Re: Terrible performance of a specific query with lots of connections

[Rick James]

Trouble with open tables? Increase the limits -- esp. open_files_limit. If the OS is restricting you, then increase its per-process limit.

Split this into two DELETEs:

DELETE FROM document_references
  WHERE referenced_document_id = '118084217'
                OR document_id = '118084217'

Why? MySQL did not used to be able to use two indexes in a single query (which this would need). What version are you running? Also, you could perhaps get a good clue via

EXPLAIN SELECT *
    FROM document_references
      WHERE referenced_document_id = '118084217'
                    OR document_id = '118084217' ;

In any case need something like these on document_references:
INDEX(referenced_document_id) and
INDEX(document_id)

To assist in analyzing slow SELECTs, please provide
* SHOW CREATE TABLE tbl\G -- engine, indexes
* SHOW TABLE STATUS LIKE 'tbl'\G -- sizes
* EXPLAIN SELECT ...\G -- clues of inefficiencies
* SHOW VARIABLES LIKE '%buffer%'; -- cache size
and surround them with [ code ] and [ / code ]

Please do the EXPLAIN on any SELECTs that may be running when the things are slow. What do you see running? SHOW FULL PROCESSLIST.