Percona Toolkit’s pt-table-checksum is a great tool to find data inconsistencies between a MySQL master and its replicas. However it is sometimes not enough to know that there are inconsistencies and let pt-table-sync fix the issue: you may want to know which exact rows are different to identify the statements that created the inconsistency. This post shows one way to achieve that goal.

The issue

Let’s assume you have 2 servers running MySQL 5.5: db1 the master and db2 the replica. You want to upgrade to MySQL 5.6 using an in-place upgrade and to play safe, you will upgrade db2 (the slave) first. If all goes well you will promote it and upgrade db1.

A good thing to do after upgrading db2 is to check for potential data inconsistencies with pt-table-checksum. Once checksumming is done, you can run the following query on db2 to see if there is any data drift:

This indicates that inconsistencies can be found in mydb.items in 17 chunks. Now the question is: which rows are different on db1 and db2?

The solution

The previous query shows that we will find inconsistencies in 17 of the chunks pt-table-checksum used. But what is a chunk?

So the first chunk with inconsistencies is chunk #28, which is the set of rows where the primary key is >= 7487511 and <= 7563474.

Let’s export all these rows on db1 and db2 instance ::

Then let’s use diff to isolate non-matching rows

We can see that some datetime fields are off by 1 second on the 5.6 instance.

In this case, the binlogs showed queries like:

MySQL 5.5 rounds '2014-10-22 02:51:33.835249' to '2014-10-22 02:51:33' (ignoring the fractional part), while MySQL 5.6 rounds it to '2014-10-22 02:51:34'.

Now it’s easy to fix the application so that it works both with MySQL 5.5 and 5.6 and then continue testing MySQL 5.6.


The method shown above is an easy way to find the exact records that are inconsistent between the MySQL master and a replica. It is not useful if you only want to resync the slave (in this case, just run pt-table-sync) but it can be a first step in understanding how inconsistencies are created.

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Josh Boon

Don’t forget about –ignore-columns offered by pt-table-checksum–ignore-columns This followed by pt-table-sync using the differences found can help make quick work of replication issues.

Jacques Grove

Also note that you don’t need 5.5 involved to run into this “off by a second” issue: