startup error upgrading 1.69 -> 1.70 or greater: constraint "receipts_graph_uniqueness" does not exist #14377

kylrth · 2022-11-06T16:24:34Z

After upgrading the Docker container from v1.68.0 to v1.70.1, I see this error on startup:

Starting synapse with args -m synapse.app.homeserver --config-path /data/homeserver.yaml
2022-11-06 16:17:37,820 - root - 345 - WARNING - main - ***** STARTING SERVER *****
2022-11-06 16:17:37,820 - root - 346 - WARNING - main - Server /usr/local/lib/python3.9/site-packages/synapse/app/homeserver.py version 1.70.1
2022-11-06 16:17:37,820 - root - 351 - INFO - main - Server hostname: kylrth.com
2022-11-06 16:17:37,820 - root - 352 - INFO - main - Instance name: master
2022-11-06 16:17:37,820 - root - 353 - INFO - main - Twisted reactor: EPollReactor
2022-11-06 16:17:37,820 - synapse.app.homeserver - 372 - INFO - main - Setting up server
2022-11-06 16:17:37,820 - synapse.server - 307 - INFO - main - Setting up.
2022-11-06 16:17:37,825 - synapse.storage.databases - 66 - INFO - main - [database config 'master']: Checking database server
2022-11-06 16:17:37,827 - synapse.storage.databases - 69 - INFO - main - [database config 'master']: Preparing for databases ['main', 'state']
2022-11-06 16:17:37,827 - synapse.storage.prepare_database - 115 - INFO - main - ['main', 'state']: Checking existing schema version
2022-11-06 16:17:37,830 - synapse.storage.prepare_database - 119 - INFO - main - ['main', 'state']: Existing schema is 73 (+8 deltas)
2022-11-06 16:17:37,830 - synapse.storage.databases.main - 311 - INFO - main - Checking database for consistency with configuration...
2022-11-06 16:17:37,831 - synapse.storage.prepare_database - 411 - INFO - main - Applying schema deltas for v73
2022-11-06 16:17:37,832 - synapse.storage.prepare_database - 519 - INFO - main - Applying schema 73/06thread_notifications_thread_id_idx.sql
2022-11-06 16:17:37,833 - synapse.storage.prepare_database - 527 - INFO - main - Applying engine-specific schema 73/08thread_receipts_non_null.sql.postgres
2022-11-06 16:17:37,834 - synapse.app._base - 205 - ERROR - main - Exception during startup
Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/synapse/app/homeserver.py", line 375, in setup
    hs.setup()
  File "/usr/local/lib/python3.9/site-packages/synapse/server.py", line 309, in setup
    self.datastores = Databases(self.DATASTORE_CLASS, self)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/databases/__init__.py", line 74, in __init__
    prepare_database(
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/prepare_database.py", line 136, in prepare_database
    _upgrade_existing_database(
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/prepare_database.py", line 528, in _upgrade_existing_database
    database_engine.execute_script_file(cur, absolute_path)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/engines/_base.py", line 145, in execute_script_file
    cls.executescript(cursor, f.read())
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/engines/postgres.py", line 224, in executescript
    cursor.execute(script)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/database.py", line 388, in execute
    self._do_execute(self.txn.execute, sql, *args)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/database.py", line 436, in _do_execute
    return func(sql, *args, **kwargs)
psycopg2.errors.UndefinedObject: constraint "receipts_graph_uniqueness" of relation "receipts_graph" does not exist

**********************************************************************************
 Error during initialisation:
    constraint "receipts_graph_uniqueness" of relation "receipts_graph" does not exist
 
 There may be more information in the logs.
**********************************************************************************

I then proceeded to downgrade to 1.70.0, and then 1.69.0, at which point the server worked correctly. Just to be sure, I then tried to upgrade back to 1.70.1, but I saw the same issue. Currently running 1.69.0 now.

squahtx · 2022-11-07T13:19:18Z

The Synapse database is missing the receipts_graph_uniqueness constraint for some reason.
That constraint was added in schema version 21, 7 years ago, so it's not clear how it went missing. (see https://github.com/matrix-org/synapse/blob/develop/synapse/storage/schema/main/delta/21/receipts.sql#L23)

Can you try running

ALTER TABLE ONLY receipts_graph
    ADD CONSTRAINT receipts_graph_uniqueness UNIQUE (room_id, receipt_type, user_id);

in psql, then upgrading again?

kylrth · 2022-11-07T13:53:37Z

What do I do if there's a duplicate key?

synapse=# ALTER TABLE ONLY receipts_graph ADD CONSTRAINT receipts_graph_uniqueness UNIQUE (room_id, receipt_type, user_id);
ERROR:  could not create unique index "receipts_graph_uniqueness"
DETAIL:  Key (room_id, receipt_type, user_id)=(!LZirCxnkkeBudrQzPj:matrix.org, m.read, @f:whomst.online) is duplicated.

