How Apache Spark makes your slow MySQL queries 10x faster (or more)

Datetime:2016-08-23 02:22:30          Topic: MySQL  Spark           Share

In this blog post, we’ll discuss how to improve the performance of slow MySQL queries using Apache Spark.

Introduction

In my previous blog post, I wrote about using Apache Spark with MySQL for data analysis and showed how to transform and analyze a large volume of data (text files) with Apache Spark. Vadim also performed a benchmark comparing performance of MySQL and Spark with Parquet columnar format (using Air traffic performance data). That works great, but what if we don’t want to move our data from MySQL to another storage (i.e., columnar format), and instead want to use “ad hock” queries on top of an existing MySQL server? Apache Spark can help here as well.

TL;DR version:

Using Apache Spark on top of the existing MySQL server(s) (without the need to export or even stream data to Spark or Hadoop), we can increase query performance more than ten times. Using multiple MySQL servers (replication or Percona XtraDB Cluster) gives us an additional performance increase for some queries. You can also use the Spark cache function to cache the whole MySQL query results table.

The idea is simple: Spark can read MySQL data via JDBC and can also execute SQL queries, so we can connect it directly to MySQL and run the queries. Why is this faster? For long running (i.e., reporting or BI) queries, it can be much faster as Spark is a massively parallel system. MySQL can only use one CPU core per query, whereas Spark can use all cores on all cluster nodes. In my examples below, MySQL queries are executed inside Spark and run 5-10 times faster (on top of the same MySQL data).

In addition, Spark can add “cluster” level parallelism. In the case of MySQL replication or Percona XtraDB Cluster, Spark can split the query into a set of smaller queries (in the case of a partitioned table it will run one query per each partition for example) and run those in parallel across multiple slave servers of multiple Percona XtraDB Cluster nodes. Finally, it will use map/reduce the type of processing to aggregate the results.

I’ve used the same “ Airlines On-Time Performance ” database as in previous posts. Vadim created some scripts to download data and upload it to MySQL. You can find the scripts here: https://github.com/Percona-Lab/ontime-airline-performance. I’ve also used Apache Spark 2.0 , which was released July 26, 2016.

Apache Spark Setup

Starting Apache Spark in standalone mode is easy. To recap:

  1. Download the Apache Spark 2.0 and place it somewhere.
  2. Start master
  3. Start slave (worker) and attach it to the master
  4. Start the app (in this case spark-shell or spark-sql)

Example:

root@thor:~/spark# ./sbin/start-master.sh
less ../logs/spark-root-org.apache.spark.deploy.master.Master-1-thor.out
15/08/25 11:21:21 INFOMaster: StartingSparkmasterat spark://thor:7077
15/08/25 11:21:21 INFOUtils: Successfullystartedservice 'MasterUI' onport 8080.
15/08/25 11:21:21 INFOMasterWebUI: StartedMasterWebUIat http://10.60.23.188:8080
root@thor:~/spark# ./sbin/start-slave.sh spark://thor:7077

To connect to Spark we can use spark-shell (Scala), pyspark (Python) or spark-sql. Since spark-sql is similar to MySQL cli, using it would be the easiest option (even “show tables” works). I also wanted to work with Scala in interactive mode so I’ve used spark-shell as well. In all the examples I’m using the same SQL query in MySQL and Spark, so working with Spark is not that different.

To work with MySQL server in Spark we need Connector/J for MySQL . Download the package and copy the mysql-connector-java-5.1.39-bin.jar to the spark directory, then add the class path to the conf/spark-defaults.conf:

spark.driver.extraClassPath = /usr/local/spark/mysql-connector-java-5.1.39-bin.jar
spark.executor.extraClassPath = /usr/local/spark/mysql-connector-java-5.1.39-bin.jar

Running MySQL queries via Apache Spark

For this test I was using one physical server with 12 CPU cores (older Intel(R) Xeon(R) CPU L5639 @ 2.13GHz) and 48G of RAM, SSD disks. I’ve installed MySQL and started spark master and spark slave on the same box.

