Mysql hand machine due to high load average and CPU
From your screenshot, it seems you are running on a machine just under 4GB of RAM. You also have ~4GB of SWAP space that MySQL could use if necessary. A rough calculation of how much memory your settings will allow is ~11.5GB. 

From mysqlcalculator.com: 


Due to the complex nature of memory allocation, this is an estimate of a worst-case scenario only.

Out of the box, your join_buffer_size is extremely large. This is a per-session thread that can be allocated multiple times in a query:


  For a complex join between several tables for which indexes are not used, multiple join buffers might be necessary.


I recommend setting this back to the default (in 5.6, that is 256kb). If you find many queries that are starting to show 'join_buffer' in the explain plan, then you should examine them for better index usage. If that fails, you might consider increasing join_buffer_size at the SESSION level for specific queries.