/.singularity.d/libs/faked: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found

[sorenwacker]

Version of Apptainer

What version of Apptainer (or Singularity) are you using? Run

apptainer version 1.2.5

Expected behavior

Bootstrap: docker
From: condaforge/miniforge3:latest

%files
    environment.yaml /environment.yaml
    requirements.txt /requirements.txt

%post
    # Update and install necessary packages
    apt-get update && apt-get install -y tree time vim ncdu speedtest-cli build-essential

    # Create a new Conda environment with JupyterLab
    mamba env create --quiet -n __apptainer-env__ --file /environment.yaml
    
    # Clean up
    apt-get clean && rm -rf /var/lib/apt/lists/*
    mamba clean --all -y

    # Now add the script to activate the Conda environment
    echo '. "/opt/conda/etc/profile.d/conda.sh"' >> $SINGULARITY_ENVIRONMENT
    echo 'conda activate __apptainer-env__' >> $SINGULARITY_ENVIRONMENT

apptainer build data-science-mamba.sif Apptainer.def

expected to build the container.

Actual behavior

INFO:    User not listed in /etc/subuid, trying root-mapped namespace
INFO:    The %post section will be run under fakeroot
Build target 'data-science-mamba.sif' already exists and will be deleted during the build process. Do you want to continue? [N/y] y
INFO:    Starting build...
Getting image source signatures
Copying blob 37f6c0865591 skipped: already exists  
Copying blob 17d0386c2fff skipped: already exists  
Copying config 7e59039f1c done  
Writing manifest to image destination
Storing signatures
2024/03/19 12:04:13  info unpack layer: sha256:17d0386c2fff30a5b92652bbef2b84639dba9b9f17bdbb819c8d10badd827fdb
2024/03/19 12:04:14  info unpack layer: sha256:37f6c08655917c7151130443c1cfe24492f41aef032347a9bc5af447c166cdc9
INFO:    Copying environment.yaml to /environment.yaml
INFO:    Copying requirements.txt to /requirements.txt
INFO:    Running post scriptlet
/.singularity.d/libs/faked: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.33' not found (required by /.singularity.d/libs/faked)
/.singularity.d/libs/faked: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by /.singularity.d/libs/faked)
fakeroot: error while starting the `faked' daemon.
/.singularity.d/libs/fakeroot: 1: kill: Usage: kill [-s sigspec | -signum | -sigspec] [pid | job]... or
kill -l [exitstatus]
FATAL:   While performing build: while running engine: exit status 1

What OS/distro are you running

PRETTY_NAME="Ubuntu 22.04.4 LTS"
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04.4 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy
ID=ubuntu
ID_LIKE=debian
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"
UBUNTU_CODENAME=jammy

How did you install Apptainer

sudo apt-get install apptainer
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
apptainer is already the newest version (1.2.5).

I tried updating glibc

sudo apt-get install libc6
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
libc6 is already the newest version (2.35-0ubuntu3.6).

And installed fakeroot

sudo apt-get install fakeroot
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
fakeroot is already the newest version (1.28-1ubuntu1).

[DrDaveD]

Since the fakeroot command is bind-mapped in from the host, it requires the container glibc library to be at least as new as the host's. This can be avoided by either setting up the /etc/subuid mapping, for example by using sudo apptainer config fakeroot --add $USER, or by installing apptainer with install-unprivileged.sh because that installs an older (EL7) fakeroot command to use.