Navigating Post-Upgrade Anomalies: Addressing Strange Behaviors After Upgrading from Ubuntu 22.04.5 LTS to 24.04.2 LTS

The transition to a new Long Term Support (LTS) release of Ubuntu, such as upgrading from 22.04.5 LTS to 24.04.2 LTS, is often anticipated with a mixture of excitement and trepidation. While promising enhanced features, improved performance, and updated software, these significant system overhauls can occasionally introduce unexpected behaviors. At revWhiteShadow, we understand the frustration that arises when familiar workflows are disrupted. This comprehensive guide aims to meticulously dissect the peculiar issues encountered after such an upgrade, drawing upon user experiences and offering in-depth troubleshooting steps. Our goal is to provide the most detailed and actionable information to help you regain full system stability and performance.

Understanding the Upgrade Process and Potential Pitfalls

The leap from Ubuntu 22.04.5 LTS to 24.04.2 LTS represents a substantial evolution in the operating system’s core components, kernel, desktop environment, and underlying libraries. While the upgrade path is generally designed to be as seamless as possible, the sheer volume of changes means that conflicts can arise, particularly with custom configurations, third-party software, or even specific hardware drivers.

Factors that can contribute to post-upgrade anomalies include:

  • Driver Incompatibilities: Newer kernels or system libraries might have altered or removed support for older graphics drivers, Wi-Fi drivers, or other hardware-specific modules.
  • Configuration File Divergences: System configuration files, especially those that have been manually modified or are specific to older versions, may not translate perfectly to the new release.
  • Application Dependencies: Applications installed from sources other than the official repositories, or older applications with complex dependency chains, can sometimes falter if their dependencies are updated or changed in the new release.
  • Desktop Environment Changes: Significant updates to the GNOME desktop environment, for instance, can impact how extensions and themes function, or even how the display manager (GDM) handles user sessions.
  • Package Management Conflicts: Residual packages or configuration remnants from the previous installation can sometimes interfere with the new system’s package management, leading to ongoing issues.

We aim to address these potential areas of conflict systematically.

Dissecting Specific Post-Upgrade Issues and Their Solutions

Based on reported experiences, several distinct problems commonly emerge after upgrading to Ubuntu 24.04.2 LTS from 22.04.5 LTS. We will tackle each of these with a focus on providing the most thorough diagnostic and resolution steps.

#### The Elusive GDM Crash and Missing System Tray on First Boot

A particularly unsettling issue is the occasional crash of the GNOME Display Manager (GDM) upon the initial boot after a shutdown, resulting in a login session devoid of the system tray and other expected graphical elements. Subsequent logins, however, often proceed without incident. This intermittent behavior suggests a race condition or a timing issue during the system’s startup sequence, where certain services or components are not fully initialized before GDM attempts to load the user session.

Diagnostic Steps:

  1. Examine System Logs for GDM Errors: The primary source of information for display manager issues lies within the system logs.

    • Open a terminal and execute: sudo journalctl -u gdm
    • This command will display logs specifically for the GDM service. Look for any error messages, segmentation faults, or critical failures occurring around the time of the problematic boot.
    • To pinpoint the exact boot instance, you can use sudo journalctl -u gdm -b -1 to view logs from the previous boot. If the issue occurs on the current boot, sudo journalctl -u gdm -b 0 can be helpful.
    • Additionally, examine general system logs for related errors: sudo journalctl -p err -b -1 for critical errors on the previous boot.

  2. Investigate Wayland vs. Xorg Sessions: Ubuntu 24.04.2 LTS defaults to Wayland. If your previous installation was heavily reliant on Xorg, or if there are Wayland-specific driver issues with your Intel Iris Xe graphics, this could be a contributing factor.

    • During the GDM login screen, before entering your password, look for a gear icon or a session selection option. Try switching to an “Ubuntu on Xorg” session and see if the problem persists on the next boot.

  3. Check for GNOME Shell Extension Conflicts: While user extensions are addressed separately, a core GNOME Shell component might be encountering an issue.

    • If you are logged into a problematic session (e.g., no tray), try running gnome-shell --replace & in a terminal. This command attempts to restart the GNOME Shell. If it successfully restores the tray, it points to a GNOME Shell internal issue or an extension conflict that manifests during startup.

