Create Index is Dead slow after upgrading percona from 5.5.36-34.2 to 5.6.32-78

Hi All,

We have upgraded our percona servers from 5.5.36-34.2 to 5.6.32-78 version.

We use this database for creating caches daily, We truncate the table drop the secondary indexes on the table and load data into them and recreate those secondary indexes back.
There is one tables whose size is around 66GB and two secondary indexes of total size 52 GB.
In 5.5 version create index used to take about 1.5 hours but in 5.6 it is taking around 14 hours.
Ram on the server is 140GB and innodb_buffer_pool is 100GB.
I already disabled the performance schema thinking that it may be an overhead on memory.

Still the index creation is dead slow, any suggestions would be helpful to improve the index creation speed…

Any solution for this issue? I use MySQL 5.7 and index creation is awful slow. Thanks