MySQL Geo Spatial Query is very slow although index is used

MySQLperformancequery-performancespatial

I need to fetch records from a InnoDb Table by distance (must not be exactly) and sort by distance.
The table has 10 million records.

My best time is so far 8 sec (3 sec without order by distance), which make this not usable. How I could improve this?

I have a point column defined as SRID 4326.
I'm using MySQL 8.0.12.

SELECT mp.hash_id, 
ROUND(ST_Distance(ST_SRID(POINT(8.53955, 47.37706), 4326), mp.geo_pt), 2) AS distance
  FROM member_profile mp 
  WHERE
    MBRCONTAINS(ST_GeomFromText(
      CONCAT('POLYGON((', ST_X(POINT (8.53955, 47.37706)) - 0.43415340086831, ' ',
        ST_Y(POINT (8.53955, 47.37706)) - 0.43415340086831, ',',
        ST_X(POINT (8.53955, 47.37706)) + 0.43415340086831, ' ',
        ST_Y(POINT (8.53955, 47.37706)) - 0.43415340086831, ',',
        ST_X(POINT (8.53955, 47.37706)) + 0.43415340086831, ' ',
        ST_Y(POINT (8.53955, 47.37706)) + 0.43415340086831, ',',
        ST_X(POINT (8.53955, 47.37706)) - 0.43415340086831, ' ',
        ST_Y(POINT (8.53955, 47.37706)) + 0.43415340086831, ',',
        ST_X(POINT (8.53955, 47.37706)) - 0.43415340086831, ' ',
        ST_Y(POINT (8.53955, 47.37706)) - 0.43415340086831, ')) ')
           , 4326), geo_pt)
-- ST_Distance(ST_GeomFromText('POINT (8.53955 47.37706)', 4326), mp.geo_pt) <= 25000 -- need 16 sec
-- order by distance -- need 8 sec with MBRContains, 100 sec with ST_Distance
LIMIT 50;

A spatial Index was created:

CREATE SPATIAL INDEX geo_pt_index ON mp (geo_pt);

EXPLAIN shows me that my geo_pt Index is used.

my.cnf

[mysqld]
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
symbolic-links=0
log-error=/var/log/mysqld.log
pid-file=/var/run/mysqld/mysqld.pid
innodb_buffer_pool_size = 12G
innodb_log_file_size = 512M
innodb_flush_log_at_trx_commit = 2
innodb_flush_method = O_DIRECT
key_buffer_size = 1G
secure-file-priv = ""

This Server is only allocated for this database, no load on it (except when I execute a Query). There is no IOPS bottleneck.
innodb_buffer_pool_size is sized to hold the whole dataset in Memory.

Server Instance has 16 GB Memory, uses fast NVMe SSD (There is no IOPS bottleneck). The Server only hosts this one Database and has except the Querys no load. 30% of Disk is used.

SHOW GLOBAL STATUS Output: https://pastebin.com/EMeNL8yT

SHOW GLOBAL VARIABLES Output: https://pastebin.com/yxzYn10E

MySQL Tuner Output: https://pastebin.com/NRWFQDMQ

I have today updated from 8.0.11 to 8.0.12 but followed mostly all related proposal of earlier MySQL Tuner Recommendations. The MySQL update was done regarding some fixed Bug with Spatial Search before the speed was the same.

SHOW WARNINGS (after Query execute):

Level,Code,Message
Note,1003,/* select#1 */ select `***`.`mp`.`member_id` AS `member_id`,round(st_distance(st_pointfromtext('POINT(8.53955 47.37706)',4326),`***`.`mp`.`geo_pt`),2) AS `distance` from `***`.`member_profile` `mp` where mbrcontains(<cache>(st_geomfromtext(concat('POLYGON((',(st_x(point(8.53955,47.37706)) - 0.43415340086831),' ',(st_y(point(8.53955,47.37706)) - 0.43415340086831),',',(st_x(point(8.53955,47.37706)) + 0.43415340086831),' ',(st_y(point(8.53955,47.37706)) - 0.43415340086831),',',(st_x(point(8.53955,47.37706)) + 0.43415340086831),' ',(st_y(point(8.53955,47.37706)) + 0.43415340086831),',',(st_x(point(8.53955,47.37706)) - 0.43415340086831),' ',(st_y(point(8.53955,47.37706)) + 0.43415340086831),',',(st_x(point(8.53955,47.37706)) - 0.43415340086831),' ',(st_y(point(8.53955,47.37706)) - 0.43415340086831),')) '),4326)),`***`.`mp`.`geo_pt`) order by `distance` limit 50

EXPLAIN: 

id,select_type,table,partitions,type,possible_keys,key,
key_len,ref,rows,filtered,Extra
1,SIMPLE,mp,\N,range,geo_pt_index,geo_pt_index,34,\N,23,100.00,Using where; Using filesort

CREATE TABLE:

CREATE TABLE `member_profile` (
  `member_id` bigint(20) NOT NULL AUTO_INCREMENT,
  `hash_id` varchar(32)
        CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci DEFAULT NULL,
  `geo_pt` point NOT NULL /*!80003 SRID 4326 */,
  PRIMARY KEY (`member_id`),
  UNIQUE KEY `hash_id` (`hash_id`),
  SPATIAL KEY `geo_pt_index` (`geo_pt`)
) ENGINE=InnoDB AUTO_INCREMENT=10498210
            DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci

SHOW INDEX FROM:

Table,Non_unique,Key_name,Seq_in_index,Column_name,Collation,
Cardinality,Sub_part,
Packed,Null,Index_type,Comment,Index_comment,Visible

member_profile,0,PRIMARY,1,member_id,A,9936492,\N,\N,,BTREE,,,YES
member_profile,0,hash_id,1,hash_id,A,9936492,\N,\N,YES,BTREE,,,YES
member_profile,1,geo_pt_index,1,geo_pt,A,9936492,32,\N,,SPATIAL,,,YES

Best Answer

"I have a point column defined as SRID 4326. I'm using MySQL 8.0.12."

I have a similar problem and changing the SRID to 0 improves performance significantly. I don't know if the side effect are unbearable for you, but at least you should try! Dont forget the other order of the lat and lon if you do that ;)

KR Pete

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