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I have a BP site with ~335,000 members. Updated to WP 1.9 today with no problem. On a clone of the real server, I’ve updated to BP 2.0, and it is not working. With all other plugins disabled, whenever BP is active, I can’t get into the WP admin. Front-end seems fine.

When I try to access wp-admin, looking at the MySQL slow query log, I see a whole bunch of ridiculously long queries trying to take place. I suppose at some point, it is just timing out, and I get a white screen instead of any admin. It times out after ~10 seconds or more.
Some of the queries are examining millions of rows.

Pasting here some of the (slow-logged) queries that happen when I go in to wp-admin:

# Time: 140417 22:27:15
# User@Host: digitaljustice[digitaljustice] @ localhost []  Id:    61
# Query_time: 2.940681  Lock_time: 0.000449 Rows_sent: 0  Rows_examined: 508756
SET timestamp=1397788035;
INSERT INTO wp_bp_activity (<code>user_id</code>, <code>component</code>, <code>type</code>, <code>action</code>, <code>content</code>, <code>primary_link</code>, <code>item_id</code>, <code></code>
date_reco
                  SELECT user_id, 'members' as component, 'last_activity' as type, '' as action, '' as content, '' as
                  FROM wp_usermeta
                  WHERE
                    meta_key = 'last_activity'
                    AND
                    user_id NOT IN (
                      SELECT user_id
                      FROM wp_bp_activity
                      WHERE component = 'members' AND type = 'last_activity'
                    )
        );
# Time: 140417 22:27:18
# User@Host: XXXXXXXXXXXXXXXXX] @ localhost []  Id:    61
# Query_time: 0.944158  Lock_time: 0.062164 Rows_sent: 79994  Rows_examined: 313319
SET timestamp=1397788038;
SELECT * FROM wp_users WHERE ID IN (181294,78917,192535,216692,105318,198052,148003,208531,151466,147363,208714,204709

# note: the above line goes on with hundreds of thousands of user IDs!

# Time: 140417 22:27:37
# User@Host: digitaljustice[digitaljustice] @ localhost []  Id:    61
# Query_time: 9.810006  Lock_time: 0.045841 Rows_sent: 1694105  Rows_examined: 3388210
SET timestamp=1397788057;
SELECT user_id, meta_key, meta_value FROM wp_usermeta WHERE user_id IN (38731,38733,38735,38739,38740,38741,38746,3874

#the above also seems to go on with hundreds of thousands of IDs.

Tried restarting MySQL and PHP-FPM.
Server is a 8GB VPS with 8 cores and SSD, Ubuntu Server 10.04 LTS.
MySQL is Percona: mysql Ver 14.14 Distrib 5.6.12
PHP is 5.3.8
Don’t think it’s relevant, but the webserver is current stable version of nginx.
I tried getting rid of my bp-custom.php in case I was hooking into something that doesn’t work in 2.0, but it had no effect.

Hope someone can help.