MySQL cpu at 400% on c5.xlarge box

Question

Box is running only mysql and CPU is at 400% constantly. I can't seem to find anything that would be causing it. I've changed a few values in my.cnf based on some research, but had no luck reducing the CPU usage.

my.cnf as follows:

[mysqld]
basedir=/opt/bitnami/mysql
datadir="/opt/bitnami/mysql/data"
port=3306
socket=/opt/bitnami/mysql/tmp/mysql.sock
tmpdir=/opt/bitnami/mysql/tmp
#bind-address=127.0.0.1
skip-name-resolve=1
skip-external-locking
key_buffer_size = 64M
table_open_cache = 256
sort_buffer_size = 1M
read_buffer_size = 1M
read_rnd_buffer_size = 256K
myisam_sort_buffer_size = 64M
thread_cache_size = 40
join_buffer_size = 1M
query_cache_limit=0
innodb_lru_scan_depth=100
max_connections = 100
open_files_limit=30000
# Try number of CPU's x 2 for thread_concurrency
thread_concurrency = 16

Answer 1

Remove these for a start, they are almost certainly counterproductive:

table_open_cache = 256
join_buffer_size = 1M
thread_concurrency = 16

There is also a conspicuous absence of innodb_buffer_pool_size being set.

Configuration isn't going to be the root cause of your problem, though - you need to identify what queries are eating all of your CPU and address those specifically, either by rewriting them or by making sure that appropriate indexes for them exist.