Some Flatpak AppsFail to Start (Crash) on Kernel 6.7.x

I’ve got a range of Flatpak apps that no longer start after updating to Kernel 6.7. The applications crash and cannot be started. I tried starting form the previous 6.7 kernel but the behaviour persists.

  • Chromium
  • Gnome Extensions Manager
  • Flatseal
  • Obsidian
  • Signal

The problem definitely seems to be Flathub/Flatpak related. A couple of these apps are available as .rpm packages. If I uninstall, and reinstall the rpm, they all start fine. Both Chromium and Flatseal run fine as rpm packages.

But the kicker is not all flatpaks are broken. Libre Office, VLC, Bitwarden, etc… all run fine as flatpaks. I’ve got another machine still running F38 and all these apps run fine as flatpaks.

I’m not seeing much chat about flatpaks being broken for all F39 users, so I’m assuming it is just me. Anyone see any commonality in the apps that are broken that would point me in the direction of what needs to be fixed?

TIA.

The common link appears to be that the problem apps are flatpaks.

Flatpaks are not maintained the same as rpms from the fedora repo and may not be quickly updated to function with newer kernels. You identified that there are at least 2 of those apps that function when installed by rpm but fail as a flatpak.

Without having exactly the same config as you do it is difficult to be more specific.
What happens if you boot to the older kernel where the apps were previously working? By default fedora retains 3 kernels, so there should be 2 older kernels that could be tested.

It also may be other packages that were updated the same time as the newer kernel. Without detailed testing a definitive solution or cause is out of reach.

Thanks for the reply @computersavvy

In the boot list there are two 6.7 kernels. Both have the same problem with the flatpak apps. The 6.6 kernel wouldn’t boot when I tried to start it. So that didn’t help me much.

Flatpak updates lagging coule be an explanation but the Obsidian flatpak was updated 9 days ago. Hard to imagine current kernel support wasn’t included.

Looking at the journal, it’s problem seems to be video drivers?

Mar 01 10:21:14 arkady md.obsidian.Obsidian.desktop[22996]: /app/bin/obsidian.sh: line 66:    14 Trace/breakpoint trap   (core dumped) zypak-wrapper /app/obsidian $@ ${EXTRA_ARGS[@]}
Mar 01 10:21:13 arkady md.obsidian.Obsidian.desktop[23008]: [14:0301/102113.649207:FATAL:gpu_data_manager_impl_private.cc(448)] GPU process isn't usable. Goodbye.
Mar 01 10:21:13 arkady md.obsidian.Obsidian.desktop[23008]: [14:0301/102113.649190:ERROR:gpu_process_host.cc(993)] GPU process exited unexpectedly: exit_code=139
Mar 01 10:21:13 arkady md.obsidian.Obsidian.desktop[23566]: [233:0301/102113.232470:ERROR:vaapi_wrapper.cc(1122)] FillProfileInfo_Locked failed for va_profile VAProfileH264High and entrypoint VAEntrypointVLD
Mar 01 10:21:13 arkady md.obsidian.Obsidian.desktop[23566]: [233:0301/102113.232439:ERROR:vaapi_wrapper.cc(1213)] Empty codec maximum resolution
Mar 01 10:21:13 arkady md.obsidian.Obsidian.desktop[23566]: [233:0301/102113.232406:ERROR:vaapi_wrapper.cc(1122)] FillProfileInfo_Locked failed for va_profile VAProfileH264Main and entrypoint VAEntrypointVLD

I’ll trace through the other apps and see if there’s some commonality.

If you suspect graphics as the cause then please post the output of inxi -Fzxx so we can see details of hardware and drivers installed.

System:
  Kernel: 6.7.6-200.fc39.x86_64 arch: x86_64 bits: 64 compiler: gcc
    v: 2.40-14.fc39
  Console: pty pts/1 wm: gnome-shell DM: GDM Distro: Fedora Linux 39
    (Workstation Edition)
Machine:
  Type: Desktop System: Apple product: iMac15,1 v: 1.0 serial: <filter>
    Chassis: type: 13 v: Mac-42FD25EABCABB274 serial: <filter>
  Mobo: Apple model: Mac-42FD25EABCABB274 v: iMac15,1 serial: <filter>
    UEFI: Apple v: 474.0.0.0.0 date: 08/23/2022
Battery:
  Device-1: hid-98:5a:eb:af:16:03-battery model: Apple Wireless Keyboard
    serial: N/A charge: N/A status: discharging
CPU:
  Info: quad core model: Intel Core i5-4690 bits: 64 type: MCP arch: Haswell
    rev: 3 cache: L1: 256 KiB L2: 1024 KiB L3: 6 MiB
  Speed (MHz): avg: 3836 high: 3890 min/max: 800/3900 cores: 1: 3791 2: 3889
    3: 3774 4: 3890 bogomips: 27935
  Flags: avx avx2 ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
Graphics:
  Device-1: AMD Curacao XT / Trinidad [Radeon R7 370 R9 270X/370X]
    vendor: Apple driver: radeon v: kernel arch: GCN-1 pcie: speed: 8 GT/s
    lanes: 16 ports: active: eDP-1 empty: DP-1,DP-2,DP-3 bus-ID: 01:00.0
    chip-ID: 1002:6810 temp: 51.0 C
  Device-2: Realtek RTL2838 DVB-T driver: dvb_usb_rtl28xxu type: USB
    rev: 2.0 speed: 480 Mb/s lanes: 1 bus-ID: 1-5:2 chip-ID: 0bda:2838
  Device-3: Apple FaceTime HD Camera (Built-in) driver: uvcvideo type: USB
    rev: 2.0 speed: 480 Mb/s lanes: 1 bus-ID: 1-7:4 chip-ID: 05ac:8511
  Display: server: X.Org v: 23.2.4 with: Xwayland v: 23.2.4
    compositor: gnome-shell driver: X: loaded: radeon
    unloaded: fbdev,modesetting,vesa dri: radeonsi gpu: radeon display-ID: :0
    screens: 1
  Screen-1: 0 s-res: 3840x2160 s-dpi: 96
  Monitor-1: eDP-1 model: Apple iMac res: 3840x2160 dpi: 163
    diag: 685mm (27")
  API: OpenGL v: 4.5 vendor: amd mesa v: 23.3.6 glx-v: 1.4 es-v: 3.2
    direct-render: yes renderer: PITCAIRN (radeonsi LLVM 17.0.6 DRM 2.50
    6.7.6-200.fc39.x86_64) device-ID: 1002:6810
  API: EGL Message: EGL data requires eglinfo. Check --recommends.
Audio:
  Device-1: Intel 8 Series/C220 Series High Definition Audio
    driver: snd_hda_intel v: kernel bus-ID: 00:1b.0 chip-ID: 8086:8c20
  Device-2: AMD Oland/Hainan/Cape Verde/Pitcairn HDMI Audio [Radeon HD 7000
    Series] driver: snd_hda_intel v: kernel pcie: speed: 8 GT/s lanes: 16
    bus-ID: 01:00.1 chip-ID: 1002:aab0
  Device-3: GN Netcom Jabra EVOLVE 20 SE MS
    driver: jabra,snd-usb-audio,usbhid type: USB rev: 2.0 speed: 12 Mb/s
    lanes: 1 bus-ID: 1-6.1.1:12 chip-ID: 0b0e:0302
  API: ALSA v: k6.7.6-200.fc39.x86_64 status: kernel-api
  Server-1: PipeWire v: 1.0.3 status: n/a (root, process) with:
    1: pipewire-pulse status: active 2: wireplumber status: active
    3: pipewire-alsa type: plugin 4: pw-jack type: plugin
Network:
  Device-1: Broadcom BCM4360 802.11ac Dual Band Wireless Network Adapter
    vendor: Apple driver: bcma-pci-bridge v: N/A pcie: speed: 2.5 GT/s lanes: 1
    bus-ID: 03:00.0 chip-ID: 14e4:43a0
  Device-2: Broadcom NetXtreme BCM57766 Gigabit Ethernet PCIe driver: tg3
    v: kernel pcie: speed: 2.5 GT/s lanes: 1 port: N/A bus-ID: 04:00.0
    chip-ID: 14e4:1686
  IF: enp4s0f0 state: up speed: 1000 Mbps duplex: full mac: <filter>
Bluetooth:
  Device-1: Apple Bluetooth Host Controller driver: btusb v: 0.8 type: USB
    rev: 2.0 speed: 12 Mb/s lanes: 1 bus-ID: 1-8.3:11 chip-ID: 05ac:828d
  Report: btmgmt ID: hci0 rfk-id: 0 state: up address: <filter> bt-v: 4.0
    lmp-v: 6
Drives:
  Local Storage: total: 1.02 TiB used: 72.53 GiB (6.9%)
  ID-1: /dev/sda vendor: Apple model: HDD ST1000DM003 size: 931.51 GiB
    speed: 3.0 Gb/s serial: <filter> temp: 42 C
  ID-2: /dev/sdb vendor: Apple model: SSD SD0128F size: 113 GiB
    speed: 6.0 Gb/s serial: <filter> temp: 59 C
Partition:
  ID-1: / size: 111.4 GiB used: 72.14 GiB (64.8%) fs: btrfs dev: /dev/dm-0
    mapped: luks-69ed407d-34f1-4eed-9c1b-69ce6d1fe938
  ID-2: /boot size: 973.4 MiB used: 358.6 MiB (36.8%) fs: ext4
    dev: /dev/sdb2
  ID-3: /boot/efi size: 600 MiB used: 36.5 MiB (6.1%) fs: hfsplus
    dev: /dev/sdb1
  ID-4: /home size: 111.4 GiB used: 72.14 GiB (64.8%) fs: btrfs
    dev: /dev/dm-0 mapped: luks-69ed407d-34f1-4eed-9c1b-69ce6d1fe938
Swap:
  ID-1: swap-1 type: zram size: 8 GiB used: 0 KiB (0.0%) priority: 100
    dev: /dev/zram0
Sensors:
  System Temperatures: cpu: 55.0 C mobo: N/A gpu: radeon temp: 51.0 C
  Fan Speeds (rpm): N/A
Info:
  Memory: total: 32 GiB available: 31.28 GiB used: 5.19 GiB (16.6%)
  Processes: 351 Power: uptime: 2h 1m wakeups: 0 Init: systemd v: 254
    target: graphical (5) default: graphical
  Packages: pm: flatpak pkgs: 65 Compilers: gcc: 13.2.1 Shell: Sudo
    v: 1.9.15p5 running-in: gnome-terminal inxi: 3.3.33

