Mysql is consuming xtremely high CPU above 1000%

[Eric Leung]

I have been experiencing high CPU load, caused by Mysql. I have 12 cores CPU with 64GB memory.

On checking on processlist showed mostly reads and did not appear to have unusual activites. It did not make any sense to me.

The following is my.cnf and I appreciate if anyone could advise me.

[mysqld]
skip-name-resolve
myisam_use_mmap=1

bind-address = 127.0.0.1
skip-networking
#myisam-recover = quick

innodb_file_per_table = 1
innodb_buffer_pool_size= 4G
innodb_file_per_table = 1
innodb_read_io_threads = 8
innodb_write_io_threads = 8
innodb_flush_log_at_trx_commit = 2
innodb_log_file_size = 256MB
innodb_log_buffer_size = 4MB
innodb_thread_concurrency = 4
innodb_flush_method = O_DIRECT
transaction-isolation = READ-COMMITTED

default-storage-engine=MyISAM
low_priority_updates = 1

local-infile = 0
max_connections = 400
max_user_connections = 200
key_buffer_size = 1GB
myisam_sort_buffer_size = 256M
read_buffer_size = 8M
thread_cache = 12
thread_concurrency = 8
thread_cache_size = 384
wait_timeout = 900
connect_timeout = 1200
tmp_table_size = 640M
max_heap_table_size = 640M
table_open_cache_instances = 8
table_open_cache = 13000
table_definition_cache = 13000
max_allowed_packet=268435456
net_buffer_length = 16384
max_connect_errors = 10
concurrent_insert = 2
read_rnd_buffer_size = 786432
bulk_insert_buffer_size = 8M
query_cache_limit = 12M
query_cache_size = 128M
query_cache_type = 1
query_prealloc_size = 262144
query_alloc_block_size = 65535
transaction_alloc_block_size = 8192
transaction_prealloc_size = 4096
max_write_lock_count = 1000
log-error
external-locking = FALSE
open_files_limit = 50000

max_allowed_packet = 256M

#### Per connection configuration ####
sort_buffer_size = 2M
join_buffer_size = 4M
thread_stack = 192K


#slow query
slow-query-log = 1
long-query-time = 1
log_queries_not_using_indexes = 0
min_examined_row_limit = 100

#[mysqld_safe]

[mysqldump]
quick
max_allowed_packet = 16M

[isamchk]
key_buffer = 256M
sort_buffer = 256M
read_buffer = 2M
write_buffer = 2M

[myisamchk]
key_buffer = 256M
sort_buffer = 256M
read_buffer = 2M
write_buffer = 2M

[mysqlhotcopy]
interactive-timeout