Now we are ready to run MySQL queries inside Spark. First, start the shell (from the Spark directory, /usr/local/spark in my case):

$ ./bin/spark-shell --driver-memory 4G --masterspark://server1:7077

Then we will need to connect to MySQL from spark and register the temporary view:

val jdbcDF = spark.read.format("jdbc").options(
  Map("url" ->  "jdbc:mysql://localhost:3306/ontime?user=root&password=",
  "dbtable" -> "ontime.ontime_part",
  "fetchSize" -> "10000",
  "partitionColumn" -> "yeard", "lowerBound" -> "1988", "upperBound" -> "2016", "numPartitions" -> "28"
  )).load()
 
jdbcDF.createOrReplaceTempView("ontime")

So we have created a “datasource” for Spark (or in other words, a “link” from Spark to MySQL). The Spark table name is “ontime” (linked to MySQL ontime.ontime_part table) and we can run SQL queries in Spark, which in turn parse it and translate it in MySQL queries.

partitionColumn ” is very important here. It tells Spark to run multiple queries in parallel, one query per each partition.

Now we can run the query:

val sqlDF = sql("select min(year), max(year) as max_year, Carrier, count(*) as cnt, sum(if(ArrDelayMinutes>30, 1, 0)) as flights_delayed, round(sum(if(ArrDelayMinutes>30, 1, 0))/count(*),2) as rate FROM ontime WHERE DayOfWeek not in (6,7) and OriginState not in ('AK', 'HI', 'PR', 'VI') and DestState not in ('AK', 'HI', 'PR', 'VI') and (origin = 'RDU' or dest = 'RDU') GROUP by carrier HAVING cnt > 100000 and max_year > '1990' ORDER by rate DESC, cnt desc LIMIT  10")
sqlDF.show()

MySQL Query Example

Let’s go back to MySQL for a second and look at the query example. I’ve chosen the following query (from my older blog post):

selectmin(year), max(year) as max_year, Carrier, count(*) as cnt, 
sum(if(ArrDelayMinutes>30, 1, 0)) as flights_delayed, 
round(sum(if(ArrDelayMinutes>30, 1, 0))/count(*),2) as rate
FROMontime
WHERE
DayOfWeeknot in (6,7) 
and OriginStatenot in ('AK', 'HI', 'PR', 'VI') 
and DestStatenot in ('AK', 'HI', 'PR', 'VI') 
GROUPbycarrierHAVINGcnt > 100000 and max_year > '1990' 
ORDERbyrateDESC, cntdesc
LIMIT  10

The query will find the total number of delayed flights per each airline. In addition, the query will calculate the smart “ontime” rating, taking into consideration the number of flights (we do not want to compare smaller air carriers with the large ones, and we want to exclude the older airlines who are not in business anymore).

The main reason I’ve chosen this query is that it is hard to optimize it in MySQL. All conditions in the “where” clause will only filter out ~70% of rows. I’ve done a basic calculation:

mysql> select count(*) FROM ontime WHERE DayOfWeek not in (6,7) and OriginState not in ('AK', 'HI', 'PR', 'VI') and DestState not in ('AK', 'HI', 'PR', 'VI');
+-----------+
| count(*)  |
+-----------+
| 108776741 |
+-----------+
 
mysql> select count(*) FROM ontime;
+-----------+
| count(*)  |
+-----------+
| 152657276 |
+-----------+
 
mysql> select round((108776741/152657276)*100, 2);
+-------------------------------------+
| round((108776741/152657276)*100, 2) |
+-------------------------------------+
|                              71.26 |
+-------------------------------------+

Table structure:

