System is not healthy

I’ve been running my Home Assistant operating system for about a year now. I’m running it on a Rapberry Pi 3 with a 32GB SD card and have not had any major issues until now. I was trying to update the operating system last night, but the supervisor wouldn’t let me, saying my system was “unhealthy”. One of the recommended fixes was to restart the supervisor, so I did. The supervisor gave its own error and did not start back up. One of the suggested fixes was to reboot the host, which I did. That’s where it went bad. I tried connecting to my home assistant from the IP address for about an hour. I could ping it just fine, but nothing worked (I tested it with my hue dimmer switch and the automations for it did not work). I decided to reinstall.

The installer ran for about 9 hours, but was still stuck on “Preparing Home Assistant”. I don’t have access to another SD Card at the moment. Is there anything I can do about this?
Here are my logs so far for the installer:

[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...
[fix-attrs.d] done.
[cont-init.d] executing container initialization scripts...
[cont-init.d] udev.sh: executing... 
[13:35:37] INFO: Using udev information from host
[cont-init.d] udev.sh: exited 0.
[cont-init.d] done.
[services.d] starting services
[services.d] done.
[13:35:37] INFO: Starting local supervisor watchdog...
21-09-13 13:35:46 INFO (MainThread) [__main__] Initializing Supervisor setup
21-09-13 13:35:46 INFO (MainThread) [supervisor.docker.network] Can't find Supervisor network, creating a new network
21-09-13 13:35:47 INFO (MainThread) [supervisor.bootstrap] Initializing Supervisor Sentry
21-09-13 13:35:47 INFO (MainThread) [supervisor.bootstrap] Seting up coresys for machine: raspberrypi3-64
21-09-13 13:35:47 INFO (SyncWorker_0) [supervisor.docker.supervisor] Attaching to Supervisor homeassistant/aarch64-hassio-supervisor with version 2021.08.1
21-09-13 13:35:47 INFO (SyncWorker_0) [supervisor.docker.supervisor] Connecting Supervisor to hassio-network
21-09-13 13:35:48 WARNING (SyncWorker_0) [supervisor.docker.interface] Can't find homeassistant/aarch64-hassio-supervisor for cleanup
21-09-13 13:35:48 INFO (MainThread) [supervisor.resolution.evaluate] Starting system evaluation with state CoreState.INITIALIZE
21-09-13 13:35:49 INFO (MainThread) [supervisor.resolution.evaluate] System evaluation complete
21-09-13 13:35:49 INFO (MainThread) [__main__] Setting up Supervisor
21-09-13 13:35:49 INFO (MainThread) [supervisor.api] Starting API on 172.30.32.2
21-09-13 13:35:49 INFO (MainThread) [supervisor.hardware.monitor] Started Supervisor hardware monitor
21-09-13 13:35:49 INFO (MainThread) [supervisor.dbus.manager] Load dbus interface io.hass.os
21-09-13 13:35:50 INFO (MainThread) [supervisor.dbus.manager] Load dbus interface org.freedesktop.systemd1
21-09-13 13:35:50 INFO (MainThread) [supervisor.dbus.manager] Load dbus interface org.freedesktop.login1
21-09-13 13:35:50 INFO (MainThread) [supervisor.dbus.manager] Load dbus interface org.freedesktop.hostname1
21-09-13 13:35:51 INFO (MainThread) [supervisor.dbus.manager] Load dbus interface org.freedesktop.timedate1
21-09-13 13:35:51 INFO (MainThread) [supervisor.dbus.manager] Load dbus interface org.freedesktop.NetworkManager
21-09-13 13:35:51 INFO (MainThread) [supervisor.dbus.manager] Load dbus interface de.pengutronix.rauc
21-09-13 13:35:52 INFO (MainThread) [supervisor.host.info] Updating local host information
21-09-13 13:35:52 INFO (MainThread) [supervisor.host.services] Updating service information
21-09-13 13:35:52 INFO (MainThread) [supervisor.host.network] Updating local network information
21-09-13 13:35:55 INFO (MainThread) [supervisor.host.sound] Updating PulseAudio information
