My company uses Anaconda python, so I’m trying to use pyjulia. I tried building a system image following the instructions in the docs, and ran into a segfault:
(pyjulia) evans-mbp:pyjl_test evan$ which python3
/Users/evan/anaconda3/envs/pyjulia/bin/python3
(pyjulia) evans-mbp:pyjl_test evan$ otool -L /Users/evan/anaconda3/envs/pyjulia/bin/python | grep libpython
(pyjulia) evans-mbp:pyjl_test evan$ python3 -m julia.sysimage sys.dylib
Output of build attempt
[ Info: activating new environment at /var/folders/q2/ynpv3jg56j54gy_ycgh3wnjr0000gn/T/tmp.pyjulia.sysimage.c8mgu6ip/compiler_env.
[ Info: Installing PackageCompiler...
Updating registry at `~/.julia/registries/General`
Updating git-repo `https://github.com/JuliaRegistries/General.git`
Resolving package versions...
Updating `/private/var/folders/q2/ynpv3jg56j54gy_ycgh3wnjr0000gn/T/tmp.pyjulia.sysimage.c8mgu6ip/compiler_env/Project.toml`
[9b87118b] + PackageCompiler v0.6.3
Updating `/private/var/folders/q2/ynpv3jg56j54gy_ycgh3wnjr0000gn/T/tmp.pyjulia.sysimage.c8mgu6ip/compiler_env/Manifest.toml`
[c7e460c6] + ArgParse v0.6.2
[9e28174c] + BinDeps v0.8.10
[b99e7846] + BinaryProvider v0.5.4
[e1450e63] + BufferedStreams v1.0.0
[34da2185] + Compat v2.1.0
[0862f596] + HTTPClient v0.2.1
[b27032c2] + LibCURL v0.5.0
[522f3ed2] + LibExpat v0.5.0
[2ec943e9] + Libz v1.0.0
[9b87118b] + PackageCompiler v0.6.3
[b718987f] + TextWrap v0.3.0
[30578b45] + URIParser v0.4.0
[c17dfb99] + WinRPM v0.4.2
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[ Info: Installing GCC
[ Info: Using `cc` as C compiler
[ Info: Loading PackageCompiler...
[ Info: PackageCompiler is successfully installed at /var/folders/q2/ynpv3jg56j54gy_ycgh3wnjr0000gn/T/tmp.pyjulia.sysimage.c8mgu6ip/compiler_env
[ Info: Loading PackageCompiler...
[ Info: Installing PyCall...
Updating registry at `~/.julia/registries/General`
Updating git-repo `https://github.com/JuliaRegistries/General.git`
Resolving package versions...
Updating `/private/var/folders/q2/ynpv3jg56j54gy_ycgh3wnjr0000gn/T/tmp.pyjulia.sysimage.c8mgu6ip/Project.toml`
[1914dd2f] + MacroTools v0.5.0
[438e738f] + PyCall v1.91.2
Updating `/private/var/folders/q2/ynpv3jg56j54gy_ycgh3wnjr0000gn/T/tmp.pyjulia.sysimage.c8mgu6ip/Manifest.toml`
[00ebfdb7] + CSTParser v0.5.2
[34da2185] + Compat v2.1.0
[8f4d0f93] + Conda v1.2.0
[864edb3b] + DataStructures v0.15.0
[682c06a0] + JSON v0.20.0
[1914dd2f] + MacroTools v0.5.0
[bac558e1] + OrderedCollections v1.1.0
[438e738f] + PyCall v1.91.2
[0796e94c] + Tokenize v0.5.3
[81def892] + VersionParsing v1.1.3
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[ Info: Compiling system image...
