Add to /etc/my.cnf under [mysqld] stanza
MySQL5
log_slow_queries = /var/log/mysqld-slow.log
long_query_time = 1
long_query_time = 1
MySQL3, MySQL4
log-slow-queries=/var/log/mysqld-slow.log
set-variable = long_query_time=1
set-variable = long_query_time=1
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