CREATE TABLE `ontime_part` (
  `YearD` int(11) NOT NULL,
  `Quarter` tinyint(4) DEFAULT NULL,
  `MonthD` tinyint(4) DEFAULT NULL,
  `DayofMonth` tinyint(4) DEFAULT NULL,
  `DayOfWeek` tinyint(4) DEFAULT NULL,
  `FlightDate` date DEFAULT NULL,
  `UniqueCarrier` char(7) DEFAULT NULL,
  `AirlineID` int(11) DEFAULT NULL,
  `Carrier` char(2) DEFAULT NULL,
  `TailNum` varchar(50) DEFAULT NULL,
...
  `id` int(11) NOT NULL AUTO_INCREMENT,
  PRIMARY KEY (`id`,`YearD`),
  KEY `covered` (`DayOfWeek`,`OriginState`,`DestState`,`Carrier`,`YearD`,`ArrDelayMinutes`)
) ENGINE=InnoDB AUTO_INCREMENT=162668935 DEFAULT CHARSET=latin1
/*!50100 PARTITION BY RANGE (YearD)
(PARTITION p1987 VALUES LESS THAN (1988) ENGINE = InnoDB,
PARTITION p1988 VALUES LESS THAN (1989) ENGINE = InnoDB,
PARTITION p1989 VALUES LESS THAN (1990) ENGINE = InnoDB,
PARTITION p1990 VALUES LESS THAN (1991) ENGINE = InnoDB,
PARTITION p1991 VALUES LESS THAN (1992) ENGINE = InnoDB,
PARTITION p1992 VALUES LESS THAN (1993) ENGINE = InnoDB,
PARTITION p1993 VALUES LESS THAN (1994) ENGINE = InnoDB,
PARTITION p1994 VALUES LESS THAN (1995) ENGINE = InnoDB,
PARTITION p1995 VALUES LESS THAN (1996) ENGINE = InnoDB,
PARTITION p1996 VALUES LESS THAN (1997) ENGINE = InnoDB,
PARTITION p1997 VALUES LESS THAN (1998) ENGINE = InnoDB,
PARTITION p1998 VALUES LESS THAN (1999) ENGINE = InnoDB,
PARTITION p1999 VALUES LESS THAN (2000) ENGINE = InnoDB,
PARTITION p2000 VALUES LESS THAN (2001) ENGINE = InnoDB,
PARTITION p2001 VALUES LESS THAN (2002) ENGINE = InnoDB,
PARTITION p2002 VALUES LESS THAN (2003) ENGINE = InnoDB,
PARTITION p2003 VALUES LESS THAN (2004) ENGINE = InnoDB,
PARTITION p2004 VALUES LESS THAN (2005) ENGINE = InnoDB,
PARTITION p2005 VALUES LESS THAN (2006) ENGINE = InnoDB,
PARTITION p2006 VALUES LESS THAN (2007) ENGINE = InnoDB,
PARTITION p2007 VALUES LESS THAN (2008) ENGINE = InnoDB,
PARTITION p2008 VALUES LESS THAN (2009) ENGINE = InnoDB,
PARTITION p2009 VALUES LESS THAN (2010) ENGINE = InnoDB,
PARTITION p2010 VALUES LESS THAN (2011) ENGINE = InnoDB,
PARTITION p2011 VALUES LESS THAN (2012) ENGINE = InnoDB,
PARTITION p2012 VALUES LESS THAN (2013) ENGINE = InnoDB,
PARTITION p2013 VALUES LESS THAN (2014) ENGINE = InnoDB,
PARTITION p2014 VALUES LESS THAN (2015) ENGINE = InnoDB,
PARTITION p2015 VALUES LESS THAN (2016) ENGINE = InnoDB,
PARTITION p_new VALUES LESS THAN MAXVALUE ENGINE = InnoDB) */

Even with a “covered” index, MySQL will have to scan ~70M-100M of rows and create a temporary table:

mysql>  explain select min(yearD), max(yearD) as max_year, Carrier, count(*) as cnt, sum(if(ArrDelayMinutes>30, 1, 0)) as flights_delayed, round(sum(if(ArrDelayMinutes>30, 1, 0))/count(*),2) as rate FROM ontime_part WHERE DayOfWeek not in (6,7) and OriginState not in ('AK', 'HI', 'PR', 'VI') and DestState not in ('AK', 'HI', 'PR', 'VI') GROUP by carrier HAVING cnt > 1000 and max_year > '1990' ORDER by rate DESC, cnt desc LIMIT  10G
*************************** 1. row ***************************
          id: 1
  select_type: SIMPLE
        table: ontime_part
        type: range
possible_keys: covered
          key: covered
      key_len: 2
          ref: NULL
        rows: 70483364
        Extra: Using where; Using index; Using temporary; Using filesort
1 row in set (0.00 sec)

