MySQL NOT IN Query much slower after Mysql Upgrade

Question

It's a very simple query:

SELECT * FROM temp_company WHERE number NOT IN (SELECT number FROM company)

It was taking 15 minutes before but that was on a Mysql installation with too low buffer pool size and 15 minutes was OK because this is a monthly task. I upgraded to Mysql 5.7 (from something like 5.1 or 5.2) as the original install was 32bit and I couldn't up the innodb buffer pool size to the minimum required 10gb for this DB (I've set it to 16GB on a machine with 32GB RAM. I've now gone to run this query a month later and it was still running after 6 hours.

The EXPLAIN for the above is:

id | select_type        | table        | partitions | type  | possible_keys | key    | key_len | ref | rows    | filtered | Extra       |
1  | PRIMARY            | temp_company |            | ALL   |               |        |         |     | 3226661 | 100.00   | Using where |
2  | DEPENDENT SUBQUERY | company      |            | index | number        | number | 33      |     | 3383517 | 100.00   | Using where |

The PRIMARY index on company and temp_company is id, but number is what they match on and that is a KEY in both but does the above suggest it's not using the index for the temp_company table?

The other logical query I thought to try was:

EXPLAIN SELECT tc.* FROM temp_company tc
LEFT JOIN company c on c.number = tc.number
WHERE c.number IS NULL

This is just as slow and the EXPLAIN is:

id | select_type | table | partitions | type  | possible_keys | key    | key_len | ref | rows    | filtered | Extra                                                           |
1  | SIMPLE      | tc    |            | ALL   |               |        |         |     | 3226661 | 100.00   |                                                                 |
2  | SIMPLE      | c     |            | index | number        | number | 33      |     | 3383517 | 100.00   | Using where; Ising index; Using join buffer (block nested loop) |

Any help would be much appreciated. Perhaps Mysql changed the way it finds indexes?

**UPDATE 1-------

SHOW CREATE's: company

   CREATE TABLE `company` (
  `id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `count_telephone` mediumint(8) unsigned NOT NULL,
  `count_fax` mediumint(8) unsigned NOT NULL,
  `count_person` mediumint(8) unsigned NOT NULL,
  `person_date` date DEFAULT NULL COMMENT 'Date the company_person relation was updated',
  `count_email_address` mediumint(8) unsigned NOT NULL,
  `name` varchar(255) DEFAULT NULL,
  `url` varchar(255) DEFAULT NULL,
  `url_date` date DEFAULT NULL,
  `url_status` smallint(5) unsigned NOT NULL DEFAULT '0' COMMENT 'Failure count for crawling the URL',
  `website_stamp_start` int(10) unsigned DEFAULT NULL,
  `website_stamp` int(10) unsigned DEFAULT NULL,
  `ch_url` varchar(255) DEFAULT NULL COMMENT 'Companies house URL',
  `keywords_stamp_start` int(10) unsigned DEFAULT NULL,
  `keywords_stamp` int(11) DEFAULT NULL,
  `number` varchar(30) CHARACTER SET ascii COLLATE ascii_bin DEFAULT NULL,
  `category` varchar(255) DEFAULT NULL,
  `status` varchar(255) DEFAULT NULL,
  `status_date` date DEFAULT NULL COMMENT 'Date the status field was updated',
  `country_of_origin` varchar(80) DEFAULT NULL,
  `dissolution_date` date DEFAULT NULL,
  `incorporation_date` date DEFAULT NULL,
  `account_ref_day` smallint(5) unsigned DEFAULT NULL,
  `account_ref_month` smallint(5) unsigned DEFAULT NULL,
  `account_next_due_date` date DEFAULT NULL,
  `account_last_made_up_date` date DEFAULT NULL,
  `account_category` varchar(255) DEFAULT NULL,
  `returns_next_due_date` date DEFAULT NULL,
  `returns_last_made_up_date` date DEFAULT NULL,
  `mortgages_num_charges` smallint(5) unsigned DEFAULT NULL,
  `mortgages_num_outstanding` smallint(5) unsigned DEFAULT NULL,
  `mortgages_num_part_satisfied` smallint(5) unsigned DEFAULT NULL,
  `mortgages_num_satisfied` smallint(5) unsigned DEFAULT NULL,
  `partnerships_num_gen_partners` smallint(5) unsigned DEFAULT NULL,
  `partnerships_num_lim_partners` smallint(5) unsigned DEFAULT NULL,
  `ext_name` varchar(255) DEFAULT NULL,
  `turnover` decimal(18,2) DEFAULT NULL,
  `turnover_date` date DEFAULT NULL,
  `trade_debtors` decimal(18,2) DEFAULT NULL,
  `other_debtors` decimal(18,2) DEFAULT NULL,
  `debtors_date` date DEFAULT NULL,
  `real_turnover_band` int(11) DEFAULT NULL,
  `est_turnover_band` int(11) DEFAULT NULL,
  `ext_address_date` date DEFAULT NULL,
  `care_of` varchar(255) DEFAULT NULL,
  `po_box` varchar(60) DEFAULT NULL,
  `line_1` varchar(255) DEFAULT NULL,
  `line_2` varchar(255) DEFAULT NULL,
  `town` varchar(60) DEFAULT NULL,
  `county` varchar(60) DEFAULT NULL,
  `country` varchar(60) DEFAULT NULL,
  `post_code` varchar(20) DEFAULT NULL,
  `DirScrapeID` int(10) DEFAULT NULL,
  PRIMARY KEY (`id`),
  KEY `homepage_keywords_stamp` (`keywords_stamp`),
  KEY `number` (`number`),
  KEY `url` (`url`),
  KEY `town` (`town`),
  KEY `county` (`county`),
  KEY `post_code` (`post_code`),
  KEY `name` (`name`),
  KEY `website_stamp` (`website_stamp`),
  KEY `website_stamp_start` (`website_stamp_start`),
  KEY `keywords_stamp_start` (`keywords_stamp_start`),
  KEY `turnover` (`turnover`),
  KEY `status` (`status`),
  KEY `category` (`category`),
  KEY `incorporation_date` (`incorporation_date`),
  KEY `real_turnover_band` (`real_turnover_band`),
  KEY `est_turnover_band` (`est_turnover_band`)
) ENGINE=InnoDB AUTO_INCREMENT=3706459 DEFAULT CHARSET=utf8