Sorry, I'm a database noob.

squahtx · 2022-11-07T18:13:11Z

In that case let's try something different. We're going to execute the 73/08thread_receipts_non_null.sql.postgres migration manually and mark it as done.

First, double check that 73/06thread_notifications_thread_id_idx.sql is the last schema delta applied:

SELECT * FROM applied_schema_deltas;
 version |                               file
---------+-------------------------------------------------------------------
...
      73 | 73/04pending_device_list_updates.sql
      73 | 73/05old_push_actions.sql.postgres
      73 | 73/06thread_notifications_thread_id_idx.sql
(### rows)

If that's the case, then try:

-- It's okay if this fails because `receipts_linearized_uniqueness` does not exist.
ALTER TABLE receipts_linearized DROP CONSTRAINT receipts_linearized_uniqueness;

-- It's okay if this fails because `receipts_graph_uniqueness` does not exist.
ALTER TABLE receipts_graph DROP CONSTRAINT receipts_graph_uniqueness;

INSERT INTO applied_schema_deltas(version, file) VALUES (73, '73/08thread_receipts_non_null.sql.postgres');

Then try upgrading Synapse again.

kylrth · 2022-11-07T19:58:09Z

Wow thank you so much for the help. I'm seeing the last delta is 73/05old_push_actions.sql.postgres. What do I do in this case?

squahtx · 2022-11-08T14:25:31Z

I'm seeing the last delta is 73/05old_push_actions.sql.postgres. What do I do in this case?

We'll have to run 73/06... manually first. After running these in order, try upgrading Synapse again:

-- 73/06thread_notifications_thread_id_idx.sql
-- Allow there to be multiple summaries per user/room.
DROP INDEX IF EXISTS event_push_summary_unique_index;

INSERT INTO background_updates (ordering, update_name, progress_json, depends_on) VALUES
  (7306, 'event_push_actions_thread_id_null', '{}', 'event_push_backfill_thread_id');

INSERT INTO background_updates (ordering, update_name, progress_json, depends_on) VALUES
  (7306, 'event_push_summary_thread_id_null', '{}', 'event_push_backfill_thread_id');

INSERT INTO applied_schema_deltas(version, file) VALUES (73, '73/06thread_notifications_thread_id_idx.sql');

-- 73/08thread_receipts_non_null.sql.postgres
-- It's okay if this fails because `receipts_linearized_uniqueness` does not exist.
ALTER TABLE receipts_linearized DROP CONSTRAINT receipts_linearized_uniqueness;

-- It's okay if this fails because `receipts_graph_uniqueness` does not exist.
ALTER TABLE receipts_graph DROP CONSTRAINT receipts_graph_uniqueness;

INSERT INTO applied_schema_deltas(version, file) VALUES (73, '73/08thread_receipts_non_null.sql.postgres');

kylrth · 2022-11-08T16:23:49Z

Ok I applied the migrations, upgraded to 1.71.0, and now federation is occurring but I'm seeing this error:

2022-11-08 16:21:42,226 - synapse.metrics.background_process_metrics - 244 - ERROR - background_updates-0 - Background process 'background_updates' threw an exception
Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/background_updates.py", line 294, in run_background_updates
    result = await self.do_next_background_update(sleep)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/background_updates.py", line 424, in do_next_background_update
    await self._do_background_update(desired_duration_ms)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/background_updates.py", line 467, in _do_background_update
    items_updated = await update_handler(progress, batch_size)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/background_updates.py", line 624, in updater
    await self.db_pool.runWithConnection(runner)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/database.py", line 976, in runWithConnection
    return await make_deferred_yieldable(
  File "/usr/local/lib/python3.9/site-packages/twisted/python/threadpool.py", line 244, in inContext
    result = inContext.theWork()  # type: ignore[attr-defined]
  File "/usr/local/lib/python3.9/site-packages/twisted/python/threadpool.py", line 260, in <lambda>
    inContext.theWork = lambda: context.call(  # type: ignore[attr-defined]
  File "/usr/local/lib/python3.9/site-packages/twisted/python/context.py", line 117, in callWithContext
    return self.currentContext().callWithContext(ctx, func, *args, **kw)
  File "/usr/local/lib/python3.9/site-packages/twisted/python/context.py", line 82, in callWithContext
    return func(*args, **kw)
  File "/usr/local/lib/python3.9/site-packages/twisted/enterprise/adbapi.py", line 282, in _runWithConnection
    result = func(conn, *args, **kw)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/database.py", line 969, in inner_func
    return func(db_conn, *args, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/background_updates.py", line 575, in create_index_psql
    c.execute(sql)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/database.py", line 388, in execute
    self._do_execute(self.txn.execute, sql, *args)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/database.py", line 436, in _do_execute
    return func(sql, *args, **kwargs)
psycopg2.errors.UniqueViolation: could not create unique index "receipts_graph_unique_index"
DETAIL:  Key (room_id, receipt_type, user_id)=(!LZirCxnkkeBudrQzPj:matrix.org, m.read, @f:whomst.online) is duplicated.


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/synapse/metrics/background_process_metrics.py", line 242, in run
    return await func(*args, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/background_updates.py", line 299, in run_background_updates
    raise RuntimeError(
RuntimeError: 5 back-to-back background update failures; aborting.

In the mean time I downgraded to 1.69.0 because I worried that state wouldn't be stored correctly.

squahtx · 2022-11-15T13:00:52Z

We're working on a fix that will go in 1.72.0. It's being tracked in #14406.

kylrth · 2022-11-22T15:14:00Z

@squahtx upon upgrading to 1.72.0, I get this:

2022-11-22 15:11:46,824 - synapse.storage.background_updates - 431 - INFO - background_updates-0 - Starting update batch on background update 'receipts_graph_unique_index'
2022-11-22 15:11:46,865 - synapse.metrics.background_process_metrics - 244 - ERROR - background_updates-0 - Background process 'background_updates' threw an exception
Traceback (most recent call last):
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/background_updates.py", line 294, in run_background_updates
    result = await self.do_next_background_update(sleep)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/background_updates.py", line 424, in do_next_background_update
    await self._do_background_update(desired_duration_ms)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/background_updates.py", line 467, in _do_background_update
    items_updated = await update_handler(progress, batch_size)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/databases/main/receipts.py", line 1053, in _background_receipts_graph_unique_index
    await self._create_receipts_index(
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/databases/main/receipts.py", line 958, in _create_receipts_index
    await self.db_pool.runWithConnection(_create_index)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/database.py", line 976, in runWithConnection
    return await make_deferred_yieldable(
  File "/usr/local/lib/python3.9/site-packages/twisted/python/threadpool.py", line 244, in inContext
    result = inContext.theWork()  # type: ignore[attr-defined]
  File "/usr/local/lib/python3.9/site-packages/twisted/python/threadpool.py", line 260, in <lambda>
    inContext.theWork = lambda: context.call(  # type: ignore[attr-defined]
  File "/usr/local/lib/python3.9/site-packages/twisted/python/context.py", line 117, in callWithContext
    return self.currentContext().callWithContext(ctx, func, *args, **kw)
  File "/usr/local/lib/python3.9/site-packages/twisted/python/context.py", line 82, in callWithContext
    return func(*args, **kw)
  File "/usr/local/lib/python3.9/site-packages/twisted/enterprise/adbapi.py", line 282, in _runWithConnection
    result = func(conn, *args, **kw)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/database.py", line 969, in inner_func
    return func(db_conn, *args, **kwargs)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/databases/main/receipts.py", line 953, in _create_index
    c.execute(sql)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/database.py", line 388, in execute
    self._do_execute(self.txn.execute, sql, *args)
  File "/usr/local/lib/python3.9/site-packages/synapse/storage/database.py", line 436, in _do_execute
    return func(sql, *args, **kwargs)
psycopg2.errors.DuplicateTable: relation "receipts_graph_unique_index" already exists

That's repeated 5 times before giving up. I'm guessing this is because of the manual upgrades I did?

squahtx · 2022-11-22T15:22:39Z

Was the receipts_graph_unique_index index created manually after we tried #14377 (comment) ?

