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ERROR: IOError: stat: permission denied (EACCES) on udocker #34918

Closed dr-br closed 4 years ago

dr-br commented 4 years ago

Intro+Relevance

udocker is a basic user tool to execute simple docker containers in user space without requiring root privileges.
It is the only means to deploy containerized jupyter+X on our super computers.
podman, docker and singularity can not be used (subuid/guid issues…) on the server nodes.

Problem

Current Julia versions (including nightly build) fail to run within a udocker-container. The container OSses testet are ubuntu (18.04) and centos:latest.
Older Julia versions like 1.0.5 and older perfectly work.
Tests with podman or docker are successful for all versions of Julia.

When I execute julia inside a udocker container I get the following error message (the same under ubuntu and centos):

./julia-1.3.1/bin/julia 
ERROR: IOError: stat: permission denied (EACCES) for file "/root/julia-1.3.1/bin/../etc/julia/startup.jl"
Stacktrace:
 [1] stat(::String) at ./stat.jl:69
 [2] isfile at ./stat.jl:311 [inlined]
 [3] load_julia_startup() at ./client.jl:314
 [4] exec_options(::Base.JLOptions) at ./client.jl:258
 [5] _start() at ./client.jl:460

Steps to reproduce

Install udocker

curl https://raw.githubusercontent.com/indigo-dc/udocker/devel/udocker.py > udocker
chmod u+rx ./udocker
./udocker install

Start ubuntu container

export PROOT_NO_SECCOMP=1
udocker pull ubuntu
udocker create --name=ubuntu ubuntu
udocker run --user=root --env="HOME=/root" --workdir="/root" ubuntu

Download and run Julia

Within the ubuntu container run:

apt update && apt install wget
wget https://julialang-s3.julialang.org/bin/linux/x64/1.3/julia-1.3.1-linux-x86_64.tar.gz
tar xvzf julia-1.3.1-linux-x86_64.tar.gz
./julia-1.3.1/bin/julia
DilumAluthge commented 4 years ago

What happens if you start Julia with the flag --startup-file=no?

For example: (inside the container)

./julia-1.3.1/bin/julia --startup-file=no
dr-br commented 4 years ago 
./julia-1.3.1/bin/julia --startup-file=no
               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.3.1 (2019-12-30)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

ERROR: IOError: stat: permission denied (EACCES) for file "/root/.julia/logs"
Stacktrace:
 [1] stat(::String) at ./stat.jl:69
 [2] isdir at ./stat.jl:311 [inlined]
 [3] #mkpath#8(::UInt16, ::typeof(mkpath), ::String) at ./file.jl:217
 [4] mkpath at ./file.jl:215 [inlined]
 [5] setup_interface(::REPL.LineEditREPL, ::Bool, ::Any) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/REPL/src/REPL.jl:859
 [6] #setup_interface#45(::Bool, ::Any, ::typeof(REPL.setup_interface), ::REPL.LineEditREPL) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/REPL/src/REPL.jl:769
 [7] setup_interface at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/REPL/src/REPL.jl:769 [inlined]
 [8] (::Pkg.var"#1#2")(::REPL.LineEditREPL) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.3/Pkg/src/Pkg.jl:432
 [9] __atreplinit(::REPL.LineEditREPL) at ./client.jl:338
 [10] #invokelatest#1 at ./essentials.jl:709 [inlined]
 [11] invokelatest at ./essentials.jl:708 [inlined]
 [12] _atreplinit at ./client.jl:345 [inlined]
 [13] (::Base.var"#770#772"{Bool,Bool,Bool,Bool})(::Module) at ./client.jl:381
 [14] #invokelatest#1 at ./essentials.jl:709 [inlined]
 [15] invokelatest at ./essentials.jl:708 [inlined]
 [16] run_main_repl(::Bool, ::Bool, ::Bool, ::Bool, ::Bool) at ./client.jl:366
 [17] exec_options(::Base.JLOptions) at ./client.jl:304
 [18] _start() at ./client.jl:460

[ Info: Disabling history file for this session
DilumAluthge commented 4 years ago

Alright let’s try this: (inside the container)

./julia-1.3.1/bin/julia --startup-file=no --history-file=no
Keno commented 4 years ago

It's a bit odd for stat to throw. Usually that only happens when the permissions are really odd. Can you show the permissions, as seen inside the container for the /root directory, the /root/.julia directory and the /root/julia-1.3.1/bin/../etc/julia directory?

