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Recently I bought new database server and installed percona mysql server 5.5.32-31 and transferred my /var/lib/mysql directory from old database server having Percona mysql server 5.5.28 to new server. My both servers configurations files are same. The new server has double storage and thrice Ram than old one. I am getting slow queries on new database server.

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What values have you set for: innodb_buffer_pool_size, innodb_write_io_threads, innodb_* ? We can't help you without this. –  cerd Feb 11 at 4:35

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