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Build error: IOError: sendfile: operation not supported on socket (ENOTSUP)
#341
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Thanks for reporting this. This appears to be a bug with Julia itself. I suspect it may have something to do with copying files across file systems. Can you outline what your file system setup is in the container? |
I'm not sure if it's related, but as shown above, I have a custom Besides that, I think that singularity auto-mounts the current working directory (which was inside What other details could I provide? |
Can you run the following code in your container? using Pkg
Pkg.add(PackageSpec(name="TimeZones", rev="cv/build-debug"))
using TimeZones
TimeZones.build() Also the output from |
The Resolving package versions...
Updating `/mnt/storage/epoch/dev/Project.toml`
[f269a46b] + TimeZones v1.5.5 `https://github.com/JuliaTime/TimeZones.jl.git#cv/build-debug`
Updating `/mnt/storage/epoch/dev/Manifest.toml`
[8f5d6c58] + EzXML v1.1.0
[78c3b35d] + Mocking v0.7.1
[f269a46b] + TimeZones v1.5.5 `https://github.com/JuliaTime/TimeZones.jl.git#cv/build-debug`
Building TimeZones → `/mnt/storage/sebastian/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/8856fa551085f6bbb29e0e9800d3be7ecf8e0db8/build.log`
ERROR: Error building `TimeZones`:
[ Info: Installing 2021a tzdata region data
[ Info: /mnt/storage/sebastian/.julia/artifacts/6d94ada27957590cbd0d7678f5ae711232a4d714/africa -> /mnt/storage/sebastian/.julia/packages/TimeZones/UQZUE/deps/tzsource/africa
ERROR: LoadError: IOError: sendfile: operation not supported on socket (ENOTSUP)
Stacktrace:
[1] uv_error
@ ./libuv.jl:97 [inlined]
[2] sendfile(dst::Base.Filesystem.File, src::Base.Filesystem.File, src_offset::Int64, bytes::Int64)
@ Base.Filesystem ./filesystem.jl:119
[3] sendfile(src::String, dst::String)
@ Base.Filesystem ./file.jl:960
[4] cp(src::String, dst::String; force::Bool, follow_symlinks::Bool)
@ Base.Filesystem ./file.jl:355
[5] build(version::String, regions::Vector{String}, archive_dir::String, tz_source_dir::String, compiled_dir::String; verbose::Bool)
@ TimeZones.TZData /mnt/storage/sebastian/.julia/packages/TimeZones/UQZUE/src/tzdata/build.jl:67
[6] build(version::String)
@ TimeZones.TZData /mnt/storage/sebastian/.julia/packages/TimeZones/UQZUE/src/tzdata/build.jl:124
[7] build(version::String; force::Bool)
@ TimeZones /mnt/storage/sebastian/.julia/packages/TimeZones/UQZUE/src/build.jl:11
[8] build (repeats 2 times)
@ /mnt/storage/sebastian/.julia/packages/TimeZones/UQZUE/src/build.jl:11 [inlined]
[9] top-level scope
@ /mnt/storage/sebastian/.julia/packages/TimeZones/UQZUE/deps/build.jl:3
[10] include(fname::String)
@ Base.MainInclude ./client.jl:444
[11] top-level scope
@ none:5
in expression starting at /mnt/storage/sebastian/.julia/packages/TimeZones/UQZUE/deps/build.jl:3
Stacktrace:
[1] pkgerror(msg::String)
@ Pkg.Types /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:55
[2] (::Pkg.Operations.var"#82#87"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec})()
@ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1044
[3] withenv(::Pkg.Operations.var"#82#87"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec}, ::Pair{String, String}, ::Vararg{Pair{String, B} where B, N} where N)
@ Base ./env.jl:161
[4] (::Pkg.Operations.var"#109#113"{String, Pkg.Operations.var"#82#87"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec}, Pkg.Types.PackageSpec})()
@ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1542
[5] with_temp_env(fn::Pkg.Operations.var"#109#113"{String, Pkg.Operations.var"#82#87"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec}, Pkg.Types.PackageSpec}, temp_env::String)
@ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1444
[6] (::Pkg.Operations.var"#108#112"{Pkg.Operations.var"#82#87"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, Pkg.Types.Project, String})(tmp::String)
@ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1517
[7] mktempdir(fn::Pkg.Operations.var"#108#112"{Pkg.Operations.var"#82#87"{Bool, Pkg.Types.Context, String, Pkg.Types.PackageSpec}, Pkg.Types.Context, Pkg.Types.PackageSpec, String, Pkg.Types.Project, String}, parent::String; prefix::String)
@ Base.Filesystem ./file.jl:729
[8] mktempdir(fn::Function, parent::String) (repeats 2 times)
@ Base.Filesystem ./file.jl:727
[9] sandbox(fn::Function, ctx::Pkg.Types.Context, target::Pkg.Types.PackageSpec, target_path::String, sandbox_path::String, sandbox_project_override::Pkg.Types.Project)
@ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1483
[10] build_versions(ctx::Pkg.Types.Context, uuids::Vector{Base.UUID}; verbose::Bool)
@ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1025
[11] build_versions
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:952 [inlined]
[12] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Vector{Base.UUID}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform)
@ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1241
[13] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::Base.Iterators.Pairs{Symbol, Base.TTY, Tuple{Symbol}, NamedTuple{(:io,), Tuple{Base.TTY}}})
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:203
[14] add(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.TTY, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:79
[15] add(pkgs::Vector{Pkg.Types.PackageSpec})
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:77
[16] #add#22
@ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:74 [inlined]
[17] add(pkg::Pkg.Types.PackageSpec)
@ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:74
[18] top-level scope
@ REPL[2]:1 I'm not sure if it helps, but I also followed with the following commands
The output from shell> mount
overlay on / type overlay (ro,nodev,relatime,seclabel,lowerdir=/var/singularity/mnt/session/overlay-lowerdir:/var/singularity/mnt/session/rootfs)
devtmpfs on /dev type devtmpfs (rw,nosuid,seclabel,size=65840508k,nr_inodes=16460127,mode=755)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev,seclabel)
devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,seclabel,gid=5,mode=620,ptmxmode=000)
mqueue on /dev/mqueue type mqueue (rw,relatime,seclabel)
hugetlbfs on /dev/hugepages type hugetlbfs (rw,relatime,seclabel)
