Saturday, April 18, 2009

An algorithm to find and resolve data differences between MySQL tables

An algorithm to find and resolve data differences between MySQL tables
with 10 comments
I’ve been designing an algorithm to resolve data differences between MySQL tables, specifically so I can ‘patch’ a replication slave that has gotten slightly out of sync without completely re-initializing it. I intend to create a tool that can identify which rows are different and bring them into sync. I would like your thoughts on this.
Background and requirements
I see this as the next step in my recent series of posts on MySQL tools and techniques to keep replication running reliably and smoothly. Sometimes slaves “drift” a little bit, even when there don’t seem to be any issues with replication (this is one reason I submitted a bug report to add checksums on binlog events). Once a table differs on the slave, it gets more and more different from the master, possibly causing other tables to differ too.
I need a tool that, given a table known to differ on master and slave(s), will efficiently compare the tables and resolve the differences. Finding tables that differ is easy with MySQL Table Checksum, but I am not sure the best way to find which rows differ.
Here are my requirements. The algorithm needs to be:
Designed for statement-based replication, which means no temp tables, no expensive queries that will propagate to the slave, and so forth.
Efficient in terms of network load and server load, both when finding and when resolving differences. No huge tables or un-indexed data, no high-impact INSERT.. SELECT locking, etc.
Efficient on the client-side where the tool is executed.
Must work well on “very large” tables.
Some things I assume:
Tables must have primary keys. Without primary keys, it’s hard or a waste of time at best, and a disaster at worst.
It is not a good idea to do this unless the fraction of rows that differ is very small. If much of the table is different, then mysqldump is a better idea.
Other tools I’ve found
I’ve found a number of tools that are either not complete or don’t quite address the need, but reading the source code has been very productive. There’s Giuseppe Maxia’s work in remote MySQL table comparison. I based the MySQL Table Checksum tool on some of this work. Read the comments on that link, and you’ll see some follow-up from Fabien Coelho, who wrote pg_comparator. The documentation for this tool is an excellent read, as it goes into great detail on the algorithm used.
There are also a few projects that don’t do what I’m looking for. datadiff does a two-way in-server comparison of two tables with OUTER JOIN, a fine technique but inherently limited to two tables on one server, and not practical for extremely large tables. coldiff is a more specialized variant of that tool. mysqldiff diffs the structure of two tables, which I mention for completeness though it is not the problem I’m trying to solve.
The Maxia/Coelho bottom-up algorithm
Without restating everything these smart people have written, here’s a high-level overview of the algorithm as presented by Maxia and Coelho:
Compute a “folding factor” based on the number of rows in the table and/or user parameters.
Build successive levels of checksum tables bottom-up, starting at a row-level granularity and decreasing granularity by the “folding factor” with each level, until the final table has a single row.
Each row in the first table contains key column(s), a checksum of the key column(s), and a checksum of the whole row.
Each row in an intermediate-level summary table contains checksums for a group of rows in the next more granular level of summary data.
Groups are defined by taking checksums from the previous level modulo the folding factor.
Beginning at the most aggregated level, walk the “tree” looking for the differences, honing in eventually to the offending rows.
The “folding factor” is really a “branching factor” for the tree of summary tables. If the factor is 128, each level in an intermediate summary table will contain the groupwise checksum of about 128 rows in the next most granular level summary table.
This algorithm has many strengths. For example, it uses a logarithmic search to find rows that differ. It makes no assumptions about key distributions; the modulo operation on the checksum should randomize the distribution of which rows need to be fixed. It’s also very generic, which means it works pretty much the same on all tables. There’s no need to think about the “best way to do it” on a given table.
I am concerned about a few things, though. There’s a lot of data in all these summary tables. The first summary table contains as many rows as the table to analyze. If I were to calculate and store these rows for a table with lots of relatively narrow rows, I might be better off just copying the whole table from one server to the other. Also, creating these tables is not replication-friendly; the queries that run on the master will run on the slave too. This might not be a problem for everyone, but it would not be acceptable for my purposes.
The second part of the algorithm, walking the “tree” of summary tables to find rows that differ, doesn’t use any indexes in the implementations I’ve seen. Suppose I have a table with 128 million rows I want to analyze on two servers, using a branching factor of 128 (the default). The first checksum table has 128 million rows; the second has 1 million, and so on. Repeated scans on these tables will be inefficient, and given the randomization caused by the summary checksums, will cause lots of random I/O. Indexes could be added on the checksum modulo branching factor, but that’s another column, plus an index — this makes the table even bigger.
The checksum/modulo approach has another weakness. It defeats any optimizations I might be able to make based on knowledge of where in the table the rows differ. If the differences are grouped at the end of the table, for example in an append-only table that just missed a few inserts on the slave, the algorithm will distribute the “pointers” to these corrupt rows randomly through the summary tables, even though the rows really live near each other. Likewise, if my table contains client data and only one client is bad, the same situation will happen. This is a major issue, especially in some large tables I work with where we do things a client or account at a time. These and other spatial and temporal locality scenarios are realistic, because lots of real data is unevenly distributed. The checksum/modulo approach isn’t optimal for this.
Finally, the bottom-up approach doesn’t allow for early optimization or working in-memory. It builds the entire tree, then does the search. There’s no chance to “prune” the tree or try to keep a small working set. The flip side of this is actually a strength: assuming that the whole tree needs to be built, bottom-up is optimal. But most of my data isn’t like that. If much of the table is corrupt, I’m going to do a mysqldump instead, so I want to optimize for cases where I’ll be able to prune the tree.
One solution: a top-down approach
