Precompilation Fails on HPC

[aadam]

I tried adding IJulia to the base environment first, but it gave the precompilation error where it wasn’t able to precompile Parsers, JSON, Conda, IJulia.

I then tried adding CSV and it again fails at the precompilation step. Based on some suggestions from the threads on this forum, I’ve tried the following already:

• Remove compiled directory under ~/.julia.
• Run instantiate, resolve, update commands.
• Update FileIO package.
• Install the latest CSV package using add CSV#main command.

Nothing seems to be working for now. This is the error that I get when I import CSV:

julia> import CSV
[ Info: Precompiling CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b]
Invalid instruction at 0x7fa9cf9b40c6: 0xc4, 0x42, 0x81, 0xf7, 0xe4, 0x31, 0xf6, 0x48, 0xc1, 0xfa, 0x06, 0x48, 0xc1, 0xe2, 0x03

[31641] signal (4.2): Illegal instruction
in expression starting at /N/u/mraadam/Carbonate/.julia/packages/Parsers/w5O1u/src/floats.jl:646
mpfr_set_ui_2exp at /N/soft/rhel7/gcc/infrastructure/lib/libmpfr.so.6 (unknown line)
mpfr_ui_pow at /N/soft/rhel7/gcc/infrastructure/lib/libmpfr.so.6 (unknown line)
exp10 at ./mpfr.jl:637
exp10 at ./math.jl:1491 [inlined]
#37 at ./none:0 [inlined]
iterate at ./generator.jl:47 [inlined]
collect at ./array.jl:782
unknown function (ip: 0x7fa9cabde692)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
_include at ./loading.jl:1963
include at ./Base.jl:457
jfptr_include_35036.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
jl_f__call_latest at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/builtins.c:774
include at /N/u/mraadam/Carbonate/.julia/packages/Parsers/w5O1u/src/Parsers.jl:1
unknown function (ip: 0x7fa9cabd3122)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_eval_module_expr at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:203 [inlined]
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:715
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/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_38866.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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_40034.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
true_main at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/jlapi.c:573
jl_repl_entrypoint at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/jlapi.c:717
main at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/cli/loader_exe.c:59
__libc_start_main at /lib64/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 2998 (Pool: 2986; Big: 12); GC: 0
ERROR: LoadError: Failed to precompile Parsers [69de0a69-1ddd-5017-9359-2bf0b02dc9f0] to "/N/u/mraadam/Carbonate/.julia/compiled/v1.9/Parsers/jl_TTJxBy".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:2300
  [3] compilecache
    @ ./loading.jl:2167 [inlined]
  [4] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1805
  [5] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1660
  [6] macro expansion
    @ ./loading.jl:1648 [inlined]
  [7] macro expansion
    @ ./lock.jl:267 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1611
  [9] include
    @ ./Base.jl:457 [inlined]
 [10] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2049
 [11] top-level scope
    @ stdin:3
in expression starting at /N/u/mraadam/Carbonate/.julia/packages/CSV/Aa41C/src/CSV.jl:1
in expression starting at stdin:3
ERROR: Failed to precompile CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b] to "/N/u/mraadam/Carbonate/.julia/compiled/v1.9/CSV/jl_Pf9TLo".
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:35
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
   @ Base ./loading.jl:2300
 [3] compilecache
   @ ./loading.jl:2167 [inlined]
 [4] _require(pkg::Base.PkgId, env::String)
   @ Base ./loading.jl:1805
 [5] _require_prelocked(uuidkey::Base.PkgId, env::String)
   @ Base ./loading.jl:1660
 [6] macro expansion
   @ ./loading.jl:1648 [inlined]
 [7] macro expansion
   @ ./lock.jl:267 [inlined]
 [8] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1611

julia> 

If anyone can help me figure out the solution, I’d really appreciate it. I’m very new to HPC. Everything works fine on my local setup though.

