Похожая ситуация описана здесь: http://bugs.mysql.com/bug.php?id=42041. В конце есть описание изменений в настройках MySQL, которые вроде как помогли:
Not sure if this helps, but we seemed to solve the issue on our servers by changing some db settings.
table_open_cache 128=>16384
table_definition_cache 1024=>16384
tmp_table_size 32M=>64M
join_buffer_size 256k=>512k
Not sure if this helps, but we seemed to solve the issue on our servers by changing some db settings.
table_open_cache 128=>16384
table_definition_cache 1024=>16384
tmp_table_size 32M=>64M
join_buffer_size 256k=>512k