What is the query response time in MySQL:

mysql> select min(yearD), max(yearD) as max_year, Carrier, count(*) as cnt, sum(if(ArrDelayMinutes>30, 1, 0)) as flights_delayed, round(sum(if(ArrDelayMinutes>30, 1, 0))/count(*),2) as rate FROM ontime_part WHERE DayOfWeek not in (6,7) and OriginState not in ('AK', 'HI', 'PR', 'VI') and DestState not in ('AK', 'HI', 'PR', 'VI') GROUP by carrier HAVING cnt > 1000 and max_year > '1990' ORDER by rate DESC, cnt desc LIMIT  10;
+------------+----------+---------+----------+-----------------+------+
| min(yearD) | max_year | Carrier | cnt      | flights_delayed | rate |
+------------+----------+---------+----------+-----------------+------+
|      2003 |    2013 | EV      |  2962008 |          464264 | 0.16 |
|      2003 |    2013 | B6      |  1237400 |          187863 | 0.15 |
|      2006 |    2011 | XE      |  1615266 |          230977 | 0.14 |
|      2003 |    2005 | DH      |  501056 |          69833 | 0.14 |
|      2001 |    2013 | MQ      |  4518106 |          605698 | 0.13 |
|      2003 |    2013 | FL      |  1692887 |          212069 | 0.13 |
|      2004 |    2010 | OH      |  1307404 |          175258 | 0.13 |
|      2006 |    2013 | YV      |  1121025 |          143597 | 0.13 |
|      2003 |    2006 | RU      |  1007248 |          126733 | 0.13 |
|      1988 |    2013 | UA      | 10717383 |        1327196 | 0.12 |
+------------+----------+---------+----------+-----------------+------+
10 rows in set (19 min 16.58 sec)

19 minutes is definitely not great.

SQL in Spark

Now we want to run the same query inside Spark and let Spark read data from MySQL. We will create a “datasource” and execute the query:

scala> val jdbcDF = spark.read.format("jdbc").options(
    |  Map("url" ->  "jdbc:mysql://localhost:3306/ontime?user=root&password=mysql",
    |  "dbtable" -> "ontime.ontime_sm",
    |  "fetchSize" -> "10000",
    |  "partitionColumn" -> "yeard", "lowerBound" -> "1988", "upperBound" -> "2015", "numPartitions" -> "48"
    |  )).load()
16/08/02 23:24:12 WARNJDBCRelation: Thenumberofpartitionsis reducedbecausethespecifiednumberofpartitionsis lessthanthedifferencebetweenupperboundand lowerbound. Updatednumberofpartitions: 27; Inputnumberofpartitions: 48; Lowerbound: 1988; Upperbound: 2015.
dbcDF: org.apache.spark.sql.DataFrame = [id: int, YearD: date ... 19 morefields]
 
scala> jdbcDF.createOrReplaceTempView("ontime")
 
scala> val sqlDF = sql("select min(yearD), max(yearD) as max_year, Carrier, count(*) as cnt, sum(if(ArrDelayMinutes>30, 1, 0)) as flights_delayed, round(sum(if(ArrDelayMinutes>30, 1, 0))/count(*),2) as rate FROM ontime WHERE OriginState not in ('AK', 'HI', 'PR', 'VI') and DestState not in ('AK', 'HI', 'PR', 'VI') GROUP by carrier HAVING cnt > 1000 and max_year > '1990' ORDER by rate DESC, cnt desc LIMIT  10")
sqlDF: org.apache.spark.sql.DataFrame = [min(yearD): date, max_year: date ... 4 morefields]
 
scala> sqlDF.show()
+----------+--------+-------+--------+---------------+----+
|min(yearD)|max_year|Carrier|    cnt|flights_delayed|rate|
+----------+--------+-------+--------+---------------+----+
|      2003|    2013|    EV| 2962008|        464264|0.16|
|      2003|    2013|    B6| 1237400|        187863|0.15|
|      2006|    2011|    XE| 1615266|        230977|0.14|
|      2003|    2005|    DH|  501056|          69833|0.14|
|      2001|    2013|    MQ| 4518106|        605698|0.13|
|      2003|    2013|    FL| 1692887|        212069|0.13|
|      2004|    2010|    OH| 1307404|        175258|0.13|
|      2006|    2013|    YV| 1121025|        143597|0.13|
|      2003|    2006|    RU| 1007248|        126733|0.13|
|      1988|    2013|    UA|10717383|        1327196|0.12|
+----------+--------+-------+--------+---------------+----+

spark-shell does not show the query time. This can be retrieved from Web UI or from spark-sql. I’ve re-run the same query in spark-sql:

