F41 Workstation (GNOME) dual-boot, desktop environmnet freezes at least once everyday for the last 3 days. Fresh installation (<1month)

Good day people!

I am new to the community, please let me know if I have made any mistakes in putting up this new topic. I have browsed through many topics that is similar to my issue here, yet none have conclusive solution. I will list out the context and problems regarding my current situation with the hopes that someone may be able to shed some light onto it :sob:. Once again, as a newbie (in the world of Linux and Fedora), my truest apologies if I were to make any mistakes in formatting, issue declaration, etc. Any feedback and suggestions are welcomed.

Context
I have recently decided to install Fedora 41 Workstation onto a free partition on my disk (SSD), which effectively makes this a dual-boot setup (with Windows 11 as its roommate.) After a few surprisingly easy-to-set-up steps, I managed to get it running smoothly, install updates, extensions, run a few more system updates suggested by GNOME ‘Software’ app, and it is all settled. I have also meddled with Bottles, managed to run a few games and software on it with no problems. While there were some hiccups, they were not too severe (nothing that the system can’t fix by itself.)

The Problem
Lately (3-4 days), I have started noticing random (yet disruptive) freezes on the desktop environment. The closest one was yesterday (01/01/2025), around 14:12:00, to which I have managed to capture a journalctl -b results (shared in this pastebin source .) This is a truncated result recording logs from the system ~30 minutes prior to the freeze/crash up to my hard reboot where the system starts running again.

I looked through them and saw that other than Flatpak’s Spotify constantly crashing and Bottles throwing some logs (that I do not yet understand), there was nothing of note to me. I do wonder if someone can share any insights into this matter?

