Mysql bottleneck

Drupal and MySQl located in two different servers:

Configuration: Drupal server: Dual core processor, 4GB RAM
MySQL Server: Xeon Processor, 4GB RAM

MySQL Enterprise edition 5

In an exercise to Pre populate the database with 1 million records, record insertions in the tables are very slow since the requests are getting queued up in the database. Insertion is done using a special tool that records our drupal application and plays back the scripts in a loop to populate the database.

Please see the below data collected by the team.