Precompilation failure of GMT.jl v1.42.0 on macOS

[melodyjulia]

It fails on macOS with Julia 1.12.6 on both Apple Silicon and Intel chip:

julia> err
PkgPrecompileError: The following 3 direct dependencies failed to precompile:

GMT 

Failed to precompile GMT [5752ebe1-31b9-557e-87aa-f909b540aa54] to "/Users/test/.julia/compiled/v1.12/GMT/jl_YgkuFf".
[37108] signal 6: Abort trap: 6
in expression starting at /Users/test/.julia/packages/GMT/rA3mT/src/GMT.jl:417
__pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
Allocations: 255935437 (Pool: 255931851; Big: 3586); GC: 45
GMT → GMTDGTLidarExt 

Failed to precompile GMTDGTLidarExt [1f1582e6-6292-5a9d-a98c-a412d01b6888] to "/Users/test/.julia/compiled/v1.12/GMTDGTLidarExt/jl_Wm6xGi".
[37116] signal 6: Abort trap: 6
in expression starting at /Users/test/.julia/packages/GMT/rA3mT/src/GMT.jl:417
__pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
Allocations: 256476526 (Pool: 256472917; Big: 3609); GC: 44
ERROR: LoadError: Failed to precompile GMT [5752ebe1-31b9-557e-87aa-f909b540aa54] to "/Users/test/.julia/compiled/v1.12/GMT/jl_jMvxqs".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3315
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})()
    @ Base ./loading.jl:2683
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.6+0.aarch64.apple.darwin14/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:96
  [5] #mkpidlock#7
    @ ~/.julia/juliaup/julia-1.12.6+0.aarch64.apple.darwin14/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:91 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.6+0.aarch64.apple.darwin14/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:117
  [7] #invokelatest_gr#232
    @ ./reflection.jl:1297 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1289 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3886
 [10] maybe_cachefile_lock
    @ ./loading.jl:3883 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2669
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2495
 [13] macro expansion
    @ ./loading.jl:2423 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2388
 [16] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2364
 [17] top-level scope
    @ ~/.julia/packages/GMT/rA3mT/ext/GMTDGTLidarExt/GMTDGTLidarExt.jl:6
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:306
 [19] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:3028
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2874
 [23] include_string
    @ ./loading.jl:2884 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:315
 [25] _start()
    @ Base ./client.jl:550
in expression starting at /Users/test/.julia/packages/GMT/rA3mT/ext/GMTDGTLidarExt/GMTDGTLidarExt.jl:5
in expression starting at stdin:5

GMT → GMTDataFramesExt 

Failed to precompile GMTDataFramesExt [b0121151-b40e-578b-8798-214dacfa5da6] to "/Users/test/.julia/compiled/v1.12/GMTDataFramesExt/jl_359owM".
[37113] signal 6: Abort trap: 6
in expression starting at /Users/test/.julia/packages/GMT/rA3mT/src/GMT.jl:417
__pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
Allocations: 256531922 (Pool: 256528312; Big: 3610); GC: 45
ERROR: LoadError: Failed to precompile GMT [5752ebe1-31b9-557e-87aa-f909b540aa54] to "/Users/test/.julia/compiled/v1.12/GMT/jl_nklO5g".
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
    @ Base ./loading.jl:3315
  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})()
    @ Base ./loading.jl:2683
  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.6+0.aarch64.apple.darwin14/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:96
  [5] #mkpidlock#7
    @ ~/.julia/juliaup/julia-1.12.6+0.aarch64.apple.darwin14/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:91 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.12.6+0.aarch64.apple.darwin14/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:117
  [7] #invokelatest_gr#232
    @ ./reflection.jl:1297 [inlined]
  [8] invokelatest_gr
    @ ./reflection.jl:1289 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3886
 [10] maybe_cachefile_lock
    @ ./loading.jl:3883 [inlined]
 [11] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2669
 [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2495
 [13] macro expansion
    @ ./loading.jl:2423 [inlined]
 [14] macro expansion
    @ ./lock.jl:376 [inlined]
 [15] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2388
 [16] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2364
 [17] top-level scope
    @ ~/.julia/packages/GMT/rA3mT/ext/GMTDataFramesExt/GMTDataFramesExt.jl:2
 [18] include(mod::Module, _path::String)
    @ Base ./Base.jl:306
 [19] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:3028
 [20] top-level scope
    @ stdin:5
 [21] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:2874
 [23] include_string
    @ ./loading.jl:2884 [inlined]
 [24] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:315
 [25] _start()
    @ Base ./client.jl:550
in expression starting at /Users/test/.julia/packages/GMT/rA3mT/ext/GMTDataFramesExt/GMTDataFramesExt.jl:1
in expression starting at stdin:5

[joa-quim]

Oops, but the worse is that I have no idea what this is. I could find that it only occurs on Macs and started with the commit in last day 26
#2024
Can you try to go back to the commit before that to see if it makes a difference?