Given that I won’t even be looking at a table unless the global checksum has already found it differs, I am considering the following top-down approach, or some variation thereof:
Generate groupwise checksums for the whole table in a top-level grouping (more on that later).
If more than a certain fraction of the groups differ, quit. Too much of the table is different.
Otherwise descend depth-first into each group that has differences.
I think this algorithm, with some tuning, will address most of my concerns above. In particular, it will allow a smart DBA to specify how the grouping and recursion should happen. The choice of grouping is actually the most complicated part.
I’d do this client-side, not server-side. I’d generate the checksums server-side, but then fetch them back to the client code and keep them in memory. Given a good grouping, this shouldn’t require much network traffic or memory client-side, and will avoid locks, eliminate scratch tables, and keep the queries from replicating.
In the best case, all other things being equal, it will require the server to read about as many rows as the bottom-up approach, but it will exploit locality — a client at a time, a day at a time, and so on. This is a huge help, in my opinion; reducing random I/O is a high priority for me.
Given all this, I think top-down is better if there are not many changes to resolve, or if they’re grouped tightly together.
Some of the weaknesses I see are complexity, a proliferation of recursion and grouping strategies, perhaps more network traffic, and susceptibility to edge cases. Whereas the bottom-up approach has identical best and worst cases for different distributions of corrupt rows (assuming the number of corrupt rows is constant), the top-down approach suffers if there’s no locality to exploit. I’m a bit worried about edge cases causing this to happen more than I think it ought to.
Finally, and this could be either a strength or weakness, this approach lets every level of the recursion have a different branching factor, which might be appropriate or not — the DBA needs to decide.
Smart grouping and recursion
I think the hardest part is choosing appropriate ways to group and “drill down” into the table. Here are some possible strategies:
Date groupings. We have a lot of data in InnoDB tables with day-first or week-first primary keys, which as you know creates a day-first or week-first clustered index. The first checksum I’d run on these tables would be grouped by day.
Numeric groupings. Tables whose primary key is an auto-incremented number would probably be best grouped by division, for example, floor(id/5000) to group about 5000 neighboring rows together at a time.
Character groupings. If the primary key is a character string, I might group on the first few letters of the string.
Drill-down. Take for example one of our tables that is primary-keyed on IDs, which are auto-incremented numbers, and client account numbers. The best way to do the table I’m thinking of is by account number, then numerically within that on ID. For the day-first table, I’d group by day, then account number, and then by ID.
Exploit append-only tables. If a table is append-only, then corruption is likely in the most recent data, and I might try to examine only that part of the table. If there are updates and deletes to existing rows, this approach might not work.
Use defaults if the DBA doesn’t specify anything. If there’s a multi-column primary key, recurse one column at a time. If a single-column key, look for another key whose cardinality is less, and recurse from that to the primary key instead.
I think the DBA will have to choose the best strategy on a table-by-table basis, because I can’t think of a good automatic way to do it. Even analyzing the index structures on the table, and then trying to decide which are good choices, is too risky to do automatically. For example, SHOW INDEX will show estimated index cardinalities, but they’re based on random dives into the index tree and can be off by an order of magnitude or more.
How to resolve the differences
Again assuming that this reconciliation is taking place between a master and slave server, it’s important to fix the rows without causing more trouble while the fixing happens. For example, I don’t want to do something that’ll propagate to another slave that’s okay, and thereby mess it up, too.
Fixing the rows on the master, and letting the fixes propagate to the slave via the normal means, might actually be a good idea. If a row doesn’t exist or is different on the slave, REPLACE or INSERT .. ON DUPLICATE KEY UPDATE should fix the row on the slave without altering it on the master. If the row exists on the slave but not the master, DELETE on the master should delete it on the slave.
Peripheral benefits of this approach are that I don’t need to set up an account with write privileges on the slave. Also, if more than one slave has troubles with the same rows, this should fix them all at the same time.
Issues I need to research are whether the different number of rows affected on the slave will cause trouble, and if this can be solved with a temporary slave-skip-errors setting. The manual may document this, but I can’t find it.
Next steps
I’m looking forward to your feedback, and then I plan to build a tool that’ll implement whatever algorithm emerges from that discussion. At this point, assuming the above algorithm is as good as we can come up with together, I’m planning to actually implement both top-down and bottom-up approaches in the tool, so the DBA can decide what to use. The tool will, like the rest of the scripts in the MySQL Toolkit, be command-line friendly (there are lots of proprietary “visual tools” to compare and sync tables, but they don’t interest me — plus, why would I ever trust customer data to something I can’t see source code for?). I also understand that not everyone has the same narrowly-defined use case of re-syncing a slave, so of course I’ll make the tool more generic.
For my own use, ideally I’ll be making sure the tool is rock-solid, then defining rules for tables that frequently drift, and running a cron job to automatically find which tables are different and fix them. If the MySQL Table Checksum tool finds a table is out of sync and I don’t have a rule for it, it’ll just notify me and not try to fix it.
In this article I proposed some ideas for a top-down, in-client, replication-centric way to compare a table known to differ on a master and slave, find the rows that differ, and resolve them. I’m thinking about building a tool to implement this algorithm, and would like your feedback on efficient ways to do this.
Written by Xaprb
March 5th, 2007 at 11:46 pm
Posted in SQL
« MySQL Table Checksum bug fix
What to do when MySQL says skip-innodb is defined »
10 Responses to 'An algorithm to find and resolve data differences between MySQL tables'
Subscribe to comments with RSS or TrackBack to 'An algorithm to find and resolve data differences between MySQL tables'.
Nice article!
We have a similar tool called SQLyog Job Agent which incorporates most of what you have discussed in this article. Unfortunately, it is not open-source.
We are always trying to improve the algorithm and look forward to more articles on this topic!

