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JuliaLang / PackageCompiler.jl

Compile your Julia Package
https://julialang.github.io/PackageCompiler.jl/dev/
MIT License
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Inability to use a gamma cdf #683

Open Deduction42 opened 2 years ago

Deduction42 commented 2 years ago

In version 1.2.5 I was able to have the entire project compile properly

In version 2.0.5, it managed to run through the precompiliaion workflow, but when building the incremental system image, there was an issue:

could not load symbol "pgamma":
/usr/local/julia/bin/julia: undefined symbol: pgamma
Stacktrace:
  [1] gammacdf
    @ ~/.julia/packages/StatsFuns/mQJB7/src/rmath.jl:83 [inlined]
  [2] cdf
    @ ~/.julia/packages/Distributions/O4ZJg/src/univariates.jl:622 [inlined]

This looks like a problem generated by the macro in this file, line 83 where the actual symbol couldn't be loaded https://github.com/JuliaStats/StatsFuns.jl/blob/master/src/rmath.jl

I would almost say it was a problem with the StatsFuns.jl package, except that PackageCompiler.jl v1.2.5 was able to handle it.

Deduction42 commented 2 years ago

This is my package manifest:

# This file is machine-generated - editing it directly is not advised

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deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
git-tree-sha1 = "25405d7016a47cf2bd6cd91e66f4de437fd54a07"
uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
version = "0.9.16"

[[SuiteSparse]]
deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"

[[SymDict]]
deps = ["Test"]
git-tree-sha1 = "0108ccdaea3ef69d9680eeafc8d5ad198b896ec8"
uuid = "2da68c74-98d7-5633-99d6-8493888d7b1e"
version = "0.3.0"

[[TOML]]
deps = ["Dates"]
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"

[[TableTraits]]
deps = ["IteratorInterfaceExtensions"]
git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39"
uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
version = "1.0.1"

[[Tables]]
deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"]
git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1"
uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
version = "1.7.0"

[[Tar]]
deps = ["ArgTools", "SHA"]
uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"

[[Test]]
deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[[TranscodingStreams]]
deps = ["Random", "Test"]
git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c"
uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
version = "0.9.6"

[[URIs]]
git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355"
uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
version = "1.3.0"

[[UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"

[[Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

[[WeakRefStrings]]
deps = ["DataAPI", "InlineStrings", "Parsers"]
git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23"
uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5"
version = "1.4.2"

[[XML2_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"]
git-tree-sha1 = "1acf5bdf07aa0907e0a37d3718bb88d4b687b74a"
uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
version = "2.9.12+0"

[[XMLDict]]
deps = ["EzXML", "IterTools", "OrderedCollections"]
git-tree-sha1 = "d9a3faf078210e477b291c79117676fca54da9dd"
uuid = "228000da-037f-5747-90a9-8195ccbf91a5"
version = "0.4.1"

[[Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"

[[libsodium_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "848ab3d00fe39d6fbc2a8641048f8f272af1c51e"
uuid = "a9144af2-ca23-56d9-984f-0d03f7b5ccf8"
version = "1.0.20+0"

[[nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"

[[p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
Deduction42 commented 2 years ago

After doing a lot of tests (on Julia 1.6.5), it looks like this problem started appearing at PackageCompiler v1.6.0

could not load symbol "pgamma":
/usr/local/julia/bin/julia: undefined symbol: pgamma
Stacktrace:
  [1] gammacdf
    @ ~/.julia/packages/StatsFuns/mQJB7/src/rmath.jl:83 [inlined]
  [2] cdf
    @ ~/.julia/packages/Distributions/O4ZJg/src/univariates.jl:622 [inlined]