temp_company:

CREATE TABLE `temp_company` (
  `id` int(10) unsigned NOT NULL AUTO_INCREMENT,
  `name` varchar(255) DEFAULT NULL,
  `url` varchar(255) DEFAULT NULL,
  `ch_url` varchar(255) DEFAULT NULL,
  `number` varchar(30) DEFAULT NULL,
  `category` varchar(255) DEFAULT NULL,
  `status` varchar(255) DEFAULT NULL,
  `country_of_origin` varchar(80) DEFAULT NULL,
  `dissolution_date` date DEFAULT NULL,
  `incorporation_date` date DEFAULT NULL,
  `account_ref_day` smallint(5) unsigned DEFAULT NULL,
  `account_ref_month` smallint(5) unsigned DEFAULT NULL,
  `account_next_due_date` date DEFAULT NULL,
  `account_last_made_up_date` date DEFAULT NULL,
  `account_category` varchar(255) DEFAULT NULL,
  `returns_next_due_date` date DEFAULT NULL,
  `returns_last_made_up_date` date DEFAULT NULL,
  `mortgages_num_charges` smallint(5) unsigned DEFAULT NULL,
  `mortgages_num_outstanding` smallint(5) unsigned DEFAULT NULL,
  `mortgages_num_part_satisfied` smallint(5) unsigned DEFAULT NULL,
  `mortgages_num_satisfied` smallint(5) unsigned DEFAULT NULL,
  `partnerships_num_gen_partners` smallint(5) unsigned DEFAULT NULL,
  `partnerships_num_lim_partners` smallint(5) unsigned DEFAULT NULL,
  `ext_name` varchar(255) DEFAULT NULL,
  `turnover` decimal(18,2) DEFAULT NULL,
  `turnover_date` date DEFAULT NULL,
  `trade_debtors` decimal(18,2) DEFAULT NULL,
  `other_debtors` decimal(18,2) DEFAULT NULL,
  `debtors_date` date DEFAULT NULL,
  `real_turnover_band` int(11) DEFAULT NULL,
  `est_turnover_band` int(11) DEFAULT NULL,
  `ext_address_date` date DEFAULT NULL,
  `care_of` varchar(255) DEFAULT NULL,
  `po_box` varchar(60) DEFAULT NULL,
  `line_1` varchar(255) DEFAULT NULL,
  `line_2` varchar(255) DEFAULT NULL,
  `town` varchar(60) DEFAULT NULL,
  `county` varchar(60) DEFAULT NULL,
  `country` varchar(60) DEFAULT NULL,
  `post_code` varchar(20) DEFAULT NULL,
  `sic_code` varchar(10) DEFAULT NULL,
  `DirScrapeID` int(10) DEFAULT NULL,
  PRIMARY KEY (`id`),
  KEY `number` (`number`),
  KEY `status` (`status`),
  KEY `name` (`name`),
  KEY `sic_code` (`sic_code`)
) ENGINE=InnoDB AUTO_INCREMENT=3297833 DEFAULT CHARSET=utf8

UPDATE 2: Profile of the query (with limit 5)

