Upgrade

• 1: Vulnerabilities
• 2: Clickhouse Function/Engines/Settings Report
• 3: Removing empty parts
• 4: Removing lost parts

1 - Vulnerabilities

2022-03-15: 7 vulnerabulities in ClickHouse were published.

See the details https://jfrog.com/blog/7-rce-and-dos-vulnerabilities-found-in-clickhouse-dbms/

Those vulnerabilities were fixed by 2 PRs:

• https://github.com/ClickHouse/ClickHouse/pull/27136
• https://github.com/ClickHouse/ClickHouse/pull/27743

All releases starting from v21.10.2.15 have that problem fixed.

Also, the fix was backported to 21.3 and 21.8 branches - versions v21.8.11.4-lts and v21.3.19.1-lts accordingly have the problem fixed (and all newer releases in those branches).

The latest Altinity stable releases also contain the bugfix.

• 21.8.13
• 21.3.20

If you use some older version we recommend upgrading.

Before the upgrade - please ensure that ports 9000 and 8123 are not exposed to the internet, so external clients who can try to exploit those vulnerabilities can not access your clickhouse node.

2 - Clickhouse Function/Engines/Settings Report

Follow this link for a complete report on ClickHouse features with their availability: https://github.com/anselmodadams/ChMisc/blob/main/report/report.md. It is frequently updated (at least once a month).

3 - Removing empty parts

Removing of empty parts is a new feature introduced in 20.12. Earlier versions leave empty parts (with 0 rows) if TTL removes all rows from a part (https://github.com/ClickHouse/ClickHouse/issues/5491). If you set up TTL for your data it is likely that there are quite many empty parts in your system.

The new version notices empty parts and tries to remove all of them immediately. This is a one-time operation which runs right after an upgrade. After that TTL will remove empty parts on its own.

There is a problem when different replicas of the same table start to remove empty parts at the same time. Because of the bug they can block each other (https://github.com/ClickHouse/ClickHouse/issues/23292).

What we can do to avoid this problem during an upgrade:

1. Drop empty partitions before upgrading to decrease the number of empty parts in the system.

   SELECT concat('alter table ',database, '.', table, ' drop partition id ''', partition_id, ''';')
   FROM system.parts WHERE active
   GROUP BY database, table, partition_id
   HAVING count() = countIf(rows=0)
   

2. Upgrade/restart one replica (in a shard) at a time. If only one replica is cleaning empty parts there will be no deadlock because of replicas waiting for one another. Restart one replica, wait for replication queue to process, then restart the next one.

Removing of empty parts can be disabled by adding remove_empty_parts=0 to the default profile.

$ cat /etc/clickhouse-server/users.d/remove_empty_parts.xml
<clickhouse>
    <profiles>
        <default>
            <remove_empty_parts>0</remove_empty_parts>
        </default>
    </profiles>
</clickhouse>

4 - Removing lost parts

There might be parts left in ZooKeeper that don’t exist on disk

The explanation is here https://github.com/ClickHouse/ClickHouse/pull/26716

The problem is introduced in 20.1.

The problem is fixed in 21.8 and backported to 21.3.16, 21.6.9, 21.7.6.

Regarding the procedure to reproduce the issue:

The procedure was not confirmed, but I think it should work.

1. Wait for a merge on a particular partition (or run an OPTIMIZE to trigger one) At this point you can collect the names of parts participating in the merge from the system.merges table, or the system.parts table.

2. When the merge finishes, stop one of the replicas before the inactive parts are dropped (or detach the table).

3. Bring the replica back up (or attach the table). Check that there are no inactive parts in system.parts, but they stayed in ZooKeeper. Also check that the inactive parts got removed from ZooKeeper for another replica. Here is the query to check ZooKeeper:

select name, ctime from system.zookeeper
where path='<table_zpath>/replicas/<replica_name>/parts/'
  and name like '<put an expression for the parts that were merged>'

4. Drop the partition on the replica that DOES NOT have those extra parts in ZooKeeper. Check the list of parts in ZooKeeper. We hope that after this the parts on disk will be removed on all replicas, but one of the replicas will still have some parts left in ZooKeeper. If this happens, then we think that after a restart of the replica with extra parts in ZooKeeper it will try to download them from another replica.

A query to find ‘forgotten’ parts

https://kb.altinity.com/altinity-kb-useful-queries/parts-consistency/#compare-the-list-of-parts-in-zookeeper-with-the-list-of-parts-on-disk

A query to drop empty partitions with failing replication tasks

select 'alter table '||database||'.'||table||' drop partition id '''||partition_id||''';' 
from (
select database, table, splitByChar('_',new_part_name)[1] partition_id
from system.replication_queue
where type='GET_PART' and not is_currently_executing and create_time < toStartOfDay(yesterday())
group by database, table, partition_id) q
left join 
(select database, table, partition_id, countIf(active) cnt_active, count() cnt_total
from system.parts group by  database, table, partition_id
) p using database, table, partition_id
where cnt_active=0