MySQL Slow? Check for Fragmentation.

June 8, 2011

Let's say you have a website and you notice that any calls to your MySQL database take longer to render. If you don't have a Database Administrator (DBA), this can be pretty frustrating. SoftLayer's Managed Hosting line of business employs some of the best DBAs in the country and is one of the only managed hosting providers that offers MySQL and MsSQL DBA services, and I don't just say that because I'm one of them ... We've got the certifications to prove it. :-)

Given my area of expertise, I wanted to share a few some simple tips with you to help you tweak variables and improve the performance of your MySQL server. Given that every application is different, this isn't necessarily a one-size-fits-all solution, but it'll at least give you a starting point for troubleshooting.

First: Get mysqltuner.pl. This is a fine script by Major Hayden that will give you some valuable information regarding the performance of your MySQL server.

Second: Look for fragmented tables. What are fragmented tables? If there are random insertions into or deletions from the indexes of a table, the indexes may become fragmented. Fragmentation means that the physical ordering of the index pages on the disk is not close to the index ordering of the records on the pages or that there are many unused pages in the 64-page blocks that were allocated to the index. The symptoms of fragmented tables can be that table can take more disk space than needed or the results may return slower with more disk I/O than needed. INNODB users need to check the fragmentation often because when INNODB marks data as deleted, it never overwrites the blocks with new data ... It just marks them as unusable. As a result, the data size is artificially inflated and data retrieval is slowed.

Fortunately, there is a way to see your table fragmentation and that is to run a query against the information_schemea to show all tables that are fragmented and the percentage of fragmentation:

SELECT TABLE_SCHEMA, TABLE_NAME, CONCAT(ROUND(data_length / ( 1024 * 1024 ), 2), 'MB') DATA, CONCAT(ROUND(data_free  / ( 1024 * 1024 ), 2), 'MB')FREE from information_schema.TABLES where TABLE_SCHEMA NOT IN ('information_schema','mysql') and Data_free < 0;

Fixing the fragmentation is easy, but there are a few caveats. When defragmenting a table, it will lock the table, so make sure you can afford the lock. To fix fragmented tables, you can simply run optimize table <table name>; to rebuild the table and all indexes or you can change the engine of the table with alter table <table name> engine = INNODB;

I have written a simple bash script in bash to go through, defragment and optimize your tables:

#!/bin/bash
 
MYSQL_LOGIN='-u<user name> --password=<passowrd>'
 
for db in $(echo "SHOW DATABASES;" | mysql $MYSQL_LOGIN | grep -v -e "Database" -e "information_schema")
do
        TABLES=$(echo "USE $db; SHOW TABLES;" | mysql $MYSQL_LOGIN |  grep -v Tables_in_)
        echo "Switching to database $db"
        for table in $TABLES
        do
                echo -n " * Optimizing table $table ... "
                echo "USE $db; OPTIMIZE TABLE $table" | mysql $MYSQL_LOGIN >/dev/null
                echo "done."
        done
done

You'd be surprised how much of an impact table fragmentation has on MySQL performance, and this is an easy way to quickly troubleshoot your database that "isn't as fast as it used to be." If you follow the above steps and still can't make sense of what's causing your database to lag, our Managed Hosting team is always here to work with you to get your servers back in shape ... And with the flexibility of month-to-month contract terms and the ability to add managed capabilities to specific pieces of your infrastructure, we have to earn your business every month with spectacular service.

-Lee