Flatpak Applications Suddenly "Break" after kernel update

Flatpak apps suddenly slow down after a while, and most apps never finish booting (empty window) after reopening or starting them after the slow-down.

Re-opening the app doesn't help, the boot process is slow, and even after it's done, it's still slow. The solution is OS restart.

Running Wayland Zorin OS 17.2.
I am using auto-cpufreq.

This started to happen after a kernel update.

Extensions:

What happens if you roll back to the previous kernel by selecting it from the Grub Menu?

Additionally, have you tried running a flatpak from the command line to see any error output? That would help us pinpoint what broke. After a driver update, I needed to update libraries Flatpak needed for example.

flatpak run  com.super_productivity.SuperProductivity

[3:0129/073050.987010:ERROR:bus.cc(407)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory
Start app...
07:30:51.137 › { enabled: null, showDevTools: false, mode: 'bottom' }
Gtk-Message: 07:30:51.181: Failed to load module "canberra-gtk-module"
Gtk-Message: 07:30:51.182: Failed to load module "canberra-gtk-module"
[3:0129/073051.196215:ERROR:bus.cc(407)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory
[3:0129/073051.196256:ERROR:bus.cc(407)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory
Saving backups to /home/futoshdirozini/.var/app/com.super_productivity.SuperProductivity/config/superProductivity/backups
07:30:51.271 › Saving backups to /home/futoshdirozini/.var/app/com.super_productivity.SuperProductivity/config/superProductivity/backups
[3:0129/073051.274403:ERROR:bus.cc(407)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory
[3:0129/073051.274458:ERROR:bus.cc(407)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory
[3:0129/073051.274486:ERROR:bus.cc(407)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory

^C

flatpak run  io.gdevelop.ide

07:32:03.510 › GDevelop Electron app starting...
Gtk-Message: 07:32:03.591: Failed to load module "canberra-gtk-module"
Gtk-Message: 07:32:03.593: Failed to load module "canberra-gtk-module"
[3:0129/073203.636468:ERROR:bus.cc(397)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory
[3:0129/073203.636546:ERROR:bus.cc(397)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory
[3 preload-host-spawn-strategy] Dropping 0x33740026d140 (3) because of connection closed
^C
flatpak run  com.rtosta.zapzap

setHighDpiScaleFactorRoundingPolicy must be called before creating the QGuiApplication instance
Failed to create wl_display (No such file or directory)
qt.qpa.plugin: Could not load the Qt platform plugin "wayland" in "" even though it was found.
Qt: Session management error: Could not open network socket
qt.gui.imageio: libpng warning: iCCP: known incorrect sRGB profile
QPropertyAnimation: you're trying to animate the non-writable property width of your QObject


I gave details to you in another reply

Using the Linux 6.8.0-51-generic x86_64 kernel,
everything works fine.

