Very poor insert performance MySQL / Percona Server
OBSERVATION #1

Since your buffer pool is 6G (6144M), the innodb_log_file_size should be 1536M (25% of 6G)

OBSERVATION #2

You have sync_binlog set to 1. This provides the safest ACID compliant setup. It can also slow things down dramatically. You say it seems as though its writing each row 1 at a time to disk. That's the case because each completed DML (INSERT, UPDATE, DELETE) and DDL (ALTER TABLE) statement gets written to the binary logs. The default for sync_binlog is 0. That let's the OS be responsible for flush binary log changes to disk.

OBSERVATION #3

You have innodb_io_capacity set at 10000. That's really 10000 IOPs you are expecting of mysql. Try lowering it.

There are some things to do in this respect


When it comes to sync_binlog

Comment it out of my.cnf
Set sync_binlog to 100 or 200 to pace the flushing of binary logs

You should make sure data disk has a battery-backed cache (with a good battery)


RECOMMENDATION

STEP 01) Set these options in my.cnf

[mysqld]
innodb_fast_shutdown = 0
innodb_log_file_size = 1536M
sync_binlog = ( you choose 0 or 100 )


STEP 02) Remove innodb_io_capacity. Let it be set to default.

STEP 03) Run this command in mysql

mysql&gt; SET GLOBAL innodb_fast_shutdown = 0;


STEP 04) Apply settings

cd /mnt/Storage/mysql
service mysql stop
mv ib_logfile0 ib_logfile0.bak
mv ib_logfile2 ib_logfile1.bak
service mysql start


This should speed things up