Unable to compile system image in Docker

[opus111]

I was trying to build a Docker containing a custom system image. I created the image in my Dockerfile. Unfortunately it blows up

[ Info: Compiling system image...
Activating environment at `/tmp/tmp.pyjulia.sysimage.7sjkrpb1/Project.toml`
ERROR: LoadError: LoadError: 
signal (11): Segmentation fault
in expression starting at none:1
unknown function (ip: 0x7fc012b28bff)
_pycall! at /root/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:29
_pycall! at /root/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:11 [inlined]
#pycall#109 at /root/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:83 [inlined]
pycall at /root/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:83 [inlined]
show at /root/.julia/packages/PyCall/ttONZ/src/exception.jl:41
showerror at ./errorshow.jl:30 [inlined]
#626 at ./errorshow.jl:80
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
#with_output_color#674 at ./util.jl:366
with_output_color at ./util.jl:364
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
#showerror#625 at ./errorshow.jl:79
#showerror at ./none:0
unknown function (ip: 0x7fc015284d9b)
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
#showerror#628 at ./errorshow.jl:89
#showerror at ./none:0
unknown function (ip: 0x7fc01528413b)
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2191
#showerror#628 at ./errorshow.jl:89
#showerror at ./none:0
unknown function (ip: 0x7fc01528413b)
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
show_exception_stack at ./errorshow.jl:652
display_error at ./client.jl:110
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
display_error at ./client.jl:112
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1614 [inlined]
jl_f__apply at /buildworker/worker/package_linux64/build/src/builtins.c:563
jl_f__apply_latest at /buildworker/worker/package_linux64/build/src/builtins.c:601
#invokelatest#1 at ./essentials.jl:790 [inlined]
invokelatest at ./essentials.jl:789 [inlined]
exec_options at ./client.jl:297
_start at ./client.jl:464
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1614 [inlined]
jl_f__apply at /buildworker/worker/package_linux64/build/src/builtins.c:563
jl_f__apply_latest at /buildworker/worker/package_linux64/build/src/builtins.c:601
#invokelatest#1 at ./essentials.jl:790 [inlined]
invokelatest at ./essentials.jl:789
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2197
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:323
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:411
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:362 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:772
jl_interpret_toplevel_thunk_callback at /buildworker/worker/package_linux64/build/src/interpreter.c:884
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x7fc01806ad0f)
unknown function (ip: 0x1)
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:893
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:815
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:764
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:844
jl_eval_string at /buildworker/worker/package_linux64/build/src/jlapi.c:94
ffi_call_unix64 at /usr/lib/x86_64-linux-gnu/libffi.so.6 (unknown line)
ffi_call at /usr/lib/x86_64-linux-gnu/libffi.so.6 (unknown line)
_ctypes_callproc at /usr/lib/python3.7/lib-dynload/_ctypes.cpython-37m-x86_64-linux-gnu.so (unknown line)
unknown function (ip: 0x7fc02807f683)
_PyObject_FastCallKeywords at /usr/bin/python3 (unknown line)
unknown function (ip: 0x54aec0)
_PyEval_EvalFrameDefault at /usr/bin/python3 (unknown line)
_PyEval_EvalCodeWithName at /usr/bin/python3 (unknown line)
_PyFunction_FastCallDict at /usr/bin/python3 (unknown line)
_PyEval_EvalFrameDefault at /usr/bin/python3 (unknown line)
_PyEval_EvalCodeWithName at /usr/bin/python3 (unknown line)
_PyFunction_FastCallKeywords at /usr/bin/python3 (unknown line)
_PyEval_EvalFrameDefault at /usr/bin/python3 (unknown line)
_PyEval_EvalCodeWithName at /usr/bin/python3 (unknown line)
PyEval_EvalCode at /usr/bin/python3 (unknown line)
unknown function (ip: 0x630af1)
PyRun_FileExFlags at /usr/bin/python3 (unknown line)
PyRun_SimpleFileExFlags at /usr/bin/python3 (unknown line)
unknown function (ip: 0x653f7d)
_Py_UnixMain at /usr/bin/python3 (unknown line)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_start at /usr/bin/python3 (unknown line)
Allocations: 7688631 (Pool: 7686558; Big: 2073); GC: 16
ERROR: LoadError: failed process: Process(`/usr/bin/julia-py --optimize=3 --output-o=/root/.julia/packages/PackageCompiler/4yNnV/sysimg/sys.a -g1 --track-allocation=none --startup-file=no --code-coverage=none --history-file=yes --inline=yes --math-mode=ieee --handle-signals=yes --warn-overwrite=no --compile=yes --depwarn=yes --cpu-target=native --track-allocation=none --sysimage-native-code=yes --sysimage=/usr/local/julia/lib/julia/sys.so -g1 --compiled-modules=yes --optimize=2 /root/.julia/packages/PackageCompiler/4yNnV/sysimg/run_julia_code.jl`, ProcessSignaled(11)) [0]