Signal is exiting with exactly the same errors, so that does see to be a theme.

Mar 01 10:58:02 arkady org.signal.Signal.desktop[29264]: [2:0301/105802.505922:FATAL:gpu_data_manager_impl_private.cc(448)] GPU process isn't usable. Goodbye.
Mar 01 10:58:02 arkady org.signal.Signal.desktop[29264]: [2:0301/105802.505898:ERROR:gpu_process_host.cc(993)] GPU process exited unexpectedly: exit_code=139
Mar 01 10:58:02 arkady org.signal.Signal.desktop[29655]: [180:0301/105802.248267:ERROR:vaapi_wrapper.cc(1122)] FillProfileInfo_Locked failed for va_profile VAProfileH264High and entrypoint VAEntrypointVLD
Mar 01 10:58:02 arkady org.signal.Signal.desktop[29655]: [180:0301/105802.248234:ERROR:vaapi_wrapper.cc(1213)] Empty codec maximum resolution
Mar 01 10:58:02 arkady org.signal.Signal.desktop[29655]: [180:0301/105802.248197:ERROR:vaapi_wrapper.cc(1122)] FillProfileInfo_Locked failed for va_profile VAProfileH264Main and entrypoint VAEntrypointVLD

Did this coincide with a Mesa update?

You could try clearing the mesa_shader_cache.

$HOME/.var/app/com.app.name/cache/mesa_shader_cache.

Hi @grumpey

No, it doesn’t look like it. The Mesa libraries look like they have not been updated for weeks. This has just popped up in the last few days.