6 Mar 07 at 2:32 am

Very interesting. I’ve already developed a simple tool to do just that, albeit based on a simple row-by-row comparison, with the correcting actions being inserts or updates directly on the slave.
It can recurse all the databases and tables to repair an entire database, or just operate on a single table.
I’d not considered doing the corrective action on the master, but it’s an interesting idea.
You’re absolutely correct that tables that lack a primary key are barely worth attempting, and so far my script ignores them.
One thing that I’ve found in practice, is that you must perform the synchronisation while replication is actually running. If you don’t, you will inevitably end up replicating ahead of the normal replication process and breaking it.
I’ve found that this tool is useful for bringing up a new replica where it’s impossible for the master to be affected in any ways, such as through table locking.
If you do develop a working implementation of your own, do let me know!

James Holden
6 Mar 07 at 7:48 am

Rohit, if I read your comment right, you’re subtly saying I’m going a good direction, which is encouraging :-)
James, you’ve reinforced my belief that lots of people need a tool that doesn’t disrupt replication.

6 Mar 07 at 8:57 am

I finally read the stuff (this article and the source code). The various discussions are very interesting.
I’m not sure that I understand fully the “index” issue with the bottom-up approach. Basically each summary table is build (once) and then it is scanned just once, so having an index built on some attribute would not be amortized. The only exception may be for bulk deletes or inserts, but that should not happen.
On the “exploit append-only tables” idea, the bottom-up approach can have a “where” clause on the initial table so that the comparison is only performed on part of the data. Moreover, if the candidate tuples are somehow an identifiable fraction of the table, it might be simpler to just
download them directly for comparison, that would be a third algorithm:-)
Do you have performance figures with your tool in different settings?

Fabien Coelho
15 May 07 at 5:06 am

Hello Fabien. The issue with the indexing is not scans, but lookups from a child table to its parent tables, including the group-by queries. These happen potentially many times. I could benchmark with and without indexes fairly easily and see for sure, but after writing all the queries I’m satisfied the index is important.
The WHERE clause has proven to be very important, as you guessed.
I did some testing with real data, and the results are here: Comparison of Table Sync Algorithms.

15 May 07 at 7:57 am

I have some problem with query sql.
I want you correct for me.
this is my query :
$queryselect=”select Distinct student.id_student,first_name,last_name,promotion,class
from student,applicationrecieve where student.id_student applicationrecieve.id_student”;
the query that I write to you, I want to select data that it don’t have in the table applicationrecieve from table student.

27 Jun 07 at 5:57 am

Nice article. I’ve studied the algorithm before, but wasn’t so clearly.
Actually I met he same need for keeping my databases synchronized, and for some days I’m trying to build a suitable algorithm for that. The Top-Down algorithm is good, but, as you mentioned, is too hard to find a good grouping. And how what is to be done if there is only one indexed column as Primary Key? So I find the Bottom-Up more suitable for that purpose, but with some differences, I’m going to build a B*-Tree based on row checksums for each table, keep it saved locally (I think a XML structure is a good way) and, for saving time and traffic, do the comparison locally too. I’m not sure it’s the best way for that, but i want to try.
Best regards.

Negruzzi Cristian
9 Oct 07 at 8:38 am

Please take a look at MySQL Table Sync in the MySQL Toolkit ( It may save you a lot of work. I’ve implemented both algorithms there.

9 Oct 07 at 8:50 am

But by all means, explore your algorithm too! I don’t mean to say you shouldn’t. It may be a much better way.

9 Oct 07 at 8:52 am

i want the algorithm to find the table of any no.

14 Oct 08 at 8:01 am

No comments: