This might be related to one of the filesystem slowdowns I posted at I need your best performance tips! - #12 by garrett a while ago.
Specifically: Having encrypted partitions (using LUKS) prevents your SSD from trimming properly on Fedora Silverblue. (I’m not sure if this affects traditional package based Fedora too, or just Atomic.)
Over time, every Fedora Atomic installation will hit this bug and get slower and slower when IO happens.
The solution I found was to run this:
sudo cryptsetup --allow-discards --persistent refresh /dev/mapper/luks*
I’ve seen other people mention there are other ways to do this, but this command worked for me, and I’ve tested it on a few Silverblue installs over the past couple years.
You can test to see if you’re affected or not by running sudo fstrim -va — this will take a while and show you filesystems more than just /boot/efi and /boot if it’s working. (It should show / for example.) If you don’t see /, then you probably need to run the command above (or some other command to enable discards).