macOS: System image file fails consistency check on binary startup #738

ghyatzo · 2022-11-09T23:48:25Z

Upon creating an app, the process goes on smoothly, untill it is time to actually call the binary.
I get the error: ERROR: System image file failed consistency check: maybe opened the wrong version?

Julia Version 1.8.2
Commit 36034abf260 (2022-09-29 15:21 UTC)
Platform Info:
  OS: macOS (arm64-apple-darwin21.3.0)
  CPU: 10 × Apple M1 Pro
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, apple-m1)
  Threads: 8 on 8 virtual cores
Environment:
  JULIA_NUM_THREADS = 8
  JULIA_DEPOT_PATH = /Users/cshen/.local/julia

I installed julia through juliaup. the juliaup folder is in ~/.local/juliaup and the julia versions in ~/.local/julia/juliaup.
the binaries in ~/.local/juliaup/bin are symlinked to ~/.local/bin which is in the PATH.
I also have julia aliased to julia --project=@.

Could it be that the symlinking throws some pathing off somewhere?

The text was updated successfully, but these errors were encountered:

FerreolS · 2023-01-26T15:14:32Z

Similar issue here on

Julia Version 1.8.4
Commit 00177ebc4fc (2022-12-23 21:32 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin21.4.0)
  CPU: 16 × Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, skylake)
  Threads: 16 on 16 virtual cores
Environment:
  JULIA_NUM_THREADS = auto

the app execute smoothly when it is in the folder where it has been compiled but fail with ERROR: System image file failed consistency check: maybe opened the wrong version? when relocated anywhere else.
Using the example of the package

> Code/Julia/PackageCompiler.jl/examples/MyAppCompiled/bin/MyApp 
  Downloaded artifact: MKL
ARGS = String[]
Base.PROGRAM_FILE = "Code/Julia/PackageCompiler.jl/examples/MyAppCompiled/bin/MyApp"
...

> cp -r Code/Julia/PackageCompiler.jl/examples/MyAppCompiled .
> MyAppCompiled/bin/MyApp                                     
ERROR: System image file failed consistency check: maybe opened the wrong version?

PhilReinhold · 2023-09-25T19:23:13Z

I'm running into this issue as well, just trying to build any sysimage, e.g.

PackageCompiler.create_sysimage(String[], sysimage_path="test_image.so")

then

julia --sysimage=test_image.so gives the same error as above.

Julia Version 1.9.3
Commit bed2cd540a1 (2023-08-24 14:43 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: macOS (arm64-apple-darwin22.4.0)
  CPU: 12 × Apple M2 Pro
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, apple-m1)
  Threads: 1 on 8 virtual cores
Environment:
  JULIA_PKG_USE_CLI_GIT = true

kevmoor · 2023-09-27T16:08:54Z

Same issue, tried on Julia 1.9.3, 1.9.2, 1.10.0-beta2, all with PackageCompiler version 2.1.9, also tried on Julia 1.9.2 with PackageCompiler version 2.1.7 (the mix I had when I last had it running a few weeks ago), this versioninfo() below is from this latest combination.

Julia Version 1.9.2
Commit e4ee485e909 (2023-07-05 09:39 UTC)
Platform Info:
  OS: macOS (arm64-apple-darwin22.4.0)
  CPU: 10 × Apple M1 Pro
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, apple-m1)
  Threads: 1 on 8 virtual cores
Environment:
  JULIA_PKG_USE_CLI_GIT = true

KwatMDPhD · 2023-10-26T16:02:16Z

I'm seeing the same error when building KwatMDPhD/GSEA.jl@79364ca

comonicon/Comonicon.jl#264

sloede · 2023-10-26T16:19:56Z

I'm seeing the same error when building KwatMDPhD/GSEA.jl@79364ca

comonicon/Comonicon.jl#264

This happens on macOS only?

