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Difficulty importing PySR #64146

Closed kyleosung closed 1 year ago

kyleosung commented 1 year ago 
julia> import Pkg; Pkg.add("SymbolicRegression")
   Resolving package versions...
  No Changes to `~/.julia/environments/v1.9/Project.toml`
  No Changes to `~/.julia/environments/v1.9/Manifest.toml`
Precompiling project...
  Progress [>                                        ]  0/9
  ◑ ConstructionBase
PLEASE submit a bug report to https://github.com/llvm/llvm-project/issues/ and include the crash backtrace.
Stack dump:
0.      Program arguments: /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/libexec/julia/lld -flavor gnu  -shared -o /home/USER/.julia/compiled/v1.9/ConstructionBase/jl_sFymoM --whole-archive /home/USER/.julia/compiled/v1.9/ConstructionBase/jl_GGOxVN --no-whole-archive -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/lib -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/lib/julia -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/lib -ljulia -ljulia-internal
Stack dump without symbol names (ensure you have llvm-symbolizer in your PATH or set the environment var `LLVM_SYMBOLIZER_PATH` to point to it):
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/lib/julia/libLLVM-14jl.so(+0x9991c0)[0x7f34913df1c0]
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/lib/julia/libLLVM-14jl.so(+0x996b2e)[0x7f34913dcb2e]
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/lib/julia/libpthread.so.0(+0x130f0)[0x7f349574d0f0]
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/libexec/julia/lld(_ZN3lld3elf9writeEhdrIN4llvm6object7ELFTypeILNS2_7support10endiannessE1ELb1EEEEEvPhRNS0_9PartitionE+0xc)[0x64afec]
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/libexec/julia/lld[0x6bae72]
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/libexec/julia/lld(_ZN3lld3elf11writeResultIN4llvm6object7ELFTypeILNS2_7support10endiannessE1ELb1EEEEEvv+0x19)[0x6bbbc9]
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/libexec/julia/lld(_ZN3lld3elf12LinkerDriver4linkERN4llvm3opt12InputArgListE+0x1e7d)[0x57140d]
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/libexec/julia/lld(_ZN3lld3elf12LinkerDriver10linkerMainEN4llvm8ArrayRefIPKcEE+0x1109)[0x573f09]
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/libexec/julia/lld(_ZN3lld3elf4linkEN4llvm8ArrayRefIPKcEERNS1_11raw_ostreamES7_bb+0x552)[0x575122]
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/libexec/julia/lld[0x48024a]
/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/libexec/julia/lld(main+0x6c)[0x47e38c]
/cvmfs/soft.computecanada.ca/gentoo/2020/lib64/libc.so.6(__libc_start_main+0xeb)[0x7f3490535e1b]
  ◑ ConstructionBase
┌ Error: Pkg.precompile error
│   exception =
│    failed process: Process(setenv(`/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/libexec/julia/lld -flavor gnu '' -shared -o /home/USER/.julia/compiled/v1.9/ConstructionBase/jl_sFymoM --whole-archive /home/USER/.julia/compiled/v1.9/ConstructionBase/jl_GGOxVN --no-whole-archive -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/lib -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/lib/julia -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/lib -ljulia -ljulia-internal`,["LMOD_ROOT=/cvmfs/soft.computecanada.ca/custom/software/lmod", "LD_LIBRARY_PATH=/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/lib/julia:/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/lib", "EBVERSIONOPENMPI=4.0.3", "DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/3129193/bus", "SQUEUE_SORT=-t,e,S", "MODULEPATH=/opt/software/modulefiles:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/avx2/MPI/intel2020/openmpi4:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/avx2/Compiler/intel2020:/home/USER/.local/easybuild/modules/2020/avx2/Core:/home/USER/.local/easybuild/modules/2020/Core:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/avx2/Core:/cvmfs/soft.computecanada.ca/easybuild/modules/2020/Core:/cvmfs/soft.computecanada.ca/custom/modules", "EBDEVELBLIS=/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/blis/0.8.1/easybuild/avx2-Compiler-intel2020-blis-0.8.1-easybuild-devel", "EBVERSIONPYTHON=3.9.6", "_ModuleTable_Sz_=13", "JULIA_IMAGE_THREADS=1"  …  "EBROOTFLEXIBLAS=/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Compiler/intel2020/flexiblas/3.0.4", "RSNT_ARCH=avx2", "XDG_SESSION_ID=278292", "_ModuleTable013_=dWxlcy8yMDIwL0NvcmUiLCAiL2N2bWZzL3NvZnQuY29tcHV0ZWNhbmFkYS5jYS9jdXN0b20vbW9kdWxlcyIsCn0sCnN5c3RlbUJhc2VNUEFUSCA9ICIvY3ZtZnMvc29mdC5jb21wdXRlY2FuYWRhLmNhL2N1c3RvbS9tb2R1bGVzIiwKfQo=", "EASYBUILD_BUILDPATH=/tmp/USER", "CC_RESTRICTED=true", "EBDEVELLIBFABRIC=/cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/libfabric/1.10.1/easybuild/avx2-Core-libfabric-1.10.1-easybuild-devel", "EBVERSIONIMKL=2020.1.217", "EPREFIX=/cvmfs/soft.computecanada.ca/gentoo/2020", "LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.m4a=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.oga=01;36:*.opus=01;36:*.spx=01;36:*.xspf=01;36::su=00:sg=00:ca=00:ow=00:st=00:tw=00:ex=00:or=00::"]), ProcessSignaled(7)) [0]
│
│    Stacktrace:
│      [1] pipeline_error
│        @ ./process.jl:565 [inlined]
│      [2] run(::Cmd, ::Base.DevNull, ::Vararg{Any}; wait::Bool)
│        @ Base ./process.jl:480
│      [3] run
│        @ ./process.jl:477 [inlined]
│      [4] link_image (repeats 2 times)
│        @ ./linking.jl:166 [inlined]
│      [5] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
│        @ Base ./loading.jl:2202
│      [6] #249
│        @ /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/share/julia/stdlib/v1.9/Pkg/src/API.jl:1438 [inlined]
│      [7] withenv(f::Pkg.API.var"#249#280"{IOBuffer, String, Base.PkgId}, keyvals::Pair{String, String})
│        @ Base ./env.jl:197
│      [8] (::Pkg.API.var"#248#279"{IOBuffer, String, Base.PkgId})()
│        @ Pkg.API /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/share/julia/stdlib/v1.9/Pkg/src/API.jl:1436
│      [9] with_logstate(f::Function, logstate::Any)
│        @ Base.CoreLogging ./logging.jl:514
│     [10] with_logger
│        @ ./logging.jl:626 [inlined]
│     [11] macro expansion
│        @ ./timing.jl:393 [inlined]
│     [12] macro expansion
│        @ /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/share/julia/stdlib/v1.9/Pkg/src/API.jl:1434 [inlined]
│     [13] (::Pkg.API.var"#245#276"{Bool, Bool, Pkg.Types.Context, Vector{Task}, Dict{Base.PkgId, String}, Dict{Base.PkgId, IOBuffer}, Pkg.API.var"#color_string#266", Base.Event, Base.Event, ReentrantLock, Vector{Base.PkgId}, Vector{Base.PkgId}, Dict{Base.PkgId, String}, Vector{Base.PkgId}, Vector{Base.PkgId}, Dict{Base.PkgId, Bool}, Dict{Base.PkgId, Base.Event}, Dict{Base.PkgId, Bool}, Vector{Pkg.Types.PackageSpec}, Dict{Base.PkgId, String}, Dict{Tuple{Base.PkgId, UInt128, String, String}, Bool}, Vector{Base.PkgId}, Bool, Base.TTY, Base.Semaphore, String, Vector{String}, Vector{Base.PkgId}, Base.PkgId})()
│        @ Pkg.API ./task.jl:514
└ @ Pkg.API /cvmfs/soft.computecanada.ca/easybuild/software/2020/avx2/Core/julia/1.9.1/share/julia/stdlib/v1.9/Pkg/src/API.jl:1302
asl commented 1 year ago

Consider reporting this issue to Julia issue tracker instead