With an overall error message of

ERROR: LoadError: failed process: Process(`/usr/local/julia/bin/julia --color=yes --startup-file=no --cpu-target=generic --sysimage=/usr/local/julia/lib/julia/sys.so --project=/home/ccg/.julia/environments/v1.6 --output-o=/tmp/jl_r2TZqJ.o -e "Base.reinit_stdio()                                    
@eval Sys BINDIR = ccall(:jl_get_julia_bindir, Any, ())::String                                                                                      
@eval Sys STDLIB = \"/usr/local/julia/share/julia/stdlib/v1.6\"                                                                                      
Base.init_load_path()                                                                                                                                
if isdefined(Base, :init_active_project)                                                                                                             
    Base.init_active_project()                                                                                                                       
end                                                                                                                                                  
Base.init_depot_path()                                                                                                                               
import CCG_Server                                                                                                                                    
import HTTP                                                                                                                                          
import Joseki                                                                                                                                        
import JSON                                                                                                                                          
# This @eval prevents symbols from being put into Main                                                                                               
@eval Module() begin                                                                                                                                 
    using Base.Meta                                                                                                                                  
    PrecompileStagingArea = Module()                                                                                                                 
    for (_pkgid, _mod) in Base.loaded_modules                                                                                                        
        if !(_pkgid.name in (\"Main\", \"Core\", \"Base\"))                                                                                          
            eval(PrecompileStagingArea, :(const \$(Symbol(_mod)) = \$_mod))                                                                          
        end                                                                                                                                          
    end                                                                                                                                              
    precompile_files = String[                                                                                                                       
        \"/tmp/jl_qcDbkJ\"                                                                                                                           
    ]                                                                                                                                                
    for file in precompile_files, statement in eachline(file)                                                                                        
        try                                                                                                                                          
            # println(statement)                                                                                                                     
            # This is taken from https://github.com/JuliaLang/julia/blob/2c9e051c460dd9700e6814c8e49cc1f119ed8b41/contrib/generate_precompile.jl#L375-L393                                                                                                                                                
            ps = Meta.parse(statement)                                                                                                               
            isexpr(ps, :call) || continue                                                                                                            
            popfirst!(ps.args) # precompile(...)                                                                                                     
            ps.head = :tuple                                                                                                                         
            l = ps.args[end]                                                                                                                         
            if (isexpr(l, :tuple) || isexpr(l, :curly)) && length(l.args) > 0 # Tuple{...} or (...)                                                  
                # XXX: precompile doesn't currently handle overloaded Vararg arguments very well.                                                    
                # Replacing N with a large number works around it.                                                                                   
                l = l.args[end]                                                                                                                      
                if isexpr(l, :curly) && length(l.args) == 2 && l.args[1] === :Vararg # Vararg{T}
                    push!(l.args, 100) # form Vararg{T, 100} instead
                end
            end
            # println(ps)
            ps = Core.eval(PrecompileStagingArea, ps)
            # XXX: precompile doesn't currently handle overloaded nospecialize arguments very well.
            # Skipping them avoids the warning.
            ms = length(ps) == 1 ? Base._methods_by_ftype(ps[1], 1, Base.get_world_counter()) : Base.methods(ps...)
            ms isa Vector || continue
            precompile(ps...)
        catch e
            # See julia issue #28808
            @debug \"failed to execute \$statement\"
        end
    end
end # module
empty!(LOAD_PATH)
empty!(DEPOT_PATH)
"`, ProcessExited(1)) [1]

Stacktrace:
 [1] pipeline_error
   @ ./process.jl:525 [inlined]
 [2] run(::Cmd; wait::Bool)
   @ Base ./process.jl:440
 [3] run
   @ ./process.jl:438 [inlined]
 [4] create_sysimg_object_file(object_file::String, packages::Vector{String}; project::String, base_sysimage::String, precompile_execution_file::Vector{String}, precompile_statements_file::Vector{String}, cpu_target::String, script::Nothing, isapp::Bool, sysimage_build_args::Cmd)
   @ PackageCompiler ~/.julia/packages/PackageCompiler/r8Xcy/src/PackageCompiler.jl:371
 [5] create_sysimage(packages::Vector{Symbol}; sysimage_path::String, project::String, precompile_execution_file::String, precompile_statements_file::Vector{String}, incremental::Bool, filter_stdlibs::Bool, replace_default::Bool, base_sysimage::Nothing, isapp::Bool, julia_init_c_file::Nothing, version::Nothing, compat_level::String, soname::Nothing, cpu_target::String, script::Nothing, sysimage_build_args::Cmd)
   @ PackageCompiler ~/.julia/packages/PackageCompiler/r8Xcy/src/PackageCompiler.jl:538
 [6] top-level scope
   @ ./timing.jl:210
in expression starting at /home/ccg/julia_server/precompile_server.jl:26

It looks like symbols aren't allowed to be put into main, and this seems what is causing StatsFuns.jl to choke on the cdf.

KristofferC commented 2 years ago

it looks like this problem started appearing at version 1.6

Do you mean Julia 1.6?

Deduction42 commented 2 years ago

No I'm talking about PackageCompiler 1.6. Everything before PackageCompiler v1.6 seems to work. I'm testing all this on Julia v1.6.5

KristofferC commented 2 years ago

Maybe you can even find the exact commit that made it start erroring.