stdatomic.h: No such file or directory

[visr]

I noticed a build that works on julia 1.7.0-rc2 but fails on 1.7.0-rc3. This happens on Linux, Windows works for both. After looking at JuliaLang/julia@v1.7.0-rc2...v1.7.0-rc3 I suspect it is because of JuliaLang/julia#42828.

PackageCompiler: compiling incremental system image
In file included from /opt/teamcityagent/work/44830c4db5199711/julia-1.7.0-rc3/include/julia/julia.h:100:0,
 from /u/svc-teamcity-ansible/.julia/packages/PackageCompiler/R3n2H/src/embedding_wrapper.c:7:
/opt/teamcityagent/work/44830c4db5199711/julia-1.7.0-rc3/include/julia/julia_atomics.h:38:23: fatal error: stdatomic.h: No such file or directory
 #include <stdatomic.h>
 ^
compilation terminated.
ERROR: LoadError: failed process: Process(`gcc '-DJULIA_MAIN="wflow_cli.julia_main"' -DNEW_DEFINE_FAST_TLS_SYNTAX -m64 -march=x86-64 -o wflow_bundle/bin/wflow_cli /u/svc-teamcity-ansible/.julia/packages/PackageCompiler/R3n2H/src/embedding_wrapper.c -O2 '-Wl,-rpath,$ORIGIN/../lib:$ORIGIN/../lib/julia' -std=gnu99 -I/opt/teamcityagent/work/44830c4db5199711/julia-1.7.0-rc3/include/julia -fPIC -L/opt/teamcityagent/work/44830c4db5199711/julia-1.7.0-rc3/lib -L/opt/teamcityagent/work/44830c4db5199711/julia-1.7.0-rc3/lib/julia -Wl,--export-dynamic -Wl,-rpath-link,/opt/teamcityagent/work/44830c4db5199711/julia-1.7.0-rc3/lib -Wl,-rpath-link,/opt/teamcityagent/work/44830c4db5199711/julia-1.7.0-rc3/lib/julia -ljulia -ljulia-internal`, ProcessExited(1)) [1]

Stacktrace:
 [1] pipeline_error
 @ ./process.jl:531 [inlined]
 [2] run(::Cmd; wait::Bool)
 @ Base ./process.jl:446
 [3] run
 @ ./process.jl:444 [inlined]
 [4] run_compiler(cmd::Cmd; cplusplus::Bool)
 @ PackageCompiler ~/.julia/packages/PackageCompiler/R3n2H/src/PackageCompiler.jl:163
 [5] run_compiler
 @ ~/.julia/packages/PackageCompiler/R3n2H/src/PackageCompiler.jl:120 [inlined]
 [6] create_executable_from_sysimg(exe_path::String, c_driver_program::String, julia_main::String)
 @ PackageCompiler ~/.julia/packages/PackageCompiler/R3n2H/src/PackageCompiler.jl:726
 [7] create_app(package_dir::String, app_dir::String; executables::Vector{Pair{String, String}}, precompile_execution_file::String, precompile_statements_file::Vector{String}, incremental::Bool, filter_stdlibs::Bool, force::Bool, c_driver_program::String, cpu_target::String, include_lazy_artifacts::Bool, sysimage_build_args::Cmd, include_transitive_dependencies::Bool)
 @ PackageCompiler ~/.julia/packages/PackageCompiler/R3n2H/src/PackageCompiler.jl:713
 [8] top-level scope
 @ /opt/teamcityagent/work/44830c4db5199711/create_app/create_app.jl:8
 [9] include(fname::String)
 @ Base.MainInclude ./client.jl:451
 [10] top-level scope
 @ /opt/teamcityagent/work/44830c4db5199711/contrib/build_steps.jl:32
in expression starting at /opt/teamcityagent/work/44830c4db5199711/create_app/create_app.jl:8
in expression starting at /opt/teamcityagent/work/44830c4db5199711/contrib/build_steps.jl:32
Process exited with code 1

The code to the app that is being built here, if relevant, is https://gitlab.com/deltares/wflow/wflow_cli.

[KristofferC]

Can you try with #638?

[visr]

Thanks for looking into it. Unfortunately I still get the same error:

/opt/teamcityagent/work/44830c4db5199711/julia-1.7.0-rc3/include/julia/julia_atomics.h:38:23: fatal error: stdatomic.h: No such file or directory
 #include <stdatomic.h>
                       ^
compilation terminated.
ERROR: LoadError: failed process: Process(`gcc '-DJULIA_MAIN="wflow_cli.julia_main"' -DNEW_DEFINE_FAST_TLS_SYNTAX -m64 -march=x86-64 -o wflow_bundle/bin/wflow_cli /u/svc-teamcity-ansible/.julia/packages/PackageCompiler/voMQc/src/embedding_wrapper.c -O2 '-Wl,-rpath,$ORIGIN/../lib:$ORIGIN/../lib/julia' -std=gnu11 -I/opt/teamcityagent/work/44830c4db5199711/julia-1.7.0-rc3/include/julia -fPIC -L/opt/teamcityagent/work/44830c4db5199711/julia-1.7.0-rc3/lib -L/opt/teamcityagent/work/44830c4db5199711/julia-1.7.0-rc3/lib/julia -Wl,--export-dynamic -Wl,-rpath-link,/opt/teamcityagent/work/44830c4db5199711/julia-1.7.0-rc3/lib -Wl,-rpath-link,/opt/teamcityagent/work/44830c4db5199711/julia-1.7.0-rc3/lib/julia -ljulia -ljulia-internal`, ProcessExited(1)) [1]

I now see -std=gnu11 in the gcc call, so it did use the right branch.

[KristofferC]

What version of gcc do you have?

[visr]

Aha. This is on a CentOS 7 machine with gcc 4.8.5. It seems from gcc 4.9 this should work, according to the gcc changelog:

ISO C11 atomics (the _Atomic type specifier and qualifier and the <stdatomic.h> header) are now supported.

I'll see if I can use a newer gcc on those build servers.

[visr]

Ok I tried gcc 7.3.0, and that works with and without #638. Though that makes sense since for that version -std=gnu11 is the default according to https://gcc.gnu.org/onlinedocs/gcc-7.2.0/gcc/Standards.html.

So I think it'd be good to merge #638 anyway. Regarding the documentation, I guess:

Having a decently modern gcc or clang available should be enough to use PackageCompiler on Linux or macOS.

would not include gcc 4.8 😅