Problem with Juno at startup on Garuda linux

Tooling Juno
1

I installed Garuda Linux on my laptop and am trying to run Julia using atom as I used to.

I can use julia in a terminal but in Atom I have the following failure.

Upon pressing Enter to start a new session, everything seems fine and I can run a few commands, but a few seconds later I have the following error message

julia: /build/julia/src/julia-1.7.1/src/llvm-late-gc-lowering.cpp:562: std::pair<llvm::Value*, int> FindBaseValue(const State&, llvm::Value*, bool): Assertion `isa<LoadInst>(CurrentV) || isa<CallInst>(CurrentV) || isa<AtomicCmpXchgInst>(CurrentV) || isa<AtomicRMWInst>(CurrentV) || isa<Argument>(CurrentV) || isa<SelectInst>(CurrentV) || isa<PHINode>(CurrentV) || isa<AddrSpaceCastInst>(CurrentV) || isa<Constant>(CurrentV) || isa<AllocaInst>(CurrentV) || isa<InsertValueInst>(CurrentV) || isa<ExtractValueInst>(CurrentV) || isa<InsertElementInst>(CurrentV) || isa<ShuffleVectorInst>(CurrentV)' failed.

signal (6): Aborted
in expression starting at none:0
gsignal at /usr/bin/../lib/libc.so.6 (unknown line)
abort at /usr/bin/../lib/libc.so.6 (unknown line)
__assert_fail_base.cold at /usr/bin/../lib/libc.so.6 (unknown line)
__assert_fail at /usr/bin/../lib/libc.so.6 (unknown line)
unknown function (ip: 0x7f6282fb4274)
unknown function (ip: 0x7f6282fb8bb3)
unknown function (ip: 0x7f6282fb8dc0)
unknown function (ip: 0x7f6282fbf209)
unknown function (ip: 0x7f6282fc9f92)
_ZN4llvm13FPPassManager13runOnFunctionERNS_8FunctionE at /usr/bin/../lib/julia/../libLLVM-13.so (unknown line)
_ZN4llvm13FPPassManager11runOnModuleERNS_6ModuleE at /usr/bin/../lib/julia/../libLLVM-13.so (unknown line)
_ZN4llvm6legacy15PassManagerImpl3runERNS_6ModuleE at /usr/bin/../lib/julia/../libLLVM-13.so (unknown line)
unknown function (ip: 0x7f6282f9a83f)
_ZN4llvm3orc14IRCompileLayer4emitESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EENS0_16ThreadSafeModuleE at /usr/bin/../lib/julia/../libLLVM-13.so (unknown line)
_ZN4llvm3orc31BasicIRLayerMaterializationUnit11materializeESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EE at /usr/bin/../lib/julia/../libLLVM-13.so (unknown line)
_ZN4llvm3orc19MaterializationTask3runEv at /usr/bin/../lib/julia/../libLLVM-13.so (unknown line)
unknown function (ip: 0x7f627f0829f7)
_ZN4llvm3orc16ExecutionSession22dispatchOutstandingMUsEv at /usr/bin/../lib/julia/../libLLVM-13.so (unknown line)
_ZN4llvm3orc16ExecutionSession17OL_completeLookupESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EESt10shared_ptrINS0_23AsynchronousSymbolQueryEESt8functionIFvRKNS_8DenseMapIPNS0_8JITDylibENS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISF_EEEENSG_ISD_EENS_6detail12DenseMapPairISD_SI_EEEEEE at /usr/bin/../lib/julia/../libLLVM-13.so (unknown line)
unknown function (ip: 0x7f627f0a23f9)
_ZN4llvm3orc16ExecutionSession19OL_applyQueryPhase1ESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EENS_5ErrorE at /usr/bin/../lib/julia/../libLLVM-13.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS0_10LookupKindERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS8_EENS0_15SymbolLookupSetENS0_11SymbolStateENS_15unique_functionIFvNS_8ExpectedINS_8DenseMapINS0_15SymbolStringPtrENS_18JITEvaluatedSymbolENS_12DenseMapInfoISI_EENS_6detail12DenseMapPairISI_SJ_EEEEEEEEESt8functionIFvRKNSH_IS6_NS_8DenseSetISI_SL_EENSK_IS6_EENSN_IS6_SV_EEEEEE at /usr/bin/../lib/julia/../libLLVM-13.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS7_EERKNS0_15SymbolLookupSetENS0_10LookupKindENS0_11SymbolStateESt8functionIFvRKNS_8DenseMapIS5_NS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISK_EEEENSL_IS5_EENS_6detail12DenseMapPairIS5_SN_EEEEEE at /usr/bin/../lib/julia/../libLLVM-13.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS7_EENS0_15SymbolStringPtrENS0_11SymbolStateE at /usr/bin/../lib/julia/../libLLVM-13.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS_8ArrayRefIPNS0_8JITDylibEEENS0_15SymbolStringPtrENS0_11SymbolStateE at /usr/bin/../lib/julia/../libLLVM-13.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS_8ArrayRefIPNS0_8JITDylibEEENS_9StringRefENS0_11SymbolStateE at /usr/bin/../lib/julia/../libLLVM-13.so (unknown line)
unknown function (ip: 0x7f6282f96406)
unknown function (ip: 0x7f6282f981d4)
unknown function (ip: 0x7f6282f99334)
unknown function (ip: 0x7f6282f98c3b)
unknown function (ip: 0x7f6282f98c3b)
unknown function (ip: 0x7f628305a9a2)
unknown function (ip: 0x7f6282f93fff)
unknown function (ip: 0x7f6282f1b8dd)
jl_apply_generic at /usr/bin/../lib/julia/libjulia-internal.so.1 (unknown line)
#270 at /home/benoitseron/.julia/packages/Atom/BUIFZ/src/outline.jl:10
handlemsg at /home/benoitseron/.julia/packages/Atom/BUIFZ/src/comm.jl:169
unknown function (ip: 0x7f625bc1776e)
jl_f__call_latest at /usr/bin/../lib/julia/libjulia-internal.so.1 (unknown line)
unknown function (ip: 0x7f6282f256d1)
unknown function (ip: 0x7f626b854fd0)
unknown function (ip: 0x7f6282f256d1)
unknown function (ip: 0x7f626b6e95b7)
unknown function (ip: 0x7f6282f256d1)
#31 at ./task.jl:423
unknown function (ip: 0x7f625bbfc4ff)
unknown function (ip: 0x7f6282f30264)
Allocations: 40427226 (Pool: 40416840; Big: 10386); GC: 34