21-09-13 13:35:55 INFO (MainThread) [supervisor.host.manager] Host information reload completed
21-09-13 13:35:55 INFO (MainThread) [supervisor.host.apparmor] Loading AppArmor Profiles: {'hassio-supervisor'}
21-09-13 13:35:55 INFO (MainThread) [supervisor.host.services] Reloading local service hassos-apparmor.service
21-09-13 09:35:55 INFO (SyncWorker_0) [supervisor.docker.interface] Found ghcr.io/home-assistant/aarch64-hassio-dns versions: [<AwesomeVersion CalVer '2021.06.0'>]
21-09-13 09:35:55 INFO (SyncWorker_0) [supervisor.docker.interface] Attaching to ghcr.io/home-assistant/aarch64-hassio-dns with version 2021.06.0
21-09-13 09:35:55 INFO (MainThread) [supervisor.plugins.dns] Starting CoreDNS plugin
21-09-13 09:35:58 INFO (SyncWorker_0) [supervisor.docker.dns] Starting DNS ghcr.io/home-assistant/aarch64-hassio-dns with version 2021.06.0 - 172.30.32.3
21-09-13 09:35:58 INFO (MainThread) [supervisor.plugins.dns] Updated /etc/resolv.conf
21-09-13 09:35:58 INFO (SyncWorker_0) [supervisor.docker.interface] Found ghcr.io/home-assistant/aarch64-hassio-audio versions: [<AwesomeVersion CalVer '2021.07.0'>]
21-09-13 09:35:58 INFO (SyncWorker_0) [supervisor.docker.interface] Attaching to ghcr.io/home-assistant/aarch64-hassio-audio with version 2021.07.0
21-09-13 09:35:58 INFO (MainThread) [supervisor.plugins.audio] Starting Audio plugin
21-09-13 09:36:01 INFO (SyncWorker_0) [supervisor.docker.audio] Starting Audio ghcr.io/home-assistant/aarch64-hassio-audio with version 2021.07.0 - 172.30.32.4
21-09-13 09:36:01 INFO (SyncWorker_0) [supervisor.docker.interface] Found ghcr.io/home-assistant/aarch64-hassio-cli versions: [<AwesomeVersion CalVer '2021.08.1'>]
21-09-13 09:36:01 INFO (SyncWorker_0) [supervisor.docker.interface] Attaching to ghcr.io/home-assistant/aarch64-hassio-cli with version 2021.08.1
21-09-13 09:36:02 INFO (MainThread) [supervisor.plugins.cli] Starting CLI plugin
21-09-13 09:36:05 INFO (SyncWorker_0) [supervisor.docker.cli] Starting CLI ghcr.io/home-assistant/aarch64-hassio-cli with version 2021.08.1 - 172.30.32.5
21-09-13 09:36:05 INFO (SyncWorker_0) [supervisor.docker.interface] Found ghcr.io/home-assistant/aarch64-hassio-observer versions: [<AwesomeVersion CalVer '2021.06.0'>]
21-09-13 09:36:05 INFO (SyncWorker_0) [supervisor.docker.interface] Attaching to ghcr.io/home-assistant/aarch64-hassio-observer with version 2021.06.0
21-09-13 09:36:05 INFO (MainThread) [supervisor.plugins.observer] Starting observer plugin
21-09-13 09:36:09 INFO (SyncWorker_0) [supervisor.docker.observer] Starting Observer ghcr.io/home-assistant/aarch64-hassio-observer with version 2021.06.0 - 172.30.32.6
21-09-13 09:36:09 INFO (SyncWorker_1) [supervisor.docker.interface] Found ghcr.io/home-assistant/aarch64-hassio-multicast versions: [<AwesomeVersion CalVer '2021.04.0'>]
21-09-13 09:36:09 INFO (SyncWorker_0) [supervisor.docker.interface] Attaching to ghcr.io/home-assistant/aarch64-hassio-multicast with version 2021.04.0
21-09-13 09:36:09 INFO (MainThread) [supervisor.plugins.multicast] Starting Multicast plugin
21-09-13 09:36:11 INFO (SyncWorker_0) [supervisor.docker.multicast] Starting Multicast ghcr.io/home-assistant/aarch64-hassio-multicast with version 2021.04.0 - Host
21-09-13 09:36:11 INFO (MainThread) [supervisor.updater] Fetching update data from https://version.home-assistant.io/stable.json
21-09-13 09:36:18 INFO (MainThread) [supervisor.homeassistant.secrets] Loaded 0 Home Assistant secrets
21-09-13 09:36:18 INFO (SyncWorker_1) [supervisor.docker.interface] No version found for ghcr.io/home-assistant/raspberrypi3-64-homeassistant
21-09-13 09:36:18 INFO (MainThread) [supervisor.homeassistant.core] No Home Assistant Docker image ghcr.io/home-assistant/raspberrypi3-64-homeassistant found.