./bin/spark-sql --driver-memory 4G  --masterspark://thor:7077 
spark-sql> CREATETEMPORARYVIEWontime
        > USINGorg.apache.spark.sql.jdbc
        > OPTIONS (
        >      url  "jdbc:mysql://localhost:3306/ontime?user=root&password=",
        >      dbtable "ontime.ontime_part",
        >      fetchSize "1000",
        >      partitionColumn "yearD", lowerBound "1988", upperBound "2014", numPartitions "48"
        > );
16/08/04 01:44:27 WARNJDBCRelation: Thenumberofpartitionsis reducedbecausethespecifiednumberofpartitionsis lessthanthedifferencebetweenupperboundand lowerbound. Updatednumberofpartitions: 26; Inputnumberofpartitions: 48; Lowerbound: 1988; Upperbound: 2014.
Time taken: 3.864 seconds
 
spark-sql> selectmin(yearD), max(yearD) as max_year, Carrier, count(*) as cnt, sum(if(ArrDelayMinutes>30, 1, 0)) as flights_delayed, round(sum(if(ArrDelayMinutes>30, 1, 0))/count(*),2) as rateFROMontimeWHEREDayOfWeeknot in (6,7) and OriginStatenot in ('AK', 'HI', 'PR', 'VI') and DestStatenot in ('AK', 'HI', 'PR', 'VI') GROUPbycarrierHAVINGcnt > 1000 and max_year > '1990' ORDERbyrateDESC, cntdescLIMIT  10;
16/08/04 01:45:13 WARNUtils: Truncatedthestring representationof a plansinceitwastoolarge. This behaviorcanbeadjustedbysetting 'spark.debug.maxToStringFields' in SparkEnv.conf.
2003    2013    EV      2962008 464264  0.16
2003    2013    B6      1237400 187863  0.15
2006    2011    XE      1615266 230977  0.14
2003    2005    DH      501056  69833  0.14
2001    2013    MQ      4518106 605698  0.13
2003    2013    FL      1692887 212069  0.13
2004    2010    OH      1307404 175258  0.13
2006    2013    YV      1121025 143597  0.13
2003    2006    RU      1007248 126733  0.13
1988    2013    UA      10717383        1327196 0.12
Time taken: 139.628 seconds, Fetched 10 row(s)

So the response time of the same query is almost 10x faster (on the same server, just one box). But now how was this query translated to MySQL queries, and why it is so much faster? Here is what is happening inside MySQL:

Inside MySQL

Spark:

scala> sqlDF.show()                                                                                                                                                              
[Stage 4:>                                                        (0 + 26) / 26]

MySQL:

mysql> select id, info from information_schema.processlist where info is not NULL and info not like '%information_schema%';
+-------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| id    | info                                                                                                                                                                                                                                                    |
+-------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| 10948 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2001 AND yearD < 2002) |
| 10965 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2007 AND yearD < 2008) |
| 10966 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 1991 AND yearD < 1992) |
| 10967 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 1994 AND yearD < 1995) |
| 10968 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 1998 AND yearD < 1999) |
| 10969 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2010 AND yearD < 2011) |
| 10970 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2002 AND yearD < 2003) |
| 10971 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2006 AND yearD < 2007) |
| 10972 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 1990 AND yearD < 1991) |
| 10953 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2009 AND yearD < 2010) |
| 10947 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 1993 AND yearD < 1994) |
| 10956 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD < 1989 or yearD is null)  |
| 10951 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2005 AND yearD < 2006) |
| 10954 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 1996 AND yearD < 1997) |
| 10955 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2008 AND yearD < 2009) |
| 10961 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 1999 AND yearD < 2000) |
| 10962 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2011 AND yearD < 2012) |
| 10963 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2003 AND yearD < 2004) |
| 10964 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 1995 AND yearD < 1996) |
| 10957 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2004 AND yearD < 2005) |
| 10949 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 1989 AND yearD < 1990) |
| 10950 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 1997 AND yearD < 1998) |
| 10952 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2013)                  |
| 10958 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 1992 AND yearD < 1993) |
| 10960 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2000 AND yearD < 2001) |
| 10959 | SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2012 AND yearD < 2013) |
+-------+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
26 rows in set (0.00 sec)