---

Julia Version Info:

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: 32 × Intel(R) Xeon(R) CPU E5-2650 v2 @ 2.60GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, ivybridge)
  Threads: 1 on 32 virtual cores
Environment:
  LD_LIBRARY_PATH = /N/soft/rhel7/cuda/11.7/lib64:/N/soft/rhel7/intel/19.5/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64:/N/soft/rhel7/intel/19.5/compilers_and_libraries_2019.5.281/linux/ipp/lib/intel64:/N/soft/rhel7/intel/19.5/compilers_and_libraries_2019.5.281/linux/compiler/lib/intel64_lin:/N/soft/rhel7/intel/19.5/compilers_and_libraries_2019.5.281/linux/mkl/lib/intel64_lin:/N/soft/rhel7/intel/19.5/compilers_and_libraries_2019.5.281/linux/tbb/lib/intel64/gcc4.7:/N/soft/rhel7/intel/19.5/debugger_2019/iga/lib:/N/soft/rhel7/intel/19.5/debugger_2019/libipt/intel64/lib:/N/soft/rhel7/intel/19.5/compilers_and_libraries_2019.5.281/linux/daal/lib/intel64_lin:/N/soft/rhel7/gcc/12.1.0/lib64:/N/soft/rhel7/gcc/12.1.0/lib:/N/soft/rhel7/gcc/infrastructure/lib:/opt/thinlinc/lib64:/opt/thinlinc/lib:/N/u/mraadam/Carbonate/applications/VSCode-linux-x64/:/N/u/mraadam/Carbonate/applications/VSCode-linux-x64/
  LD_RUN_PATH = /N/soft/rhel7/gcc/12.1.0/lib64:/N/soft/rhel7/gcc/12.1.0/lib:/N/soft/rhel7/gcc/infrastructure/lib
  LD_PRELOAD = /N/soft/rhel7/xalt/2.10.30/lib64/libxalt_init.so
  JULIA_IMAGE_THREADS = 1

[Salmon]

The stacktrace mentions an error in Parsers.
What happens if you only add Parsers in a fresh environment, does it precompile fine?
If it does precompile try to add the other packages starting with CSV one by one to see at which point it throws the error.
Maybe that helps finding the issue. It might be that there is a bug in Parsers that needs to be fixed by the package dev but it would probably help them if you find out whether it’s due to some incompatibility

[BioTurboNick]

Possibly related to this: Segmentation fault in LLVM frames on Julia 1.9.3 when precompiling CSV.jl on Intel Sapphire Rapids CPU · Issue #51482 · JuliaLang/julia · GitHub ?

I see the CPU is older for you, but weird that it’s also in CSV.

Does Julia 1.8 or 1.10 work?

[mkitti]

I’m guessing your HPC nodes are heterogeneous.

An immediate fix is to use julia --pkgimages=no. You could also try setting JULIA_CPU_TARGET.

See Package Images · The Julia Language

Also see julia -C help

[Sevi]

Sounds a bit similar to an issue I ran into a while ago (if the problem appears when you have a shared depot and precompile certain things on a different machine compared to where you run the code). Maybe the discussion there is helpful:

Julia 1.9, same depot with different machines?

Hi! I’m using Julia 1.9 on an HPC cluster and ran into a strange error on some of the machines. I have a hunch that it’s related to native code caching and the fact that I currently use the same depot for all machines, but I’m a bit stuck investigating the actual issue and finding a good solution. Problem Running certain code on the affected machines gives an Illegal instruction error. So far I could only trigger the error when using Cthulhu.jl, but I’m not sure if it’s really related to that p…

The bottom line is exactly what @mkitti wrote above.

[aadam]

Nope, the Parsers doesn’t work as well. It doesn’t precompile. I get the following error:

julia> using Parsers
[ Info: Precompiling Parsers [69de0a69-1ddd-5017-9359-2bf0b02dc9f0]
Invalid instruction at 0x7f84237810c6: 0xc4, 0x42, 0x81, 0xf7, 0xe4, 0x31, 0xf6, 0x48, 0xc1, 0xfa, 0x06, 0x48, 0xc1, 0xe2, 0x03