dr-br commented 4 years ago

./julia-1.3.1/bin/julia --startup-file=no --history-file=no works without errors, but nothing can be installed:

julia> using Pkg
ERROR: IOError: stat: permission denied (EACCES) for file "/root/.julia/environments/v1.3"
Stacktrace:
 [1] stat(::String) at ./stat.jl:69
 [2] isdir at ./stat.jl:311 [inlined]
 [3] load_path_expand(::String) at ./initdefs.jl:241
 [4] load_path() at ./initdefs.jl:288
 [5] identify_package(::String) at ./loading.jl:219
 [6] identify_package(::Base.PkgId, ::String) at ./loading.jl:206
 [7] identify_package at ./loading.jl:200 [inlined]
 [8] require(::Module, ::Symbol) at ./loading.jl:882

No /root/.julia directory is created.

ls -la
total 180352
drwxr-xr-x  5 root root     4096 Feb 29 16:51 .
drwxr-xr-x 21 root root     4096 Feb 29 16:43 ..
-rw-------  1 root root     1460 Feb 29 16:52 .bash_history
-rw-r--r--  1 root root     3106 Apr  9  2018 .bashrc
drwxr-xr-x  3 root root     4096 Feb 29 16:50 .local
-rw-r--r--  1 root root      148 Aug 17  2015 .profile
-rw-r--r--  1 root root      248 Feb 29 16:50 .wget-hsts
drwxr-xr-x  7 root root     4096 Sep  9 21:08 julia-1.0.5
-rw-r--r--  1 root root 88706549 Sep 11 21:22 julia-1.0.5-linux-x86_64.tar.gz
drwxr-xr-x  8 root root     4096 Dec 30 22:12 julia-1.3.1
-rw-r--r--  1 root root 95929584 Dec 31 00:20 julia-1.3.1-linux-x86_64.tar.gz
ls -la /root/julia-1.3.1/bin/../etc/julia
total 12
drwxr-xr-x 2 root root 4096 Dec 30 22:12 .
drwxr-xr-x 3 root root 4096 Dec 30 22:12 ..
-rw-r--r-- 1 root root  162 Dec 30 22:12 startup.jl

With ./julia-1.0.5/bin/julia everything works as expected.

DilumAluthge commented 4 years ago

First, try this: (inside the container)

export JULIA_DEPOT_PATH="$HOME/.julia:"
./julia-1.3.1/bin/julia --startup-file=no --history-file=no

If that does not work, then try this instead: (inside the container)

export JULIA_DEPOT_PATH="$HOME/.julia"
./julia-1.3.1/bin/julia --startup-file=no --history-file=no
DilumAluthge commented 4 years ago

I have a few additional questions:

  1. Can you show the permissions (as seen inside the container) for the / directory?
  2. What do you get when you run whoami, groups, and id inside the container?
  3. Inside the container, start Julia with ./julia-1.3.1/bin/julia --startup-file=no --history-file=no, and then run the following commands in the Julia REPL and post the results:
    • julia> @show homedir()
    • julia> @show Base.DEPOT_PATH
    • julia> versioninfo(stdout; verbose = true)
  4. What happens if you delete your ~/.udocker directory (on the host machine) and then try again to reproduce?
dr-br commented 4 years ago 
export JULIA_DEPOT_PATH="$HOME/.julia:"
./julia-1.3.1/bin/julia --startup-file=no --history-file=no

and

export JULIA_DEPOT_PATH="$HOME/.julia"
./julia-1.3.1/bin/julia --startup-file=no --history-file=no

both lead to ERROR: IOError: stat: permission denied (EACCES) for file "/root/.julia/environments/v1.3" when trying to using Pkg.

