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mysqljoinoptimizationdistinctinnodb

MySQL distinct performance

When I add 'distinct' to my query, query time increases from 0.015 to over 6 seconds.

I want to join several tables, which are linked via foreign keys and get a distinct column from it:

select distinct table3.idtable3 from 
    table1
    join table2 on table1.idtable1 = table2.fkey
    join table3 on table2.idtable2 = table3.fkey
    where table1.idtable1 = 1

The distinct query takes 6 seconds which seems to me to be improvable.

With select:

duration : 0.015s / fetch:5.532s (5.760.434 rows)

Explain:

id, select_type, table, partitions, type, possible_keys, key, key_len, ref, rows, filtered, Extra
1   SIMPLE  table1      index   asd asd 137     10  10.00   Using where; Using index
1   SIMPLE  table2      ALL idtable2                200 25.00   Using where; Using join buffer (Block Nested Loop)
1   SIMPLE  table3      ref fkey_table2_table_3_idx fkey_table2_table_3_idx 138 mydb.table2.idtable2    66641   100.00

With distinct select:

duration : 6.625s / fetch:0.000s (1000 rows)

Explain:

id, select_type, table, partitions, type, possible_keys, key, key_len, ref, rows, filtered, Extra
1   SIMPLE  table1      index   asd asd 137     10  10.00   Using where; Using index; Using temporary
1   SIMPLE  table2      ALL idtable2                200 25.00   Using where; Using join buffer (Block Nested Loop)
1   SIMPLE  table3      ref fkey_table2_table_3_idx fkey_table2_table_3_idx 138 mydb.table2.idtable2    66641   100.00

Database: Database snippet

Code for testing / MCRE:

import mysql.connector
import time
import numpy as np




""" 
-- MySQL Script generated by MySQL Workbench
-- Fri Jan 17 12:19:26 2020
-- Model: New Model    Version: 1.0
-- MySQL Workbench Forward Engineering

SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0;
SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0;
SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='ONLY_FULL_GROUP_BY,STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_ENGINE_SUBSTITUTION';

-- -----------------------------------------------------
-- Schema mydb
-- -----------------------------------------------------

-- -----------------------------------------------------
-- Schema mydb
-- -----------------------------------------------------
CREATE SCHEMA IF NOT EXISTS `mydb` DEFAULT CHARACTER SET utf8 ;
USE `mydb` ;

-- -----------------------------------------------------
-- Table `mydb`.`table1`
-- -----------------------------------------------------
CREATE TABLE IF NOT EXISTS `mydb`.`table1` (
  `idtable1` VARCHAR(45) NOT NULL,
  INDEX `asd` (`idtable1` ASC) VISIBLE)
ENGINE = InnoDB;


-- -----------------------------------------------------
-- Table `mydb`.`table2`
-- -----------------------------------------------------
CREATE TABLE IF NOT EXISTS `mydb`.`table2` (
  `idtable2` VARCHAR(45) NOT NULL,
  `fkey` VARCHAR(45) NULL,
  INDEX `link_table1_table2_idx` (`fkey` ASC) INVISIBLE,
  INDEX `idtable2` (`idtable2` ASC) VISIBLE,
  CONSTRAINT `link_table1_table2`
    FOREIGN KEY (`fkey`)
    REFERENCES `mydb`.`table1` (`idtable1`)
    ON DELETE NO ACTION
    ON UPDATE NO ACTION)
ENGINE = InnoDB;


-- -----------------------------------------------------
-- Table `mydb`.`table3`
-- -----------------------------------------------------
CREATE TABLE IF NOT EXISTS `mydb`.`table3` (
  `idtable3` VARCHAR(45) NOT NULL,
  `fkey` VARCHAR(45) NULL,
  INDEX `fkey_table2_table_3_idx` (`fkey` ASC) VISIBLE,
  CONSTRAINT `fkey_table2_table_3`
    FOREIGN KEY (`fkey`)
    REFERENCES `mydb`.`table2` (`idtable2`)
    ON DELETE NO ACTION
    ON UPDATE NO ACTION)
ENGINE = InnoDB;