Stacktrace:
 [1] pipeline_error at ./process.jl:813 [inlined]
 [2] #run#536(::Bool, ::typeof(run), ::Cmd) at ./process.jl:728
 [3] #run_julia#1 at ./process.jl:726 [inlined]
 [4] #run_julia at ./none:0 [inlined]
 [5] #compile_incremental#62(::Bool, ::Bool, ::Bool, ::Nothing, ::typeof(compile_incremental), ::String, ::String) at /root/.julia/packages/PackageCompiler/4yNnV/src/incremental.jl:137
 [6] compile_incremental(::String, ::String) at /root/.julia/packages/PackageCompiler/4yNnV/src/incremental.jl:134
 [7] top-level scope at /usr/local/lib/python3.7/dist-packages/julia/compile.jl:27
 [8] include at ./boot.jl:328 [inlined]
 [9] include_relative(::Module, ::String) at ./loading.jl:1094
 [10] include(::Module, ::String) at ./Base.jl:31
 [11] exec_options(::Base.JLOptions) at ./client.jl:295
 [12] _start() at ./client.jl:464
 [13] #invokelatest#1 at ./essentials.jl:790 [inlined]
 [14] invokelatest(::Any) at ./essentials.jl:789
 [15] top-level scope at none:1
in expression starting at /usr/local/lib/python3.7/dist-packages/julia/compile.jl:27
Command '['/usr/bin/julia-py', '--julia', 'julia', '/usr/local/lib/python3.7/dist-packages/julia/compile.jl', '/tmp/tmp.pyjulia.sysimage.7sjkrpb1/compiler_env', '/usr/local/lib/python3.7/dist-packages/julia/precompile.jl', '/app/bug.so']' returned non-zero exit status 1.
The command '/bin/sh -c python3 -m julia.sysimage  /app/bug.so' returned a non-zero code: 1

Dockerfile to recreate problem

FROM julia:latest

WORKDIR /app

RUN apt-get update
RUN apt-get install python3 python3-pip -y
RUN pip3 install --upgrade pip

RUN python3 -m pip install julia
RUN python3 -c "import julia; julia.install()"

RUN cp -r /usr/local/bin/* /usr/bin
RUN python3 -m julia.sysimage  /app/bug.so

[xiaodaigh]

@opus11 you might want to check this out https://discourse.julialang.org/t/docker-image-with-compiled-packages-for-instant-loading/32871

See https://hub.docker.com/r/xiaodaidocker2019/julia-data-science-base

[KristofferC]

I ran the docker script again and it works fine:

[ Info: Compiling system image...
[ Info: ===== Start precompile execution =====
[ Info: ===== End precompile execution =====
[ Info: PackageCompiler: creating system image object file, this might take a while...
[ Info: System image is created at /app/bug.so

So I think this has been fixed in newer Julia versions.