Mysqltuner suggestions and changes to my.cnf
I'll do my best to help here. The MysqlTuner report implies that you have 4GB of RAM in this VPS, so my suggestions are based on that.
query_cache_size - This is the amount of RAM MySQL can use to cache the results of database queries. Results stored in the query cache are returned much faster than normal selects, so this variable can significantly speed things up (more so than any of the other suggested changes).
Exactly what the correct value is for you will take some experimentation. You currently have this set to 8M. If you have 4GB of RAM in this box I'd start at 64M, increasing to 128M and then 256M if required. After each change, leave things for a few days and then run MysqlTuner again and compare the percentage for 'Query cache efficiency' to what it was before. For a server mainly hosting 5 Wordpress blogs I doubt you'd see any improvement beyond 256M, and I wouldn't recommend going beyond an eighth of your total RAM.
Personally I find Munin (a free server monitoring tool) quite handy for keeping an eye on this sort of thing, as it will graph the cache hits vs. other queries.
tmp_table_size - for some complex queries (particularly those using GROUP BY or complex sorting), MySQL needs to first create a temporary table containing the data and then run some operations on it in order to create the result set. It will try and create these temp tables in memory, as this is much faster than creating them on disk; but for large result sets this isn't always possible. tmp_table_size controls this threshold.
I can't imagine Wordpress is doing any hugely complex queries so I wouldn't go overboard with this one. MysqlTuner is suggesting a value greater than 32MB, so start with 64M and see how this affects the 'Temporary tables created on disk' value after a few days. Set max_heap_table_size while you're at it as it suggests.
thread_cache_size - Wordpress doesn't use persistent connections by default (which is good), so each request is making a new connection to your database and then closing this once the page has been generated. This overhead is not significant, but using thread_cache_size allows MySQL to reuse these connection threads which will help a little.
I'd go with the suggested value of 4 which I'd imagine will be fine unless you get a high number of concurrent users.
table_cache - I'm a little hazy on this one, it seems to relate to MySQL's cache of table structure. I'd go with 128 for this.
innodb_buffer_pool_size - this is the amount of memory MySQL can use to cache indexes and data for InnoDB tables. This one puzzles me a bit as I don't think Wordpress uses InnoDB at all - do you have some other sites on this server as well?
To answer your other questions, the configuration after [mysqld_safe] only apply to the MySQL daemon in safe mode, rather than MySQL overall, so that's why some of the variables are duplicated. If you do change innodb_buffer_pool_size, you'll want to change the first one. The variables not in the file you can add, yes, but add them above the [mysqld_safe] block for the same reason.
Lastly, since you're in the mood for optimising, if you are not already using a PHP bytecode cache such as APC then this is worth exploring. APC can give some significant speed improvements to PHP apps without any negative effects.
There are more tools out there to tune your mysql database: http://www.day32.com/MySQL/ and http://www.maatkit.org/doc/ and http://hackmysql.com/mysqlsla
In most cases you don't no need to write queries and test them against the server. Just enable the slow query log to identify your slow queries aggregate them with mysqlsla and explain them with maatkit:
You could paste the slowest queries from the mysqla results to a text file and execute them with maatkit.
mk-visual-explain –host hostname –user username –password passwort –database \
databasename -c query1.sql >> query1_data.txt
-
mk-query-profiler –host hostname –user username –password passwort –database \
databasename query1_data.txt >> query1_data.txt
Often coosing a newer mysql version is critical to performance. I experienced that the execution plans for complex queries are very different when you compare for example mysql 5.0.23 to 5.1.4. They are executed in our environment much faster with 5.1.4.
Lot's of useful information about mysql can be found at http://www.mysqlperformanceblog.com/ and in the book "High Performance MySQL".
Tabe Cache: According to the book "the table cache stores objects that represent tables. Each object in the cache contains the associated table's parsed .frm file plus other data, depending on the table's storage engine.
The table cache's design is a little MyISAM centric - this is one of the areas where the seperation between the server and the storage engine is not completely clean, for historical reasons. The table cache is a little less important for InnoDB, because InnoDB doesn't rely on it for as many purposes(such as holding file descriptors; it has its own version of a table cache for this purpose). However, even InnoDB benefits from caching the parsed .frm files.".
If you raise the table cache, there might be errors with the open files limit. You also need to increase the open_files_limit variable on the server and perhaps the operating system open files limit: http://www.cyberciti.biz/faq/linux-increase-the-maximum-number-of-open-files/.
Thread Cache:
The thread cache holds the threads that aren't currently associated with a connection but are ready to serve new connections. As long as MySQL has a free thread in the cache, it can respond very rapidly to connect requests, because it doesn't have to create a new thread for each connection.
[!!] Temporary tables created on disk: 46% (400K on disk / 869K total) If tmp_table_size and max_heap_table_size are not set yet, increase them. Disk operations are very slow compared to RAM-operations. Does wordpress use lots of blob/text columns? then you won't see much benefits, because BLOB and Text columns are not allowed in memory tables.
[OK] Highest usage of available connections: 53% (53/100) To save RAM you could decrease the allowed max connections. On the other hand you might run out of connections in peak times.
Using an opcode cache for PHP is a very good idea!