Permissions of / 

ls -la /
total 72
drwxr-xr-x  21 root root 4096 Mar  1 08:15 .
drwxr-xr-x  21 root root 4096 Mar  1 08:15 ..
drwxr-xr-x   2 root root 4096 Feb 19 01:17 bin
drwxr-xr-x   2 root root 4096 Apr 24  2018 boot
drwxr-xr-x  19 root root 4400 Mar  1 07:52 dev
drwxr-xr-x  31 root root 4096 Mar  1 08:16 etc
drwxr-xr-x   2 root root 4096 Apr 24  2018 home
drwxr-xr-x   9 root root 4096 Mar  1 08:15 lib
drwxr-xr-x   2 root root 4096 Feb 19 01:15 lib64
drwxr-xr-x   2 root root 4096 Feb 19 01:14 media
drwxr-xr-x   2 root root 4096 Feb 19 01:14 mnt
drwxr-xr-x   2 root root 4096 Feb 19 01:14 opt
dr-xr-xr-x 298 root root    0 Mar  1 07:50 proc
drwx------   3 root root 4096 Mar  1 08:16 root
drwxr-xr-x   5 root root 4096 Feb 21 22:20 run
drwxr-xr-x   2 root root 4096 Feb 21 22:20 sbin
drwxr-xr-x   2 root root 4096 Feb 19 01:14 srv
dr-xr-xr-x  13 root root    0 Mar  1 07:50 sys
drwxr-xr-x   2 root root 4096 Mar  1 08:16 tmp
drwxr-xr-x  10 root root 4096 Feb 19 01:14 usr
drwxr-xr-x  11 root root 4096 Feb 19 01:17 var
root@desktop:~# whoami 
root
root@desktop:~# groups
root adm cdrom sudo audio dip video plugdev G111 G114 G121 G127 G133 G134 G1000 G1002
root@desktop:~# id
uid=0(root) gid=0(root) groups=0(root),4(adm),24(cdrom),27(sudo),29(audio),30(dip),44(video),46(plugdev),111(G111),114(G114),121(G121),127(G127),133(G133),134(G134),1000(G1000),1002(G1002)

and finally: 

julia> @show homedir()
homedir() = "/root"
"/root"

julia> @show Base.DEPOT_PATH
Base.DEPOT_PATH = ["/root/.julia", "/root/julia-1.3.1/local/share/julia", "/root/julia-1.3.1/share/julia"]
3-element Array{String,1}:
 "/root/.julia"                       
 "/root/julia-1.3.1/local/share/julia"
 "/root/julia-1.3.1/share/julia"      

julia> versioninfo(stdout; verbose = true)
Julia Version 1.3.1
Commit 2d5741174c (2019-12-30 21:36 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  uname: Linux 5.4.0-16-generic #19-Ubuntu SMP Wed Feb 26 18:35:11 UTC 2020 x86_64 x86_64
  CPU: Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz: 
              speed         user         nice          sys         idle          irq
       #1  3800 MHz       5963 s         62 s       1828 s     220891 s          0 s
       #2  3800 MHz       6187 s         56 s       2048 s     215920 s          0 s
       #3  3801 MHz       6060 s        214 s       1964 s     219314 s          0 s
       #4  3800 MHz       6131 s        154 s       2024 s     219160 s          0 s
       #5  3808 MHz       6243 s         84 s       1872 s     220415 s          0 s
       #6  3808 MHz       5916 s          3 s       1852 s     221188 s          0 s
       #7  3800 MHz       5134 s         32 s       1829 s     221457 s          0 s
       #8  3800 MHz       5726 s         19 s       1886 s     220930 s          0 s

  Memory: 15.52651596069336 GB (10002.5703125 MB free)
  Uptime: 2303.0 sec
  Load Avg:  0.3193359375  0.29736328125  0.34814453125
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.1 (ORCJIT, skylake)
Environment:
  JULIA_DEPOT_PATH = /root/.julia:
  JULIA_DEPOT_PATH = /root/.julia:
  HOME = /root
  TERM = xterm-256color
  PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
DilumAluthge commented 4 years ago

Can you run println(mktempdir()) in the Julia REPL and post the results?

dr-br commented 4 years ago 
./julia-1.3.1/bin/julia --startup-file=no --history-file=no

julia> println(mktempdir())
/tmp/jl_5ejX2C
DilumAluthge commented 4 years ago

In the Julia REPL, try the following:


julia> rm("/root/.julia"; force = true, recursive = true)
julia> mkpath("/root/.julia")
julia> open("/root/.julia/foo.txt", "w") do io
              println(io, "hello world")
           end
julia> println(read("/root/.julia/foo.txt", String))
julia> println(realpath("/root/.julia/foo.txt"))
DilumAluthge commented 4 years ago

Also:

  1. What happens if you delete your ~/.udocker directory (on the host machine) and then try again to reproduce?

Oh, and also:

julia> Base.stat("/")
julia> Base.stat("/root")
julia> Base.stat("/tmp")

Also, is there any chance that your host system is running SELinux?