[joa-quim]

Or, before that. Try to comment the lines 481-483 of GMT.jl (Those that call the fft1 and fft2 functions)

[Julian-Patzner]

Similar issue on our MacOS test pipeline:

  ERROR: LoadError: The following 5 direct dependencies failed to precompile:
  
  GMT → GMTParkerFFTExt --code-coverage=@/Users/runner/work/GEMS/GEMS --color=yes --check-bounds=yes --warn-overwrite=yes --depwarn=yes --inline=yes --startup-file=no --track-allocation=none --check-bounds=yes --compiled-modules=yes --depwarn=yes 
  
  Failed to precompile GMTParkerFFTExt [35a23bc9-6f20-5cbc-8971-9cdf66427582] to "/Users/runner/.julia/compiled/v1.12/GMTParkerFFTExt/jl_tlT8kf".
  [16950] signal 6: Abort trap: 6
  in expression starting at /Users/runner/.julia/packages/GMT/rA3mT/src/GMT.jl:417
  __pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
  Allocations: 254914386 (Pool: 254910808; Big: 3578); GC: 35
  ERROR: LoadError: Failed to precompile GMT [5752ebe1-31b9-557e-87aa-f909b540aa54] to "/Users/runner/.julia/compiled/v1.12/GMT/jl_bEfGOz".
  Stacktrace:
    [1] error(s::String)
      @ Base ./error.jl:44
    [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
      @ Base ./loading.jl:3315
    [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})()
      @ Base ./loading.jl:2683
    [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
      @ FileWatching.Pidfile ~/hostedtoolcache/julia/1.12.6/aarch64/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:96
    [5] #mkpidlock#7
      @ ~/hostedtoolcache/julia/1.12.6/aarch64/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:91 [inlined]
    [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
      @ FileWatching.Pidfile ~/hostedtoolcache/julia/1.12.6/aarch64/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:117
    [7] #invokelatest_gr#232
      @ ./reflection.jl:1297 [inlined]
    [8] invokelatest_gr
      @ ./reflection.jl:1289 [inlined]
    [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
      @ Base ./loading.jl:3886
   [10] maybe_cachefile_lock
      @ ./loading.jl:3883 [inlined]
   [11] __require_prelocked(pkg::Base.PkgId, env::String)
      @ Base ./loading.jl:2669
   [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
      @ Base ./loading.jl:2495
   [13] macro expansion
      @ ./loading.jl:2423 [inlined]
   [14] macro expansion
      @ ./lock.jl:376 [inlined]
   [15] __require(into::Module, mod::Symbol)
      @ Base ./loading.jl:2388
   [16] require(into::Module, mod::Symbol)
      @ Base ./loading.jl:2364
   [17] top-level scope
      @ ~/.julia/packages/GMT/rA3mT/ext/GMTParkerFFTExt/GMTParkerFFTExt.jl:2
   [18] include(mod::Module, _path::String)
      @ Base ./Base.jl:306
   [19] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
      @ Base ./loading.jl:3028
   [20] top-level scope
      @ stdin:5
   [21] eval(m::Module, e::Any)
      @ Core ./boot.jl:489
   [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
      @ Base ./loading.jl:2874
   [23] include_string
      @ ./loading.jl:2884 [inlined]
   [24] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:315
   [25] _start()
      @ Base ./client.jl:550
  in expression starting at /Users/runner/.julia/packages/GMT/rA3mT/ext/GMTParkerFFTExt/GMTParkerFFTExt.jl:1
  in expression starting at stdin:5
  GEMS --code-coverage=@/Users/runner/work/GEMS/GEMS --color=yes --check-bounds=yes --warn-overwrite=yes --depwarn=yes --inline=yes --startup-file=no --track-allocation=none --check-bounds=yes --compiled-modules=yes --depwarn=yes 
  