/dev/sda2 on /usr/share/zoneinfo/UCT type xfs (rw,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /etc/hosts type xfs (rw,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
172.16.9.1:/data1 on /mnt/storage type nfs4 (rw,nosuid,nodev,relatime,vers=4.1,rsize=1048576,wsize=1048576,namlen=255,soft,proto=tcp,timeo=600,retrans=2,sec=sys,clientaddr=172.16.9.11,local_lock=none,addr=172.16.9.1)
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=29,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=374563956)
sysfs on /sys type sysfs (rw,nosuid,nodev,relatime,seclabel)
/dev/sda5 on /home/sebastian type xfs (rw,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /tmp type xfs (rw,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /var/tmp type xfs (rw,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
tmpfs on /.singularity.d/libs type tmpfs (ro,nosuid,nodev,relatime,seclabel,size=16384k,uid=1000,gid=1000)
/dev/sda2 on /.singularity.d/libs/libcuda.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libcuda.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libEGL_nvidia.so.0 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libEGL.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libEGL.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libGLdispatch.so.0 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libGLdispatch.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libGLESv1_CM_nvidia.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libGLESv1_CM.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libGLESv1_CM.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libGLESv2_nvidia.so.2 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libGLESv2.so.2 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libGLESv2.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libGL.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libGL.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libGLX_nvidia.so.0 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libGLX.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libGLX.so.0 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvcuvid.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvcuvid.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-cbl.so.410.48 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-cbl.so.460.32.03 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-cfg.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-cfg.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-compiler.so.410.48 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-compiler.so.460.32.03 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-eglcore.so.410.48 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-eglcore.so.460.32.03 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-encode.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-encode.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-fatbinaryloader.so.410.48 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-fbc.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-fbc.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-glcore.so.460.32.03 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-glcore.so.410.48 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-glsi.so.460.32.03 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-glsi.so.410.48 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-glvkspirv.so.460.32.03 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-glvkspirv.so.410.48 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-gtk2.so.410.48 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-gtk3.so.460.32.03 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-gtk3.so.410.48 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-ifr.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-ifr.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-ml.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-ml.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-opencl.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-opticalflow.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-ptxjitcompiler.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-ptxjitcompiler.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-rtcore.so.410.48 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-rtcore.so.460.32.03 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-tls.so.410.48 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvidia-tls.so.460.32.03 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libnvoptix.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libOpenCL.so.1 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libOpenCL.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libOpenGL.so type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /.singularity.d/libs/libOpenGL.so.0 type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /usr/bin/nvidia-smi type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /usr/bin/nvidia-debugdump type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /usr/bin/nvidia-persistenced type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /usr/bin/nvidia-cuda-mps-control type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
/dev/sda2 on /usr/bin/nvidia-cuda-mps-server type xfs (ro,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota)
tmpfs on /etc/resolv.conf type tmpfs (rw,nosuid,relatime,seclabel,size=16384k,uid=1000,gid=1000)
tmpfs on /etc/passwd type tmpfs (rw,nosuid,relatime,seclabel,size=16384k,uid=1000,gid=1000)
tmpfs on /etc/group type tmpfs (rw,nosuid,relatime,seclabel,size=16384k,uid=1000,gid=1000)
172.16.9.1:/data1 on /mnt/storage type nfs4 (rw,nosuid,nodev,relatime,vers=4.1,rsize=1048576,wsize=1048576,namlen=255,soft,proto=tcp,timeo=600,retrans=2,sec=sys,clientaddr=172.16.9.11,local_lock=none,addr=172.16.9.1)
/dev/sda2 on /usr/local/cuda type xfs (rw,nosuid,nodev,relatime,seclabel,attr2,inode64,noquota) From outside the container form bash:
|
I got the following error while building
TimeZones v1.5.5
:This is on:
I'm not sure if it helps, but my system info is the following: I'm using the julia docker image (in a singularity container) with
on a host with
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