innodb_flush_method=O_DIRECT
innodb_file_per_table
innodb-flush-log-at-trx-commit = 2

# number of cpus * number of disks * 2
#innodb_thread_concurrency=16
_____
Lowering the value of swappiness may help mysql

# default 60
echo '50' > /proc/sys/vm/swappiness

Make the change permanent:
/etc/sysctrl.conf
vm.swappiness = 50

# innodb basic settings
innodb_buffer_pool_size=1G
innodb_log_file_size=512M

# MyISAM only cnf setting
user=root
skip-innodb
default-storage-engine=myisam
bulk_insert_buffer_size=1G
key-buffer=1G

# increase default 2 GB on 32 bit OS
myisam_max_sort_file_size=40G
myisam_sort_buffer_size=512M

# make sure temp directory has sufficient space
# and mysql has permission to write
tmpdir=/