KwatMDPhD · 2023-10-26T17:38:56Z

I have only tried on macOS Sonoma 14.0.
If you have a non-mac machine, you can clone the above commit and try julia --project deps/build.lj app.

jayscook · 2023-10-30T16:16:23Z

I'm still getting the error on PackageCompiler 2.1.11 (which specifically addresses this issue) on macOS Ventura (13.6). Running Julia 1.8.5, not sure if 1.9 is required for the fix.

sloede · 2023-10-30T16:18:45Z

Thanks for reporting. Just to clarify: There is no fix available as of yet (also not in PC v2.1.11)

jayscook · 2023-10-30T16:21:48Z

Thanks for reporting. Just to clarify: There is no fix available as of yet (also not in PC v2.1.11)

Thanks for clarifying! I assumed that the closed issue indicated that it was fixed.

Please let me know if I can contribute to a fix in some way.

sloede · 2023-10-30T16:23:34Z

Please let me know if I can contribute to a fix in some way.

At the moment we are lacking an understanding of why the consistency check fails. If you manage to find out about this, we could start looking for a remedy 🙂

KwatMDPhD · 2023-10-30T21:49:07Z

I'm using 1.9.3

Would be great if this error can be fixed...

ctarn · 2023-10-31T12:31:01Z

I was able to build apps using Julia 1.9.0, PackageCompiler 2.1.7, and macOS 13. Recently I upgraded Julia to 1.9.3, PackageCompiler to 2.1.2, and macOS to 14, and the error occurred.

I tried to restore Julia to 1.9.0 and PackageCompiler to 2.1.7, and the error still occurs. So I guess macOS should cause it since Xcode Command Line Tools was also upgraded to 15, which is required by PackageCompiler to compile executables.

Unfortunately, when I tried to downgrade Xcode Command Line Tools, it warned that older version Xcode C. L. T. can not be installed on macOS 14... And I can not downgrade the OS... :(

I would recommend anyone (@jayscook ?) still using macOS 13 try to install an older version (v14.3?)of Xcode. It can be downloaded from: https://developer.apple.com/download/all/

bjarthur · 2023-10-31T21:43:40Z

i can't build sysimages on apple silicon either. please let me know how i can help fix it.

hycakir · 2023-11-02T21:57:13Z

I can confirm it is related to clang version. I have compiled MyLib with gcc from homebrew and it works.

ctarn · 2023-11-03T02:27:55Z

it really works! but remember to set the compiler to gcc-13 instead of just gcc since gcc is just an alias of clang by default.

you can specify the compiler by running an export in your shell:

export JULIA_CC="gcc-13"

sloede · 2023-11-03T03:35:54Z

Great catch! Could you please report which version of clang/gcc you are each using by default on your systems that works (using gcc --version), which version did not work, and the output of your Julia versioninfo()?

ctarn · 2023-11-03T04:04:02Z

clang v15 from Xcode CLT doesn't work

$ gcc --version
Apple clang version 15.0.0 (clang-1500.0.40.1)
Target: x86_64-apple-darwin23.1.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

(clang v14 should work, but older version Xcode CLT can not be installed on latest macOS)

gcc v13 from brew works

$ gcc-13 --version
gcc-13 (Homebrew GCC 13.2.0) 13.2.0
Copyright (C) 2023 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

versioninfo

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: macOS (x86_64-apple-darwin22.4.0)
  CPU: 16 × Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, skylake)
  Threads: 1 on 16 virtual cores
Environment:
  JULIA_CC = gcc-13

jayscook · 2023-11-03T15:59:55Z

Good catch!

I've installed gcc-13 with brew install gcc@13 and set it as an env var but am still getting the error after restarting the shell. Any thoughts on what I'm missing here?

$ gcc-13 --version
gcc-13 (Homebrew GCC 13.2.0) 13.2.0
Copyright (C) 2023 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

julia> versioninfo()
Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
  OS: macOS (arm64-apple-darwin21.5.0)
  CPU: 10 × Apple M1 Pro
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, apple-m1)
  Threads: 1 on 8 virtual cores
Environment:
  JULIA_CC = gcc-13

ctarn · 2023-11-03T16:48:46Z

Since the versions of Julia and LLVM are different, maybe you should try older versions of gcc or upgrade Julia to 1.9.

sloede · 2023-11-04T06:10:57Z

I've installed gcc-13 with brew install gcc@13 and set it as an env var but am still getting the error after restarting the shell. Any thoughts on what I'm missing here?

