Precompilation issue in Ubuntu 22.04.2 LTS (libLLVM-14jl.so (unknown line)) #1103
Comments
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@vchuravy, any idea if this is related to new pkgimages perhaps? Any ideas of what to try here? |
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No this is a segmentation fault inside LLVM proper. Is it reproducible? It might be Sapphire Rapids specific. |
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@ssouyris right now we don't have enough information to act on this issue. Does this issue occur repeatedly for you? Can you post Manifest.toml and Project.toml that reproduce this issue? |
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You can also use |
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@vchuravy, yes, the issue occur repeatedly. I tried to recompile CSV many times and got the same result. |
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@vchuravy , @quinnj, I am having other issues with this new tower, so I am sending it back to Dell for diagnosis and fixing. Let me get you back in a couple of weeks with an update. If the Sapphire Rapids compatibility is relevant for the development of CSV.jl, I would be happy to connect with you and do some testing. I am closing the issue. Thanks again. |
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Hi @vchuravy, I am reopening this issue with an update. We got a new machine with the same hardware configuration but with Windows instead of Ubuntu. I installed Julia and CSV and got the same pre-compilation issue. Please see the code information below. Is this something that can be instigated? I tried using CSVFiles.jl, but the running time is much longer than CSV.jl (on my laptop, reading and writing 5GB+ files). Thanks for looking at this. julia> versioninfo() julia> ] (@v1.9) pkg> st (@v1.9) pkg> add CSV (@v1.9) pkg> precompile ERROR: The following 1 direct dependency failed to precompile: CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b] Failed to precompile CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b] to "C:\Users\SOUYRS\.julia\compiled\v1.9\CSV\jl_A63.tmp". Please submit a bug report with steps to reproduce this fault, and any error messages that follow (in their entirety). Thanks. |
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@quinnj, @vchuravy, I installed the Upcoming release: v1.10.0-alpha1 (July 6, 2023), and that allowed me to add CSV without issues. Nice! That installation was both in Ubuntu and Windows machines described above. I am closing this issue now. |
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I am also running into CSV.jl precompilation issues on an HPC with Sapphire Rapids CPUs. I have tried to build Julia from source and also use the generic-linux Julia binary and both give the same error. The following outputs are with the latter: julia> versioninfo()
Julia Version 1.9.3
Commit bed2cd540a1 (2023-08-24 14:43 UTC)
Build Info:
Official https://julialang.org/ release
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 104 × Intel(R) Xeon(R) Platinum 8470QL
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-14.0.6 (ORCJIT, sapphirerapids)
Threads: 1 on 104 virtual cores
Environment:
LD_LIBRARY_PATH = /nopt/nrel/apps/software/julia/generic-linux-julia-1.9.3/lib:/nopt/nrel/apps/compilers/08-23/spack/opt/spack/linux-rhel8-icelake/gcc-8.4.0/gcc-13.1.0-hiekcz5owm5hgiw7xnwd55reo3wfxwmp/lib64:/nopt/nrel/apps/compilers/08-23/spack/opt/spack/linux-rhel8-icelake/gcc-8.4.0/gcc-13.1.0-hiekcz5owm5hgiw7xnwd55reo3wfxwmp/lib:/nopt/slurm/current/lib::
JULIA_ROOT_DIR = /nopt/nrel/apps/software/julia/generic-linux-julia-1.9.3/This is the environment that I am using And when I try to use CSV, I get the set fault error. I was able to reproduce this error with Julia v1.9.0 as well. Any suggestions? Thanks in advance! |
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Can you check v1.10-beta? This is likely an upstream LLVM issue. Without access to a Sapphire Rapids machine this is going to be hard to reproduce. |
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Alternativly you could use |
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The error does go away in v1.10.0-beta2 and I submitted a bug report as well. Do you know when one can expect a stable release for v1.10.0? |
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In the next few weeks |
Hello,
I have used CVS in multiple projects and platforms, but now on a new computer and latest version of CSV, I am getting the following compilation error I can't get around.
I think the error at precompilation is at:
_ZN4llvm19MachineRegisterInfo22addRegOperandToUseListEPNS_14MachineOperandE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
Let me copy and paste step by step in RELP:
julia> versioninfo()
Julia Version 1.9.2
Commit e4ee485e909 (2023-07-05 09:39 UTC)
Platform Info:
OS: Linux (x86_64-linux-gnu)
CPU: 16 × Intel(R) Xeon(R) w3-2435
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-14.0.6 (ORCJIT, sapphirerapids)
Threads: 1 on 16 virtual cores
]
(@v1.9) pkg> activate test
Activating new project at
~/test(test) pkg> st
Status
~/test/Project.toml(empty project)(test) pkg> add CSV
Resolving package versions...
