MySQL/Optimization

Caching

One thing you should look at is the query cache. By default, the query cache is turned off. You should turn it on, and set it in the tens of megabytes to see how it affects performance (like 80MB for starters). A huge cache will hurt performance (don't give it 4GB just because you have 32GB of RAM). But some amount of cache will definitely improve performance. So you just have to find the sweetspot for your hardware and application. That being said, if your tables are exclusively InnoDB tables, then you might be able to turn query cache off.

The cache is for SELECT queries obviously. Any insert or update invalidates the cache so you can't get stale data from cache. Low memory prunes indicates how many queries are being removed to make room for new queries that are being cached and the cache prune strategy is LRU (least recently used) so that queries that are seen the most frequently are the ones that get priority for caching. It wouldn't make much sense to cache a query that is rare v. a query that is used on every page load.

-- check the settings
SHOW VARIABLES LIKE '%cache%';
-- check the status
SHOW STATUS LIKE 'Qcache%';
-- turn it on 
SET GLOBAL query_cache_size = 80000000;
-- Measure performance
-- Uncomment line 2 to check the math
SELECT FORMAT(((QCACHE_HITS / (Qcache_hits + Qcache_inserts + Qcache_not_cached))*100),2) AS query_cache_hit_rate_percentage
--, QCACHE_FREE_BLOCKS, QCACHE_FREE_MEMORY, QCACHE_HITS, QCACHE_INSERTS, QCACHE_LOWMEM_PRUNES, QCACHE_NOT_CACHED, QCACHE_QUERIES_IN_CACHE, QCACHE_TOTAL_BLOCKS
FROM (
SELECT
MAX(IF(VARIABLE_NAME = 'QCACHE_FREE_BLOCKS', VARIABLE_VALUE, NULL)) QCACHE_FREE_BLOCKS,
MAX(IF(VARIABLE_NAME = 'QCACHE_FREE_MEMORY', VARIABLE_VALUE, NULL)) QCACHE_FREE_MEMORY,
MAX(IF(VARIABLE_NAME = 'QCACHE_HITS', VARIABLE_VALUE, NULL)) QCACHE_HITS,
MAX(IF(VARIABLE_NAME = 'QCACHE_INSERTS', VARIABLE_VALUE, NULL)) QCACHE_INSERTS,
MAX(IF(VARIABLE_NAME = 'QCACHE_LOWMEM_PRUNES', VARIABLE_VALUE, NULL)) QCACHE_LOWMEM_PRUNES,
MAX(IF(VARIABLE_NAME = 'QCACHE_NOT_CACHED', VARIABLE_VALUE, NULL)) QCACHE_NOT_CACHED,
MAX(IF(VARIABLE_NAME = 'QCACHE_QUERIES_IN_CACHE', VARIABLE_VALUE, NULL)) QCACHE_QUERIES_IN_CACHE,
MAX(IF(VARIABLE_NAME = 'QCACHE_TOTAL_BLOCKS', VARIABLE_VALUE, NULL)) QCACHE_TOTAL_BLOCKS
FROM information_schema.global_status
WHERE VARIABLE_NAME LIKE 'QCACHE%'
) AS stats;

InnoDB status

Look for long-running transactions; and deadlocks

The best tuning parameters are

1. innodb_buffer_pool_size as much as you can spare after OS and MySQL
2. innodb_log_file_size at least enough for 60 minutes of log writes (because sequential writes to a log file are faster than disk)
3. innodb_io_capacity based on your disk IOPS

SHOW ENGINE INNODB STATUS\G;