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There numerous ways to speed up the database one way is just to optimize the my.cnf file.

If you have access to this file here are some key areas I found to speed up Civi. I especially have seen huge improvements in Importing Contacts.

For example we have three servers that are all the same specs 

Intel(R) Core(TM)2 CPU          6600  @ 2.40GHz

2 gigs of memory and standard sata drives (one may be NCQ for multi processing)

But out of the box the settings for in this case Ubuntu was somewhat slow. We installed CentOS on the third server 

and it came out of the box a bit faster but not perfect either.

They all now benefit from this mysql setup as well as additions to php settings.

in ubuntu or debian /etc/mysql/my.cnf

in centos /etc/my.cnf

key_buffer = 64M

key_buffer_size = 32M

thread_cache_size = 64

query_cache_limit = 8M

query_cache_size = 64M

query_cache_type = 1

join_buffer_size = 512K

max_connections = 150

long_query_time = 5

log-slow-queries = /var/log/mysql/mysql-slow.log

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