Appreciate your reply. Thanks

Obsidian and Signal are both Electron (so, Chromium-based). Extension Manager and Flatseal are GTK4. Can you check the output from one of the latter?

flatpak run com.github.tchx84.Flatseal

Hi @chrisawi

Thanks for your assistance. I have reinstalled flatseal as an rpm package. So I ran

flatpak run com.mattjakeman.ExtensionManager

It returns…

A fatal error has occurred.
Please report this to 'https://github.com/mjakeman/extension-manager' and attach the following crash report:

START BACKTRACE

../src/exm-backtrace.c:92 'exm_backtrace_print'
../src/main.c:41 'handler'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
(null):0 '(null)'
../src/main.c:109 'run_app'
(null):0 '(null)'
(null):0 '(null)'
../sysdeps/x86_64/start.S:115 '_start'
(null):0 '(null)'

END BACKTRACE

@chrisawi I uninstalled the Flatseal rpm so I could install and run the flatpak from the command line.

Installed the flathub flatpak and it failed. I got an error message through notifications, but nothing reported on the command line.

“gjs-console quit unexpectedly
The application encountered a problem and could not continue.”

I uninstalled the flathub flatpak and installed Flatseal from the Fedora Linux repository and the app runs fine. I don’t really understand what that means but thought it may trigger a thought in those more learned than I.

Neither of those are very helpful, unfortunately. As previously suggested, this could be caused by a mesa update, but flatpaks don’t use mesa from the host. You can try downgrading the flatpak mesa extension:

sudo flatpak update --commit=d095240fc8e7a7c0889cef1ab561726b0a94304292024f66771fbf1c3d6c3088 org.freedesktop.Platform.GL.default//23.08
sudo flatpak update --commit=e437b679eda2d7eb9f73f5a735a6f323c74c5f3f6758380bded07013eac64192 org.freedesktop.Platform.GL.default//23.08-extra

How long has this been happening? The most recent update was just today, so I went back two releases to the one published on 2024-01-05.

Thanks @chrisawi. The problems started today. So it’s only very recent. I will have a go with the instructions provided when I get a chance. Rest of the day is locked up with meetings. :frowning:

In that case, you may want to try the mesa update from 2024-02-05 instead:

sudo flatpak update --commit=6896a1e84f623eba039b3a0eeabe21a16537f297460a3f3fcbcaab724cd97aaf org.freedesktop.Platform.GL.default//23.08
sudo flatpak update --commit=0f90faaea3e66a353bb667ee87b39eb49626d37d6117f37bba33b770b398b6c9 org.freedesktop.Platform.GL.default//23.08-extra
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First step when debugging any crash is to get a useful stack trace.

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I had a similar issue with the GIMP a similar issue with the GIMP 2.99.18RC flatpak, What fixed it, was starting it from the terminal once. . . Strangely it’s worked ever since. Can also provide info on why it’s not starting for you.

Similar issues here. iMac15,1. Will try downgrading mesa and report back later today by editing this message.

Edit: Yup: mesa was the problem, and downgrading fixed it.

For those unable to launch their browsers in order to copy the commit hashes, you can try using the w3m text browser from terminal.

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This is not a Fedora Problem. It also happens un Ububtu. The cause is the flatpaks runtime/org.freedesktop.Platform.GL.default/x86_64/23.08 (system) runtime/org.freedesktop.Platform.GL.default/x86_64/23.08-extra (system) and runtime/org.freedesktop.Platform.GL32.default/x86_64/23.08 (system)
These contain mesa 24.0.1. Mesa 24.0.1 has a bug in the AMD radeon driver. Soluutions (all of these work) 1) change to the amdgpu driver 2) wait for flathub to get the mesa 24.02 driver 3) remove 23.08 and use 22.08 which has the mesa 23.3.5 driver.

This was first seen in Arch Linux were it caused Display Managers to crash so normal booting was impossible. Arch has since upgraded to the mesa 24.0.2 driver

See radeon: Crash in radeon_bo_can_reclaim_slab (#10613) · Issues · Mesa / mesa · GitLab

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I have opened a discussion on the flathub forum Bug in Mesa 24.0.1 - Flathub Discourse The Radeon Bug is discudded in radeon: Crash in radeon_bo_can_reclaim_slab (#10613) · Issues · Mesa / mesa · GitLab

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