[11820] signal (4.2): Illegal instruction
in expression starting at /N/u/mraadam/Carbonate/.julia/packages/Parsers/w5O1u/src/floats.jl:646
mpfr_set_ui_2exp at /N/soft/rhel7/gcc/infrastructure/lib/libmpfr.so.6 (unknown line)
mpfr_ui_pow at /N/soft/rhel7/gcc/infrastructure/lib/libmpfr.so.6 (unknown line)
exp10 at ./mpfr.jl:637
exp10 at ./math.jl:1491 [inlined]
#37 at ./none:0 [inlined]
iterate at ./generator.jl:47 [inlined]
collect at ./array.jl:782
unknown function (ip: 0x7f841e9ab692)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
_include at ./loading.jl:1963
include at ./Base.jl:457
jfptr_include_35036.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
jl_f__call_latest at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/builtins.c:774
include at /N/u/mraadam/Carbonate/.julia/packages/Parsers/w5O1u/src/Parsers.jl:1
unknown function (ip: 0x7f841e9a0122)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_eval_module_expr at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:203 [inlined]
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:715
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/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_38844.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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_40034.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
true_main at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/jlapi.c:573
jl_repl_entrypoint at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/jlapi.c:717
main at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/cli/loader_exe.c:59
__libc_start_main at /lib64/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 2999 (Pool: 2987; Big: 12); GC: 0
ERROR: Failed to precompile Parsers [69de0a69-1ddd-5017-9359-2bf0b02dc9f0] to "/N/u/mraadam/Carbonate/.julia/compiled/v1.9/Parsers/jl_2ZnNpq".
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:35
 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
   @ Base ./loading.jl:2300
 [3] compilecache
   @ ./loading.jl:2167 [inlined]
 [4] _require(pkg::Base.PkgId, env::String)
   @ Base ./loading.jl:1805
 [5] _require_prelocked(uuidkey::Base.PkgId, env::String)
   @ Base ./loading.jl:1660
 [6] macro expansion
   @ ./loading.jl:1648 [inlined]
 [7] macro expansion
   @ ./lock.jl:267 [inlined]
 [8] require(into::Module, mod::Symbol)
   @ Base ./loading.jl:1611

[aadam]

I’ve tried it on Julia v1.6 as well. It doesn’t work there either. I think the problem is in Parsers library and that’s making all the others fail as well.

(v1.9) pkg> precompile
Precompiling project...
  ✗ Parsers
  ✗ JSON
  ✗ InlineStrings
  ✗ WeakRefStrings
  ✗ Conda
  ✗ CSV
  ✗ IJulia
  0 dependencies successfully precompiled in 16 seconds. 29 already precompiled.

ERROR: The following 4 direct dependencies failed to precompile:

Parsers [69de0a69-1ddd-5017-9359-2bf0b02dc9f0]

Failed to precompile Parsers [69de0a69-1ddd-5017-9359-2bf0b02dc9f0] to "/N/u/mraadam/Carbonate/.julia/compiled/v1.9/Parsers/jl_tCLg7D".
Invalid instruction at 0x7f03baa820c6: 0xc4, 0x42, 0x81, 0xf7, 0xe4, 0x31, 0xf6, 0x48, 0xc1, 0xfa, 0x06, 0x48, 0xc1, 0xe2, 0x03

[14405] signal (4.2): Illegal instruction
in expression starting at /N/u/mraadam/Carbonate/.julia/packages/Parsers/w5O1u/src/floats.jl:646
mpfr_set_ui_2exp at /N/soft/rhel7/gcc/infrastructure/lib/libmpfr.so.6 (unknown line)
mpfr_ui_pow at /N/soft/rhel7/gcc/infrastructure/lib/libmpfr.so.6 (unknown line)
exp10 at ./mpfr.jl:637
exp10 at ./math.jl:1491 [inlined]
#37 at ./none:0 [inlined]
iterate at ./generator.jl:47 [inlined]
collect at ./array.jl:782
unknown function (ip: 0x7f03ba9174f2)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
_include at ./loading.jl:1963
include at ./Base.jl:457
jfptr_include_35036.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
jl_f__call_latest at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/builtins.c:774
include at /N/u/mraadam/Carbonate/.julia/packages/Parsers/w5O1u/src/Parsers.jl:1
unknown function (ip: 0x7f03ba90d2d2)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_eval_module_expr at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:203 [inlined]
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:715
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/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_38844.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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_40034.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
true_main at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/jlapi.c:573
jl_repl_entrypoint at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/jlapi.c:717
main at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/cli/loader_exe.c:59
__libc_start_main at /lib64/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 2997 (Pool: 2985; Big: 12); GC: 0