21-09-13 09:36:18 INFO (SyncWorker_0) [supervisor.docker.interface] Attaching to ghcr.io/home-assistant/raspberrypi3-64-homeassistant with version landingpage
21-09-13 09:36:18 INFO (MainThread) [supervisor.homeassistant.core] Using preinstalled landingpage
21-09-13 09:36:18 INFO (MainThread) [supervisor.homeassistant.core] Starting HomeAssistant landingpage
21-09-13 09:36:18 INFO (MainThread) [supervisor.homeassistant.module] Update pulse/client.config: /data/tmp/homeassistant_pulse
21-09-13 09:36:20 INFO (SyncWorker_0) [supervisor.docker.homeassistant] Starting Home Assistant ghcr.io/home-assistant/raspberrypi3-64-homeassistant with version landingpage
21-09-13 09:36:20 INFO (MainThread) [supervisor.hassos] Detect Home Assistant Operating System 6.3 / BootSlot A
21-09-13 09:36:20 INFO (MainThread) [supervisor.store.git] Cloning add-on https://github.com/hassio-addons/repository repository
21-09-13 09:36:20 INFO (MainThread) [supervisor.store.git] Cloning add-on https://github.com/home-assistant/addons repository
21-09-13 09:36:25 WARNING (MainThread) [supervisor.addons.validate] Add-on config 'snapshot_exclude' is deprecated, 'backup_exclude' should be used instead. Please report this to the maintainer of AdGuard Home
21-09-13 09:36:25 WARNING (MainThread) [supervisor.addons.validate] Add-on config 'snapshot_exclude' is deprecated, 'backup_exclude' should be used instead. Please report this to the maintainer of ESPHome
21-09-13 09:36:26 WARNING (MainThread) [supervisor.addons.validate] Add-on config 'snapshot' is deprecated, 'backup' should be used instead. Please report this to the maintainer of UniFi Controller
21-09-13 09:36:26 INFO (MainThread) [supervisor.store] Loading add-ons from store: 63 all - 63 new - 0 remove
21-09-13 09:36:26 INFO (MainThread) [supervisor.addons] Found 0 installed add-ons
21-09-13 09:36:26 INFO (MainThread) [supervisor.backups.manager] Found 0 backup files
21-09-13 09:36:26 INFO (MainThread) [supervisor.discovery] Loaded 0 messages
21-09-13 09:36:26 INFO (MainThread) [supervisor.ingress] Loaded 0 ingress sessions
21-09-13 09:36:26 INFO (MainThread) [supervisor.resolution.check] Starting system checks with state CoreState.SETUP
21-09-13 09:36:26 INFO (MainThread) [supervisor.resolution.check] System checks complete
21-09-13 09:36:26 INFO (MainThread) [supervisor.resolution.evaluate] Starting system evaluation with state CoreState.SETUP
21-09-13 09:36:26 INFO (MainThread) [supervisor.resolution.evaluate] System evaluation complete
21-09-13 09:36:26 INFO (MainThread) [supervisor.jobs] 'ResolutionFixup.run_autofix' blocked from execution, system is not running - CoreState.SETUP
21-09-13 09:36:26 INFO (MainThread) [supervisor.resolution.evaluate] Starting system evaluation with state CoreState.SETUP
21-09-13 09:36:26 INFO (MainThread) [supervisor.resolution.evaluate] System evaluation complete
21-09-13 09:36:26 INFO (MainThread) [__main__] Running Supervisor
21-09-13 09:36:27 INFO (MainThread) [supervisor.hassos] Rauc: A - marked slot kernel.0 as good
21-09-13 09:36:27 INFO (MainThread) [supervisor.supervisor] Fetching AppArmor profile https://version.home-assistant.io/apparmor.txt
21-09-13 09:36:28 INFO (MainThread) [supervisor.host.apparmor] Adding/updating AppArmor profile: hassio-supervisor
21-09-13 09:36:28 INFO (MainThread) [supervisor.host.services] Reloading local service hassos-apparmor.service
21-09-13 09:36:28 INFO (MainThread) [supervisor.supervisor] Update Supervisor to version 2021.09.0
21-09-13 09:36:28 INFO (SyncWorker_1) [supervisor.docker.interface] Downloading docker image ghcr.io/home-assistant/aarch64-hassio-supervisor with tag 2021.09.0.