SET SQL_MODE=@OLD_SQL_MODE;
SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS;
SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS;


"""


def insertData():
    for i in range(2):
        num_distinct_table1_values = 5
        num_distinct_table2_values = 10
        num_distinct_table3_values = 1000

        num_entries_table1 = int(num_distinct_table1_values)
        num_entries_table2 = int(num_distinct_table2_values * 10)
        num_entries_table3 = int(num_distinct_table3_values * 300)

        random_numbers_table1_id = range(num_distinct_table1_values)

        random_numbers_table2_id = np.random.randint(num_distinct_table2_values, size=int(num_entries_table2))
        random_numbers_table2_fkey = np.random.randint(num_distinct_table1_values, size=int(num_entries_table2))

        random_numbers_table3_id = np.random.randint(num_distinct_table3_values, size=int(num_entries_table3))
        random_numbers_table3_fkey = np.random.randint(num_distinct_table2_values, size=int(num_entries_table3))

        value_string_table1 = ','.join([f"('{i_name}')" for i_name in random_numbers_table1_id])
        value_string_table2=""
        for i in range(num_entries_table2):
            value_string_table2 = value_string_table2+','.join(
                ["('{id}','{fkey}'),".format(id=random_numbers_table2_id[i], fkey=random_numbers_table2_fkey[i])])

        value_string_table3=""
        for i in range(num_entries_table3):
            value_string_table3 = value_string_table3+','.join(
                ["('{id}','{fkey}'),".format(id=random_numbers_table3_id[i], fkey=random_numbers_table3_fkey[i])])

        # fill table 1
        mySql_insert_query = f"INSERT INTO table1 (idtable1) VALUES {value_string_table1}"
        cursor.execute(mySql_insert_query)
        conn.commit()
        print("Done table 1")
        # fill table 2
        mySql_insert_query = f"INSERT INTO table2 (idtable2, fkey) VALUES {value_string_table2}"
        mySql_insert_query=mySql_insert_query[0:-1]
        cursor.execute(mySql_insert_query)
        print("Done table 2")
        # fill table 3
        mySql_insert_query = f"INSERT INTO table3 (idtable3, fkey) VALUES {value_string_table3}"
        mySql_insert_query = mySql_insert_query[0:- 1]
        cursor.execute(mySql_insert_query)
        print("Done table 3")

        conn.commit()

conn = mysql.connector.connect(user='root', password='admin', host='127.0.0.1',
                               database='mydb', raise_on_warnings=True, autocommit=False)
cursor = conn.cursor()


insertData()


conn.close()
Solution

  • Thanks for the CREATE TABLEs; you might never have gotten an Answer without them.

    • Every table should have a PRIMARY KEY. If you have a column (or combination of columns) that 'naturally' works, use that. Else use an AUTO_INCREMENT.
    • When timing queries, (1) make sure the "Query cache" is not being used, and (2) run the query twice to check for other variations in timing.
    • INDEX(fkey) is INVISIBLE, hence not used. Don't waste learning time on VISIBLE/INVISIBLE, you may never need them in your career.
    • When experimenting, be sure to have more than a few rows in each table, and have their values varying in a realistic way. Else, the Optimizer may take shortcuts that will only confuse your learning experience.

    • And...

      duration : 0.015s / fetch:5.532s (5.760.434 rows)
duration : 6.625s / fetch:0.000s (1000 rows)

    Notice how both are about 6 seconds. It is just that the time is split up differently.

    • With 6M rows and no DISTINCT, the query can pump out the data immediately, but takes a long time due to network latency.
    • With the DISTINCT, the first row cannot come out until after preforming the "de-duplication", which probably involves a "temporary" (see the EXPLAIN) and a sort. So, now all the time is involved in computing before sending the data.
    • The confusion is that you looked only at the "duration" not the sum of the two times. That is, the total time is the important one to note.
    • The DISTINCT one is slightly slower (total time) because of the extra step of collecting and sorting 5.7M rows.