Windows suddenly freeze up for 30-45 seconds, cursor still moves

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Somewhat frequently, my desktop will just suddenly freeze up. I’ll typically have a few browser tabs open, a terminal or two, qBittorrent, Mullvad VPN, KeepassXC, and maybe some other program; suddenly I am unable to type, move any windows, switch focus, switch to TTY or do any input other than move the mouse. The cursor still moves around, but that’s it. I have to wait maybe 30-45 seconds before things work again. If i right clicked or moved any windows, it would show when the freezing stopped.

I initially thought this might have been with qBittorrent as I often have it running in the background, so I stopped running it for a little while to see if the issue went away, it didn’t. I ran my browser through the terminal with to see if it outputted anything when it occured, and didn’t see anything. Nothing stands out in .xsession_errors. Rebooting my system doesn’t make it go away. I checked GsmartControl to see if it was a drive issue and things seemed fine. No errors or warnings about the drives having issues.

How do I go about checking what process(es) are causing my windows to freeze up like this? I don’t know if it’s cinnamon sucking, some other software causing problems, or worst of all a hardware issue. I doubt it’s amount of memory, I have 16GB and things have been working fine until maybe the past couple weeks.

Kernel: 6.9.9-100.fc39.x86_64
DE: Cinnamon 6.0.4
WM: Mutter 45.7
qBittorrent: 4.6.5
KeepassXC: 2.7.9
Mullvad: 2024.3

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I often see similar when tracker-miner3 is running. As soon as that ends the performance returns to normal.

My thoughts are that tracker-miner should be running (by default) at a very low priority and niced to allow the desktop to operate normally.

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Thanks for the suggestion. I found this reddit comment that instructed to run the following commands:

systemctl --user mask tracker-extract-3.service tracker-miner-fs-3.service tracker-miner-rss-3.service tracker-writeback-3.service tracker-xdg-portal-3.service tracker-miner-fs-control-3.service
tracker3 reset -s -r

I ran them, and I’ll see if the issue comes up again. I might have to take note to disable this on future installs.
Just in case it happens to be relevant, I saw these errors in journalctl when I checked right after another freeze:

Jul 18 02:44:05 hostname kernel: ata2.00: exception Emask 0x0 SAct 0x460000 SErr 0xd0000 action 0x6 frozen
Jul 18 02:44:05 hostname kernel: ata2: SError: { PHYRdyChg CommWake 10B8B }
Jul 18 02:44:06 hostname kernel: ata2.00: failed command: READ FPDMA QUEUED
Jul 18 02:44:06 hostname kernel: ata2.00: cmd 60/20:88:e0:92:21/00:00:00:00:00/40 tag 17 ncq dma 16384 in
                                          res 40/00:01:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
Jul 18 02:44:06 hostname kernel: ata2.00: status: { DRDY }
Jul 18 02:44:06 hostname kernel: ata2.00: failed command: READ FPDMA QUEUED
Jul 18 02:44:06 hostname kernel: ata2.00: cmd 60/20:90:00:69:2a/00:00:00:00:00/40 tag 18 ncq dma 16384 in
                                          res 40/00:01:00:4f:c2/00:00:00:00:00/00 Emask 0x4 (timeout)
Jul 18 02:44:06 hostname kernel: ata2.00: status: { DRDY }
Jul 18 02:44:06 hostname kernel: ata2.00: failed command: READ FPDMA QUEUED
Jul 18 02:44:06 hostname kernel: ata2.00: cmd 60/20:b0:40:1c:cb/00:00:0c:00:00/40 tag 22 ncq dma 16384 in
                                          res 40/00:ff:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
Jul 18 02:44:06 hostname kernel: ata2.00: status: { DRDY }

Update: Eventually it froze again, although it didn’t last as long. Only about 10-15 seconds. This was in journalctl:

Jul  21:57:39 thedisco kernel: ata2.00: exception Emask 0x0 SAct 0x4 SErr 0xd0000 action 0x6 frozen
Jul  21:57:39 thedisco kernel: ata2: SError: { PHYRdyChg CommWake 10B8B }
Jul  21:57:39 thedisco kernel: ata2.00: failed command: READ FPDMA QUEUED
Jul  21:57:39 thedisco kernel: ata2.00: cmd 60/20:10:80:67:cd/00:00:0c:00:00/40 tag 2 ncq dma 16384 in
                                          res 40/00:ff:00:00:00/00:00:00:00:00/00 Emask 0x4 (timeout)
Jul  21:57:39 thedisco kernel: ata2.00: status: { DRDY }
Jul  21:57:39 thedisco kernel: ata2: hard resetting link
Jul  21:57:39 thedisco kernel: ata2: found unknown device (class 0)
Jul  21:57:39 thedisco kernel: ata2: SATA link up 6.0 Gbps (SStatus 133 SControl 300)
Jul  21:57:39 thedisco kernel: ata2.00: supports DRM functions and may not be fully accessible
Jul  21:57:39 thedisco kernel: ata2.00: supports DRM functions and may not be fully accessible
Jul  21:57:39 thedisco kernel: ata2.00: configured for UDMA/133
Jul  21:57:39 thedisco kernel: ahci 0000:03:00.1: port does not support device sleep
Jul  21:57:39 thedisco kernel: ata2: EH complete
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Final update on this for now.
After transferring my data to another drive, the freezing seems to have gone away.
The ata2.00: status: { DRDY } indicated that my drive was aging and starting to fail, which was likely causing the issues.

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