Potential Solutions:

  • Disable Non-Essential GNOME Shell Extensions: Even if you plan to re-enable them later, temporarily disabling all GNOME Shell extensions (including those that come pre-installed) can help isolate if one of them is causing the GDM crash. You can manage extensions through the “Extensions” application or via GNOME Tweaks if installed.
  • Ensure Graphics Drivers are Properly Configured: While Intel Iris Xe is generally well-supported, ensuring the correct Mesa drivers and Intel-specific packages are installed and up-to-date is crucial.
    • sudo apt update && sudo apt upgrade
    • Consider installing mesa-utils (sudo apt install mesa-utils) and running glxinfo | grep "OpenGL renderer string" to confirm your GPU is being correctly identified.
  • Reinstall GDM: In rare cases, the GDM package itself might have become corrupted during the upgrade.
    • sudo apt remove gdm3
    • sudo apt autoremove
    • sudo apt install gdm3
    • This action requires careful consideration as it will affect your login screen. Ensure you have a way to access a terminal (e.g., Ctrl+Alt+F3 to switch to a TTY) before proceeding.
  • Clear GDM Configuration: Corrupted GDM configuration files might exist.
    • sudo rm -rf /etc/gdm3/custom.conf (Backup this file first: sudo cp /etc/gdm3/custom.conf /etc/gdm3/custom.conf.backup)
    • Restart GDM: sudo systemctl restart gdm3

#### The Persistent “Major System Upgrade, Review” Notification

Receiving a persistent notification for a “major system upgrade, review” on every boot is a clear indication that the system believes an upgrade process has not been fully completed or has encountered an error that prevents it from recognizing the current state as stable. This notification is often tied to the update-manager or related package management services.

Diagnostic Steps:

  1. Check the Status of update-manager-core: This package is often responsible for managing upgrade-related notifications.

    • dpkg -s update-manager-core
    • Look for any status messages indicating errors or inconsistencies.

  2. Review the Upgrade Log Files: The apt system maintains detailed logs of all package operations, including upgrades.

    • The primary log file is /var/log/apt/history.log. Examine entries around the time of your upgrade.
    • Look for files in /var/log/apt/term.log.* which capture the terminal output of apt operations.

  3. Inspect /etc/update-motd.d/: The “Message of the Day” system, which often displays these notifications at login, populates its messages from scripts in this directory.

    • ls -l /etc/update-motd.d/
    • Look for any scripts that seem related to upgrade status or pending actions. Sometimes, a script might be failing to execute correctly, leading to the persistent notification.

  4. Verify Package Integrity: Ensure that all packages related to the upgrade process are in a consistent state.

    • sudo dpkg --configure -a
    • sudo apt --fix-broken install

Potential Solutions:

  • Manually Triggering a Status Check: Sometimes, forcing a re-evaluation of the upgrade status can resolve this.

    • sudo dpkg-reconfigure -f noninteractive update-notifier-common
    • Consider running sudo update-manager -c to manually check for updates, even if it doesn’t find new ones, it might refresh the status.

  • Removing or Disabling the Specific Message Script: If you can identify the script in /etc/update-motd.d/ responsible for the notification, you can temporarily disable it.

    • For example, if 00-update-notifier is the culprit: sudo mv /etc/update-motd.d/00-update-notifier /etc/update-motd.d/00-update-notifier.disabled
    • This is a workaround, and ideally, the underlying cause should be fixed.

  • Resetting Package Management State: If other methods fail, you might need to reset the state of the package manager. This is a more advanced step.

    • Back up /var/lib/dpkg/status and /var/lib/apt/extended_states before proceeding.
    • sudo rm /var/lib/dpkg/lock-frontend
    • sudo dpkg --remove --force-remove-essential ubuntu-advantage-tools (If present and suspected)
    • Then, re-run the repair commands: sudo dpkg --configure -a and sudo apt --fix-broken install.

#### User Extensions (GsConnect, Just Perfect) Disabling on Every Boot

The automatic disabling of user-installed GNOME Shell extensions like GsConnect and Just Perfect on each boot is a common symptom of the GNOME Shell not properly recognizing or loading these extensions’ metadata or dependencies after a system restart. This can be triggered by changes in GNOME Shell’s internal structure, extension management processes, or even minor inconsistencies in how extensions are registered.

Diagnostic Steps:

  1. Check GNOME Shell Extension Compatibility: Ensure that the installed versions of GsConnect and Just Perfect are explicitly compatible with GNOME Shell 46, which is what Ubuntu 24.04.2 LTS uses.

