Upgrading the mysql server from 5.1 to 5.6?
I have a more direct way to upgrade from MySQL 5.1 to 5.6

The idea is to do the following:


Dump the mysql schema from MySQL 5.1 as pure SQL into a grants file


Use pt-show-grants
Emulate pt-show-grants

Dump the data from MySQL 5.1 without the mysql schema into a data file
Uninstall MySQL 5.1
Install MySQL 5.6
Load grants file into MySQL 5.6
Load data file into MySQL 5.6


CAPTURE DATA

MYSQL_USER=root
MYSQL_PASS=rootpassword
MYSQL_CONN="-u${MYSQL_USER} -p${MYSQL_PASS}"
SQL="SET group_concat_max_len = 1048576;"
SQL="${SQL} SELECT GROUP_CONCAT(schema_name) FROM information_schema.schemata"
SQL="${SQL} WHERE schema_name NOT IN"
SQL="${SQL} ('information_schema','mysql','performance_schema')"
DBLIST=`mysql -ANe"${SQL}" | sed 's/,/ /g'`
mysqldump ${MYSQL_CONN} --databases ${DBLIST} &gt; MySQLData.sql


CAPTURE GRANTS

Here is my personal emulation of pt-show-grants to capture SQL Grants

MYSQL_USER=root
MYSQL_PASS=rootpassword
MYSQL_CONN="-u${MYSQL_USER} -p${MYSQL_PASS}"
SQL="SELECT CONCAT('SHOW GRANTS FOR ''',user,'''@''',host,''';')"
SQL="${SQL} FROM mysql.user WHERE user&lt;&gt;''"
mysql ${MYSQL_CONN} -ANe"${SQL}"|mysql ${MYSQL_CONN} -AN|sed 's/$/;/g' &gt; MySQLGrants.sql


Here are my posts where I discussed these things before


Mar 26, 2015 : mysql upgrading from 5.1 --&gt; 5.6 do I have to do mysqldump before upgrade?
Oct 17, 2014 : Any known issues upgrading from MySQL 5.1.73 to 5.6.21?


GIVE IT A TRY !!!