GDAL does not compile in Alpine:3.14 Linux docker container #151
Comments
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So this is on an older Julia version, and probably requires a musl based build. I advise to move to more recent Julia versions, it will probably work out of the box. |
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We do have musl builds for GDAL_jll: https://github.com/JuliaBinaryWrappers/GDAL_jll.jl/releases It would be good to know what version of GDAL_jll and dependencies you see this on ( |
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@evetion @visr Thanks for the quick responses. I have put together a Dockerfile that I can use to test different combinations of julia and Alpine. All of the docker images fail to build GDAL_jl. I use Dockerfile RUN apk add --update --upgrade --no-cache gcc openssh netcat-openbsd zip unzip curl gnu-libiconv musl-dev postgresql-client aws-cli RUN adduser -u 1000 -S runtime --home /runtime ENV JULIA_DEPOT_PATH=/runtime/.julia WORKDIR /app RUN julia -e 'using Pkg; Pkg.instantiate()' RUN julia -e 'using Pkg; Pkg.add("GDAL"); Pkg.precompile()'
Running (@v1.8) pkg> st -m |
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Thanks for the info. So this happens on the latest GDAL_jll and latest Julia. The key error is this: This could be caused by new libzstd builds breaking the libtiff build, you could try Zstd_jll v1.5.2, see if that resolves it. If so, we probably need to trigger a new build of libtiff and possibly GDAL in Yggdrasil. https://github.com/JuliaBinaryWrappers/Zstd_jll.jl/releases |
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@visr How do I enforce the use of Zstd_jll@1.5.2. I tried the following inside a Julia project within an Alpine docker container and it didn't work: bash> docker run -it julia:1.8-alpine3.17
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What you did worked to get that version, although unfortunately it doesn't seem to work. I saw you opened the same issue in Yggdrasil. Probably the workaround suggested there would be the next thing to try: JuliaPackaging/Yggdrasil#6557 (comment). |
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Thanks @visr . I'll give that workaround a go and see if that fixes things. I'm not sure if I will be able to use that workaround in our production system but atleast that will help us pinpoint the issue. I'll update here once I've tried that. |
We use a Linux Alpine image for our production servers however, GDAL does not compile on the docker container. The steps to reproduce this are:
`
sh> docker pull julia:1.6.2-alpine3.14
sh> docker run -it julia:1.6.2-alpine3.14
julia> ]
Pkg> add GDAL
to see detailed errors run the below
Pkg> precompile
`
Test environment:
Things I have tried so far:
Error relocating /usr/lib/libgssapi_krb5.so.2: k5_sname_compare: symbol not found.Error:
`
(@v1.6) pkg> precompile
Precompiling project...
✗ PROJ_jll
✗ LittleCMS_jll
✗ OpenJpeg_jll
✗ libgeotiff_jll
✗ GDAL_jll
✗ GDAL
0 dependencies successfully precompiled in 8 seconds (29 already precompiled)
ERROR: The following 1 direct dependency failed to precompile:
GDAL [add2ef01-049f-52c4-9ee2-e494f65e021a]
Failed to precompile GDAL [add2ef01-049f-52c4-9ee2-e494f65e021a] to /root/.julia/compiled/v1.6/GDAL/jl_iHjPOh.
ERROR: LoadError: LoadError: InitError: could not load library "/root/.julia/artifacts/4d94fac9395da1d9e54143cd9329aa4ed2882f36/lib/libtiff.so"
Error loading shared library libzstd.so.1: No such file or directory (needed by /root/.julia/artifacts/4d94fac9395da1d9e54143cd9329aa4ed2882f36/lib/libtiff.so)
Stacktrace:
[1] dlopen(s::String, flags::UInt32; throw_error::Bool)
@ Base.Libc.Libdl ./libdl.jl:114
[2] dlopen(s::String, flags::UInt32)
@ Base.Libc.Libdl ./libdl.jl:114
[3] macro expansion
@ ~/.julia/packages/JLLWrappers/QpMQW/src/products/library_generators.jl:54 [inlined]
[4] init()
@ Libtiff_jll ~/.julia/packages/Libtiff_jll/5VD1s/src/wrappers/x86_64-linux-musl.jl:12
[5] _include_from_serialized(path::String, depmods::Vector{Any})
@ Base ./loading.jl:696
[6] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:782
[7] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1020
[8] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:936
[9] require(into::Module, mod::Symbol)
@ Base ./loading.jl:923
[10] include(mod::Module, _path::String)
@ Base ./Base.jl:386
[11] top-level scope
@ ~/.julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
[12] include
@ ./Base.jl:386 [inlined]
[13] 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, UInt64}}, source::String)
@ Base ./loading.jl:1235
[14] top-level scope
@ none:1
[15] eval
@ ./boot.jl:360 [inlined]
[16] eval(x::Expr)
@ Base.MainInclude ./client.jl:446
[17] top-level scope
@ none:1
during initialization of module Libtiff_jll
in expression starting at /root/.julia/packages/PROJ_jll/oT9sV/src/wrappers/x86_64-linux-musl-cxx11.jl:5
in expression starting at /root/.julia/packages/PROJ_jll/oT9sV/src/PROJ_jll.jl:2
ERROR: LoadError: LoadError: Failed to precompile PROJ_jll [58948b4f-47e0-5654-a9ad-f609743f8632] to /root/.julia/compiled/v1.6/PROJ_jll/jl_PjLclO.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{IOStream}, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1385
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1329
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1043
[5] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:936
[6] require(into::Module, mod::Symbol)
@ Base ./loading.jl:923
[7] include(mod::Module, _path::String)
@ Base ./Base.jl:386
[8] top-level scope
@ ~/.julia/packages/JLLWrappers/QpMQW/src/toplevel_generators.jl:188
[9] include
@ ./Base.jl:386 [inlined]
[10] 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, UInt64}}, source::String)
@ Base ./loading.jl:1235
[11] top-level scope
@ none:1
[12] eval
@ ./boot.jl:360 [inlined]
[13] eval(x::Expr)
@ Base.MainInclude ./client.jl:446
[14] top-level scope
@ none:1
in expression starting at /root/.julia/packages/GDAL_jll/mKGP0/src/wrappers/x86_64-linux-musl-cxx11.jl:5
in expression starting at /root/.julia/packages/GDAL_jll/mKGP0/src/GDAL_jll.jl:2
ERROR: LoadError: Failed to precompile GDAL_jll [a7073274-a066-55f0-b90d-d619367d196c] to /root/.julia/compiled/v1.6/GDAL_jll/jl_AKFeLI.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{IOStream}, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1385
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1329
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1043
[5] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:936
[6] require(into::Module, mod::Symbol)
@ Base ./loading.jl:923
[7] include
@ ./Base.jl:386 [inlined]
[8] 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, UInt64}}, source::Nothing)
@ Base ./loading.jl:1235
[9] top-level scope
@ none:1
[10] eval
@ ./boot.jl:360 [inlined]
[11] eval(x::Expr)
@ Base.MainInclude ./client.jl:446
[12] top-level scope
@ none:1
in expression starting at /root/.julia/packages/GDAL/wjbw2/src/GDAL.jl:1
`
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