    • Visit the GNOME Extensions website (extensions.gnome.org) or the respective GitHub repositories for these extensions and check their compatibility statements.

  2. Examine dconf Settings for Extensions: GNOME Shell stores extension settings and status in the dconf database.

    • Use dconf-editor (install with sudo apt install dconf-editor) to navigate to /org/gnome/shell/extensions/.
    • Look for entries related to gsconnect and just-perfect. Check their enabled status. You can manually enable them here, but the goal is to find out why they are being disabled.

  3. Inspect GNOME Shell Logs: Similar to GDM crashes, GNOME Shell logs can reveal why extensions are failing to load.

    • journalctl /usr/bin/gnome-shell
    • Again, use -b -1 to examine logs from the previous boot if the issue occurs after a reboot. Look for errors related to loading extensions, missing dependencies, or parsing extension metadata.

  4. Verify Extension Installation Method: If these extensions were installed manually rather than through the extensions.gnome.org website or a distribution package, they might not be managed correctly by GNOME Shell.

Potential Solutions:

  • Reinstall Extensions via extensions.gnome.org: The most robust way to install GNOME extensions is through the official website using the browser integration.

    • Uninstall existing versions.
    • Navigate to extensions.gnome.org, find GsConnect and Just Perfect, and install them from there. This ensures they are installed in the correct user directory (~/.local/share/gnome-shell/extensions/) and registered properly.

  • Update Extensions: Ensure you have the latest available versions of both extensions, as developers often release updates to address compatibility with new GNOME Shell versions.

  • Check Extension Dependencies: Some extensions may have dependencies on specific libraries or other extensions. If these dependencies are missing or incompatible, the extension might fail to load.

    • For GsConnect, ensure gsconnect package is installed: sudo apt install gsconnect.
    • For Just Perfect, check its specific documentation for any required system packages.

  • Manually Enable and Lock Extension Settings: While not a fix for the root cause, you can try enabling them and then using dconf-editor to set the enabled key to true and potentially prevent further modification (though this is unlikely to solve a persistent disabling issue).

  • Consider gnome-extensions-app (or similar): If not already installed, sudo apt install gnome-extensions-app provides a dedicated GUI for managing extensions, which can sometimes offer clearer error messages or management options.

#### Drastic Performance Degradation on Intel Iris Xe Graphics

This is perhaps the most critical issue: a severe drop in GPU performance, reducing Minecraft frame rates from 60 FPS at 4K to a mere 16 FPS. This indicates a fundamental problem with how the graphics drivers are being utilized or initialized in the new Ubuntu release, specifically impacting the Intel Iris Xe integrated graphics. The difference between 60 FPS and 16 FPS is monumental and points to either a missing driver component, incorrect driver loading, or a significant performance regression.

Diagnostic Steps:

  1. Verify Mesa and Intel Graphics Driver Installation: The Iris Xe GPU relies heavily on the Mesa 3D graphics library and specific Intel kernel drivers.

    • Ensure you have the latest Mesa packages: sudo apt update && sudo apt upgrade.
    • Install essential Intel graphics packages: sudo apt install intel-media-va-driver-non-free vainfo libva-drm2 libva-x11-2. The intel-media-va-driver-non-free package often provides hardware acceleration capabilities.
    • Check installed driver versions: dpkg -l | grep mesa. Compare these versions to what is recommended or known to work well.

  2. Confirm Hardware Acceleration Status: Verify that hardware acceleration is actually being utilized.

    • vainfo: This utility checks the status of Video Acceleration API (VA-API).
      • vainfo
      • The output should list your Intel GPU as a VA-API driver and should not report significant errors. If it shows errors or doesn’t list your GPU, hardware acceleration is likely not working.
    • glxinfo: Confirms OpenGL renderer and extensions.
      • glxinfo | grep "OpenGL renderer string" should show your Iris Xe graphics.
      • glxinfo | grep "OpenGL version string" should show a recent OpenGL version.

  3. Check Kernel Modules: Ensure the correct Intel graphics kernel modules are loaded.

    • lsmod | grep i915 should show the i915 module (Intel graphics driver) loaded.

  4. Examine Xorg vs. Wayland Performance: As mentioned earlier, driver behavior can differ significantly between Wayland and Xorg.

