Clustered Index : Help to store table data on on pages in sorted order according to key column. So you can say it's sorted table (clustered table).
Non-Clustered Index : Store key value on IAM (Index Allocation Map) pages along with row address, like page id and row offset, that helps query to find rows on data pages.
So you can say, after creating ...
So with the updated index the First Update works fine,it uses the updated Non Clustered Index , but for second update it ask me to create a non clustered index on column3.
The updates will always work fine. Is this an update query you run very frequently?
Because in general (extra) non clustered indexes slow down inserts.
All your data is in the Clustered ...
(Long-winded, but incomplete, answer)
The graph moves up and down rather smoothly. This puzzled me. With your latest numbers, I can explain some of what is going on.
Data is written to the binlog until it exceeds max_binlog_size (128M, in your case). At that point, a new binlog file is created.
Slave(s) pull the data from the binlogs continually, and ...