JSON [682c06a0-de6a-54ab-a142-c8b1cf79cde6]

Failed to precompile JSON [682c06a0-de6a-54ab-a142-c8b1cf79cde6] to "/N/u/mraadam/Carbonate/.julia/compiled/v1.9/JSON/jl_IfXkJt".
Invalid instruction at 0x7efffb6830c6: 0xc4, 0x42, 0x81, 0xf7, 0xe4, 0x31, 0xf6, 0x48, 0xc1, 0xfa, 0x06, 0x48, 0xc1, 0xe2, 0x03

[14423] signal (4.2): Illegal instruction
in expression starting at /N/u/mraadam/Carbonate/.julia/packages/Parsers/w5O1u/src/floats.jl:646
mpfr_set_ui_2exp at /N/soft/rhel7/gcc/infrastructure/lib/libmpfr.so.6 (unknown line)
mpfr_ui_pow at /N/soft/rhel7/gcc/infrastructure/lib/libmpfr.so.6 (unknown line)
exp10 at ./mpfr.jl:637
exp10 at ./math.jl:1491 [inlined]
#37 at ./none:0 [inlined]
iterate at ./generator.jl:47 [inlined]
collect at ./array.jl:782
unknown function (ip: 0x7efffb518542)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
_include at ./loading.jl:1963
include at ./Base.jl:457
jfptr_include_35036.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
jl_f__call_latest at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/builtins.c:774
include at /N/u/mraadam/Carbonate/.julia/packages/Parsers/w5O1u/src/Parsers.jl:1
unknown function (ip: 0x7efffb50e322)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_eval_module_expr at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:203 [inlined]
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:715
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/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_38866.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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_40034.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
true_main at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/jlapi.c:573
jl_repl_entrypoint at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/jlapi.c:717
main at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/cli/loader_exe.c:59
__libc_start_main at /lib64/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 2998 (Pool: 2986; Big: 12); GC: 0
ERROR: LoadError: Failed to precompile Parsers [69de0a69-1ddd-5017-9359-2bf0b02dc9f0] to "/N/u/mraadam/Carbonate/.julia/compiled/v1.9/Parsers/jl_PHVob0".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:2300
  [3] compilecache
    @ ./loading.jl:2167 [inlined]
  [4] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1805
  [5] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1660
  [6] macro expansion
    @ ./loading.jl:1648 [inlined]
  [7] macro expansion
    @ ./lock.jl:267 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1611
  [9] include(mod::Module, _path::String)
    @ Base ./Base.jl:457
 [10] include(x::String)
    @ JSON ~/.julia/packages/JSON/93Ea8/src/JSON.jl:3
 [11] top-level scope
    @ ~/.julia/packages/JSON/93Ea8/src/JSON.jl:11
 [12] include
    @ ./Base.jl:457 [inlined]
 [13] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2049
 [14] top-level scope
    @ stdin:3
in expression starting at /N/u/mraadam/Carbonate/.julia/packages/JSON/93Ea8/src/Parser.jl:1
in expression starting at /N/u/mraadam/Carbonate/.julia/packages/JSON/93Ea8/src/JSON.jl:3
in expression starting at stdin:3


CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b]

Failed to precompile CSV [336ed68f-0bac-5ca0-87d4-7b16caf5d00b] to "/N/u/mraadam/Carbonate/.julia/compiled/v1.9/CSV/jl_M0W1Io".
Invalid instruction at 0x7fca9298a0c6: 0xc4, 0x42, 0x81, 0xf7, 0xe4, 0x31, 0xf6, 0x48, 0xc1, 0xfa, 0x06, 0x48, 0xc1, 0xe2, 0x03

