Pkg.instantiate errors with signal 6 (abort) in emulated arm64 container on docker on macOS

[stemann]

julia --eval 'using Pkg; Pkg.instantiate()' errors with signal 6 (abort) from libc when run as the entrypoint in a qemu-emulated linux/arm64 Julia 1.6 container on Docker for Mac on x86_64:

docker run -it --rm --platform=linux/arm64 -v `pwd`/Foo:/project julia:1.6 julia --project=/project --eval 'using Pkg; Pkg.instantiate()'

See stack trace below. Foo is just an empty project.

Oddly, it works in the REPL:

docker run -it --rm --platform=linux/arm64 -v `pwd`/Foo:/project julia:1.6 julia --project=/project
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.6.5 (2021-12-19)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> versioninfo()
Julia Version 1.6.5
Commit 9058264a69 (2021-12-19 12:30 UTC)
Platform Info:
  OS: Linux (aarch64-unknown-linux-gnu)
  CPU: unknown
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-11.0.1 (ORCJIT, generic)
Environment:
  JULIA_VERSION = 1.6.5
  JULIA_GPG = 3673DF529D9049477F76B37566E3C7DC03D6E495
  JULIA_PATH = /usr/local/julia

(Foo) pkg> instantiate
  Installing known registries into `~/.julia`
       Added registry `General` to `~/.julia/registries/General`
  No Changes to `/project/Project.toml`
  No Changes to `/project/Manifest.toml`

(Foo) pkg>

Minimal reproducible example on Julia 1.6

Generate a project:

julia --eval 'using Pkg; Pkg.generate("Foo")'

Instantiate in a linux/arm64 container (on macOS):

docker run -it --rm --platform=linux/arm64 -v `pwd`/Foo:/project julia:1.6 julia --project=/project --eval 'using Pkg; Pkg.instantiate()'

  Installing known registries into `~/.julia`
       Added
signal (6): Aborted
in expression starting at none:1
gsignal at /lib/aarch64-linux-gnu/libc.so.6 (unknown line)
abort at /lib/aarch64-linux-gnu/libc.so.6 (unknown line)
uv__io_poll at /workspace/srcdir/libuv/src/unix/epoll.c:288
uv_run at /workspace/srcdir/libuv/src/unix/core.c:383
jl_task_get_next at /buildworker/worker/package_linuxaarch64/build/src/partr.c:472
poptask at ./task.jl:760
wait at ./task.jl:769
uv_write at ./stream.jl:992
unsafe_write at ./stream.jl:1064
write at ./strings/io.jl:185 [inlined]
print at ./strings/io.jl:187 [inlined]
#with_output_color#815 at ./util.jl:91
with_output_color##kw at ./util.jl:71 [inlined]
#printstyled#816 at ./util.jl:105 [inlined]
printstyled##kw at ./util.jl:105 [inlined]
#printpkgstyle#106 at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:1406
printpkgstyle at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:1404
jfptr_printpkgstyle_53959 at /usr/local/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linuxaarch64/build/src/gf.c:2237 [inlined]
jl_apply_generic at /buildworker/worker/package_linuxaarch64/build/src/gf.c:2419
printpkgstyle at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:1401
printpkgstyle at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:1401 [inlined]
#82 at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:1076
#mktempdir#21 at ./file.jl:729
mktempdir at ./file.jl:727 [inlined]
mktempdir at ./file.jl:727 [inlined]
clone_or_cp_registries at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:1027
clone_or_cp_registries at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:1020 [inlined]
#clone_default_registries#67 at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:920
clone_default_registries at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:908 [inlined]
find_registered! at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:1291
find_registered! at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:1252 [inlined]
deps_graph at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:523
resolve_versions! at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:407
up at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1323
#up#109 at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:261
up##kw at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:237 [inlined]
#up#41 at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:84 [inlined]
up##kw at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:84 [inlined]
#instantiate#253 at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:1342
instantiate at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:1325 [inlined]
#instantiate#252 at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:1321 [inlined]
instantiate at /buildworker/worker/package_linuxaarch64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:1321
unknown function (ip: 0x55258040ef)
_jl_invoke at /buildworker/worker/package_linuxaarch64/build/src/gf.c:2237 [inlined]
jl_apply_generic at /buildworker/worker/package_linuxaarch64/build/src/gf.c:2419
jl_apply at /buildworker/worker/package_linuxaarch64/build/src/julia.h:1703 [inlined]
do_call at /buildworker/worker/package_linuxaarch64/build/src/interpreter.c:115
eval_value at /buildworker/worker/package_linuxaarch64/build/src/interpreter.c:204
eval_stmt_value at /buildworker/worker/package_linuxaarch64/build/src/interpreter.c:155 [inlined]
eval_body at /buildworker/worker/package_linuxaarch64/build/src/interpreter.c:576
jl_interpret_toplevel_thunk at /buildworker/worker/package_linuxaarch64/build/src/interpreter.c:670
jl_toplevel_eval_flex at /buildworker/worker/package_linuxaarch64/build/src/toplevel.c:877
jl_toplevel_eval_flex at /buildworker/worker/package_linuxaarch64/build/src/toplevel.c:825
jl_toplevel_eval_flex at /buildworker/worker/package_linuxaarch64/build/src/toplevel.c:825
jl_toplevel_eval_in at /buildworker/worker/package_linuxaarch64/build/src/toplevel.c:929
eval at ./boot.jl:360 [inlined]
exec_options at ./client.jl:261
_start at ./client.jl:485
jfptr__start_30860 at /usr/local/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linuxaarch64/build/src/gf.c:2237 [inlined]
jl_apply_generic at /buildworker/worker/package_linuxaarch64/build/src/gf.c:2419
jl_apply at /buildworker/worker/package_linuxaarch64/build/src/julia.h:1703 [inlined]
true_main at /buildworker/worker/package_linuxaarch64/build/src/jlapi.c:560
repl_entrypoint at /buildworker/worker/package_linuxaarch64/build/src/jlapi.c:702
main at /buildworker/worker/package_linuxaarch64/build/cli/loader_exe.c:51
__libc_start_main at /lib/aarch64-linux-gnu/libc.so.6 (unknown line)
_start at /usr/local/julia/bin/julia (unknown line)
_start at /usr/local/julia/bin/julia (unknown line)
Allocations: 3571658 (Pool: 3570672; Big: 986); GC: 5
qemu: uncaught target signal 6 (Aborted) - core dumped

[vtjnash]

I wonder if this will be fixed by #43664

[dnadlinger]

#43664 only changes the codegen for aarch64-darwin, so it probably won't be. The backtrace also appears to be in C code, while the segfaults due to invalid far jumps were in JIT-compiled code.