    • If you are on Wayland, try switching to an “Ubuntu on Xorg” session at the login screen and re-test Minecraft. This can help isolate if the issue is Wayland-specific.

  5. Investigate Game-Specific Settings: While the system-wide performance drop is the primary concern, ensure that within Minecraft itself, the graphics settings are appropriate and not inadvertently capping performance. (Though a drop from 60 to 16 FPS suggests a deeper system issue).

  6. Monitor GPU Usage and Temperatures: Tools like intel_gpu_top (part of intel-gpu-tools) can provide real-time insights into GPU utilization and power states.

    • Install: sudo apt install intel-gpu-tools
    • Run: sudo intel_gpu_top
    • Observe if the GPU is being utilized at all during gameplay, or if it’s stuck in a low-power state.

Potential Solutions:

  • Reinstall Mesa Packages: Sometimes, a clean reinstallation of Mesa can resolve corrupted files.

    • sudo apt purge mesa-va-drivers mesa-vdpau-drivers mesa-vulkan-drivers libgl1-mesa-dri libglx-mesa0
    • sudo apt install mesa-va-drivers mesa-vdpau-drivers mesa-vulkan-drivers libgl1-mesa-dri libglx-mesa0
    • Follow up with sudo apt update && sudo apt upgrade.

  • Install intel-gpu-tools and vainfo: Ensure these diagnostic tools are installed to help further troubleshoot.

    • sudo apt install intel-gpu-tools vainfo

  • Force Specific Driver Options (Advanced): For Intel graphics, certain kernel parameters can sometimes influence performance or stability, though this is generally not recommended unless advised by specific troubleshooting guides for your hardware. Example (do NOT apply without research): You might find discussions about i915.enable_psr=0 or similar.

  • Consider Alternative Mesa Builds (PPA - Use with Caution): For bleeding-edge performance or fixes, some users opt for Mesa PPAs (e.g., kisak-mesa or oibaf). However, using PPAs can introduce instability if not managed carefully. If you go this route, ensure you understand how to revert changes.

    • Example PPA installation (for illustrative purposes only):
      sudo add-apt-repository ppa:kisak/kisak-mesa
sudo apt update
sudo apt upgrade
    • Always back up your system or critical data before installing PPAs.

  • Check BIOS/UEFI Settings: Ensure that integrated graphics are enabled in your system’s BIOS/UEFI settings and that there are no unusual power-saving modes enabled that might throttle the GPU excessively.

  • Reinstall Ubuntu (Last Resort): If all troubleshooting steps fail to restore GPU performance, and given the severity of the performance drop, a clean installation of Ubuntu 24.04.2 LTS might be the most effective solution. This ensures that all system components and drivers are installed from a known good state, avoiding any potential corruption or lingering configuration issues from the upgrade process.

Preventative Measures and Maintaining a Stable System

While troubleshooting is crucial, adopting proactive measures can minimize the chances of encountering such issues in future upgrades:

  • Perform Regular Backups: Before any major system upgrade, always back up your important data. Consider creating a full system image if possible.
  • Review Release Notes: Familiarize yourself with the official release notes for Ubuntu 24.04 LTS. They often highlight known issues and potential incompatibilities.
  • Test in a Virtual Machine: If you have critical workflows, consider testing the new Ubuntu version in a virtual machine environment before upgrading your primary system.
  • Keep System Updated: Regularly applying security updates and minor patches for your current Ubuntu version can sometimes resolve underlying issues that might exacerbate during a major upgrade.
  • Manage Third-Party Repositories Carefully: If you use PPAs or other third-party repositories, ensure they are compatible with the target Ubuntu version before upgrading. Disabling them during the upgrade process is often a good practice.

Conclusion

The journey from Ubuntu 22.04.5 LTS to 24.04.2 LTS can be remarkably smooth, but when unexpected behaviors manifest, a systematic and detailed approach to diagnostics and solutions is paramount. By meticulously examining logs, understanding the interplay between system components, and applying targeted fixes, we can overcome the challenges of GDM crashes, persistent notifications, extension disablings, and significant performance regressions. At revWhiteShadow, we are committed to providing the in-depth information necessary to restore your Ubuntu system to its optimal working condition. While a reinstall is always a fallback, the detailed steps outlined here offer a strong path towards resolving these post-upgrade anomalies and continuing to enjoy the advancements brought by Ubuntu 24.04.2 LTS.