precompilation.var"#24#64"{Bool, Bool, Vector{Task}, Dict{Tuple{Base.PkgId, Pair{Cmd, Base.CacheFlags}}, String}, Dict{Tuple{Base.PkgId, Pair{Cmd, Base.CacheFlags}}, IOBuffer}, Base.Event, Base.Event, ReentrantLock, Vector{Tuple{Base.PkgId, Pair{Cmd, Base.CacheFlags}}}, Dict{Tuple{Base.PkgId, Pair{Cmd, Base.CacheFlags}}, String}, Vector{Tuple{Base.PkgId, Pair{Cmd, Base.CacheFlags}}}, Vector{Base.PkgId}, Dict{Tuple{Base.PkgId, Pair{Cmd, Base.CacheFlags}}, Bool}, Dict{Tuple{Base.PkgId, Pair{Cmd, Base.CacheFlags}}, Base.Event}, Dict{Tuple{Base.PkgId, Pair{Cmd, Base.CacheFlags}}, Bool}, Vector{Base.PkgId}, Pkg.API.Precompilation.var"#describe_pkg#37"{Dict{Base.PkgId, Base.PkgId}, Pkg.API.Precompilation.var"#color_string#36"{Bool}, Int64}, Dict{Base.PkgId, Base.PkgId}, Dict{Base.PkgId, Vector{Base.PkgId}}, Dict{Tuple{Base.PkgId, UInt128, String, String}, Bool}, Pkg.API.Precompilation.var"#color_string#36"{Bool}, Bool, Base.Semaphore, Bool, String, Vector{String}, Vector{Base.PkgId}, Base.PkgId, Base.CacheFlags, Cmd, Pair{Cmd, Base.CacheFlags}, Tuple{Base.PkgId, Pair{Cmd, Base.CacheFlags}}})()
    @ Pkg.API.Precompilation ~/software/julia-1.10.8/share/julia/stdlib/v1.10/Pkg/src/precompilation.jl:864

@navidcy
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navidcy commented Mar 9, 2025

Really strange this last one... Remove Manifest.toml and try again?

@navidcy navidcy added the package 📦 Quite meta label Mar 9, 2025
@glwagner
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glwagner commented Mar 9, 2025

I'd just try again, not even sure you need to remove Manifest.toml

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@navidcy @francispoulin @glwagner @simone-silvestri