Updating
~/test/Project.toml[336ed68f] + CSV v0.10.11
Updating
~/test/Manifest.toml[336ed68f] + CSV v0.10.11
[944b1d66] + CodecZlib v0.7.1
[34da2185] + Compat v4.7.0
[9a962f9c] + DataAPI v1.15.0
[e2d170a0] + DataValueInterfaces v1.0.0
[48062228] + FilePathsBase v0.9.20
[842dd82b] + InlineStrings v1.4.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[bac558e1] + OrderedCollections v1.6.0
[69de0a69] + Parsers v2.7.1
[2dfb63ee] + PooledArrays v1.4.2
[aea7be01] + PrecompileTools v1.1.2
[21216c6a] + Preferences v1.4.0
[91c51154] + SentinelArrays v1.4.0
[3783bdb8] + TableTraits v1.0.1
[bd369af6] + Tables v1.10.1
[3bb67fe8] + TranscodingStreams v0.9.13
[ea10d353] + WeakRefStrings v1.4.2
[76eceee3] + WorkerUtilities v1.6.1
[56f22d72] + Artifacts
[2a0f44e3] + Base64
[ade2ca70] + Dates
[9fa8497b] + Future
[b77e0a4c] + InteractiveUtils
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[de0858da] + Printf
[9a3f8284] + Random
[ea8e919c] + SHA v0.7.0
[9e88b42a] + Serialization
[fa267f1f] + TOML v1.0.3
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[e66e0078] + CompilerSupportLibraries_jll v1.0.5+0
[4536629a] + OpenBLAS_jll v0.3.21+4
[83775a58] + Zlib_jll v1.2.13+0
[8e850b90] + libblastrampoline_jll v5.8.0+0
Precompiling project...
✗ CSV
0 dependencies successfully precompiled in 4 seconds. 21 already precompiled.
1 dependency errored. To see a full report either run
import Pkg; Pkg.precompile()or load the package(test) pkg> precompile
Precompiling project...
✗ CSV
0 dependencies successfully precompiled in 4 seconds. 21 already precompiled.
ERROR: The following 1 direct dependency failed to precompile:
CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b]
Failed to precompile CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b] to "/home/souyrs/.julia/compiled/v1.9/CSV/jl_aRd8kH".
[55625] signal (11.1): Segmentation fault
in expression starting at /home/souyrs/.julia/packages/CSV/OnldF/src/precompile.jl:3
_ZN4llvm19MachineRegisterInfo22addRegOperandToUseListEPNS_14MachineOperandE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm12MachineInstr10addOperandERNS_15MachineFunctionERKNS_14MachineOperandE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm7BuildMIERNS_17MachineBasicBlockERNS_12MachineInstrERKNS_8DebugLocERKNS_11MCInstrDescENS_8RegisterE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZNK4llvm17X86TargetLowering27EmitInstrWithCustomInserterERNS_12MachineInstrEPNS_17MachineBasicBlockE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN12_GLOBAL__N_112FinalizeISel20runOnMachineFunctionERN4llvm15MachineFunctionE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm19MachineFunctionPass13runOnFunctionERNS_8FunctionE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm13FPPassManager13runOnFunctionERNS_8FunctionE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm13FPPassManager11runOnModuleERNS_6ModuleE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm6legacy15PassManagerImpl3runERNS_6ModuleE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm3orc14SimpleCompilerclERNS_6ModuleE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
operator() at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/jitlayers.cpp:1206
_ZN4llvm3orc14IRCompileLayer4emitESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EENS0_16ThreadSafeModuleE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm3orc16IRTransformLayer4emitESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EENS0_16ThreadSafeModuleE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
emit at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/jitlayers.cpp:631
_ZN4llvm3orc31BasicIRLayerMaterializationUnit11materializeESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm3orc19MaterializationTask3runEv at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
ZN4llvm6detail18UniqueFunctionBaseIvJSt10unique_ptrINS_3orc4TaskESt14default_deleteIS4_EEEE8CallImplIPFvS7_EEEvPvRS7 at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession22dispatchOutstandingMUsEv at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession17OL_completeLookupESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EESt10shared_ptrINS0_23AsynchronousSymbolQueryEESt8functionIFvRKNS_8DenseMapIPNS0_8JITDylibENS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISF_vEEEENSG_ISD_vEENS_6detail12DenseMapPairISD_SI_EEEEEE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm3orc25InProgressFullLookupState8completeESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession19OL_applyQueryPhase1ESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EENS_5ErrorE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS0_10LookupKindERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS8_EENS0_15SymbolLookupSetENS0_11SymbolStateENS_15unique_functionIFvNS_8ExpectedINS_8DenseMapINS0_15SymbolStringPtrENS_18JITEvaluatedSymbolENS_12DenseMapInfoISI_vEENS_6detail12DenseMapPairISI_SJ_EEEEEEEEESt8functionIFvRKNSH_IS6_NS_8DenseSetISI_SL_EENSK_IS6_vEENSN_IS6_SV_EEEEEE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS7_EERKNS0_15SymbolLookupSetENS0_10LookupKindENS0_11SymbolStateESt8functionIFvRKNS_8DenseMapIS5_NS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISK_vEEEENSL_IS5_vEENS_6detail12DenseMapPairIS5_SN_EEEEEE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS7_EENS0_15SymbolStringPtrENS0_11SymbolStateE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS_8ArrayRefIPNS0_8JITDylibEEENS0_15SymbolStringPtrENS0_11SymbolStateE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