Spark is running 26 queries in parallel, which is great. As the table is partitioned it only uses one partition per query, but scans the whole partition:

mysql> explain partitions SELECT `YearD`,`ArrDelayMinutes`,`Carrier` FROM ontime.ontime_part WHERE (((NOT (DayOfWeek IN (6, 7)))) AND ((NOT (OriginState IN ('AK', 'HI', 'PR', 'VI')))) AND ((NOT (DestState IN ('AK', 'HI', 'PR', 'VI'))))) AND (yearD >= 2001 AND yearD < 2002)G
*************************** 1. row ***************************
          id: 1
  select_type: SIMPLE
        table: ontime_part
  partitions: p2001
        type: ALL
possible_keys: NULL
          key: NULL
      key_len: NULL
          ref: NULL
        rows: 5814106
        Extra: Using where
1 row in set (0.00 sec)

In this case, as the box has 12 CPU cores / 24 threads, it efficently executes 26 queries in parallel and the partitioned table helps to avoid contention issues (I wish MySQL could scan partitions in parallel, but it can’t at the time of writing).

Another interesting thing is that Spark can “push down” some of the conditions to MySQL, but only those inside the “where” clause. All group by/order by/aggregations are done inside Spark. It  needs to retrieve data from MySQL to satisfy those conditions and will not push down group by/order by/etc to MySQL.

That also means that queries without “where” conditions (for example “select count(*) as cnt, carrier from ontime group by carrier order by cnt desc limit 10”) will have to retrieve all data from MySQL and load it to Spark (as opposed to MySQL will do all group by inside). Running it in Spark might be slower or faster (depending on the amount of data and use of indexes) but it also requires more resources and potentially more memory dedicated for Spark. The above query is translated to 26 queries, each does a “select carrier from ontime_part where (yearD >= N AND yearD < N)”

Pushing down the whole query into MySQL 

If we want to avoid sending all data from MySQL to Spark we have the option of creating a temporary table on top of a query (similar to MySQL’s create temporary table as select …). In Scala:

val tableQuery = 
 "(select yeard, count(*) from ontime group by yeard) tmp"
 
 val jdbcDFtmp = spark.read.format("jdbc").options(
  Map("url" ->  "jdbc:mysql://localhost:3306/ontime?user=root&password=",
  "dbtable" -> tableQuery,
  "fetchSize" -> "10000"
  )).load()
 
jdbcDFtmp.createOrReplaceTempView("ontime_tmp")

In Spark SQL:

CREATE TEMPORARY VIEW ontime_tmp
USING org.apache.spark.sql.jdbc
OPTIONS (
    url  "jdbc:mysql://localhost:3306/ontime?user=root&password=mysql",
    dbtable "(select yeard, count(*) from ontime_part group by yeard) tmp",
    fetchSize "1000"
);
 
select * from ontime_tmp;

Please note:

  1. We do not want to use “partitionColumn” here, otherwise we will see 26 queries like this in MySQL: “SELECT yeard, count(*) FROM (select yeard, count(*) from ontime_part group by yeard) tmp where (yearD >= N AND yearD < N)” (obviously not optimal)
  2. This is not a good use of Spark, more like a “hack.” The only good reason to do it is to be able to have the result of the query as a source of an additional query.

Query cache in Spark

Another option is to cache the result of the query (or even the whole table) and then use .filter in Scala for faster processing. This requires sufficient memory dedicated for Spark. The good news is we can add additional nodes to Spark and get more memory for Spark cluster.