dr-br commented 4 years ago 
julia> rm("/root/.julia"; force = true, recursive = true)

There is no .julia dir, so I can't delete it

julia> mkpath("/root/.julia")
ERROR: IOError: stat: permission denied (EACCES) for file "/root/.julia"
Stacktrace:
 [1] stat(::String) at ./stat.jl:69
 [2] isdir at ./stat.jl:311 [inlined]
 [3] #mkpath#8(::UInt16, ::typeof(mkpath), ::String) at ./file.jl:217
 [4] mkpath(::String) at ./file.jl:215
 [5] top-level scope at REPL[2]:1

no ~/.julia created

When I manually create mkdir ~/.julia, file creation under julia works then! 

julia> open("/root/.julia/foo.txt", "w") do io
                     println(io, "hello world")
                  end

julia> println(read("/root/.julia/foo.txt", String))
hello world

julia> println(realpath("/root/.julia/foo.txt"))
/root/.julia/foo.txt
julia> Base.stat("/")
StatStruct(mode=0o040755, size=4096)

julia> Base.stat("/root")
StatStruct(mode=0o040700, size=4096)

julia> Base.stat("/tmp")
StatStruct(mode=0o041777, size=2957312)

I always start with a rm -rf ~/udocker ;)

SELinux…I don't know. Tested so far on vanilla Ubuntu 19.10 and 20.04 hosts.

dr-br commented 4 years ago

Update: On Red Hat Enterprise Linux Server release 7.7 host everything works as expected with ubuntu container.

DilumAluthge commented 4 years ago

There is no .julia dir, so I can't delete it

You can run that command in Julia whether or not the file/directory exists. In Julia, if you run the rm function with force = true, it won’t throw an error if the file/directory doesn’t exist.

SELinux…I don't know.

You can run the following commands in bash to see if SELinux is enabled:

getenforce
sestatus
DilumAluthge commented 4 years ago

This seems like a bug in one of the following:

DilumAluthge commented 4 years ago

What happens if you go into a brand-new container, enter a Julia REPL, and run this:

julia> Base.stat("/root/.julia")
DilumAluthge commented 4 years ago

Also, on one of the hosts that does have this error, can you download and extract Julia on the host (not inside udocker, not inside a container), open a Julia REPL, and try to reproduce this error?

That will help us figure out of the problem is with your host machine or with udocker.

dr-br commented 4 years ago

Inside a brand new container: 

julia> Base.stat("/root/.julia")
ERROR: IOError: stat: permission denied (EACCES) for file "/root/.julia"
Stacktrace:
 [1] stat(::String) at ./stat.jl:69
 [2] top-level scope at REPL[1]:1

On the host (all machines in reach), I do not get any errors. Everything works as expected. SELinux is disabled on my Ubuntu machines and on the cluster RHEL 7.7.

Have there been substantial changes between julia 1.0.5 and the following versions with respect to directory creation/stat/security/rights management?

DilumAluthge commented 4 years ago

What about this: (inside a brand new container)

julia> run(`stat /root/.julia`)

I expect this to throw an error. The question is: will it throw an error because of stat: No such file or directory, or will it throw an error because of stat: Permission denied?

DilumAluthge commented 4 years ago

Have there been substantial changes between julia 1.0.5 and the following versions with respect to directory creation/stat/security/rights management?

I'm not sure.

Is Julia 1.0.5 the most recent version that works for you? Do any of the Julia 1.1.x versions work?

In particular, if you can confirm that Julia 1.0.5 works for you, but Julia 1.1.0 gives this error, then we can try to look at the diff between those two versions.

DilumAluthge commented 4 years ago

Here's another thing to try. Inside a fresh container:

julia> Base.stat("/root/.foo")

julia> Base.stat("/root/foo")
dr-br commented 4 years ago 
julia> run(`stat /root/.julia`)
stat: cannot stat '/root/.julia': No such file or directory
ERROR: failed process: Process(`stat /root/.julia`, ProcessExited(1)) [1]

Stacktrace:
 [1] pipeline_error at ./process.jl:525 [inlined]
 [2] #run#565(::Bool, ::typeof(run), ::Cmd) at ./process.jl:440
 [3] run(::Cmd) at ./process.jl:438
 [4] top-level scope at REPL[5]:1
julia> Base.stat("/root/.foo")
ERROR: IOError: stat: permission denied (EACCES) for file "/root/.foo"
Stacktrace:
 [1] stat(::String) at ./stat.jl:69
 [2] top-level scope at REPL[6]:1

julia> Base.stat("/root/foo")
ERROR: IOError: stat: permission denied (EACCES) for file "/root/foo"
Stacktrace:
 [1] stat(::String) at ./stat.jl:69
 [2] top-level scope at REPL[7]:1
dr-br commented 4 years ago

I tried different versions:

DilumAluthge commented 4 years ago

Can you try julia-1.3.0 also?

