Debian 13 trixie upgrade

friday.md

Debian 13

Caution Upgrading from Debian 12 to Debian 13 on machines with mdadm has intermittently failed for me; symptom is that grub EFI is not up to date and system boots into BIOS. Root cause under investigation; it might not be related to mdadm.

To start, read the official release notes.

If your install fits into "vanilla Debian plus maybe a handful of 3rd-party repos", then this guide for a simple upgrade to Debian 13 "trixie" from Debian 12 "bookworm" can be helpful. 3rd-party repos are handled with a find command.

Note upgrade is only supported from Debian 12 to Debian 13. If you are on Debian 11, upgrade to Debian 12 first. Then once on Debian 12, you can upgrade to Debian 13.

This guide is only for the OS itself. Applications are as plentiful as sand on the beach, and they may all require additional steps. Plan for that.

• Check free disk space

df -h

5 GiB free is a conservative amount. sudo apt clean and sudo apt autoremove can be used to free some disk space.

On a server with only docker installed, even 1 GiB free was sufficient. Do err on the side of caution here, however.

• Identify any 3rd-party repos that may need to be updated. They'll be changed with a find command, below.

ls /etc/apt/sources.list.d

• Update current distribution

sudo apt update && sudo apt full-upgrade

If this brought in a new kernel, sudo reboot - otherwise continue

• Change repo to trixie, from bookworm.

sudo sed -i 's/bookworm/trixie/g' /etc/apt/sources.list

non-free has been split since Debian 12 and if used, you should also use non-free-firmware. If you are unsure, check and adjust. More complete instructions are in the Debian release notes and the gist for Debian 12 upgrade

• Change all 3rd-party repos

This assumes the repos have trixie versions. Run sudo apt update after the change to trixie to confirm, and deal with any repos that aren't available in trixie.

sudo find /etc/apt/sources.list.d -type f -exec sed -i 's/bookworm/trixie/g' {} \;

• Optional: Start a screen session

So that an SSH disconnect doesn't stop your upgrade halfway through, you can run in screen:

sudo apt install -y screen && screen

• Hold mdadm if it's in use

If you use the mdadm package, as of Aug 22nd 2025, you'll want a workaround to avoid an issue where mdadm is updated before systemd and shows an error that it cannot find systemd. A bug report tracks this.

Hold mdadm, update Debian, then unhold mdadm and update again.

sudo apt-mark hold mdadm

• Update Debian

For the following, say Yes to restarting services, and keep existing config files when prompted.

sudo apt update && sudo apt full-upgrade

• Update mdadm if it's in use

This is a workaround for an order-of-operations issue, see above.

sudo apt-mark unhold mdadm

sudo apt update && sudo apt full-upgrade

mdadm should be updated without an error message about not finding systemd

• Reboot

sudo reboot

• Clean up old repos

sudo apt autoremove && sudo apt clean

• Modernize Debian sources

Optional but recommended: Switch to deb822 format for the sources.list. This will write /etc/apt/sources.list.d/debian.sources and /etc/apt/sources.list.d/debian-backports.sources

sudo apt modernize-sources

Caveat that trixie-backports might not have a Signed-By on some 3rd-party mirrors. You can fix this by manually setting Signed-By: /usr/share/keyrings/debian-archive-keyring.gpg in /etc/apt/sources.list.d/debian-backports.sources

• Clean up old /tmp

Optional: Remove files from the old /tmp directory. Debian 13 replaced it with a tmpfs, see https://www.debian.org/releases/trixie/release-notes/issues.en.html#the-temporary-files-directory-tmp-is-now-stored-in-a-tmpfs

On most systems /tmp will be empty or all-but. If you did store large files here, it can be worth the effort to clean up.

sudo mkdir /mnt/tmp-chk
sudo mount --bind / /mnt/tmp-chk
ls -lha /mnt/tmp-chk/tmp/

Remove files from /mnt/tmp-chk/tmp as you see fit, then unmount again

sudo umount /mnt/tmp-chk
sudo rm -rf /mnt/tmp-chk

Automated by Ansible

Config ansible.cfg:

[defaults]
interpreter_python = /usr/bin/python3

Playbook trixie.yml:

---
- name: Upgrade to Debian trixie
  hosts: all
  serial: 1
  gather_facts: false
  roles:
    - base/upgrade_trixie

Role base/upgrade_trixie/tasks/main.yml:

---
- name: Get distribution version
  setup:
    filter: ansible_distribution*
- name: Skip if not Debian 12
  meta: end_host
  when: ansible_distribution != 'Debian' or ansible_distribution_major_version != '12'
- name: apt clean
  apt:
    clean: yes
  become: yes
- name: Get filesystem facts
  setup:
    filter: ansible_mounts
- name: Fail if free space on / is below 5 GiB
  ansible.builtin.assert:
    that:
      - item.size_available > (5 * 1024 * 1024 * 1024)
    fail_msg: "Free disk space on {{ item.mount }} is below 5 GiB"
  loop: "{{ ansible_mounts }}"
  when: item.mount == "/"
- name: All apt packages up to date
  apt:
    upgrade: dist
    update_cache: yes
  become: yes
- name: apt autoremove
  apt:
    autoremove: yes
  become: yes
- name: apt clean
  apt:
    clean: yes
  become: yes
- name: Check if reboot required
  ansible.builtin.stat:
    path: /run/reboot-required
    get_checksum: no
  register: reboot_required_file
- name: Reboot if required
  ansible.builtin.reboot:
    msg: "Reboot initiated by Ansible"
    connect_timeout: 5
    reboot_timeout: 600
    pre_reboot_delay: 0
    post_reboot_delay: 60
    test_command: whoami
  when: reboot_required_file.stat.exists
  become: true
- name: Switch OS from bookworm to trixie
  ansible.builtin.replace:
    path: /etc/apt/sources.list
    regexp: 'bookworm'
    replace: 'trixie'
  become: yes
- name: Find all 3rd-party repos
  ansible.builtin.find:
    paths: /etc/apt/sources.list.d
    patterns: '*'
    recurse: no
  register: third_party_repos
- name: Switch 3rd-party repos from bookworm to trixie
  ansible.builtin.replace:
    path: "{{ item.path }}"
    regexp: 'bookworm'
    replace: 'trixie'
  loop: "{{ third_party_repos.files }}"
  loop_control:
    label: "{{ item.path }}"
  become: yes
- name: Use apt to move to trixie
  apt:
    upgrade: dist
    update_cache: yes
  become: yes
- name: Get distribution version
  setup:
    filter: ansible_distribution*
- name: Fail if not Debian 13
  assert:
    that:
      - ansible_distribution_major_version == '13'
    fail_msg: "Upgrade to Debian 13 failed"
- name: apt autoremove
  apt:
    autoremove: yes
  become: yes
- name: apt clean
  apt:
    clean: yes
  become: yes
- name: Reboot on trixie
  ansible.builtin.reboot:
    msg: "Reboot initiated by Ansible"
    connect_timeout: 5
    reboot_timeout: 600
    pre_reboot_delay: 0
    post_reboot_delay: 60
    test_command: whoami
  become: yes
- name: Modernize apt sources
  ansible.builtin.command:
    cmd: apt -y modernize-sources
  become: yes
- name: Pause for 5 minutes for staggered upgrades
  pause:
    minutes: 5

@pjl Good suggestion. I've added a section about that. On most systems, there won't be anything in /tmp - but some folk may have used it.