which then exists the session.

I tried what I could see in [FAQ · Juno Documentation] which says changing the location of the binaries, but I was not able to enter anything that worked (I am not sure what to write there).

Does anyone have an idea of how to solve this?

2

Hello! I am facing the exact same problem running julia on Manjaro. It works well in the command-line, but trying to use it on Atom yields the same output almost line-by-line. I have no idea so far, but if I do find out I’ll share here.

Edit: I have been trying some stuff to pin out the error and I have made some progress, though I am not sure if you have the same error. My error seems to be related to the loading of the Sundials library. Running any julia code that does not load DifferentialEquations and, thus, Sundials returns no error via the terminal. Altough this is progress, Atom seems to keep strugling even without loading this library.

ERROR: The following 2 direct dependencies failed to precompile:

Sundials [c3572dad-4567-51f8-b174-8c6c989267f4]

Failed to precompile Sundials [c3572dad-4567-51f8-b174-8c6c989267f4] to /home/lucas/.julia/compiled/v1.7/Sundials/jl_PGESDU.
ERROR: LoadError: InitError: could not load library "/home/lucas/.julia/artifacts/cb7fc2801ca0133a5bdea4bc4585d07c08284cfa/lib/libsundials_sunlinsollapackband.so"
libopenblas64_.so: cannot open shared object file: No such file or directory
Stacktrace:
 [1] macro expansion
   @ ~/.julia/packages/JLLWrappers/RYztT/src/products/library_generators.jl:54 [inlined]
 [2] __init__()
   @ Sundials_jll ~/.julia/packages/Sundials_jll/rXn1i/src/wrappers/x86_64-linux-gnu-libgfortran5.jl:99
 [3] top-level scope (repeats 2 times)
   @ none:1
during initialization of module Sundials_jll
in expression starting at /home/lucas/.julia/packages/Sundials/m1EFu/src/Sundials.jl:3

DifferentialEquations [0c46a032-eb83-5123-abaf-570d42b7fbaa]

Failed to precompile DifferentialEquations [0c46a032-eb83-5123-abaf-570d42b7fbaa] to /home/lucas/.julia/compiled/v1.7/DifferentialEquations/jl_jEOTCX.
ERROR: LoadError: InitError: could not load library "/home/lucas/.julia/artifacts/cb7fc2801ca0133a5bdea4bc4585d07c08284cfa/lib/libsundials_sunlinsollapackband.so"
libopenblas64_.so: cannot open shared object file: No such file or directory
Stacktrace:
 [1] macro expansion
   @ ~/.julia/packages/JLLWrappers/RYztT/src/products/library_generators.jl:54 [inlined]
 [2] __init__()
   @ Sundials_jll ~/.julia/packages/Sundials_jll/rXn1i/src/wrappers/x86_64-linux-gnu-libgfortran5.jl:99
 [3] top-level scope (repeats 2 times)
   @ none:1
during initialization of module Sundials_jll
in expression starting at /home/lucas/.julia/packages/Sundials/m1EFu/src/Sundials.jl:3
ERROR: LoadError: Failed to precompile Sundials [c3572dad-4567-51f8-b174-8c6c989267f4] to /home/lucas/.julia/compiled/v1.7/Sundials/jl_dvQdJL.
Stacktrace:
 [1] top-level scope (repeats 2 times)
   @ none:1
in expression starting at /home/lucas/.julia/packages/DifferentialEquations/4jfQK/src/DifferentialEquations.jl:1

Stacktrace:
 [1] top-level scope

Perhaps a somewhat similar situation is happening to you, but with only this log you showed I cannot tell. Can you try running it without some packages via the terminal to try and find which one is giving you problems, if any at all?

3

Ok, I think I got it. Not that I fully understand the reason, but I read here that the binaries in the standard arch repository tend to be buggy. Try running

sudo pacman -R julia

And, then,

yay julia-bin

to install this version. This solved all the problems I had.

1 Like