Further context include

  • My inxi -Fzxx result:
System:
  Kernel: 6.12.6-200.fc41.x86_64 arch: x86_64 bits: 64 compiler: gcc
    v: 2.43.1-5.fc41
  Desktop: GNOME v: 47.2 tk: GTK v: 3.24.43 wm: gnome-shell dm: GDM
    Distro: Fedora Linux 41 (Workstation Edition)
Machine:
  Type: Convertible System: Dell product: Inspiron 7506 2n1 v: N/A
    serial: <superuser required> Chassis: type: 31 serial: <superuser required>
  Mobo: Dell model: 0WGM6F v: A00 serial: <superuser required> part-nu: 09DE
    UEFI: Dell v: 1.32.0 date: 09/12/2024
Battery:
  ID-1: BAT0 charge: 20.3 Wh (64.9%) condition: 31.3/53.0 Wh (59.1%)
    volts: 16.1 min: 15.0 model: SMP DELL 9077G0A serial: <filter>
    status: charging
CPU:
  Info: quad core model: 11th Gen Intel Core i7-1165G7 bits: 64 type: MT MCP
    arch: Tiger Lake rev: 1 cache: L1: 320 KiB L2: 5 MiB L3: 12 MiB
  Speed (MHz): avg: 400 min/max: 400/4700 cores: 1: 400 2: 400 3: 400 4: 400
    5: 400 6: 400 7: 400 8: 400 bogomips: 44851
  Flags: avx avx2 ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
Graphics:
  Device-1: Intel TigerLake-LP GT2 [Iris Xe Graphics] vendor: Dell
    driver: i915 v: kernel arch: Gen-12.1 ports: active: eDP-1
    empty: DP-1,DP-2,HDMI-A-1 bus-ID: 0000:00:02.0 chip-ID: 8086:9a49
  Device-2: Realtek Integrated_Webcam_HD driver: uvcvideo type: USB rev: 2.0
    speed: 480 Mb/s lanes: 1 bus-ID: 3-6:3 chip-ID: 0bda:5538
  Display: wayland server: Xwayland v: 24.1.4 compositor: gnome-shell
    driver: gpu: i915 display-ID: 0
  Monitor-1: eDP-1 model: InfoVision Optronics/Kunshan 0x061f res: 1920x1080
    dpi: 142 diag: 395mm (15.5")
  API: OpenGL v: 4.6 vendor: intel mesa v: 24.2.8 glx-v: 1.4 es-v: 3.2
    direct-render: yes renderer: Mesa Intel Xe Graphics (TGL GT2)
    device-ID: 8086:9a49 display-ID: :0.0
  API: Vulkan v: 1.3.296 surfaces: xcb,xlib,wayland device: 0
    type: integrated-gpu driver: N/A device-ID: 8086:9a49 device: 1 type: cpu
    driver: N/A device-ID: 10005:0000
  API: EGL Message: EGL data requires eglinfo. Check --recommends.
Audio:
  Device-1: Intel Tiger Lake-LP Smart Sound Audio vendor: Dell
    driver: sof-audio-pci-intel-tgl bus-ID: 0000:00:1f.3 chip-ID: 8086:a0c8
  API: ALSA v: k6.12.6-200.fc41.x86_64 status: kernel-api
  Server-1: JACK v: 1.9.22 status: off
  Server-2: PipeWire v: 1.2.7 status: active with: 1: pipewire-pulse
    status: active 2: wireplumber status: active 3: pipewire-alsa type: plugin
Network:
  Device-1: Intel Wi-Fi 6 AX201 driver: iwlwifi v: kernel bus-ID: 0000:00:14.3
    chip-ID: 8086:a0f0
  IF: wlp0s20f3 state: up mac: <filter>
Bluetooth:
  Device-1: Intel AX201 Bluetooth driver: btusb v: 0.8 type: USB rev: 2.0
    speed: 12 Mb/s lanes: 1 bus-ID: 3-10:4 chip-ID: 8087:0026
  Report: btmgmt ID: hci0 rfk-id: 0 state: up address: <filter> bt-v: 5.2
    lmp-v: 11
RAID:
  Hardware-1: Intel Volume Management Device NVMe RAID Controller driver: vmd
    v: 0.6 bus-ID: 0000:00:0e.0 chip-ID: 8086:9a0b
Drives:
  Local Storage: total: 476.94 GiB used: 36.29 GiB (7.6%)
  ID-1: /dev/nvme0n1 vendor: Toshiba model: KBG40ZNS512G NVMe KIOXIA 512GB
    size: 476.94 GiB speed: 31.6 Gb/s lanes: 4 serial: <filter> temp: 30.9 C
Partition:
  ID-1: / size: 62 GiB used: 35.98 GiB (58.0%) fs: btrfs dev: /dev/nvme0n1p10
  ID-2: /boot size: 973.4 MiB used: 309.3 MiB (31.8%) fs: ext4
    dev: /dev/nvme0n1p9
  ID-3: /boot/efi size: 146 MiB used: 108.4 MiB (74.2%) fs: vfat
    dev: /dev/nvme0n1p1
  ID-4: /home size: 62 GiB used: 35.98 GiB (58.0%) fs: btrfs
    dev: /dev/nvme0n1p10
Swap:
  ID-1: swap-1 type: zram size: 8 GiB used: 0 KiB (0.0%) priority: 100
    dev: /dev/zram0
Sensors:
  System Temperatures: cpu: 51.0 C mobo: 47.0 C sodimm: SODIMM C
  Fan Speeds (rpm): cpu: 2503
Info:
  Memory: total: 16 GiB note: est. available: 15.34 GiB used: 4.37 GiB (28.5%)
  Processes: 347 Power: uptime: 45m wakeups: 0 Init: systemd v: 256
    target: graphical (5) default: graphical
  Packages: pm: rpm pkgs: N/A note: see --rpm pm: flatpak pkgs: 47
    Compilers: clang: 19.1.5 gcc: 14.2.1 Shell: Bash v: 5.2.32
    running-in: ptyxis-agent inxi: 3.3.36
  • Recent possible problematic modules/apps I have installed recently:

    1. Bottles & Wine
    2. BTRFS Assistant (where I attempted to create a default config and a first snapshot using snapper)
    3. Flatpak’s Spotify (which has been crashing recently)

Any help/insight is appreciated! Please let me know if there is any further info I can provide!

  • Check your FS and disk health (smartctl, btrfs tools), if you have a lot of VMs on top of BTRFS, and if trim isn’t executed frequently, that can stall the system. (e.g. fstrim -v / ).
  • Try to narrow down the freezing to its cause, e.g. CPU or IO or graphics, e.g. record resource usage Linux CPU usage and Process Execution History - Server Fault
  • High memory usage can sometimes trigger stalls, typically you’d see oomd being invoked

My guess in absence of more information would be your disk (wine/bottles/flatpak can cause very high IO, and can be not great for a COW filesystem).

Can be useful to check if there’s not an accidental timed task (crontab / systemd) running somewhere that invoked very high CPU/IO, e.g. package manager, snapshots, …

Hope this helps

2 Likes

Hi there vsert!