Spark SQL example:

CREATE TEMPORARY VIEW ontime_latest
USING org.apache.spark.sql.jdbc
OPTIONS (
    url  "jdbc:mysql://localhost:3306/ontime?user=root&password=",
    dbtable "ontime.ontime_part partition (p2013, p2014)",
    fetchSize "1000",
    partitionColumn "yearD", lowerBound "1988", upperBound "2014", numPartitions "26"
);
cache table ontime_latest;
 
spark-sql> cache table ontime_latest;
Time taken: 465.076 seconds    
 
spark-sql> select count(*) from ontime_latest;
5349447
Time taken: 0.526 seconds, Fetched 1 row(s)
 
spark-sql> select count(*), dayofweek from ontime_latest group by dayofweek;
790896  1
634664  6
795540  3
794667  5
808243  4
743282  7
782155  2
Time taken: 0.541 seconds, Fetched 7 row(s)
 
spark-sql> select min(yearD), max(yearD) as max_year, Carrier, count(*) as cnt, sum(if(ArrDelayMinutes>30, 1, 0)) as flights_delayed, round(sum(if(ArrDelayMinutes>30, 1, 0))/count(*),2) as rate FROM ontime_latest WHERE DayOfWeek not in (6,7) and OriginState not in ('AK', 'HI', 'PR', 'VI') and DestState not in ('AK', 'HI', 'PR', 'VI') and (origin='RDU' or dest = 'RDU') GROUP by carrier HAVING cnt > 1000 and max_year > '1990' ORDER by rate DESC, cnt desc LIMIT  10;
2013    2013    MQ      9339    1734    0.19                                    
2013    2013    B6      3302    516    0.16
2013    2013    EV      9225    1331    0.14
2013    2013    UA      1317    177    0.13
2013    2013    AA      5354    620    0.12
2013    2013    9E      5520    593    0.11
2013    2013    WN      10968  1130    0.1
2013    2013    US      5722    549    0.1
2013    2013    DL      6313    478    0.08
2013    2013    FL      2433    205    0.08
Time taken: 2.036 seconds, Fetched 10 row(s)

Here we cache partitions p2013 and p2014 in Spark. This retrieves the data from MySQL and loads it in Spark. After that all queries run on the cached data and will be much faster.

With Scala we can cache the result of a query and then use filters to only get the information we need:

val sqlDF = sql("SELECT flightdate, origin, dest, depdelayminutes, arrdelayminutes, carrier, TailNum, Cancelled, Diverted, Distance from ontime")
sqlDF.cache().show()
scala> sqlDF.filter("flightdate='1988-01-01'").count()
res5: Long = 862

Using Spark with Percona XtraDB Cluster

As Spark can be used in a cluster mode and scale with more and more nodes, reading data from a single MySQL is a bottleneck. We can use MySQL replication slave servers or Percona XtraDB Cluster (PXC) nodes as a Spark datasource. To test it out, I’ve provisioned Percona XtraDB Cluster with three nodes on AWS (I’ve used m4.2xlarge Ubuntu instances) and also started Apache Spark on each node:

  1. Node1 (pxc1): Percona Server + Spark Master + Spark worker node + Spark SQL running
  2. Node2 (pxc2): Percona Server + Spark worker node
  3. Node3 (pxc3): Percona Server + Spark worker node

All the Spark worker nodes use the memory configuration option:

cat conf/spark-env.sh
exportSPARK_WORKER_MEMORY=24g

Then I can start spark-sql (also need to have connector/J JAR file copied to all nodes):

$ ./bin/spark-sql --driver-memory 4G --masterspark://pxc1:7077

When creating a table, I still use localhost to connect to MySQL (url “jdbc:mysql://localhost:3306/ontime?user=root&password=xxx”). As Spark worker nodes are running on the same instance as Percona Cluster nodes, it will use the local connection. Then running a Spark SQL will evenly distribute all 26 MySQL queries among the three MySQL nodes.

Alternatively we can run Spark cluster on a separate host and connect it to the HA Proxy, which in turn will load balance selects across multiple Percona XtraDB Cluster nodes.

