I've been working for some weeks now to optimize a client's MySQL databases. I consider myself an apprentice MySQL DBA (e.g. there's much room for me to improve :P ), and I've found the process to be difficult. Although there is a whole lot of information about what to do and how -- some blog posts out there are absolutely invaluable -- the settings are not always straightforward to understand, since they often have many impacts and to correctly modify them, you need to understand what they do and how they change things under the hood for MySQL.
After bumping table_cache and tmp_table_size / max_heap_table_size up, I was left with one weirdness: the table cache is marked as being nearly empty (good) but there were a lot of query cache prunes (bad). This situation actually makes the cache add latency for most cases (in other words, it slows down tremendously your database).
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