Could you post the output of

 \d receipts_graph

and

\d receipts_linearized

?

kylrth · 2022-11-22T15:26:15Z

synapse=# \d receipts_graph
            Table "public.receipts_graph"
    Column    | Type | Collation | Nullable | Default 
--------------+------+-----------+----------+---------
 room_id      | text |           | not null | 
 receipt_type | text |           | not null | 
 user_id      | text |           | not null | 
 event_ids    | text |           | not null | 
 data         | text |           | not null | 
 thread_id    | text |           |          | 
Indexes:
    "receipts_graph_unique_index" UNIQUE, btree (room_id, receipt_type, user_id) WHERE thread_id IS NULL
    "receipts_graph_uniqueness_thread" UNIQUE CONSTRAINT, btree (room_id, receipt_type, user_id, thread_id)

synapse=# \d receipts_linearized
               Table "public.receipts_linearized"
        Column         |  Type  | Collation | Nullable | Default 
-----------------------+--------+-----------+----------+---------
 stream_id             | bigint |           | not null | 
 room_id               | text   |           | not null | 
 receipt_type          | text   |           | not null | 
 user_id               | text   |           | not null | 
 event_id              | text   |           | not null | 
 data                  | text   |           | not null | 
 instance_name         | text   |           |          | 
 event_stream_ordering | bigint |           |          | 
 thread_id             | text   |           |          | 
Indexes:
    "receipts_linearized_id" btree (stream_id)
    "receipts_linearized_room_stream" btree (room_id, stream_id)
    "receipts_linearized_unique_index" UNIQUE, btree (room_id, receipt_type, user_id) WHERE thread_id IS NULL
    "receipts_linearized_uniqueness_thread" UNIQUE CONSTRAINT, btree (room_id, receipt_type, user_id, thread_id)
    "receipts_linearized_user" btree (user_id)

squahtx · 2022-11-22T15:29:30Z

Thanks. That all looks okay.
I'm not sure how or why the error in #14377 (comment) cleared itself up.

Could you run SELECT * FROM background_updates? I'm expecting to see receipts_graph_unique_index in there still.

kylrth · 2022-11-22T15:31:36Z

synapse=# SELECT * FROM background_updates;
            update_name            | progress_json |          depends_on           | ordering 
-----------------------------------+---------------+-------------------------------+----------
 event_push_actions_thread_id_null | {}            | event_push_backfill_thread_id |     7306
 event_push_summary_thread_id_null | {}            | event_push_backfill_thread_id |     7306
 threads_backfill                  | {}            |                               |     7309
(3 rows)

If you're willing to help debug further somewhere other than GitHub (and huge thanks for what you've done so far), we could take this to matrix @kyle:kylrth.com

squahtx · 2022-11-23T13:15:27Z

That looks okay then. Are you still seeing errors in the logs when restarting on 1.72.0?

kylrth · 2022-11-23T13:56:54Z

Hmm, well now I restarted again with 1.72.0 and I'm not seeing any errors. Not sure how it got fixed, since I haven't made any changes since the previous attempt. Thanks so much for you help!

squahtx added S-Minor Blocks non-critical functionality, workarounds exist. T-Other Questions, user support, anything else. O-Uncommon Most users are unlikely to come across this or unexpected workflow labels Nov 7, 2022

squahtx added the X-Needs-Info This issue is blocked awaiting information from the reporter label Nov 7, 2022

erikjohnston removed the X-Needs-Info This issue is blocked awaiting information from the reporter label Nov 16, 2022

squahtx added the X-Needs-Info This issue is blocked awaiting information from the reporter label Nov 22, 2022

kylrth closed this as completed Nov 23, 2022

clokep mentioned this issue Aug 29, 2023

psycopg2.errors.UniqueViolation: duplicate key value violates unique constraint "receipts_linearized_uniqueness" #16138

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startup error upgrading 1.69 -> 1.70 or greater: constraint "receipts_graph_uniqueness" does not exist #14377

startup error upgrading 1.69 -> 1.70 or greater: constraint "receipts_graph_uniqueness" does not exist #14377

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startup error upgrading 1.69 -> 1.70 or greater: constraint "receipts_graph_uniqueness" does not exist #14377

startup error upgrading 1.69 -> 1.70 or greater: constraint "receipts_graph_uniqueness" does not exist #14377

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