Mysql – Query running slow on script and producing error 500 when run in phptheadmin

First, each time you UPDATE the status column, you are having to update the index as well (source). Evaluate your indexing to see if you really need the index on the status column. My guess is no, since it has an extremely low cardinality and MySQL probably won't use it anyway.

If you ignore me and think you do need it, follow the advice in the article to drop the index before your loop and re-add it after you're done.

Here are some other things you might do if that doesn't help:

• You are taking all the columns from the data but only using number. Don't do a SELECT *, but instead a SELECT number. That won't help your writes, but it is a good performance practice. Only select the columns you're using.

• Your number index isn't getting used at all. This means it is not unique enough to be useful for updating. (Slight tangent: how many rows does a single UPDATE affect?) I would drop it, or at least add it to process index.

• It looks like process is unique enough for MySQL to whittle the amount of rows down to 16k, instead of 1 million. In light of this, I would add AND process=x to your update statement (I'm assuming you know process from the original SELECT statement):

  -- FAILED--
  UPDATE data SET status = 2, error='$error' WHERE process=X AND number = $data['number']
  
  -- SUCCESS --
  UPDATE data SET status = 1 WHERE process=X AND number = $data['number']
  

A hint about unnecessary indexes in InnoDB. InnoDB is using a hidden 'primary key' (since you don't have one defined) and is using that when it writes the indexes. So for each Index you're using, you add the size of the index + the size of the hidden primary key to the data file. If you're not using the index (or MySQL can't use it), you are wasting space and adding overhead each time you insert a new number (same for status, as discussed earlier)

If you only want the 100 rows (with offset 100), you don't need a subquery. Use what you name B, adding the username:

SELECT username, points
FROM users
WHERE points <> 0
ORDER BY points DESC
  LIMIT $start, $limit ;

If you have an index on (points, username), it will be pretty fast (at least when the offset is not huge).

The query you have is bringing more than 100 rows because, as @Phil pointed, you are using a subquery. You are joining table A (which probably has thousands or millions of rows) with the (derived) table B (which has 100 rows at maximum). But the joining is done using points which is not unique on the table. So, for some rows of table B, there are more than one rows from A joined.