21-09-13 09:42:43 ERROR (SyncWorker_1) [supervisor.docker.interface] Can't install ghcr.io/home-assistant/aarch64-hassio-supervisor:2021.09.0: 500 Server Error for http+docker://localhost/v1.41/images/create?tag=2021.09.0&fromImage=ghcr.io%2Fhome-assistant%2Faarch64-hassio-supervisor: Internal Server Error ("Get "https://ghcr.io/v2/": context deadline exceeded (Client.Timeout exceeded while awaiting headers)")
21-09-13 09:42:43 INFO (MainThread) [supervisor.resolution.module] Create new issue IssueType.UPDATE_FAILED - ContextType.SUPERVISOR / None
21-09-13 09:42:43 ERROR (MainThread) [supervisor.supervisor] Update of Supervisor failed: Can't install ghcr.io/home-assistant/aarch64-hassio-supervisor:2021.09.0: 500 Server Error for http+docker://localhost/v1.41/images/create?tag=2021.09.0&fromImage=ghcr.io%2Fhome-assistant%2Faarch64-hassio-supervisor: Internal Server Error ("Get "https://ghcr.io/v2/": context deadline exceeded (Client.Timeout exceeded while awaiting headers)")
21-09-13 09:42:43 CRITICAL (MainThread) [supervisor.core] Can't update Supervisor! This will break some Add-ons or affect future versions of Home Assistant!
21-09-13 09:42:43 INFO (MainThread) [supervisor.addons] Phase 'AddonStartup.INITIALIZE' starting 0 add-ons
21-09-13 09:42:43 INFO (MainThread) [supervisor.addons] Phase 'AddonStartup.SYSTEM' starting 0 add-ons
21-09-13 09:42:43 INFO (MainThread) [supervisor.addons] Phase 'AddonStartup.SERVICES' starting 0 add-ons
21-09-13 09:42:43 INFO (MainThread) [supervisor.core] Skiping start of Home Assistant
21-09-13 09:42:43 INFO (MainThread) [supervisor.addons] Phase 'AddonStartup.APPLICATION' starting 0 add-ons
21-09-13 09:42:43 INFO (MainThread) [supervisor.misc.tasks] All core tasks are scheduled
21-09-13 09:42:43 INFO (MainThread) [supervisor.core] Supervisor is up and running
21-09-13 09:42:43 INFO (MainThread) [supervisor.homeassistant.core] Home Assistant setup
21-09-13 09:42:43 INFO (MainThread) [supervisor.host.info] Updating local host information
21-09-13 09:42:43 INFO (SyncWorker_1) [supervisor.docker.interface] Updating image ghcr.io/home-assistant/raspberrypi3-64-homeassistant:landingpage to ghcr.io/home-assistant/raspberrypi3-64-homeassistant:2021.9.6
21-09-13 09:42:43 INFO (SyncWorker_1) [supervisor.docker.interface] Downloading docker image ghcr.io/home-assistant/raspberrypi3-64-homeassistant with tag 2021.9.6.