  Failed to precompile GEMS [be47d99e-7859-414d-a902-bf4cb6b83c8a] to "/Users/runner/.julia/compiled/v1.12/GEMS/jl_E5DA3b".
  [21044] signal 6: Abort trap: 6
  in expression starting at /Users/runner/.julia/packages/GMT/rA3mT/src/GMT.jl:417
  __pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
  Allocations: 252980398 (Pool: 252976835; Big: 3563); GC: 41
  ERROR: LoadError: Failed to precompile GMT [5752ebe1-31b9-557e-87aa-f909b540aa54] to "/Users/runner/.julia/compiled/v1.12/GMT/jl_C6KKCJ".
  Stacktrace:
    [1] error(s::String)
      @ Base ./error.jl:44
    [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
      @ Base ./loading.jl:3315
    [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})()
      @ Base ./loading.jl:2683
    [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
      @ FileWatching.Pidfile ~/hostedtoolcache/julia/1.12.6/aarch64/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:96
    [5] #mkpidlock#7
      @ ~/hostedtoolcache/julia/1.12.6/aarch64/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:91 [inlined]
    [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
      @ FileWatching.Pidfile ~/hostedtoolcache/julia/1.12.6/aarch64/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:117
    [7] #invokelatest_gr#232
      @ ./reflection.jl:1297 [inlined]
    [8] invokelatest_gr
      @ ./reflection.jl:1289 [inlined]
    [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
      @ Base ./loading.jl:3886
   [10] maybe_cachefile_lock
      @ ./loading.jl:3883 [inlined]
   [11] __require_prelocked(pkg::Base.PkgId, env::String)
      @ Base ./loading.jl:2669
   [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
      @ Base ./loading.jl:2495
   [13] macro expansion
      @ ./loading.jl:2423 [inlined]
   [14] macro expansion
      @ ./lock.jl:376 [inlined]
   [15] __require(into::Module, mod::Symbol)
      @ Base ./loading.jl:2388
   [16] require(into::Module, mod::Symbol)
      @ Base ./loading.jl:2364
   [17] top-level scope
      @ ~/work/GEMS/GEMS/src/GEMS.jl:16
   [18] include(mod::Module, _path::String)
      @ Base ./Base.jl:306
   [19] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
      @ Base ./loading.jl:3028
   [20] top-level scope
      @ stdin:5
   [21] eval(m::Module, e::Any)
      @ Core ./boot.jl:489
   [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
      @ Base ./loading.jl:2874
   [23] include_string
      @ ./loading.jl:2884 [inlined]
   [24] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:315
   [25] _start()
      @ Base ./client.jl:550
  in expression starting at /Users/runner/work/GEMS/GEMS/src/GEMS.jl:1
  in expression starting at stdin:5
  
  GMT → GMTDataFramesExt --code-coverage=@/Users/runner/work/GEMS/GEMS --color=yes --check-bounds=yes --warn-overwrite=yes --depwarn=yes --inline=yes --startup-file=no --track-allocation=none --check-bounds=yes --compiled-modules=yes --depwarn=yes 
  