[14519] signal (4.2): Illegal instruction
in expression starting at /N/u/mraadam/Carbonate/.julia/packages/Parsers/w5O1u/src/floats.jl:646
mpfr_set_ui_2exp at /N/soft/rhel7/gcc/infrastructure/lib/libmpfr.so.6 (unknown line)
mpfr_ui_pow at /N/soft/rhel7/gcc/infrastructure/lib/libmpfr.so.6 (unknown line)
exp10 at ./mpfr.jl:637
exp10 at ./math.jl:1491 [inlined]
#37 at ./none:0 [inlined]
iterate at ./generator.jl:47 [inlined]
collect at ./array.jl:782
unknown function (ip: 0x7fca9281f542)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
_include at ./loading.jl:1963
include at ./Base.jl:457
jfptr_include_35036.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
jl_f__call_latest at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/builtins.c:774
include at /N/u/mraadam/Carbonate/.julia/packages/Parsers/w5O1u/src/Parsers.jl:1
unknown function (ip: 0x7fca92815322)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_eval_module_expr at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:203 [inlined]
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:715
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/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_38866.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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_40034.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
true_main at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/jlapi.c:573
jl_repl_entrypoint at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/jlapi.c:717
main at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/cli/loader_exe.c:59
__libc_start_main at /lib64/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 2997 (Pool: 2985; Big: 12); GC: 0
ERROR: LoadError: Failed to precompile Parsers [69de0a69-1ddd-5017-9359-2bf0b02dc9f0] to "/N/u/mraadam/Carbonate/.julia/compiled/v1.9/Parsers/jl_o2MT6c".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:2300
  [3] compilecache
    @ ./loading.jl:2167 [inlined]
  [4] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1805
  [5] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1660
  [6] macro expansion
    @ ./loading.jl:1648 [inlined]
  [7] macro expansion
    @ ./lock.jl:267 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1611
  [9] include
    @ ./Base.jl:457 [inlined]
 [10] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2049
 [11] top-level scope
    @ stdin:3
in expression starting at /N/u/mraadam/Carbonate/.julia/packages/CSV/Aa41C/src/CSV.jl:1
in expression starting at stdin:3


IJulia [7073ff75-c697-5162-941a-fcdaad2a7d2a]

Failed to precompile IJulia [7073ff75-c697-5162-941a-fcdaad2a7d2a] to "/N/u/mraadam/Carbonate/.julia/compiled/v1.9/IJulia/jl_qguxuB".
Invalid instruction at 0x7f792421a0c6: 0xc4, 0x42, 0x81, 0xf7, 0xe4, 0x31, 0xf6, 0x48, 0xc1, 0xfa, 0x06, 0x48, 0xc1, 0xe2, 0x03

[14539] signal (4.2): Illegal instruction
in expression starting at /N/u/mraadam/Carbonate/.julia/packages/Parsers/w5O1u/src/floats.jl:646
mpfr_set_ui_2exp at /N/soft/rhel7/gcc/infrastructure/lib/libmpfr.so.6 (unknown line)
mpfr_ui_pow at /N/soft/rhel7/gcc/infrastructure/lib/libmpfr.so.6 (unknown line)
exp10 at ./mpfr.jl:637
exp10 at ./math.jl:1491 [inlined]
#37 at ./none:0 [inlined]
iterate at ./generator.jl:47 [inlined]
collect at ./array.jl:782
unknown function (ip: 0x7f79240af542)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
_include at ./loading.jl:1963
include at ./Base.jl:457
jfptr_include_35036.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
jl_f__call_latest at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/builtins.c:774
include at /N/u/mraadam/Carbonate/.julia/packages/Parsers/w5O1u/src/Parsers.jl:1
unknown function (ip: 0x7f79240a5322)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_eval_module_expr at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:203 [inlined]
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:715
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/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_38866.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
do_call at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:126
eval_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:226
eval_stmt_value at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:177 [inlined]
eval_body at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:624
jl_interpret_toplevel_thunk at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/interpreter.c:762
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:912
jl_toplevel_eval_flex at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/toplevel.c:856
ijl_toplevel_eval_in at /cache/build/default-amdci5-5/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_40034.clone_1 at /geode2/soft/hps/rhel7/julia/1.9.3/lib/julia/sys.so (unknown line)
_jl_invoke at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2758 [inlined]
ijl_apply_generic at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/gf.c:2940
jl_apply at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/julia.h:1880 [inlined]
true_main at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/jlapi.c:573
jl_repl_entrypoint at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/src/jlapi.c:717
main at /cache/build/default-amdci5-5/julialang/julia-release-1-dot-9/cli/loader_exe.c:59
__libc_start_main at /lib64/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
Allocations: 2997 (Pool: 2985; Big: 12); GC: 0
ERROR: LoadError: Failed to precompile Parsers [69de0a69-1ddd-5017-9359-2bf0b02dc9f0] to "/N/u/mraadam/Carbonate/.julia/compiled/v1.9/Parsers/jl_smlrR2".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base ./loading.jl:2300
  [3] compilecache
    @ ./loading.jl:2167 [inlined]
  [4] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:1805
  [5] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:1660
  [6] macro expansion
    @ ./loading.jl:1648 [inlined]
  [7] macro expansion
    @ ./lock.jl:267 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:1611
  [9] include(mod::Module, _path::String)
    @ Base ./Base.jl:457
 [10] include(x::String)
    @ JSON ~/.julia/packages/JSON/93Ea8/src/JSON.jl:3
 [11] top-level scope
    @ ~/.julia/packages/JSON/93Ea8/src/JSON.jl:11
 [12] include
    @ ./Base.jl:457 [inlined]
 [13] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
    @ Base ./loading.jl:2049
 [14] top-level scope
    @ stdin:3
in expression starting at /N/u/mraadam/Carbonate/.julia/packages/JSON/93Ea8/src/Parser.jl:1
in expression starting at /N/u/mraadam/Carbonate/.julia/packages/JSON/93Ea8/src/JSON.jl:3
in expression starting at stdin:3