21-09-13 09:42:44 INFO (MainThread) [supervisor.updater] Fetching update data from https://version.home-assistant.io/stable.json
21-09-13 09:42:44 INFO (MainThread) [supervisor.resolution.check] Starting system checks with state CoreState.RUNNING
21-09-13 09:42:44 INFO (MainThread) [supervisor.resolution.checks.base] Run check for IssueType.TRUST/ContextType.CORE
21-09-13 09:42:44 ERROR (MainThread) [supervisor.utils] Can't execute check_trust while a task is in progress
21-09-13 09:42:44 INFO (MainThread) [supervisor.resolution.checks.base] Run check for IssueType.TRUST/ContextType.PLUGIN
21-09-13 09:42:45 INFO (MainThread) [supervisor.host.services] Updating service information
21-09-13 09:42:45 INFO (MainThread) [supervisor.host.network] Updating local network information
21-09-13 09:42:49 INFO (MainThread) [supervisor.resolution.checks.base] Run check for IssueType.FREE_SPACE/ContextType.SYSTEM
21-09-13 09:42:49 INFO (MainThread) [supervisor.resolution.module] Create new suggestion SuggestionType.CREATE_FULL_BACKUP - ContextType.SYSTEM / None
21-09-13 09:42:49 INFO (MainThread) [supervisor.resolution.checks.base] Run check for IssueType.PWNED/ContextType.ADDON
21-09-13 09:42:49 INFO (MainThread) [supervisor.resolution.checks.base] Run check for IssueType.TRUST/ContextType.SUPERVISOR
21-09-13 09:42:49 INFO (MainThread) [supervisor.resolution.checks.base] Run check for IssueType.SECURITY/ContextType.CORE
21-09-13 09:42:49 INFO (MainThread) [supervisor.resolution.check] System checks complete
21-09-13 09:42:49 INFO (MainThread) [supervisor.resolution.evaluate] Starting system evaluation with state CoreState.RUNNING
21-09-13 09:42:49 INFO (MainThread) [supervisor.host.sound] Updating PulseAudio information
21-09-13 09:42:49 INFO (MainThread) [supervisor.host.manager] Host information reload completed
21-09-13 09:42:52 INFO (MainThread) [supervisor.resolution.evaluate] System evaluation complete
21-09-13 09:42:52 INFO (MainThread) [supervisor.jobs] 'ResolutionFixup.run_autofix' blocked from execution, system is not healthy
21-09-13 09:48:49 ERROR (SyncWorker_1) [supervisor.docker.interface] Can't install ghcr.io/home-assistant/raspberrypi3-64-homeassistant:2021.9.6: 500 Server Error for http+docker://localhost/v1.41/images/create?tag=2021.9.6&fromImage=ghcr.io%2Fhome-assistant%2Fraspberrypi3-64-homeassistant: Internal Server Error ("Get "https://ghcr.io/v2/": net/http: request canceled while waiting for connection (Client.Timeout exceeded while awaiting headers)")
21-09-13 09:48:49 WARNING (MainThread) [supervisor.homeassistant.core] Error on Home Assistant installation. Retry in 30sec
21-09-13 09:49:19 INFO (SyncWorker_1) [supervisor.docker.interface] Updating image ghcr.io/home-assistant/raspberrypi3-64-homeassistant:landingpage to ghcr.io/home-assistant/raspberrypi3-64-homeassistant:2021.9.6
21-09-13 09:49:19 INFO (SyncWorker_1) [supervisor.docker.interface] Downloading docker image ghcr.io/home-assistant/raspberrypi3-64-homeassistant with tag 2021.9.6.
21-09-13 09:54:55 ERROR (SyncWorker_1) [supervisor.docker.interface] Can't install ghcr.io/home-assistant/raspberrypi3-64-homeassistant:2021.9.6: 500 Server Error for http+docker://localhost/v1.41/images/create?tag=2021.9.6&fromImage=ghcr.io%2Fhome-assistant%2Fraspberrypi3-64-homeassistant: Internal Server Error ("Get "https://ghcr.io/v2/": context deadline exceeded (Client.Timeout exceeded while awaiting headers)")
21-09-13 09:54:55 WARNING (MainThread) [supervisor.homeassistant.core] Error on Home Assistant installation. Retry in 30sec
21-09-13 09:55:25 INFO (SyncWorker_1) [supervisor.docker.interface] Updating image ghcr.io/home-assistant/raspberrypi3-64-homeassistant:landingpage to ghcr.io/home-assistant/raspberrypi3-64-homeassistant:2021.9.6
21-09-13 09:55:25 INFO (SyncWorker_1) [supervisor.docker.interface] Downloading docker image ghcr.io/home-assistant/raspberrypi3-64-homeassistant with tag 2021.9.6.

Can you SSH into it? I only ask as I had the exact same issue just now and ran the following command:
ha supervisor update
from within my console for HA in my Proxmox NUC. Now it is updated to the latest version.
Hopefully this can get you going again!
Lyall