If the data between the two data sources is supposed to be exactly the same then you could compute MD5 sums for each row and only dig deeper if the MD5 sums differ. You could even start by computing the MD5 sums for the files and check these - if the MD5 sums of two files is the same then the data in the files is almost certainly the same.

If there are whitespace or other non-significant differences then you'll either have to remove these differences between the two CSV files before performing the MD5 checks.

Michael