ERROR: LoadError: LoadError:
signal (11): Segmentation fault: 11
in expression starting at no file:0
PyObject_Call at /Users/evan/anaconda3/envs/pyjulia/lib/libpython3.7m.dylib (unknown line)
macro expansion at /Users/evan/.julia/packages/PyCall/ttONZ/src/exception.jl:81 [inlined]
__pycall! at /Users/evan/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:44
_pycall! at /Users/evan/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:29
_pycall! at /Users/evan/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:11 [inlined]
#pycall#109 at /Users/evan/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:83 [inlined]
pycall at /Users/evan/.julia/packages/PyCall/ttONZ/src/pyfncall.jl:83 [inlined]
show at /Users/evan/.julia/packages/PyCall/ttONZ/src/exception.jl:41
showerror at ./errorshow.jl:30 [inlined]
#624 at ./errorshow.jl:80
jl_fptr_trampoline at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1864
#with_output_color#671 at ./util.jl:366
unknown function (ip: 0x11c42d0c2)
jl_fptr_trampoline at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1864
with_output_color at ./util.jl:364
jl_fptr_trampoline at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1864
#showerror#623 at ./errorshow.jl:79
unknown function (ip: 0x11c428132)
jl_fptr_trampoline at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1864
#showerror at ./none:0
unknown function (ip: 0x11c427d1b)
jl_fptr_trampoline at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1864
#showerror#626 at ./errorshow.jl:89
#showerror at ./none:0
unknown function (ip: 0x11c426a4b)
jl_fptr_trampoline at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1864
#showerror#626 at ./errorshow.jl:89
unknown function (ip: 0x11c4268a2)
jl_fptr_trampoline at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1864
showerror at ./errorshow.jl:88 [inlined]
display_error at ./client.jl:99
jl_fptr_trampoline at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1864
display_error at ./client.jl:102
jl_fptr_trampoline at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1864
jl_apply at /Users/osx/buildbot/slave/package_osx64/build/src/./julia.h:1571 [inlined]
jl_f__apply at /Users/osx/buildbot/slave/package_osx64/build/src/builtins.c:556
jl_f__apply_latest at /Users/osx/buildbot/slave/package_osx64/build/src/builtins.c:594
#invokelatest#1 at ./essentials.jl:742 [inlined]
invokelatest at ./essentials.jl:741 [inlined]
exec_options at ./client.jl:269
_start at ./client.jl:436
jl_fptr_trampoline at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1864
jl_apply at /Users/osx/buildbot/slave/package_osx64/build/src/./julia.h:1571 [inlined]
jl_f__apply at /Users/osx/buildbot/slave/package_osx64/build/src/builtins.c:556
jl_f__apply_latest at /Users/osx/buildbot/slave/package_osx64/build/src/builtins.c:594
#invokelatest#1 at ./essentials.jl:742 [inlined]
invokelatest at ./essentials.jl:741
jl_fptr_trampoline at /Users/osx/buildbot/slave/package_osx64/build/src/gf.c:1864
do_call at /Users/osx/buildbot/slave/package_osx64/build/src/interpreter.c:323
eval_stmt_value at /Users/osx/buildbot/slave/package_osx64/build/src/interpreter.c:362 [inlined]
eval_body at /Users/osx/buildbot/slave/package_osx64/build/src/interpreter.c:759
jl_interpret_toplevel_thunk_callback at /Users/osx/buildbot/slave/package_osx64/build/src/interpreter.c:885
unknown function (ip: 0xfffffffffffffffe)
unknown function (ip: 0x1202a366f)
unknown function (ip: 0x1)
jl_interpret_toplevel_thunk at /Users/osx/buildbot/slave/package_osx64/build/src/interpreter.c:894
jl_toplevel_eval_flex at /Users/osx/buildbot/slave/package_osx64/build/src/toplevel.c:764
jl_toplevel_eval at /Users/osx/buildbot/slave/package_osx64/build/src/toplevel.c:773 [inlined]
jl_toplevel_eval_in at /Users/osx/buildbot/slave/package_osx64/build/src/toplevel.c:793