Hm, this is unfortunate. It also means we're back to square one, since I don't understand now (again) what the necessary conditions are to trigger the error.

hycakir · 2023-11-04T11:26:24Z

I've installed gcc-13 with brew install gcc@13 and set it as an env var but am still getting the error after restarting the shell. Any thoughts on what I'm missing here?
julia> versioninfo()
Julia Version 1.8.5
...
  JULIA_CC = gcc-13

This is expected as per JuliaLang/julia#49581. You should pick an earlier version of GCC/Clang or newer version of Julia.

sloede · 2023-11-04T11:59:02Z

@hycakir Thanks for letting us know, I didn't know about this!

@jayscook Could you please confirm that it works with gcc-12? If yes, we might want to add a note about this behavior to the docs.

KwatMDPhD · 2023-11-04T23:38:24Z

How can we make this work with the latest mac gcc? I would be nice to not have to downgrade.

sloede · 2023-11-05T05:31:07Z

How can we make this work with the latest mac gcc? I would be nice to not have to downgrade.

TBH, I do not know, since I neither know the rationale behind this check nor do I understand what it actually checks 😅 It seems this check was introduced in JuliaLang/julia@4e7ec79, specifically here.

@vtjnash can you maybe shed some light on this and help us understand

what exactly causes this error to appear when loading sysimages built with clang/gcc versions that are "too new" in some sense,
if there is anything we can do about it on PC side, and if not
what could be done on the Julia side to remedy this issue for building custom sysimages?

vtjnash · 2023-11-06T20:51:54Z

It simply checks if the symbol jl_RTLD_DEFAULT_handle_pointer exists, which is something added by codegen to the image, and that it linked to jl_RTLD_DEFAULT_handle. You may want to try setting LD_DEBUG to find out why this did not generate a completed dylib for you.

sloede · 2023-11-06T22:10:24Z

It simply checks if the symbol jl_RTLD_DEFAULT_handle_pointer exists, which is something added by codegen to the image, and that it linked to jl_RTLD_DEFAULT_handle. You may want to try setting LD_DEBUG to find out why this did not generate a completed dylib for you.

Thanks for the explanation! So you mean we should set LD_DEBUG when calling Julia with the broken sysimage? Can you tell us which value should we set the variable to? Also, this error does only seem to occur on macOS - there's no LD_DEBUG available IIRC, maybe you have an alternative?

Sorry for the many questions, we just don't have any enough experience to tackle this at the moment.

vtjnash · 2023-11-06T23:21:58Z

See man dyld for the available env options

sloede · 2023-11-07T10:53:53Z

I've been trying to reproduce the problem on my M1 Macbook, but without success so far - all my sysimages or apps I build seem to work.

@KwatMDPhD @bjarthur @hycakir @ctarn Can someone who had this problem please provide an MWE with a sysimage/app as small as possible and the exact commands you use to build it? In addition, please also post the output of gcc --version and Julia's versioninfo() such that we understand which environment is used exactly.

hycakir · 2023-11-10T20:47:58Z

@sloede I tried the same thing on my macbook with the same setup but it worked out just fine for me. One thing caught my attention: I do not receive the warning that you do with -lgcc. Reading the discussions here and here, this might be the culprit for your setup. Can you try uninstalling and installing (or updating) gcc@12 as it seems to have been resolved by Homebrew/homebrew-core#149350?

julia> versioninfo()
Julia Version 1.9.1
Commit 147bdf428cd (2023-06-07 08:27 UTC)
Platform Info:
  OS: macOS (arm64-apple-darwin22.4.0)
  CPU: 8 × Apple M1 Pro
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, apple-m1)
  Threads: 1 on 6 virtual cores
Environment:
  JULIA_CC = gcc-12

PhilReinhold · 2023-12-04T15:36:30Z

I'll admit that I don't really understand what's going on here, but I saw this exhortation of success by adding the flags -Wl,-ld_classic, and decided to try it here.