The issue happens on Linux 6.8.0-52-generic x86_64


Hardware specs:
sudo lshw -short
H/W path                 Device          Class          Description
===================================================================
                                         system         82FG (LENOVO_MT_82FG_BU_idea_FM_IdeaPad 5 15ITL05)
/0                                       bus            LNVNB161216
/0/0                                     memory         128KiB BIOS
/0/4                                     processor      11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
/0/4/6                                   memory         128KiB L1 cache
/0/4/7                                   memory         5MiB L2 cache
/0/4/8                                   memory         12MiB L3 cache
/0/5                                     memory         192KiB L1 cache
/0/24                                    memory         16GiB System Memory
/0/24/0                                  memory         8GiB Row of chips DDR4 Synchronous 3200 MHz (0.3 ns)
/0/24/1                                  memory         8GiB Row of chips DDR4 Synchronous 3200 MHz (0.3 ns)
/0/100                                   bridge         11th Gen Core Processor Host Bridge/DRAM Registers
/0/100/2                 /dev/fb0        display        TigerLake-LP GT2 [Iris Xe Graphics]
/0/100/4                                 generic        TigerLake-LP Dynamic Tuning Processor Participant
/0/100/6                                 bridge         11th Gen Core Processor PCIe Controller
/0/100/6/0                               display        TU117M [GeForce MX450]
/0/100/a                                 generic        Tigerlake Telemetry Aggregator Driver
/0/100/d                                 bus            Tiger Lake-LP Thunderbolt 4 USB Controller
/0/100/d/0               usb1            bus            xHCI Host Controller
/0/100/d/1               usb2            bus            xHCI Host Controller
/0/100/14                                bus            Tiger Lake-LP USB 3.2 Gen 2x1 xHCI Host Controller
/0/100/14/0              usb3            bus            xHCI Host Controller
/0/100/14/0/1            input7          input          SONiX USB Keyboard System Control
/0/100/14/0/4            input10         input          Lenovo Lenovo Wireless Mouse System Control
/0/100/14/0/5                            multimedia     Integrated Camera
/0/100/14/0/6            scsi1           storage        USB Storage
/0/100/14/0/6/0.0.0      /dev/sda        disk           7751MB MassStorageClass
/0/100/14/0/6/0.0.0/0    /dev/sda        disk           7751MB 
/0/100/14/0/6/0.0.0/0/1  /dev/sda1       volume         7391MiB Windows FAT volume
/0/100/14/0/7                            generic        Goodix FingerPrint Device
/0/100/14/0/a                            communication  Bluetooth 9460/9560 Jefferson Peak (JfP)
/0/100/14/1              usb4            bus            xHCI Host Controller
/0/100/14.2                              memory         RAM memory
/0/100/14.3              wlp0s20f3       network        Wi-Fi 6 AX201
/0/100/15                                bus            Tiger Lake-LP Serial IO I2C Controller #0
/0/100/15.1                              bus            Tiger Lake-LP Serial IO I2C Controller #1
/0/100/16                                communication  Tiger Lake-LP Management Engine Interface
/0/100/17                                storage        Intel Corporation
/0/100/1c                                bridge         Intel Corporation
/0/100/1c/0              /dev/nvme0      storage        Micron MTFDHBA512QFD
/0/100/1c/0/0            hwmon2          disk           NVMe disk
/0/100/1c/0/2            /dev/ng0n1      disk           NVMe disk
/0/100/1c/0/1            /dev/nvme0n1    disk           512GB NVMe disk
/0/100/1c/0/1/1                          volume         99MiB Windows FAT volume
/0/100/1c/0/1/2          /dev/nvme0n1p2  volume         15MiB reserved partition
/0/100/1c/0/1/3          /dev/nvme0n1p3  volume         229GiB Windows NTFS volume
/0/100/1c/0/1/4          /dev/nvme0n1p4  volume         545MiB Windows NTFS volume
/0/100/1c/0/1/5          /dev/nvme0n1p5  volume         246GiB EXT4 volume
/0/100/1e                                communication  Tiger Lake-LP Serial IO UART Controller #0
/0/100/1e.3                              bus            Tiger Lake-LP Serial IO SPI Controller #1
/0/100/1f                                bridge         Tiger Lake-LP LPC Controller
/0/100/1f/0                              system         PnP device PNP0c02
/0/100/1f/1                              generic        PnP device INT3f0d
/0/100/1f/2                              input          PnP device PNP0303
/0/100/1f/3                              system         PnP device PNP0c02
/0/100/1f/4                              system         PnP device PNP0c02
/0/100/1f/5                              system         PnP device PNP0c02
/0/100/1f/6                              system         PnP device PNP0c02
/0/100/1f/7              input15         input          Ideapad extra buttons
/0/100/1f.3              card0           multimedia     Tiger Lake-LP Smart Sound Technology Audio Controller
/0/100/1f.4                              bus            Tiger Lake-LP SMBus Controller
/0/100/1f.5                              bus            Tiger Lake-LP SPI Controller
/1                                       power          CRB Battery 0
/2                                       power          OEM Define 5
/3                       input0          input          Lid Switch
/4                       input1          input          Power Button
/5                       input16         input          ELAN06FA:00 04F3:3140 Mouse
/6                       input17         input          ELAN06FA:00 04F3:3140 Touchpad
/7                       input18         input          sof-hda-dsp Mic
/8                       input19         input          sof-hda-dsp Headphone
/9                       input2          input          AT Translated Set 2 keyboard
/a                       input20         input          sof-hda-dsp HDMI/DP,pcm=3
/b                       input21         input          sof-hda-dsp HDMI/DP,pcm=4
/c                       input22         input          sof-hda-dsp HDMI/DP,pcm=5
/d                       input5          input          Video Bus
/e                       input6          input          Video Bus

At first, I thought this might purely an Electron issue, but looking at your output, it applies to containerization as a whole.