[aadam]

I’ve tried using julia --pkgimages=no, but I’m still not able to import Parsers. It’s giving the same error. Do I need to do something else as well?

[giordano]

@aadam

Invalid instruction at 0x7fa9cf9b40c6: 0xc4, 0x42, 0x81, 0xf7, 0xe4, 0x31, 0xf6, 0x48, 0xc1, 0xfa, 0x06, 0x48, 0xc1, 0xe2, 0x03

[31641] signal (4.2): Illegal instruction
in expression starting at /N/u/mraadam/Carbonate/.julia/packages/Parsers/w5O1u/src/floats.jl:646
mpfr_set_ui_2exp at /N/soft/rhel7/gcc/infrastructure/lib/libmpfr.so.6 (unknown line)
mpfr_ui_pow at /N/soft/rhel7/gcc/infrastructure/lib/libmpfr.so.6 (unknown line)
exp10 at ./mpfr.jl:637

How did you install Julia? Looking at the path of libmpfr makes me think you aren’t using the official binaries. Or maybe the problem is your superlong LD_LIBRARY_PATH, there’s everything in there.

[aadam]

I loaded the module on the HPC cluster using the following command:

module load julia

I have no idea how they’ve installed it and what CPU architectures are available. I have just started my Ph.D. and everything is so new to me right now.

[giordano]

Can you please try to start Julia with

LD_LIBRARY_PATH='' julia

and see if that makes any difference? I don’t know how the system you’re using works, so this might as well be worse than before, but worth a try.

If that doesn’t work, my next attempt would be to download the official binary of Julia from Download Julia and start that one, again with LD_LIBRARY_PATH set to an empty string, to rule out interferences from the external system.

[mkitti]

It might be worthwhile to just download the official tarball and try that along with the above instructions.

[johnh]

@aadam Please tell us something about your HPC cluster. How exactly are you doing these operations. Are you ssh ing into a login node?

[aadam]

Yes. I usually use ThinLinc client to connect to the HPC. I’ve also tried ssh ing into the login node recently.

[aadam]

Sorry for the late reply. The HPC is down for maintenance. As soon as it gets back up, I’ll try the recommended steps and let you guys know. Many thanks for the help.

[johnh]

You need biscuits for this problem. Bring biscuits to your friendly system administrators.

(Yes I know they dress in black and growl at you when you approach their domain)

[aadam]

Great news guys. They took down the HPC yesterday for maintenance, and now when it’s back online, everything seems to be working fine, automagically. I wonder what the issue was, but for now, everything is precompiling and installing fine. Yay.