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sylabs / singularity

SingularityCE is the Community Edition of Singularity, an open source container platform designed to be simple, fast, and secure.
https://sylabs.io/docs/
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Cannot install vim (and any other tools) inside singularity container #576

Closed airbox11 closed 2 years ago

airbox11 commented 2 years ago

Version of Singularity:

What version of Singularity are you using? Run:

$ singularity --version
singularity-ce version 3.8.0-rc.1+113-gd7f654eae

Expected behavior

I've created a sandbox 

$ singularity pull docker://ubuntu:latest
$ singularity build --sandbox ubuntu_sandbox1 ubuntu_latest.sif

and trying to install vim inside of it with the following commands:

$ singularity shell --writable ubuntu_sandbox1
WARNING: Skipping mount /etc/localtime [binds]: /etc/localtime doesn't exist in container

$ apt update
$ apt install vim

Actual behavior

Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
  alsa-topology-conf alsa-ucm-conf file libasound2 libasound2-data libcanberra0 libexpat1 libgpm2 libltdl7 libmagic-mgc libmagic1 libmpdec2 libogg0 libpython3.8 libpython3.8-minimal libpython3.8-stdlib libreadline8 libsqlite3-0 libssl1.1 libtdb1 libvorbis0a libvorbisfile3 mime-support readline-common
  sound-theme-freedesktop vim-common vim-runtime xxd xz-utils
Suggested packages:
  libasound2-plugins alsa-utils libcanberra-gtk0 libcanberra-pulse gpm readline-doc ctags vim-doc vim-scripts
The following NEW packages will be installed:
  alsa-topology-conf alsa-ucm-conf file libasound2 libasound2-data libcanberra0 libexpat1 libgpm2 libltdl7 libmagic-mgc libmagic1 libmpdec2 libogg0 libpython3.8 libpython3.8-minimal libpython3.8-stdlib libreadline8 libsqlite3-0 libssl1.1 libtdb1 libvorbis0a libvorbisfile3 mime-support readline-common
  sound-theme-freedesktop vim vim-common vim-runtime xxd xz-utils
0 upgraded, 30 newly installed, 0 to remove and 9 not upgraded.
Need to get 14.9 MB of archives.
After this operation, 70.6 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://archive.ubuntu.com/ubuntu focal/main amd64 libmagic-mgc amd64 1:5.38-4 [218 kB]
Get:2 http://archive.ubuntu.com/ubuntu focal/main amd64 libmagic1 amd64 1:5.38-4 [75.9 kB]
Get:3 http://archive.ubuntu.com/ubuntu focal/main amd64 file amd64 1:5.38-4 [23.3 kB]
Get:4 http://archive.ubuntu.com/ubuntu focal/main amd64 libexpat1 amd64 2.2.9-1build1 [73.3 kB]
Get:5 http://archive.ubuntu.com/ubuntu focal/main amd64 libmpdec2 amd64 2.4.2-3 [81.1 kB]
Get:6 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libssl1.1 amd64 1.1.1f-1ubuntu2.10 [1322 kB]
Get:7 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libpython3.8-minimal amd64 3.8.10-0ubuntu1~20.04.2 [717 kB]
Get:8 http://archive.ubuntu.com/ubuntu focal/main amd64 mime-support all 3.64ubuntu1 [30.6 kB]
Get:9 http://archive.ubuntu.com/ubuntu focal/main amd64 readline-common all 8.0-4 [53.5 kB]
Get:10 http://archive.ubuntu.com/ubuntu focal/main amd64 libreadline8 amd64 8.0-4 [131 kB]
Get:11 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libsqlite3-0 amd64 3.31.1-4ubuntu0.2 [549 kB]
Get:12 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libpython3.8-stdlib amd64 3.8.10-0ubuntu1~20.04.2 [1675 kB]
Get:13 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 xxd amd64 2:8.1.2269-1ubuntu5.7 [50.0 kB]
Get:14 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 vim-common all 2:8.1.2269-1ubuntu5.7 [85.0 kB]
Get:15 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 xz-utils amd64 5.2.4-1ubuntu1 [82.5 kB]
Get:16 http://archive.ubuntu.com/ubuntu focal/main amd64 alsa-topology-conf all 1.2.2-1 [7364 B]
Get:17 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 alsa-ucm-conf all 1.2.2-1ubuntu0.11 [26.9 kB]
Get:18 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libasound2-data all 1.2.2-2.1ubuntu2.5 [20.1 kB]
Get:19 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libasound2 amd64 1.2.2-2.1ubuntu2.5 [335 kB]
Get:20 http://archive.ubuntu.com/ubuntu focal/main amd64 libltdl7 amd64 2.4.6-14 [38.5 kB]
Get:21 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libtdb1 amd64 1.4.3-0ubuntu0.20.04.1 [44.2 kB]
Get:22 http://archive.ubuntu.com/ubuntu focal/main amd64 libogg0 amd64 1.3.4-0ubuntu1 [24.0 kB]
Get:23 http://archive.ubuntu.com/ubuntu focal/main amd64 libvorbis0a amd64 1.3.6-2ubuntu1 [87.0 kB]
Get:24 http://archive.ubuntu.com/ubuntu focal/main amd64 libvorbisfile3 amd64 1.3.6-2ubuntu1 [16.1 kB]
Get:25 http://archive.ubuntu.com/ubuntu focal/main amd64 sound-theme-freedesktop all 0.8-2ubuntu1 [384 kB]
Get:26 http://archive.ubuntu.com/ubuntu focal/main amd64 libcanberra0 amd64 0.30-7ubuntu1 [38.1 kB]
Get:27 http://archive.ubuntu.com/ubuntu focal/main amd64 libgpm2 amd64 1.20.7-5 [15.1 kB]
Get:28 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 libpython3.8 amd64 3.8.10-0ubuntu1~20.04.2 [1625 kB]
Get:29 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 vim-runtime all 2:8.1.2269-1ubuntu5.7 [5872 kB]
Get:30 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 vim amd64 2:8.1.2269-1ubuntu5.7 [1238 kB]
Fetched 14.9 MB in 1s (13.3 MB/s)
perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
        LANGUAGE = (unset),
        LC_ALL = (unset),
        LC_TIME = "en_US.UTF-8",
        LC_MONETARY = "en_US.UTF-8",
        LC_ADDRESS = "en_US.UTF-8",
        LC_TELEPHONE = "en_US.UTF-8",
        LC_NAME = "en_US.UTF-8",
        LC_MEASUREMENT = "en_US.UTF-8",
        LC_IDENTIFICATION = "en_US.UTF-8",
        LC_NUMERIC = "en_US.UTF-8",
        LC_PAPER = "en_US.UTF-8",
        LANG = "en_US.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
debconf: delaying package configuration, since apt-utils is not installed
dpkg: error: requested operation requires superuser privilege
E: Sub-process /usr/bin/dpkg returned an error code (2)

What OS/distro are you running

$ cat /etc/os-release
NAME="Ubuntu"
VERSION="20.04.3 LTS (Focal Fossa)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 20.04.3 LTS"
VERSION_ID="20.04"
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
VERSION_CODENAME=focal
UBUNTU_CODENAME=focal
dtrudg commented 2 years ago

This is not a bug with singularity.

When you are running singularity shell as a non-root user, you are your own user account inside the container. The apt tool that installs software on a Debian type distribution needs to be run as root, as the error message mentions:

dpkg: error: requested operation requires superuser privilege

You must use singularity shell as root (e.g. sudo singularity shell), or use the --fakeroot option. See the user guide for details.

https://sylabs.io/guides/3.9/user-guide/fakeroot.html