I modified o_file_flags in PackageCompiler.jl:create_sysimg_from_object_file like so

function create_sysimg_from_object_file(object_files::Vector{String},
                                        sysimage_path::String;
                                        version,
                                        compat_level::String,
                                        soname::Union{Nothing, String})

    if soname === nothing && (Sys.isunix() && !Sys.isapple())
        soname = basename(sysimage_path)
    end
    mkpath(dirname(sysimage_path))
    # Prevent compiler from stripping all symbols from the shared lib.
    o_file_flags = Sys.isapple() ? `-Wl,-all_load $object_files -Wl,-ld_classic` : `-Wl,--whole-archive $object_files -Wl,--no-whole-archive`
    extra = get_extra_linker_flags(version, compat_level, soname)
    cmd = `$(bitflag()) $(march()) -shared -L$(julia_libdir()) -L$(julia_private_libdir()) -o $sysimage_path $o_file_flags $(Base.shell_split(ldlibs())) $extra`
    run_compiler(cmd; cplusplus=true)
    return nothing
end

and now I am able to produce sysimages following the tutorial which have symbols exported and julia happily loads, despite being on xcode CLT version 15.

Probably not the right course of action to just add this flag universally, but maybe having a mechanism for passing additional linker flags could be part of the create_sysimage interface.

DilumAluthge · 2023-12-06T14:20:34Z

Maybe helpful: you can use the open-source xcodes command-line tool to install and switch between different Xcode versions. So you could use xcodes to install Xcode 14.

Note: xcodes is a command-line tool, and it's the one that I prefer. However, there also is a GUI version, which is called Xcodes.app.

dokie · 2023-12-09T12:37:51Z

I'll admit that I don't really understand what's going on here, but I saw this exhortation of success by adding the flags -Wl,-ld_classic, and decided to try it here.

I modified o_file_flags in PackageCompiler.jl:create_sysimg_from_object_file like so
function create_sysimg_from_object_file(object_files::Vector{String},
                                        sysimage_path::String;
                                        version,
                                        compat_level::String,
                                        soname::Union{Nothing, String})

    if soname === nothing && (Sys.isunix() && !Sys.isapple())
        soname = basename(sysimage_path)
    end
    mkpath(dirname(sysimage_path))
    # Prevent compiler from stripping all symbols from the shared lib.
    o_file_flags = Sys.isapple() ? `-Wl,-all_load $object_files -Wl,-ld_classic` : `-Wl,--whole-archive $object_files -Wl,--no-whole-archive`
    extra = get_extra_linker_flags(version, compat_level, soname)
    cmd = `$(bitflag()) $(march()) -shared -L$(julia_libdir()) -L$(julia_private_libdir()) -o $sysimage_path $o_file_flags $(Basks for me on e.shell_split(ldlibs())) $extra`
    run_compiler(cmd; cplusplus=true)
    return nothing
end
and now I am able to produce sysimages following the tutorial which have symbols exported and julia happily loads, despite being on xcode CLT version 15.

Probably not the right course of action to just add this flag universally, but maybe having a mechanism for passing additional linker flags could be part of the create_sysimage interface.

I can confirm this works for me too on MacBook Air M1 with

Julia Version 1.9.4
Commit 8e5136fa297 (2023-11-14 08:46 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: macOS (arm64-apple-darwin22.4.0)
  CPU: 8 × Apple M1
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, apple-m1)
  Threads: 1 on 4 virtual cores

and

λ gcc --version
Apple clang version 15.0.0 (clang-1500.0.40.1)
Target: arm64-apple-darwin23.1.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

But as @PhilReinhold stated, that is one heck of a hack!

terasakisatoshi · 2023-12-15T03:43:23Z

#738 (comment) works on my Intel macOS :D

using PackageCompiler
using PackageCompiler: get_extra_linker_flags, julia_libdir, julia_private_libdir, ldlibs, bitflag, march, run_compiler
# https://github.com/JuliaLang/PackageCompiler.jl/issues/738#issuecomment-1838901893