+-------------------------------+----------+
| Status                        | Duration |
+-------------------------------+----------+
| executing                     | 0.000001 |
| Sending data                  | 0.000112 |
| executing                     | 0.000001 |
| Sending data                  | 0.000111 |
| executing                     | 0.000001 |
| Sending data                  | 0.000110 |
| executing                     | 0.000001 |
| Sending data                  | 0.000110 |
| executing                     | 0.000001 |
| Sending data                  | 0.000110 |
| executing                     | 0.000001 |
| Sending data                  | 0.000111 |
| executing                     | 0.000001 |
| Sending data                  | 0.000111 |
| executing                     | 0.000001 |
| Sending data                  | 0.000112 |
| executing                     | 0.000001 |
| Sending data                  | 0.000112 |
| executing                     | 0.000001 |
| Sending data                  | 0.000112 |
| executing                     | 0.000001 |
| Sending data                  | 0.000112 |
| executing                     | 0.000001 |
| Sending data                  | 0.000112 |
| executing                     | 0.000001 |
| Sending data                  | 0.000112 |
| executing                     | 0.000001 |
| Sending data                  | 0.000113 |
| executing                     | 0.000001 |
| Sending data                  | 0.000114 |
| executing                     | 0.000001 |
| Sending data                  | 0.000114 |
| executing                     | 0.000001 |
| Sending data                  | 0.000114 |
| executing                     | 0.000001 |
| Sending data                  | 0.000115 |
| executing                     | 0.000001 |
| Sending data                  | 0.000116 |
| executing                     | 0.000001 |
| Sending data                  | 0.000115 |
| executing                     | 0.000001 |
| Sending data                  | 0.000115 |
| executing                     | 0.000001 |
| Sending data                  | 0.000116 |
| executing                     | 0.000001 |
| Sending data                  | 0.000116 |
| executing                     | 0.000001 |
| Sending data                  | 0.000115 |
| executing                     | 0.000001 |
| Sending data                  | 0.000115 |
| executing                     | 0.000001 |
| Sending data                  | 0.000116 |
| executing                     | 0.000001 |
| Sending data                  | 0.000116 |
| executing                     | 0.000001 |
| Sending data                  | 0.000117 |
| executing                     | 0.000001 |
| Sending data                  | 0.000117 |
| executing                     | 0.000001 |
| Sending data                  | 0.000117 |
| executing                     | 0.000001 |
| Sending data                  | 0.000118 |
| executing                     | 0.000001 |
| Sending data                  | 0.000118 |
| executing                     | 0.000001 |
| Sending data                  | 0.000118 |
| executing                     | 0.000001 |
| Sending data                  | 0.000118 |
| executing                     | 0.000001 |
| Sending data                  | 0.000118 |
| executing                     | 0.000001 |
| Sending data                  | 0.000118 |
| executing                     | 0.000001 |
| Sending data                  | 0.000120 |
| executing                     | 0.000001 |
| Sending data                  | 0.000120 |
| executing                     | 0.000001 |
| Sending data                  | 0.000121 |
| executing                     | 0.000001 |
| Sending data                  | 0.000123 |
| executing                     | 0.000001 |
| Sending data                  | 0.000121 |
| executing                     | 0.000001 |
| Sending data                  | 0.000120 |
| executing                     | 0.000001 |
| Sending data                  | 0.000121 |
| executing                     | 0.000001 |
| Sending data                  | 0.000121 |
| executing                     | 0.000001 |
| Sending data                  | 0.000121 |
| executing                     | 0.000001 |
| Sending data                  | 0.000122 |
| executing                     | 0.000001 |
| Sending data                  | 0.000123 |
| executing                     | 0.000001 |
| Sending data                  | 0.000124 |
| executing                     | 0.000001 |
| Sending data                  | 1.063880 |
| end                           | 0.000009 |
| query end                     | 0.000008 |
| closing tables                | 0.000009 |
| freeing items                 | 0.000007 |
| Waiting for query cache lock  | 0.000002 |
| freeing items                 | 0.000062 |
| Waiting for query cache lock  | 0.000002 |
| freeing items                 | 0.000001 |
| storing result in query cache | 0.000002 |
| cleaning up                   | 0.000028 |
+-------------------------------+----------+

Answer 1

It turned out that the problem was that the temp_company table number field did not have ascii_bin set as its Collation like the Company table.

As explained on the MySQL forums (http://forums.mysql.com/read.php?24,603620,603732#msg-603732), varchar fields with different collation or character sets are regarded as being of different type and thus an index could not be used between them.

The remedy was to set the same collation on the number field of the temp_company table. The query then took 3.3 seconds (and 2.7 seconds using the left join method).

Answer 2

I don't know why it's suddenly running more slowly, but I recommend converting to a join, which should perform better:

SELECT t.*
FROM temp_company t
LEFT JOIN company c ON c.number = t.number
WHERE c.number is null

This is a fairly standard way of tackling a not in (...) via a join, and works because outer joins that don't match have nulls in the joined table's columns.

Answer 3

MySQL is probably unoptimized now, unlike before. You should check out the config files and have your sys admin optimize it. Also, there might be an underlying issue with the web applications you are running and MySQL 5, such as some older plugins not working right.