_ZN4llvm3orc16ExecutionSession6lookupENS_8ArrayRefIPNS0_8JITDylibEEENS_9StringRefENS0_11SymbolStateE at /snap/julia/83/bin/../lib/julia/libLLVM-14jl.so (unknown line)
addModule at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/jitlayers.cpp:1420
jl_add_to_ee at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/jitlayers.cpp:1815
jl_add_to_ee at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/jitlayers.cpp:1794
jl_add_to_ee at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/jitlayers.cpp:1794
jl_add_to_ee at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/jitlayers.cpp:1794
jl_add_to_ee at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/jitlayers.cpp:1794
_jl_compile_codeinst at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/jitlayers.cpp:241
jl_generate_fptr_impl at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/jitlayers.cpp:460
jl_compile_method_internal at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2348 [inlined]
jl_compile_method_internal at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2237
_jl_invoke at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2750 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2940
File at /home/souyrs/.julia/packages/CSV/OnldF/src/file.jl:290
File at /home/souyrs/.julia/packages/CSV/OnldF/src/file.jl:227 [inlined]
#File#32 at /home/souyrs/.julia/packages/CSV/OnldF/src/file.jl:223 [inlined]
File at /home/souyrs/.julia/packages/CSV/OnldF/src/file.jl:162
unknown function (ip: 0x7ff092553818)
_jl_invoke at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2940
macro expansion at /home/souyrs/.julia/packages/CSV/OnldF/src/precompile.jl:10 [inlined]
macro expansion at /home/souyrs/.julia/packages/PrecompileTools/0yi7r/src/workloads.jl:74 [inlined]
macro expansion at /home/souyrs/.julia/packages/CSV/OnldF/src/precompile.jl:7 [inlined]
top-level scope at /home/souyrs/.julia/packages/PrecompileTools/0yi7r/src/workloads.jl:136
jl_toplevel_eval_flex at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/toplevel.c:903
jl_toplevel_eval_flex at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/toplevel.c:971
eval at ./boot.jl:370 [inlined]
include_string at ./loading.jl:1903
_jl_invoke at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2940
_include at ./loading.jl:1963
include at ./Base.jl:457
jfptr_include_32440.clone_1 at /snap/julia/83/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/julia.h:1879 [inlined]
jl_f__call_latest at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/builtins.c:774
include at /home/souyrs/.julia/packages/CSV/OnldF/src/CSV.jl:24
unknown function (ip: 0x7ff092500482)
_jl_invoke at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/julia.h:1879 [inlined]
do_call at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_eval_module_expr at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/toplevel.c:203 [inlined]
jl_toplevel_eval_flex at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/toplevel.c:715
jl_toplevel_eval_flex at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/toplevel.c:856
jl_toplevel_eval_flex at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/toplevel.c:971
eval at ./boot.jl:370 [inlined]
include_string at ./loading.jl:1903
_jl_invoke at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2940
_include at ./loading.jl:1963
include at ./Base.jl:457 [inlined]
include_package_for_output at ./loading.jl:2049
jfptr_include_package_for_output_41305.clone_1 at /snap/julia/83/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/julia.h:1879 [inlined]
do_call at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/toplevel.c:971
eval at ./boot.jl:370 [inlined]
include_string at ./loading.jl:1903
include_string at ./loading.jl:1913 [inlined]
exec_options at ./client.jl:305
_start at ./client.jl:522
jfptr__start_43375.clone_1 at /snap/julia/83/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/julia.h:1879 [inlined]
true_main at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/jlapi.c:573
jl_repl_entrypoint at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/src/jlapi.c:717
main at /cache/build/default-amdci5-2/julialang/julia-release-1-dot-9/cli/loader_exe.c:59
unknown function (ip: 0x7ff0a9c98d8f)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x401098)
Allocations: 14683492 (Pool: 14664723; Big: 18769); GC: 21
Any guidance is appreciated. Thanks!
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