Query Performance Benchmark

Finally, here is the query response time test on the three AWS Percona XtraDB Cluster nodes:

Query 1: select min (yearD), max (yearD) as max_year,Carrier, count (*) as cnt, sum ( if (ArrDelayMinutes > 30,1,0)) as flights_delayed, round ( sum ( if (ArrDelayMinutes > 30,1,0))/ count (*),2) as rate FROM ontime_part WHERE DayOfWeek not in (6,7) and OriginState not in ( 'AK' , 'HI' , 'PR' , 'VI' ) and DestState not in ( 'AK' , 'HI' , 'PR' , 'VI' ) GROUP by carrier HAVING cnt > 1000 and max_year > '1990' ORDER by rate DESC ,cnt desc LIMIT 10;

Query / Index type MySQL Time Spark Time (3 nodes) Times Improvement
No covered index (partitioned) 19 min 16.58 sec 192.17 sec 6.02
Covered index (partitioned) 2 min 10.81 sec 48.38 sec 2.7

Query 2: select dayofweek , count (*) from ontime_part group by dayofweek ;

Query / Index type MySQL Time Spark Time (3 nodes) Times Improvement
No covered index (partitoned) 19 min 15.21 sec 195.058 sec 5.92
Covered index (partitioned) 1 min 10.38 sec 27.323 sec 2.58

Now, this looks really good, but it can be better. With three nodes @ m4.2xlarge we will have 8*3 = 24 cores total (although they are shared between Spark and MySQL). We can expect 10x improvement, especially without a covered index.

However, on m4.2xlarge the amount of RAM did not allow me to run MySQL out of memory, so all reads were from EBS non-provisioned IOPS, which only gave me ~120MB/sec. I’ve redone the test on a set of three dedicated servers:

  • 28 cores E5-2683 v3 @ 2.00GHz
  • 240GB of RAM
  • Samsung 850 PRO

The test was running completely off RAM:

Query 1 (from the above)

Query / Index type MySQL Time Spark Time (3 nodes) Times Improvement
No covered index (partitoned) 3 min 13.94 sec 14.255 sec 13.61
Covered index (partitioned) 2 min 2.11 sec 9.035 sec 13.52

Query 2: select dayofweek , count (*) from ontime_part group by dayofweek ;

Query / Index type MySQL Time Spark Time (3 nodes) Times Improvement
No covered index (partitoned) 2 min 0.36 sec 7.055 sec 17.06
Covered index (partitioned) 1 min 6.85 sec 4.514 sec 14.81

With this amount of cores and running out of RAM we actually do not have enough concurrency as the table only have 26 partitions. I’ve tried the unpartitioned table with ID primary key and use 128 partitions.

Note about partitioning

I’ve used partitioned table (partition by year) in my tests to help reduce MySQL level contention. At the same time the “partitionColumn” option in Spark does not require that MySQL table is partitioned. For example, if a table has a primary key, we can use this CREATE VIEW in Spark :

CREATE OR REPLACE TEMPORARY VIEW ontime
USING org.apache.spark.sql.jdbc
OPTIONS (
  url  "jdbc:mysql://127.0.0.1:3306/ontime?user=root&password=",
  dbtable "ontime.ontime",
  fetchSize "1000",
  partitionColumn "id", lowerBound "1", upperBound "162668934", numPartitions "128"
);

Assuming we have enough MySQL servers (i.e., nodes or slaves), we can increase the number of partitions and that can improve the parallelism (as opposed to only 26 partitions when running one partition by year). Actually, the above test gives us even better response time:  6.44 seconds for query 1 .

Where Spark doesn’t work well

For faster queries (those that use indexes or can efficiently use an index) it does not make sense to use Spark. Retrieving data from MySQL and loading it into Spark is not free. This overhead can be significant for faster queries. For example, a query like this select count (*) from ontime_part where YearD=2013 and DayOfWeek =7 and OriginState= 'NC' and DestState= 'NC' ; will only scan 1300 rows and will return instant (0.00 seconds reported by MySQL).

An even better example is this: select max (id) from ontime_part . In MySQL, the query will use the index and all calculations will be done inside MySQL. Spark, on the other hand, will have to retrieve all IDs (select id from ontime_part) from MySQL and calculate maximum. That took 24.267 seconds.

Conclusion

Using Apache Spark as an additional engine level on top of MySQL can help to speed up the slow reporting queries and add much-needed scalability for the long running select queries. In addition, Spark can help with query caching for frequent queries.

PS: Visual explain plan with Spark

Spark Web GUI provides lots of ways of monitoring Spark jobs. For example, it shows the “job” progress:

And SQL visual explain details:





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