Thank you for your reply and suggestions, didn’t hope anyone would have paid attention to this thread. To update on the dotpoints you’ve listed out:

  • I have attempted to run smartctl -H on my NVMe drive, from which it returned PASSED as the result, so I assume that it is generally good? If there are any more exhaustive methods of testing the drive (or run the test with smartctl), or the Fedora partition itself, I am open for more comments.
  • I was not able to retrieve such information on the last crash, but I followed your link and turned on process accounting using accton. I will be looking at such results when the next freeze/crash occurs, and update back to this thread.
  • Regarding memory usage, I did look back at the logs from systemd-oomd around the time of the mentioned crash, it showed this results, but I do not know how to intepret it.
-- Boot 14d84b9a55af4f0a99d237c98b71c504 --
Dec 31 21:33:47 fedora systemd[1]: Starting systemd-oomd.service - Userspace Out-Of-Memory (OOM) Killer...
Dec 31 21:33:47 fedora systemd[1]: Started systemd-oomd.service - Userspace Out-Of-Memory (OOM) Killer.
-- Boot c735ff3c682347968b5783907b0eb869 --
Jan 01 14:12:21 fedora systemd[1]: Starting systemd-oomd.service - Userspace Out-Of-Memory (OOM) Killer...
Jan 01 14:12:22 fedora systemd[1]: Started systemd-oomd.service - Userspace Out-Of-Memory (OOM) Killer.
Jan 01 17:01:47 fedora systemd[1]: Stopping systemd-oomd.service - Userspace Out-Of-Memory (OOM) Killer...
Jan 01 17:01:47 fedora systemd[1]: systemd-oomd.service: Deactivated successfully.
Jan 01 17:01:47 fedora systemd[1]: Stopped systemd-oomd.service - Userspace Out-Of-Memory (OOM) Killer.
Jan 01 17:01:47 fedora systemd[1]: systemd-oomd.service: Consumed 8.766s CPU time, 4.4M memory peak.
-- Boot 36050d9a19504c71ae18655c3a88ffc3 --
Jan 01 17:21:33 fedora systemd[1]: Starting systemd-oomd.service - Userspace Out-Of-Memory (OOM) Killer...
  • There are no suspicious (I assume) systemd timer, nor I have any cron tasks set up (pardon my terminologies, I do not know if I’m using the right ones.) Below are the systemd timers I found running.
NEXT                              LEFT LAST                            PASSED UNIT                         ACTIVATES                     
Sat 2025-01-04 00:00:00 AEDT       12h Fri 2025-01-03 00:01:01 AEDT         - unbound-anchor.timer         unbound-anchor.service
Sat 2025-01-04 00:18:28 AEDT       12h Fri 2025-01-03 00:33:12 AEDT         - logrotate.timer              logrotate.service
Sat 2025-01-04 00:36:16 AEDT       12h Fri 2025-01-03 00:04:56 AEDT         - plocate-updatedb.timer       plocate-updatedb.service
Sat 2025-01-04 10:52:35 AEDT       23h Fri 2025-01-03 10:52:35 AEDT 49min ago systemd-tmpfiles-clean.timer systemd-tmpfiles-clean.service
Sun 2025-01-05 01:00:00 AEDT 1 day 13h Sun 2024-12-29 01:00:00 AEDT         - raid-check.timer             raid-check.service
Mon 2025-01-06 00:45:56 AEDT    2 days Mon 2024-12-30 01:10:06 AEDT         - fstrim.timer                 fstrim.service

Also, something else that might be of note: I also have problems crashing/freezing problems when launching Flatpak application, and come by this thread on r/Fedora claiming that BTRFS Assistant was the culprit for these crashes. I tried to uninstall it, and the flatpaks apps are going better than before. I do question the merit of this claim, as they seem to be almost unrelated by nature, but if that is the solution to my recent DE crashes (and flatpak instability), it may be worth noting.

If it crashes within the next 24-48hrs, I will update back for more info.

Once again, thank you!

Quick update. Another crash just came in around 40 minutes ago. I noticed that the time logged by journalctl got messed up during boot, but recovered after boot finishes.

There were actually two crashes that occurred today:

  • One was a Gnome shell crash, which it logged me out but stayed functional after login.
  • The other was a freeze crash with the same fashion as the one I am describing in the thread’s main issue, with unresponsive cursors, screen, audio output keeps repeating the sound it was playing a second prior.

Here are the pastebins of journalctl output around the time of the two crashes

  1. GNOME Shell crash [~Jan 3 12:46:03]: f41-gnome-030125-decrash - Pastebin.com
  2. Freeze (unknown cause) crash [~Jan 3 15:44:xx]: f41-gnome-030125-freezecrash - Pastebin.com

I am very interested in seeing whether this is a common issue for the distro (and GNOME DE), or just my setup being the problem.

The logs you post do not have messages near the time of crash, suggesting they’re not even saved to disk? E.g. they stop halfway boot messages, not actual usage.
From what you describe there seem to be multiple issues, as the crashes are not the same, e.g hanging/repeating audio is more severe than a process crashing.
You can try to rule out general system instability by e.g. memtest, and test if the crashes occur when you use the system using a live disk (USB).
That said, that kind of debugging will take quite some time, and without information on narrowing the cause it may be a rabbithole.