DilumAluthge commented 4 years ago

@Keno does the fact that

run(`stat /root/.julia`)

gives "no such file or directory" (the correct answer), but 

Base.stat("/root/.julia")

gives "permission denied (EACCES)" suggest that this is a Julia bug or a libuv bug (rather than a problem with the system)?

dr-br commented 4 years ago
DilumAluthge commented 4 years ago

So, if you are able to build Julia from source inside the container, the best option will be to git bisect between 1.2.0 and 1.3.0 to figure out which commit introduces this bug.

DilumAluthge commented 4 years ago

The script for the git bisect can probably be as simple as:

make
rm -rf /root/.julia
./julia -e 'Base.stat("/root/.julia")
DilumAluthge commented 4 years ago

Pass that script to git bisect run with the tags v1.2.0 and v1.3.0 as the known good and bad commits, respectively. Then the bisect should automatically find which commit introduced this bug.

Keno commented 4 years ago

Another thing to try would be stracing Julia doing the stat call vs the native utility.

On Sun, Mar 1, 2020, 13:45 Dilum Aluthge notifications@github.com wrote:

The script for the git bisect can probably be as simple as:

make rm -rf /root/.julia ./julia -e 'Base.stat("/root/.julia")

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/JuliaLang/julia/issues/34918?email_source=notifications&email_token=AAJ3LF7POZR6DTJMLULCVYTRFKUL7A5CNFSM4K5UHN32YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENNHHHQ#issuecomment-593130398, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJ3LF5FHMAJFRAWWF7HRXLRFKUL7ANCNFSM4K5UHN3Q .

DilumAluthge commented 4 years ago

Another thing to try would be stracing Julia doing the stat call vs the native utility.

Yeah that might be the first thing to do. @dr-br inside a fresh container can you run each of the following:

strace stat /root/.julia
strace ./julia-1.3.1/bin/julia --startup-file=no --history-file=no -e 'Base.stat("/root/.julia")'
Keno commented 4 years ago

Yeah that might be the first thing to do. @dr-br inside a fresh container can you run each of the following:

In order for this to work, you'd need to strace the children also (or just strace the utility directly).

DilumAluthge commented 4 years ago

In order for this to work, you'd need to strace the children also (or just strace the utility directly).

Would this be better then?

strace stat /root/.julia
strace ./julia-1.3.1/bin/julia --startup-file=no --history-file=no -e 'Base.stat("/root/.julia")'
dr-br commented 4 years ago

All the stats on ~/.julia will return 1, as in a new container, there is no such directory.

DilumAluthge commented 4 years ago

All the stats on ~/.julia will return 1, as in a new container, there is no such directory.

I think @Keno wants to see the strace output, to figure out why the system utility stat works correctly (telling us that there is no such directory), but the Julia Base.stat function errors and claims that there is a permissions problem. strace will tell us about the system calls that are made in each situation.

dr-br commented 4 years ago

OK. command1: strace stat /root/.julia command2: strace ./julia-1.3.1/bin/julia --startup-file=no --history-file=no -e 'Base.stat("/root/.julia")' command1.txt command2.txt

Is the difference between the following commands valuable?

strace ./julia-1.3.1/bin/julia -e 'exit()'
strace ./julia-1.0.5/bin/julia -e 'exit()'
DilumAluthge commented 4 years ago

Is the difference between the following commands valuable?

It can't hurt to run it and save the output, just in case Keno wants to see it later!

DilumAluthge commented 4 years ago

By the way @dr-br, thanks for your patience with all of this!

DilumAluthge commented 4 years ago

@Keno look at line 80 of command1.txt (system stat utility):

lstat("/root/.julia", 0x7ffeb2f4d7a0)   = -1 ENOENT (No such file or directory)

Now look at line 845 of command2.txt (Julia 1.3.1 Base.stat):

statx(AT_FDCWD, "/root/.julia", AT_STATX_SYNC_AS_STAT, STATX_ALL, 0x7fff4a035940) = -1 EACCES (Permission denied)

It seems like the system stat command is calling the lstat syscall, while Julia's libuv is calling the statx syscall?