# I know this causes type piracy, which is a bad solution, but it will save life for those who want to comple for macOS somehow
function PackageCompiler.create_sysimg_from_object_file(object_files::Vector{String},
                                        sysimage_path::String;
                                        version,
                                        compat_level::String,
                                        soname::Union{Nothing, String})

    if soname === nothing && (Sys.isunix() && !Sys.isapple())
        soname = basename(sysimage_path)
    end
    mkpath(dirname(sysimage_path))
    # Prevent compiler from stripping all symbols from the shared lib.
    o_file_flags = Sys.isapple() ? `-Wl,-all_load $object_files -Wl,-ld_classic` : `-Wl,--whole-archive $object_files -Wl,--no-whole-archive`
    extra = get_extra_linker_flags(version, compat_level, soname)
    cmd = `$(bitflag()) $(march()) -shared -L$(julia_libdir()) -L$(julia_private_libdir()) -o $sysimage_path $o_file_flags $(Base.shell_split(ldlibs())) $extra`
    run_compiler(cmd; cplusplus=true)
    return nothing
end

using MyExe

create_app(pkgdir(MyExe), "build", force=true)

Apple Clang (15.0.0) and Julia 1.10:

This does not work out-of-the-box:

% ls -la MySysimagePrecompile.dylib
-rwxr-xr-x   1 justme  staff  16768 Jan 23 21:33 MySysimagePrecompile.dylib

% nm -g MySysimagePrecompile.dylib 
MySysimagePrecompile.dylib: no symbols

gcc-13 (13.2.0) and Julia 1.10:

This does not work out-of-the-box:

% ls -la MySysimagePrecompile.dylib
-rwxr-xr-x   1 justme  staff  2662912 Jan 23 21:36 MySysimagePrecompile.dylib

% nm -g MySysimagePrecompile.dylib 
00000000000143f0 T ___bid128_abs
00000000000201f0 T ___bid128_add
0000000000014410 T ___bid128_class
00000000000143d4 T ___bid128_copy
0000000000014400 T ___bid128_copySign
0000000000029de0 T ___bid128_div
000000000001bd54 T ___bid128_fma
000000000001f010 T ___bid128_from_int32
000000000001f040 T ___bid128_from_int64
000000000001f030 T ___bid128_from_uint32

... list continues ...

U _realloc
U _sys_icache_invalidate

Manual edit of PackageCompiler.jl w Apple Clang (15.0.0) and Julia 1.10

... that is addition of -Wl,-ld_classic to o_file_flags

This works:

% ls -la MySysimagePrecompile.dylib 
-rwxr-xr-x  1 justme  staff  450527424 Jan 23 22:12 MySysimagePrecompile.dylib