  Failed to precompile GMTDataFramesExt [b0121151-b40e-578b-8798-214dacfa5da6] to "/Users/runner/.julia/compiled/v1.12/GMTDataFramesExt/jl_qFzcEK".
  [14665] signal 6: Abort trap: 6
  in expression starting at /Users/runner/.julia/packages/GMT/rA3mT/src/GMT.jl:417
  __pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
  Allocations: 252236003 (Pool: 252232446; Big: 3557); GC: 36
  ERROR: LoadError: Failed to precompile GMT [5752ebe1-31b9-557e-87aa-f909b540aa54] to "/Users/runner/.julia/compiled/v1.12/GMT/jl_V0txgj".
  Stacktrace:
    [1] error(s::String)
      @ Base ./error.jl:44
    [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
      @ Base ./loading.jl:3315
    [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})()
      @ Base ./loading.jl:2683
    [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
      @ FileWatching.Pidfile ~/hostedtoolcache/julia/1.12.6/aarch64/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:96
    [5] #mkpidlock#7
      @ ~/hostedtoolcache/julia/1.12.6/aarch64/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:91 [inlined]
    [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
      @ FileWatching.Pidfile ~/hostedtoolcache/julia/1.12.6/aarch64/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:117
    [7] #invokelatest_gr#232
      @ ./reflection.jl:1297 [inlined]
    [8] invokelatest_gr
      @ ./reflection.jl:1289 [inlined]
    [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
      @ Base ./loading.jl:3886
   [10] maybe_cachefile_lock
      @ ./loading.jl:3883 [inlined]
   [11] __require_prelocked(pkg::Base.PkgId, env::String)
      @ Base ./loading.jl:2669
   [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
      @ Base ./loading.jl:2495
   [13] macro expansion
      @ ./loading.jl:2423 [inlined]
   [14] macro expansion
      @ ./lock.jl:376 [inlined]
   [15] __require(into::Module, mod::Symbol)
      @ Base ./loading.jl:2388
   [16] require(into::Module, mod::Symbol)
      @ Base ./loading.jl:2364
   [17] top-level scope
      @ ~/.julia/packages/GMT/rA3mT/ext/GMTDataFramesExt/GMTDataFramesExt.jl:2
   [18] include(mod::Module, _path::String)
      @ Base ./Base.jl:306
   [19] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
      @ Base ./loading.jl:3028
   [20] top-level scope
      @ stdin:5
   [21] eval(m::Module, e::Any)
      @ Core ./boot.jl:489
   [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
      @ Base ./loading.jl:2874
   [23] include_string
      @ ./loading.jl:2884 [inlined]
   [24] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:315
   [25] _start()
      @ Base ./client.jl:550
  in expression starting at /Users/runner/.julia/packages/GMT/rA3mT/ext/GMTDataFramesExt/GMTDataFramesExt.jl:1
  in expression starting at stdin:5
  
  GMT --code-coverage=@/Users/runner/work/GEMS/GEMS --color=yes --check-bounds=yes --warn-overwrite=yes --depwarn=yes --inline=yes --startup-file=no --track-allocation=none --check-bounds=yes --compiled-modules=yes --depwarn=yes 
  
  Failed to precompile GMT [5752ebe1-31b9-557e-87aa-f909b540aa54] to "/Users/runner/.julia/compiled/v1.12/GMT/jl_nr87PV".
  [12777] signal 6: Abort trap: 6
  in expression starting at /Users/runner/.julia/packages/GMT/rA3mT/src/GMT.jl:417
  __pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
  Allocations: 250066053 (Pool: 250062507; Big: 3546); GC: 35
  
  GMT → GMTDGTLidarExt --code-coverage=@/Users/runner/work/GEMS/GEMS --color=yes --check-bounds=yes --warn-overwrite=yes --depwarn=yes --inline=yes --startup-file=no --track-allocation=none --check-bounds=yes --compiled-modules=yes --depwarn=yes 
  
  Failed to precompile GMTDGTLidarExt [1f1582e6-6292-5a9d-a98c-a412d01b6888] to "/Users/runner/.julia/compiled/v1.12/GMTDGTLidarExt/jl_KCiFnM".
  [19298] signal 6: Abort trap: 6
  in expression starting at /Users/runner/.julia/packages/GMT/rA3mT/src/GMT.jl:417
  __pthread_kill at /usr/lib/system/libsystem_kernel.dylib (unknown line)
  Allocations: 255057514 (Pool: 255053933; Big: 3581); GC: 41
  ERROR: LoadError: Failed to precompile GMT [5752ebe1-31b9-557e-87aa-f909b540aa54] to "/Users/runner/.julia/compiled/v1.12/GMT/jl_ZboJD4".
  Stacktrace:
    [1] error(s::String)
      @ Base ./error.jl:44
    [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)
      @ Base ./loading.jl:3315
    [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}})()
      @ Base ./loading.jl:2683
    [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
      @ FileWatching.Pidfile ~/hostedtoolcache/julia/1.12.6/aarch64/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:96
    [5] #mkpidlock#7
      @ ~/hostedtoolcache/julia/1.12.6/aarch64/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:91 [inlined]
    [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
      @ FileWatching.Pidfile ~/hostedtoolcache/julia/1.12.6/aarch64/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:117
    [7] #invokelatest_gr#232
      @ ./reflection.jl:1297 [inlined]
    [8] invokelatest_gr
      @ ./reflection.jl:1289 [inlined]
    [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId, String, Dict{String, Int64}}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
      @ Base ./loading.jl:3886
   [10] maybe_cachefile_lock
      @ ./loading.jl:3883 [inlined]
   [11] __require_prelocked(pkg::Base.PkgId, env::String)
      @ Base ./loading.jl:2669
   [12] _require_prelocked(uuidkey::Base.PkgId, env::String)
      @ Base ./loading.jl:2495
   [13] macro expansion
      @ ./loading.jl:2423 [inlined]
   [14] macro expansion
      @ ./lock.jl:376 [inlined]
   [15] __require(into::Module, mod::Symbol)
      @ Base ./loading.jl:2388
   [16] require(into::Module, mod::Symbol)
      @ Base ./loading.jl:2364
   [17] top-level scope
      @ ~/.julia/packages/GMT/rA3mT/ext/GMTDGTLidarExt/GMTDGTLidarExt.jl:6
   [18] include(mod::Module, _path::String)
      @ Base ./Base.jl:306
   [19] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
      @ Base ./loading.jl:3028
   [20] top-level scope
      @ stdin:5
   [21] eval(m::Module, e::Any)
      @ Core ./boot.jl:489
   [22] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
      @ Base ./loading.jl:2874
   [23] include_string
      @ ./loading.jl:2884 [inlined]
   [24] exec_options(opts::Base.JLOptions)
      @ Base ./client.jl:315
   [25] _start()
      @ Base ./client.jl:550
  in expression starting at /Users/runner/.julia/packages/GMT/rA3mT/ext/GMTDGTLidarExt/GMTDGTLidarExt.jl:5
  in expression starting at stdin:5
  in expression starting at /Users/runner/work/_actions/julia-actions/julia-runtest/v1/test_harness.jl:67