DilumAluthge commented 4 years ago

@dr-br You said that this bug does not exist on Julia 1.2.0, right? Can you run this as well:

strace ./julia-1.2.0/bin/julia --startup-file=no --history-file=no -e 'Base.stat("/root/.julia")'
DilumAluthge commented 4 years ago

@Keno I'm wondering if maybe https://github.com/libuv/libuv/issues/2152 is the culprit?

dr-br commented 4 years ago

Here the output from 1.2.0 strace_1.2.0.txt

DilumAluthge commented 4 years ago

command1.txt (system stat utility), line 80:

lstat("/root/.julia", 0x7ffeb2f4d7a0)   = -1 ENOENT (No such file or directory)

command2.txt (Julia 1.3.1 Base.stat), line 845:

statx(AT_FDCWD, "/root/.julia", AT_STATX_SYNC_AS_STAT, STATX_ALL, 0x7fff4a035940) = -1 EACCES (Permission denied)

strace_1.2.0.txt (Julia 1.2.0 Base.stat), line 864:

stat("/root/.julia", 0x7ffc2c99fb00)    = -1 ENOENT (No such file or directory)

It certainly does seem like statx is the culprit here.

DilumAluthge commented 4 years ago

If you look at the original bug report, Base.stat is getting called by Base.isdir. I don't think we need all of the fancy information of statx just to figure out whether or not the input is a directory, right? The info we get from stat or lstat (which presumably are equivalent if the input is not a link) should be more than sufficient.

Keno commented 4 years ago

It would be good to figure out where the eaccess comes from though and at least update the man page or file a bug with somebody if that's not the expected behavior.

Keno commented 4 years ago

To add the reference, as I suspected there is no documented difference between stat and statx with respect to eaccess errors: http://man7.org/linux/man-pages/man2/statx.2.html. @dr-br could you show the output of mount inside the container, so we know what kind of car we're dealing with?

dr-br commented 4 years ago

mount inside container:

