After I upgrade to moodle 1.9+, I found our website stalls every morning. And when I check mysql-slow log, I found this:

# Time: 090410 9:33:05
# User@Host: moodle[moodle] @ localhost []
# Query_time: 26566.176123 Lock_time: 0.000264 Rows_sent: 0 Rows_examined: 3633693755
use moodle;
SET timestamp=1239327185;
UPDATE mdl_stats_daily
                   SET stat2 = (SELECT COUNT(DISTINCT ra.userid)
                                  FROM mdl_role_assignments ra JOIN mdl_context ctx
                  ON ctx.id = ra.contextid
             CROSS JOIN mdl_course c
             JOIN mdl_role_capabilities rc
                  ON rc.roleid = ra.roleid LEFT OUTER JOIN mdl_course_categories cc1
                            ON cc1.id = c.category
                                 WHERE ra.roleid = mdl_stats_daily.roleid AND
                                       c.id = mdl_stats_daily.courseid AND
                                       ((rc.capability = 'moodle/course:view' )
               AND rc.permission = 1 AND rc.contextid = 1
               AND (ctx.contextlevel = 10
                    OR (c.id = ctx.instanceid AND ctx.contextlevel = 50) OR (cc1.id = ctx.instanceid AND ctx.contextlevel = 40))) AND
                                       EXISTS (SELECT 'x'
                                                 FROM mdl_log l
                                                WHERE l.course = mdl_stats_daily.courseid AND
                                                      l.userid = ra.userid AND l.time >= 1239033600 AND l.time < 1239120000))
                 WHERE mdl_stats_daily.stattype = 'enrolments' AND
                       mdl_stats_daily.timeend = 1239120000 AND
                       mdl_stats_daily.courseid IN
                          (SELECT DISTINCT l.course
                             FROM mdl_log l
                            WHERE l.time >= 1239033600 AND l.time < 1239120000);

Is one of my table too big or it's missing some index? I have emptied log table before I upgrade because updating log uses too many time.