Database Corruption Every Second Sunday Due to Auto-Repack - Need Help

firstcolle · September 8, 2024, 8:06am

Good morning,
for 4 months I have been using Home Assistant on a virtual machine running on a Mac Mini. Everything works very well except for one issue: every second Sunday of the month at 4 a.m., my database gets corrupted and I have to restore a backup.

I believe this issue is related to the ‘repack’ function, which, according to the documentation, happens every second Sunday of the month at 4 a.m. This has always happened. At first, I thought my installation was corrupted, so I reinstalled everything from scratch, but the problem persists.

This happens both with the default recorder configuration and with my configuration, which I hoped would improve the issue. In my configuration, I exclude all devices from recorder/history/logbook except for the ones I need, but I have to keep the data for at least 2 years (I know the database will grow large, but based on my calculations, it shouldn’t exceed 20GB in 2 years, as I don’t save many devices). Now the db is 2GB. Below is my recorder configuration:

purge_keep_days: 730
auto_repack: true
exclude:
  domains:
    - alarm_control_panel
    - automation
    - binary_sensor
    - (and all the others)

include:
  entities:
    - sensor.voltage
    - (and all the sensors I need)

I also tried reverting to the default configuration and manually running the service, but the issue reoccurs. Below are the two logs:

2024-09-08 04:12:01.942 ERROR (Recorder) [homeassistant.components.recorder.core] Unrecoverable sqlite3 database corruption detected: (sqlite3.DatabaseError) database disk image is malformed
[SQL: VACUUM]
(Background on this error at: https://sqlalche.me/e/20/4xp6)
Traceback (most recent call last):
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1967, in _exec_single_context
    self.dialect.do_execute(
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/default.py", line 924, in do_execute
    cursor.execute(statement, parameters)
sqlite3.DatabaseError: database disk image is malformed

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/src/homeassistant/homeassistant/components/recorder/core.py", line 900, in _process_one_task_or_event_or_recover
    task.run(self)
  File "/usr/src/homeassistant/homeassistant/components/recorder/tasks.py", line 114, in run
    if purge.purge_old_data(
       ^^^^^^^^^^^^^^^^^^^^^
  File "/usr/src/homeassistant/homeassistant/components/recorder/util.py", line 664, in wrapper
    return job(instance, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/src/homeassistant/homeassistant/components/recorder/purge.py", line 127, in purge_old_data
    repack_database(instance)
  File "/usr/src/homeassistant/homeassistant/components/recorder/repack.py", line 28, in repack_database
    conn.execute(text("VACUUM"))
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1418, in execute
    return meth(
           ^^^^^
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/sql/elements.py", line 515, in _execute_on_connection
    return connection._execute_clauseelement(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1640, in _execute_clauseelement
    ret = self._execute_context(
          ^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1846, in _execute_context
    return self._exec_single_context(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1986, in _exec_single_context
    self._handle_dbapi_exception(
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2353, in _handle_dbapi_exception
    raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1967, in _exec_single_context
    self.dialect.do_execute(
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/default.py", line 924, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.DatabaseError: (sqlite3.DatabaseError) database disk image is malformed
[SQL: VACUUM]
(Background on this error at: https://sqlalche.me/e/20/4xp6)
2024-09-08 04:12:02.014 ERROR (Recorder) [homeassistant.components.recorder.util] The system will rename the corrupt database file //config/home-assistant_v2.db to //config/home-assistant_v2.db.corrupt.2024-09-08T02:12:02.014619+00:00 in order to allow startup to proceed

Registratore: homeassistant.components.recorder.core
Fonte: components/recorder/core.py:900
Integrazione: Recorder (documentazione, problemi)
Prima occorrenza: 09:39:23 (1 occorrenze)
Ultima registrazione: 09:39:23

Unrecoverable sqlite3 database corruption detected: (sqlite3.DatabaseError) database disk image is malformed [SQL: UPDATE states SET old_state_id=? 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?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)] [parameters: (None, 304208, 304209, 304214, 304215, 304216, 304217, 304218, 304219, 304220, 304221, 304222, 304223, 304224, 304225, 304226, 304227, 304228, 304229, 304230, 304231, 304232, 304233, 304234, 304235, 304236, 304237, 304238, 304239, 304240, 304241, 304242, 304243, 304244, 304245, 304246, 304247, 304248, 304249, 304250, 304251, 304252, 304253, 304254, 304255, 304256, 304257, 304258, 304259, 304260 ... 3901 parameters truncated ... 308162, 308163, 308164, 308165, 308166, 308167, 308168, 308169, 308170, 308171, 308172, 308173, 308174, 308175, 308176, 308177, 308178, 308179, 308180, 308181, 308182, 308183, 308184, 308185, 308186, 308187, 308188, 308189, 308190, 308191, 308192, 308193, 308194, 308195, 308196, 308197, 308198, 308199, 308200, 308201, 308202, 308203, 308204, 308205, 308206, 308207, 308208, 308209, 308210, 308211)] (Background on this error at: https://sqlalche.me/e/20/4xp6)
Traceback (most recent call last):
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1967, in _exec_single_context
    self.dialect.do_execute(
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/default.py", line 924, in do_execute
    cursor.execute(statement, parameters)
sqlite3.DatabaseError: database disk image is malformed