nm -g MySysimagePrecompile.dylib 
                 U ___divti3
                 U ___modti3
                 U ___udivti3
                 U ___umodti3
                 U _bzero
                 U _ijl_adopt_thread
                 U _ijl_apply_generic
                 U _ijl_boundp
                 U _ijl_bounds_error_int
                 U _ijl_bounds_error_ints
                 U _ijl_bounds_error_tuple_int
                 U _ijl_bounds_error_unboxed_int
                 U _ijl_box_char
                 U _ijl_box_float32
                 U _ijl_box_int16
                 U _ijl_box_int32
                 U _ijl_box_int64
                 U _ijl_box_ssavalue
                 U _ijl_box_uint16
                 U _ijl_box_uint32
                 U _ijl_box_uint64
                 U _ijl_checked_assignment
                 U _ijl_copy_ast
                 U _ijl_current_exception
                 U _ijl_enter_handler
                 U _ijl_error
                 U _ijl_excstack_state
                 U _ijl_field_index
                 U _ijl_gc_pool_alloc
                 U _ijl_gc_queue_root
                 U _ijl_get_binding_or_error
                 U _ijl_get_nth_field_checked
                 U _ijl_has_no_field_error
                 U _ijl_invoke
                 U _ijl_isa
                 U _ijl_lazy_load_and_lookup
                 U _ijl_load_and_lookup
                 U _ijl_new_structt
                 U _ijl_new_structv
                 U _ijl_object_id_
                 U _ijl_pop_handler
                 U _ijl_restore_excstack
                 U _ijl_subtype
                 U _ijl_throw
                 U _ijl_type_error
                 U _ijl_typeassert
                 U _ijl_undefined_var_error
                 U _jl_RTLD_DEFAULT_handle
00000000013bc3a8 S _jl_RTLD_DEFAULT_handle_pointer
                 U _jl_add_int
                 U _jl_boxed_int8_cache
                 U _jl_boxed_uint8_cache
                 U _jl_diverror_exception
                 U _jl_egal__unboxed
                 U _jl_emptytuple
                 U _jl_f__apply_iterate
                 U _jl_f__apply_pure
                 U _jl_f__call_in_world
                 U _jl_f__call_latest
                 U _jl_f__expr
                 U _jl_f__svec_ref
                 U _jl_f__typevar
                 U _jl_f_applicable
                 U _jl_f_apply_typ
                 U _jl_f_arraysize
                 U _jl_f_fieldtype
                 U _jl_f_finalizer
                 U _jl_f_getfield
                 U _jl_f_isa
                 U _jl_f_isdefined
                 U _jl_f_issubtype
                 U _jl_f_setfield
                 U _jl_f_sizeof
                 U _jl_f_svec
                 U _jl_f_tuple
                 U _jl_f_typeassert
                 U _jl_false
                 U _jl_field_isdefined_checked
00000000013c1580 D _jl_image_pointers
                 U _jl_libjulia_internal_handle
                 U _jl_neg_int
                 U _jl_not_int
                 U _jl_nothing
00000000013c15c0 D _jl_system_image_data
0000000001157118 S _jl_system_image_size
                 U _jl_true
                 U _jl_undefref_exception
                 U _jl_world_counter
                 U _jl_xor_int
                 U _julia__gnu_f2h_ieee
                 U _julia__gnu_h2f_ieee
                 U _julia__truncdfhf2
                 U _memcpy
                 U _memmove
                 U _memset
                 U _sigsetjmp

bjarthur · 2024-02-26T21:42:07Z

others have this problem too and used the same -ld_classic workaround: https://www.scivision.dev/xcode-ld_classic/. possibly needed because of weak references as described in the "known issues" section here: https://developer.apple.com/documentation/xcode-release-notes/xcode-15-release-notes#Linking

bjarthur · 2024-02-26T22:30:44Z

can someone with xcode version 14 or less try the -ld_classic workaround described above? if it continues to work, i'd suggest we just add it universally.

PhilReinhold · 2024-02-26T22:36:38Z

@bjarthur

Unfortunately I've seen this flag break compilation with xcode 14 since I think it's unrecognized. I've used the following locally to detect xcode version and conditionally apply the flag:

function PackageCompiler.create_sysimg_from_object_file(object_files::Vector{String},
                                        sysimage_path::String;
                                        version,
                                        compat_level::String,
                                        soname::Union{Nothing, String})

    if soname === nothing && (Sys.isunix() && !Sys.isapple())
        soname = basename(sysimage_path)
    end
    mkpath(dirname(sysimage_path))
    # Prevent compiler from stripping all symbols from the shared lib.
    if Sys.isapple()
        cltools_version_cmd = `pkgutil --pkg-info=com.apple.pkg.CLTools_Executables`
        cltools_version = match(r"version: (.*)\n", readchomp(cltools_version_cmd))[1]
        if startswith(cltools_version, "15")
            o_file_flags = `-Wl,-all_load $object_files -Wl,-ld_classic`
        else
            o_file_flags = `-Wl,-all_load $object_files`
        end
    else
        o_file_flags = `-Wl,--whole-archive $object_files -Wl,--no-whole-archive`
    end
    extra = get_extra_linker_flags(version, compat_level, soname)
    cmd = `$(bitflag()) $(march()) -shared -L$(julia_libdir()) -L$(julia_private_libdir()) -o $sysimage_path $o_file_flags $(Base.shell_split(ldlibs())) $extra`
    run_compiler(cmd; cplusplus=true)
    return nothing
end

bjarthur · 2024-02-27T23:27:53Z

@PhilReinhold submit a PR! is there any reason not to? you've found a nice solution and everyone here has verified it works for them.

thomasjankovic · 2024-03-20T17:44:04Z

I'll admit that I don't really understand what's going on here, but I saw this exhortation of success by adding the flags -Wl,-ld_classic, and decided to try it here.

