I have a table with ~100,000,000 rows.  I recently discovered that I
need to start using one of the non-indexed columns in WHERE clauses.  As
expected the performance is horrid.  I decided to bite the bullet and
create an index (innodb):

mysql> show full processlist\G
*************************** 1. row ***************************
     Id: 109496
   User: root
   Host: localhost
     db: orson
Command: Query
   Time: 161079
  State: copy to tmp table
   Info: create index ix_card on game (ender)


Its already been running 2 days.  I probably need to index some more
columns in another table -- is there anything that can be done to speed
this up?

dump and re-import is impractical.

Server is decent -- 4xcpu, 16GB RAM...

Thanks,

ds

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