Figured it out in case someone else has this issues
innodb_log_file_size = 256M is causing the error because the sites is smaller than the current log file.
[URL=“MySQL Consulting and NoSQL Consulting: MySQL DBA: Increase innodb_log_file_size: the proper way”]http://mysqldatabaseadministration.blogspot.com/2007/01/increase-innodblogfilesize-proper-way.html[/URL=“http://mysqldatabaseadministration.blogspot.com/2007/01/increase-innodblogfilesize-proper-way.html”]
I keep trying to build new my.cnf from Percona tools and every time myql fails to restart.
Starting MySQL (Percona Server).The server quit without updating PID file (/mysql//server.domain.com.pid). [FAILED]
Config from the tool
Generated by Percona Configuration Wizard ([URL=“http://tools.percona.com/”]http://tools.percona.com/[/URL=“http://tools.percona.com/”]) version REL5-20120208
Configuration name server generated for at 2013-04-24 03:55:30
[mysql]
CLIENT
port = 3306
socket = /mysql/mysql.sock
[mysqld]
GENERAL
user = mysql
default_storage_engine = InnoDB
socket = /mysql/mysql.sock
pid_file = /mysql/mysql.pid
MyISAM
key_buffer_size = 32M
myisam_recover = FORCE,BACKUP
SAFETY
max_allowed_packet = 16M
max_connect_errors = 1000000
skip_name_resolve
sql_mode = STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_ AUTO_CREATE_USER,NO_AUTO_VALUE_ON_ZERO,NO_ENGINE_S UBSTITUTION,NO_ZERO_DATE,NO_ZERO_IN_DATE,ONLY_FULL _GROUP_BY
sysdate_is_now = 1
innodb = FORCE
innodb_strict_mode = 1
DATA STORAGE
datadir = /mysql/
BINARY LOGGING
log_bin = /mysql/mysql-bin
expire_logs_days = 14
sync_binlog = 1
CACHES AND LIMITS
tmp_table_size = 32M
max_heap_table_size = 32M
query_cache_type = 0
query_cache_size = 0
max_connections = 500
thread_cache_size = 50
open_files_limit = 65535
table_definition_cache = 4096
table_open_cache = 10240
INNODB
innodb_flush_method = O_DIRECT
innodb_log_files_in_group = 2
innodb_log_file_size = 256M
innodb_flush_log_at_trx_commit = 2
innodb_file_per_table = 1
innodb_buffer_pool_size = 6G
LOGGING
log_error = /mysql/mysql-error.log
log_queries_not_using_indexes = 1
slow_query_log = 1
slow_query_log_file = /mysql/mysql-slow.log