root@myMachine:~# mount
sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
udev on /dev type devtmpfs (rw,nosuid,relatime,size=5988288k,nr_inodes=1497072,mode=755)
devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)
tmpfs on /run type tmpfs (rw,nosuid,noexec,relatime,size=1206384k,mode=755)
/dev/mapper/vgubuntu-root on / type ext4 (rw,relatime,errors=remount-ro)
securityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)
tmpfs on /run/lock type tmpfs (rw,nosuid,nodev,noexec,relatime,size=5120k)
tmpfs on /sys/fs/cgroup type tmpfs (ro,nosuid,nodev,noexec,mode=755)
cgroup2 on /sys/fs/cgroup/unified type cgroup2 (rw,nosuid,nodev,noexec,relatime,nsdelegate)
cgroup on /sys/fs/cgroup/systemd type cgroup (rw,nosuid,nodev,noexec,relatime,xattr,name=systemd)
pstore on /sys/fs/pstore type pstore (rw,nosuid,nodev,noexec,relatime)
efivarfs on /sys/firmware/efi/efivars type efivarfs (rw,nosuid,nodev,noexec,relatime)
bpf on /sys/fs/bpf type bpf (rw,nosuid,nodev,noexec,relatime,mode=700)
cgroup on /sys/fs/cgroup/devices type cgroup (rw,nosuid,nodev,noexec,relatime,devices)
cgroup on /sys/fs/cgroup/memory type cgroup (rw,nosuid,nodev,noexec,relatime,memory)
cgroup on /sys/fs/cgroup/cpuset type cgroup (rw,nosuid,nodev,noexec,relatime,cpuset)
cgroup on /sys/fs/cgroup/freezer type cgroup (rw,nosuid,nodev,noexec,relatime,freezer)
cgroup on /sys/fs/cgroup/net_cls,net_prio type cgroup (rw,nosuid,nodev,noexec,relatime,net_cls,net_prio)
cgroup on /sys/fs/cgroup/blkio type cgroup (rw,nosuid,nodev,noexec,relatime,blkio)
cgroup on /sys/fs/cgroup/hugetlb type cgroup (rw,nosuid,nodev,noexec,relatime,hugetlb)
cgroup on /sys/fs/cgroup/perf_event type cgroup (rw,nosuid,nodev,noexec,relatime,perf_event)
cgroup on /sys/fs/cgroup/pids type cgroup (rw,nosuid,nodev,noexec,relatime,pids)
cgroup on /sys/fs/cgroup/cpu,cpuacct type cgroup (rw,nosuid,nodev,noexec,relatime,cpu,cpuacct)
cgroup on /sys/fs/cgroup/rdma type cgroup (rw,nosuid,nodev,noexec,relatime,rdma)
mqueue on /dev/mqueue type mqueue (rw,nosuid,nodev,noexec,relatime)
hugetlbfs on /dev/hugepages type hugetlbfs (rw,relatime,pagesize=2M)
debugfs on /sys/kernel/debug type debugfs (rw,nosuid,nodev,noexec,relatime)
systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=44,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=20854)
configfs on /sys/kernel/config type configfs (rw,nosuid,nodev,noexec,relatime)
fusectl on /sys/fs/fuse/connections type fusectl (rw,nosuid,nodev,noexec,relatime)
/var/lib/snapd/snaps/telegram-desktop_1234.snap on /snap/telegram-desktop/1234 type squashfs (ro,nodev,relatime)
/var/lib/snapd/snaps/core18_1668.snap on /snap/core18/1668 type squashfs (ro,nodev,relatime)
/var/lib/snapd/snaps/core_8689.snap on /snap/core/8689 type squashfs (ro,nodev,relatime)
/var/lib/snapd/snaps/gnome-logs_81.snap on /snap/gnome-logs/81 type squashfs (ro,nodev,relatime)
/var/lib/snapd/snaps/gnome-3-28-1804_116.snap on /snap/gnome-3-28-1804/116 type squashfs (ro,nodev,relatime)
/var/lib/snapd/snaps/gtk-common-themes_1440.snap on /snap/gtk-common-themes/1440 type squashfs (ro,nodev,relatime)
/var/lib/snapd/snaps/gnome-calculator_544.snap on /snap/gnome-calculator/544 type squashfs (ro,nodev,relatime)
/var/lib/snapd/snaps/blender_36.snap on /snap/blender/36 type squashfs (ro,nodev,relatime)
/var/lib/snapd/snaps/skype_112.snap on /snap/skype/112 type squashfs (ro,nodev,relatime)
/var/lib/snapd/snaps/telegram-desktop_1244.snap on /snap/telegram-desktop/1244 type squashfs (ro,nodev,relatime)
/var/lib/snapd/snaps/chromium_1028.snap on /snap/chromium/1028 type squashfs (ro,nodev,relatime)
/var/lib/snapd/snaps/code-insiders_375.snap on /snap/code-insiders/375 type squashfs (ro,nodev,relatime)
/var/lib/snapd/snaps/gnome-characters_399.snap on /snap/gnome-characters/399 type squashfs (ro,nodev,relatime)
/var/lib/snapd/snaps/signal-desktop_299.snap on /snap/signal-desktop/299 type squashfs (ro,nodev,relatime)
/dev/sda2 on /boot type ext4 (rw,relatime)
/dev/sda1 on /boot/efi type vfat (rw,relatime,fmask=0077,dmask=0077,codepage=437,iocharset=iso8859-1,shortname=mixed,errors=remount-ro)
me@otherMachine: on /mnt/lsdf type fuse.sshfs (rw,relatime,user_id=0,group_id=0,allow_other)
/var/lib/snapd/snaps/code-insiders_376.snap on /snap/code-insiders/376 type squashfs (ro,nodev,relatime)
tmpfs on /run/user/1000 type tmpfs (rw,nosuid,nodev,relatime,size=1206380k,mode=700,uid=1000,gid=1000)
gvfsd-fuse on /run/user/1000/gvfs type fuse.gvfsd-fuse (rw,nosuid,nodev,relatime,user_id=1000,group_id=1000)
Keno commented 4 years ago

That's inside the container? Looks more like a host system. I wonder if it's picking up the outside world instead.

dr-br commented 4 years ago

To recall this:

Update: On Red Hat Enterprise Linux Server release 7.7 host everything works as expected with ubuntu container.

The problems seem to be the combination Ubuntu host + Udocker So I'm not sure, if further digging into this problem is worth it. However, it is strange that julia 1.2.0 and older work.

@Keno: Yes, udocker is not really what you expect, if you know docker or podman.