I modified o_file_flags in PackageCompiler.jl:create_sysimg_from_object_file like so
function create_sysimg_from_object_file(object_files::Vector{String},
                                        sysimage_path::String;
                                        version,
                                        compat_level::String,
                                        soname::Union{Nothing, String})

    if soname === nothing && (Sys.isunix() && !Sys.isapple())
        soname = basename(sysimage_path)
    end
    mkpath(dirname(sysimage_path))
    # Prevent compiler from stripping all symbols from the shared lib.
    o_file_flags = Sys.isapple() ? `-Wl,-all_load $object_files -Wl,-ld_classic` : `-Wl,--whole-archive $object_files -Wl,--no-whole-archive`
    extra = get_extra_linker_flags(version, compat_level, soname)
    cmd = `$(bitflag()) $(march()) -shared -L$(julia_libdir()) -L$(julia_private_libdir()) -o $sysimage_path $o_file_flags $(Base.shell_split(ldlibs())) $extra`
    run_compiler(cmd; cplusplus=true)
    return nothing
end
and now I am able to produce sysimages following the tutorial which have symbols exported and julia happily loads, despite being on xcode CLT version 15.

Probably not the right course of action to just add this flag universally, but maybe having a mechanism for passing additional linker flags could be part of the create_sysimage interface.

Can confirm that this worked for me too. Julia 1.9.4 and gcc-13.

jayscook · 2024-04-03T19:05:00Z

Hey folks, I went ahead and opened a PR for @PhilReinhold's fix. I'd love it if someone can review! I haven't contributed here before so please let me know if I'm missing any conventions, considerations, etc.

rallen10 · 2024-05-13T19:52:32Z

@bjarthur

Unfortunately I've seen this flag break compilation with xcode 14 since I think it's unrecognized. I've used the following locally to detect xcode version and conditionally apply the flag:

function PackageCompiler.create_sysimg_from_object_file(object_files::Vector{String},
                                        sysimage_path::String;
                                        version,
                                        compat_level::String,
                                        soname::Union{Nothing, String})

    if soname === nothing && (Sys.isunix() && !Sys.isapple())
        soname = basename(sysimage_path)
    end
    mkpath(dirname(sysimage_path))
    # Prevent compiler from stripping all symbols from the shared lib.
    if Sys.isapple()
        cltools_version_cmd = `pkgutil --pkg-info=com.apple.pkg.CLTools_Executables`
        cltools_version = match(r"version: (.*)\n", readchomp(cltools_version_cmd))[1]
        if startswith(cltools_version, "15")
            o_file_flags = `-Wl,-all_load $object_files -Wl,-ld_classic`
        else
            o_file_flags = `-Wl,-all_load $object_files`
        end
    else
        o_file_flags = `-Wl,--whole-archive $object_files -Wl,--no-whole-archive`
    end
    extra = get_extra_linker_flags(version, compat_level, soname)
    cmd = `$(bitflag()) $(march()) -shared -L$(julia_libdir()) -L$(julia_private_libdir()) -o $sysimage_path $o_file_flags $(Base.shell_split(ldlibs())) $extra`
    run_compiler(cmd; cplusplus=true)
    return nothing
end

I was experiencing the same problem and I can confirm the above fix works on

Apple M1, Sonoma 14.4.1
julia v1.8.0
PackageCompiler v2.0.9
gcc --version Apple clang version 15.0.0 (clang-1500.3.9.4)

rallen10 · 2024-05-14T20:34:54Z

Similar issue here on

Julia Version 1.8.4
Commit 00177ebc4fc (2022-12-23 21:32 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin21.4.0)
  CPU: 16 × Intel(R) Core(TM) i9-9880H CPU @ 2.30GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-13.0.1 (ORCJIT, skylake)
  Threads: 16 on 16 virtual cores
Environment:
  JULIA_NUM_THREADS = auto

the app execute smoothly when it is in the folder where it has been compiled but fail with ERROR: System image file failed consistency check: maybe opened the wrong version? when relocated anywhere else. Using the example of the package

> Code/Julia/PackageCompiler.jl/examples/MyAppCompiled/bin/MyApp 
  Downloaded artifact: MKL
ARGS = String[]
Base.PROGRAM_FILE = "Code/Julia/PackageCompiler.jl/examples/MyAppCompiled/bin/MyApp"
...