jl_eval_string at /Users/osx/buildbot/slave/package_osx64/build/src/jlapi.c:94
ffi_call_unix64 at /Users/evan/anaconda3/envs/pyjulia/lib/libffi.6.dylib (unknown line)
ffi_call at /Users/evan/anaconda3/envs/pyjulia/lib/libffi.6.dylib (unknown line)
_ctypes_callproc at /Users/evan/anaconda3/envs/pyjulia/lib/python3.7/lib-dynload/_ctypes.cpython-37m-darwin.so (unknown line)
PyCFuncPtr_call at /Users/evan/anaconda3/envs/pyjulia/lib/python3.7/lib-dynload/_ctypes.cpython-37m-darwin.so (unknown line)
_PyObject_FastCallKeywords at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
call_function at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
_PyEval_EvalFrameDefault at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
_PyEval_EvalCodeWithName at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
_PyFunction_FastCallDict at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
_PyEval_EvalFrameDefault at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
_PyEval_EvalCodeWithName at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
_PyFunction_FastCallKeywords at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
call_function at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
_PyEval_EvalFrameDefault at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
_PyEval_EvalCodeWithName at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
PyRun_FileExFlags at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
PyRun_SimpleFileExFlags at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
pymain_main at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
main at /Users/evan/anaconda3/envs/pyjulia/bin/python (unknown line)
Allocations: 8794096 (Pool: 8791813; Big: 2283); GC: 17
ERROR: LoadError: failed process: Process(`/Users/evan/anaconda3/envs/pyjulia/bin/julia-py --optimize=3 --output-o=/Users/evan/.julia/packages/PackageCompiler/oT98U/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=/Applications/Julia-1.1.app/Contents/Resources/julia/lib/julia/sys.dylib -g1 --compiled-modules=yes --optimize=2 /Users/evan/.julia/packages/PackageCompiler/oT98U/sysimg/run_julia_code.jl`, ProcessSignaled(11)) [0]
Stacktrace:
[1] error(::String, ::Base.Process, ::String, ::Int64, ::String) at ./error.jl:42
[2] pipeline_error at ./process.jl:785 [inlined]
[3] #run#515(::Bool, ::Function, ::Cmd) at ./process.jl:726
[4] run at ./process.jl:724 [inlined]
[5] #run_julia#1 at /Users/evan/.julia/packages/PackageCompiler/oT98U/src/compiler_flags.jl:225 [inlined]
[6] #run_julia at ./none:0 [inlined]
[7] #compile_incremental#62(::Bool, ::Bool, ::Bool, ::Nothing, ::Function, ::String, ::String) at /Users/evan/.julia/packages/PackageCompiler/oT98U/src/incremental.jl:82
[8] compile_incremental(::String, ::String) at /Users/evan/.julia/packages/PackageCompiler/oT98U/src/incremental.jl:79
[9] top-level scope at none:0
[10] include at ./boot.jl:326 [inlined]
[11] include_relative(::Module, ::String) at ./loading.jl:1038
[12] include(::Module, ::String) at ./sysimg.jl:29
[13] exec_options(::Base.JLOptions) at ./client.jl:267
[14] _start() at ./client.jl:436
[15] #invokelatest#1 at ./essentials.jl:742 [inlined]
[16] invokelatest(::Any) at ./essentials.jl:741
[17] top-level scope at none:0
in expression starting at /Users/evan/anaconda3/envs/pyjulia/lib/python3.7/site-packages/julia/compile.jl:27
Command '['/Users/evan/anaconda3/envs/pyjulia/bin/julia-py', '--julia', 'julia', '--color=yes', '/Users/evan/anaconda3/envs/pyjulia/lib/python3.7/site-packages/julia/compile.jl', '/var/folders/q2/ynpv3jg56j54gy_ycgh3wnjr0000gn/T/tmp.pyjulia.sysimage.c8mgu6ip/compiler_env', '/Users/evan/anaconda3/envs/pyjulia/lib/python3.7/site-packages/julia/precompile.jl', '/Users/evan/pyjl_test/sys.dylib']' returned non-zero exit status 1.
Thanks in advance for any suggestions.