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/src/homeassistant/homeassistant/components/recorder/core.py", line 900, in _process_one_task_or_event_or_recover
    task.run(self)
  File "/usr/src/homeassistant/homeassistant/components/recorder/tasks.py", line 114, in run
    if purge.purge_old_data(
       ^^^^^^^^^^^^^^^^^^^^^
  File "/usr/src/homeassistant/homeassistant/components/recorder/util.py", line 664, in wrapper
    return job(instance, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/src/homeassistant/homeassistant/components/recorder/purge.py", line 89, in purge_old_data
    has_more_to_purge |= _purge_states_and_attributes_ids(
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/src/homeassistant/homeassistant/components/recorder/purge.py", line 202, in _purge_states_and_attributes_ids
    _purge_state_ids(instance, session, state_ids)
  File "/usr/src/homeassistant/homeassistant/components/recorder/purge.py", line 521, in _purge_state_ids
    disconnected_rows = session.execute(disconnect_states_rows(state_ids))
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2351, in execute
    return self._execute_internal(
           ^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/orm/session.py", line 2236, in _execute_internal
    result: Result[Any] = compile_state_cls.orm_execute_statement(
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/orm/bulk_persistence.py", line 1624, in orm_execute_statement
    return super().orm_execute_statement(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/orm/context.py", line 293, in orm_execute_statement
    result = conn.execute(
             ^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1418, in execute
    return meth(
           ^^^^^
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/sql/lambdas.py", line 603, in _execute_on_connection
    return connection._execute_clauseelement(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1640, in _execute_clauseelement
    ret = self._execute_context(
          ^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1846, in _execute_context
    return self._exec_single_context(
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1986, in _exec_single_context
    self._handle_dbapi_exception(
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 2353, in _handle_dbapi_exception
    raise sqlalchemy_exception.with_traceback(exc_info[2]) from e
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/base.py", line 1967, in _exec_single_context
    self.dialect.do_execute(
  File "/usr/local/lib/python3.12/site-packages/sqlalchemy/engine/default.py", line 924, in do_execute
    cursor.execute(statement, parameters)
sqlalchemy.exc.DatabaseError: (sqlite3.DatabaseError) database disk image is malformed
[SQL: UPDATE states SET old_state_id=? WHERE states.old_state_id IN (?, ?, ? )]
[parameters: (None, 304208, 304209, 304214, 304215, 304216, 304217, 304218, 304219, 304220, 304221, 304222, 304223, 304224, 304225, 304226, 304227, 304228, 304229, 304230, 304231, 304232, 304233, 304234, 304235, 304236, 304237, 304238, 304239, 304240, 304241, 304242, 304243, 304244, 304245, 304246, 304247, 304248, 304249, 304250, 304251, 304252, 304253, 304254, 304255, 304256, 304257, 304258, 304259, 304260 ... 3901 parameters truncated ... 308162, 308163, 308164, 308165, 308166, 308167, 308168, 308169, 308170, 308171, 308172, 308173, 308174, 308175, 308176, 308177, 308178, 308179, 308180, 308181, 308182, 308183, 308184, 308185, 308186, 308187, 308188, 308189, 308190, 308191, 308192, 308193, 308194, 308195, 308196, 308197, 308198, 308199, 308200, 308201, 308202, 308203, 308204, 308205, 308206, 308207, 308208, 308209, 308210, 308211)]
(Background on this error at: https://sqlalche.me/e/20/4xp6)

How can I resolve this? The only solution I have left is to disable the auto-repack.
Thank you.

tom_l · September 8, 2024, 8:41am

Do not keep more than 30 days of state data.

Then do not use the the HA database to do this. Use a second time series database like InluxDB.

Or use the long term statistics feature. This data is kept forever. All you have to do is give your sensors a valid state_class.

@Ildar_Gabdullin Case in point

firstcolle · September 8, 2024, 8:56am

Thanks for the response. I don’t really like the idea of using another database. I could limit myself to long-term statistics, that’s fine. However, as I mentioned, the problem persists even if I keep the default parameters of the recorder

Ildar_Gabdullin · September 8, 2024, 10:53am

Thanks for pointing.
Faced a DB corruption as well - but it was for 10 days, it grew up to 10GB within ~ a day - it was flooded by “sys_error” events (later I excluded these events from Recorder). In normal circumstances DB size was not so high.
And after “docker stop HA”, “docker start HA” the DB was corrupted (according to HA log). There were a few GBs of free space on HDD left.
Means - corruption may happen not only for a high “purge_keep” value.
And probably HA DB should be more robust for large sizes.

tom_l · September 8, 2024, 10:55am

Apologies this is not a DB size issue. I missed this:

That is a reasonable size.

Ildar_Gabdullin · September 8, 2024, 10:56am

Could it be an issue related to HDD damaged surface etc?

firstcolle · September 9, 2024, 6:18am

I don’t think it’s an HDD-related issue because I moved the data to a secondary hard drive last month. The problem was present even when the data was on the default storage

tom_l · September 9, 2024, 7:15am

You could try repairing the database: Restore corrupt database after nightly purge - #3 by peterevers