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Has anyone here encountered such scenario before where and update statement took longer time to run when innodb_buffer_pool_size is bigger.

I've run a few tests using the same statements on around 2500 rows of data on a single table, here are the data that I manage to get.

innodb_buffer_pool_size = 16M Time taken for SQL to complete - 1 min 25 sec

innodb_buffer_pool_size = 1G Time taken for SQL to complete - 3 min 45 sec

innodb_buffer_pool_size = 2G Time taken for SQL to complete - 4 min 53 sec

I'm running MariaDB 5.5 on an AWS EC2 instance with m1.large size. Does anyone has any idea how could this happened?

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Is the increased buffer pool size causing your insurance to start using swap space? That would be my first suspicion. – Michael - sqlbot Apr 9 '14 at 12:19
My server has 7GB of RAM and has no other service running except for MariaDB. And I don't have any swap configured for this particular instance. – dctw Apr 10 '14 at 15:24

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