I can only recommend falling back to the previous kernel:

And consider filing a Linux Kernel bug.

Not a flatpak issue?
Also I clicked the link and that's a very huge wall of text I'm going to read it anyway. Dedication

Flatpaks are Containerized. Unless you use Docker and can test that too... Currently, I am thinking it is a containerization issue as a whole.

1 Like

Might be more complicated than that. I just updated my kernel to match v9um's:
6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 19:18:46 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

My flatpaks worked, so I installed two that they listed errors for (Super Productivity and GDevelop), both of which also worked.

1 Like

Uhh...


The kernel isnt supported anymore by linux.

I was able to reproduce the bug by plugging in the charger. no idea why!

Try opening them then opening Firefox try plugging in the charger and then try to open these two apps again

In that case, I would stick with the working Kernel.

I don't have a charger. My PC is a desktop I'm afraid.

1 Like

I have no problem sticking around with an old kernel. But Wouldn't that risk my security?

Depends on what the change to the kernel was. If it was a non-security related bugfix, then it's no problem. This was a relatively small update, given the version number, but I don't have a change list handy.

1 Like

I will provide a very honest answer.

Security patches should be taken seriously and should be applied. That being said...

Any risk to you as a home user are so vanishingly small, I would not lose one single second of sleep over using 6.8.0-51 over 6.8.0-52

2 Likes

Just a side comment donct know if using flatseal would improve things. Personally on any GNu/Linux I will be sticking with X11 and APT. Once these options are gone back to the Amiga if I can get a zz9000 board for it.

1 Like

I have flatseal but it doesn't help.

I'd like to stick to wayland, it's more secure and I have no problem experiencing some minor bugs that will help in improving wayland for others by reporting the bug.

X11 is too old, we need to move on

But here on Zorin 17, You can use Xorg. The Desktop is based on Gnome 43. So, the Wayland Implementation isn't as good as in the newer Versions.

1 Like

THIS HAPPENED AGAIN!!!

On the 6.8.0-51-generic kernel

[3:0130/180210.534287:ERROR:bus.cc(407)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory
Start app...
18:02:10.833 › { enabled: null, showDevTools: false, mode: 'bottom' }
Gtk-Message: 18:02:10.920: Failed to load module "canberra-gtk-module"
Gtk-Message: 18:02:10.922: Failed to load module "canberra-gtk-module"
[3:0130/180210.950208:ERROR:bus.cc(407)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory
[3:0130/180210.950286:ERROR:bus.cc(407)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory
Saving backups to /home/futoshdirozini/.var/app/com.super_productivity.SuperProductivity/config/superProductivity/backups
18:02:11.128 › Saving backups to /home/futoshdirozini/.var/app/com.super_productivity.SuperProductivity/config/superProductivity/backups
[3:0130/180211.136100:ERROR:bus.cc(407)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory
[3:0130/180211.136196:ERROR:bus.cc(407)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory
[3:0130/180211.136264:ERROR:bus.cc(407)] Failed to connect to the bus: Failed to connect to socket /run/dbus/system_bus_socket: No such file or directory
^C
futoshdirozini@futoshdirozini-IdeaPad-5-15ITL05:~$ [3 preload-host-spawn-strategy] Dropping 0x266000038d80 (3) because of connection closed
[3:0130/180704.007239:FATAL:bus.cc(1246)] D-Bus connection was disconnected. Aborting.
/app/bin/run.sh: line 2:     3 Trace/breakpoint trap   zypak-wrapper.sh /app/superproductivity/superproductivity "$@"