[joa-quim]

It is something related to the use of the GMT FFTW. Have no way of finding what but commenting the fft1|2 precompile commands at least avoids the problem for now. A 1.42.1 version is on the works.

[joa-quim]

Version 1.42.1 is out and should workaround the problem (it does on the CIs)

With it, could you guys please try to run this

fft1d(rand(64));
fft2d(rand(Float32, 32, 32));
fft2d!(ComplexF32.(rand(32, 32)); inverse=true);

and see if they all cause the crash or only one of them?

[melodyjulia]

GMT.jl v1.42.1 can now pass precompilation. That's great!
I tried the code you provided below, and all of it runs successfully with GMT.jl v1.42.1.

fft1d(rand(64));
fft2d(rand(Float32, 32, 32));
fft2d!(ComplexF32.(rand(32, 32)); inverse=true);

[joa-quim]

But that, although good, makes absolutely no sense. It was exactly by having them in the precompile block that the crashes occurred!!!!

[melodyjulia]

But that, although good, makes absolutely no sense. It was exactly by having them in the precompile block that the crashes occurred!!!!

What test can we help with?

[joa-quim]

Thanks. What I would try.

• Uncomment line 481 of GMT.jl file
• If it doesn't crash the pre-compilation, do the same to lines 482 and 483
• If it crashes, try to move the crashing line to the begining and end of the @compile_workload begin block

It must be something that is triggered inside the workload block. Either because of the interaction with other previous calls, or something to the @compile_workload environment itself.

[melodyjulia]

Uncommenting Line 481 of GMT.jl causes precompilation to crash.
Moving Line 481 to the beginning of the @compile_workload begin block also causes a crash.
However, moving Line 481 (or Lines 481–483) to the end of the @compile_workload begin block allows precompilation to succeed.

[joa-quim]

Thanks. Still don't know what to do with this info but can you please try to move them to bellow the other 3 uncommented lines. That is below 488, 489 and 491? Though my guess is that, what ever is causing the problem is clean up by the resetGMT() that starts a new C Lib pointer.

[melodyjulia]

Moving Line 481 (or Lines 481–483) below Line 488 allows precompilation to succeed as well.

arrows([0 8.2 0 6], limits=(-2,4,0,9), arrow=(len=2,stop=1,shape=0.5,fill=:red), axis=:a, pen="6p");

However, moving Line 481 (or Lines 481–483) before Line 488 causes precompilation to crash.

[joa-quim]

Ok, thanks for pinpointing it. I have no time now to investigate this. I suspect somewhere in the arrows workflow call there is a call to resetGMT and that's why it later works. But the true problem still remains hidden.

[melodyjulia]

Yes, it's weird that the same code works fine on Linux, but fails on macOS.