> cp -r Code/Julia/PackageCompiler.jl/examples/MyAppCompiled .
> MyAppCompiled/bin/MyApp                                     
ERROR: System image file failed consistency check: maybe opened the wrong version?

@FerreolS did you ever get resolution for your problem? It seems to be closely-related-yet-distinct from the workarounds mentioned in this thread. After using @PhilReinhold fix I am able to build an app and run it in its build location; but now I am facing your problem where relocating the app causes the consistency check error to re-appear.

I've created a new issue: #943

ctarn · 2024-05-25T15:34:36Z

I run into the same problem again... I previously set JULIA_CC to gcc-13, and it doesn't work after some changes to my iMac (maybe updating OS).
So I switched back clang, and changed the flag to -Wl,-ld_classic, as suggested by @PhilReinhold, and it works now.

o_file_flags = Sys.isapple() ? `-Wl,-ld_classic,-all_load $object_files` : `-Wl,--whole-archive $object_files -Wl,--no-whole-archive`

Hope we can solve the issue soon.😵‍💫

stevezhaoUS · 2024-05-26T22:24:02Z

I have face the same issue, hope it can be fix soon.

ctarn mentioned this issue Oct 9, 2023

macOS: can not build app on macOS reporting System image file failed consistency check #864

Closed

sloede mentioned this issue Nov 3, 2023

Warn about potentially incompatible compiler #886

Draft

DilumAluthge changed the title ~~System Image file fails consistency check on binary startup.~~ macOS: System Image file fails consistency check on binary startup. Dec 6, 2023

DilumAluthge changed the title ~~macOS: System Image file fails consistency check on binary startup.~~ macOS: System image file fails consistency check on binary startup Dec 6, 2023

justinesjw mentioned this issue Jan 12, 2024

Error running snakemake gustaveroussy/sopa#10

Closed

sjkelly mentioned this issue Mar 18, 2024

Building "examples/MyLib" fails on macOS #928

Closed

gbaraldi linked a pull request Mar 19, 2024 that will close this issue

Change naming convention of object files to follow what Base Julia does #930

Open

roman-schaerer mentioned this issue Mar 21, 2024

Error when creating a c-callable library on MacOS #932

Open

jayscook mentioned this issue Apr 2, 2024

Fix bug in create_sysimg_from_object_file for Xcode 15 CLT #935

Open

rallen10 mentioned this issue May 14, 2024

Failed consistency check when trying to relocate compiled app (MacOS) #943

Closed

macOS: System image file fails consistency check on binary startup #738

macOS: System image file fails consistency check on binary startup #738

Comments

ghyatzo commented Nov 9, 2022

FerreolS commented Jan 26, 2023

PhilReinhold commented Sep 25, 2023 • edited

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hbe72 commented Jan 23, 2024 • edited

hbe72 commented Jan 23, 2024 • edited

Apple Clang (15.0.0) and Julia 1.10:

gcc-13 (13.2.0) and Julia 1.10:

Manual edit of PackageCompiler.jl w Apple Clang (15.0.0) and Julia 1.10

bjarthur commented Feb 26, 2024

bjarthur commented Feb 26, 2024

PhilReinhold commented Feb 26, 2024

bjarthur commented Feb 27, 2024

thomasjankovic commented Mar 20, 2024

jayscook commented Apr 3, 2024

rallen10 commented May 13, 2024

rallen10 commented May 14, 2024

ctarn commented May 25, 2024

stevezhaoUS commented May 26, 2024

PhilReinhold commented Sep 25, 2023 •

edited

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edited

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edited

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edited

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edited

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edited