Tuning and Debugging in Apache Spark

Tuning and Debugging in Apache
Spark
Patrick Wendell @pwendell
February 20, 2015

About Me
Apache Spark committer and PMC, release
manager
Worked on Spark at UC Berkeley when the project
started
Today, managing Spark efforts at Databricks
2

About Databricks
Founded by creators of Spark in 2013
Donated Spark to ASF and remain largest
contributor
End-to-End hosted service: Databricks Cloud
3

Today’s Talk
Help you understand and debug Spark programs
Related talk this afternoon:
Assumes you know Spark core API concepts,
focused on internals
4

6
The key to tuning
Spark apps is a
sound grasp of
Spark’s internal
mechanisms.

Key Question
How does a user program get translated into units
of physical execution: jobs, stages, and tasks:
7
?

RDD API Refresher
RDDs are a distributed collection of records
rdd = spark.parallelize(range(10000), 10)
Transformations create new RDDs from existing
ones
errors = rdd.filter(lambda line: “ERROR” in
line)
Actions materialize a value in the user program
size = errors.count() 8

RDD API Example
// Read input file
val input = sc.textFile("input.txt")
val tokenized = input
.map(line => line.split(" "))
.filter(words => words.size > 0) // remove empty lines
val counts = tokenized // frequency of log levels
.map(words => (words(0), 1)).
.reduceByKey{ (a, b) => a + b, 2 }
9
INFO Server started
INFO Bound to port 8080
WARN Cannot find srv.conf
input.txt

RDD API Example
// Read input file
val input = sc.textFile( )
val tokenized = input
.map(line => line.split(" "))
.filter(words => words.size > 0) // remove empty lines
val counts = tokenized // frequency of log levels
.map(words => (words(0), 1)).
.reduceByKey{ (a, b) => a + b }
10

Transformations
sc.textFile().map().filter().map().reduceByKey()
11

DAG View of RDD’s
textFile() map() filter() map()
reduceByKey()
12
Mapped
RDD
Partition 1
Partition 2
Partition 3
Filtered
RDD
Partition 1
Partition 2
Partition 3
Mapped
RDD
Partition 1
Partition 2
Partition 3
Shuffle RDD
Partition 1
Partition 2
Hadoop
RDD
Partition 1
Partition 2
Partition 3
input tokenized counts

Transformations build up a DAG, but don’t “do
anything”
13

Evaluation of the DAG
We mentioned “actions” a few slides ago. Let’s forget
them for a minute.
DAG’s are materialized through a method sc.runJob:
def runJob[T, U](
rdd: RDD[T], 1. RDD
to compute
partitions: Seq[Int], 2.
Which partitions
func: (Iterator[T]) => U)) 3. Fn to
produce results 14

them for a minute.
def runJob[T, U](
rdd: RDD[T], 1. RDD
to compute
Which partitions
produce results 15

them for a minute.
def runJob[T, U](
rdd: RDD[T], 1. RDD
to compute
Which partitions
produce results 16

them for a minute.
def runJob[T, U](
rdd: RDD[T], 1. RDD
to compute
Which partitions
produce results 17

How runJob Works
Needs to compute my parents, parents, parents, etc all the
way back to an RDD with no dependencies (e.g.
HadoopRDD).
18
Mapped
RDD
Partition 1
Partition 2
Partition 3
Filtered
RDD
Partition 1
Partition 2
Partition 3
Mapped
RDD
Partition 1
Partition 2
Partition 3
Shuffle RDD
Partition 1
Partition 2
Hadoop
RDD
Partition 1
Partition 2
Partition 3
runJob(counts)

Physical Optimizations
1. Certain types of transformations can be
pipelined.
1. If dependent RDD’s have already been cached
(or persisted in a shuffle) the graph can be
truncated.
Once pipelining and truncation occur, Spark
produces a a set of stages each stage is composed
of tasks
19

How runJob Works
HadoopRDD).
20
Mapped
RDD
Partition 1
Partition 2
Partition 3
Filtered
RDD
Partition 1
Partition 2
Partition 3
Mapped
RDD
Partition 1
Partition 2
Partition 3
Shuffle RDD
Partition 1
Partition 2
Hadoop
RDD
Partition 1
Partition 2
Partition 3
runJob(counts)

How runJob Works
HadoopRDD).
21
Mapped
RDD
Partition 1
Partition 2
Partition 3
Filtered
RDD
Partition 1
Partition 2
Partition 3
Mapped
RDD
Partition 1
Partition 2
Partition 3
Shuffle RDD
Partition 1
Partition 2
Hadoop
RDD
Partition 1
Partition 2
Partition 3
runJob(counts)

How runJob Works
HadoopRDD).
22
Mapped
RDD
Partition 1
Partition 2
Partition 3
Filtered
RDD
Partition 1
Partition 2
Partition 3
Mapped
RDD
Partition 1
Partition 2
Partition 3
Shuffle RDD
Partition 1
Partition 2
Hadoop
RDD
Partition 1
Partition 2
Partition 3
runJob(counts)

Stage Graph
23
Task 1
Task 2
Task 3
Task 1
Task 2
Stage 1 Stage 2
Each task will:
1. Read
Hadoop
input
2. Perform
maps and
filters
3. Write
partial
sums
Each task
will:
1. Read
partial
sums
2. Invoke
user
function
passed to
runJob.Shuffle write Shuffle readInput

Units of Physical Execution
Jobs: Work required to compute RDD in runJob.
Stages: A wave of work within a job, corresponding
to one or more pipelined RDD’s.
Tasks: A unit of work within a stage,
corresponding to one RDD partition.
Shuffle: The transfer of data between stages.
24

Seeing this on your own
scala> counts.toDebugString
res84: String =
(2) ShuffledRDD[296] at reduceByKey at <console>:17
+-(3) MappedRDD[295] at map at <console>:17
| FilteredRDD[294] at filter at <console>:15
| MappedRDD[293] at map at <console>:15
| input.text MappedRDD[292] at textFile at <console>:13
| input.text HadoopRDD[291] at textFile at <console>:13
25
(indentations indicate a shuffle boundary)

Example: count() action
class RDD {
def count(): Long = {
results = sc.runJob(
this, 1. RDD
= self
0 until partitions.size, 2. Partitions = all
partitions
it => it.size() 3. Function
= size of the partition
)
return results.sum
} 26

Example: take(N) action
class RDD {
def take(n: Int) {
val results = new ArrayBuffer[T]
var partition = 0
while (results.size < n) {
result ++= sc.runJob(this, partition, it => it.toArray)
partition = partition + 1
}
return results.take(n)
}
}
27

Putting it All Together
28
Named after action calling runJob
Named after last RDD in pipeline

29
Determinants of Performance in
Spark

Quantity of Data Shuffled
In general, avoiding shuffle will make your program
run faster.
1. Use the built in aggregateByKey() operator
instead of writing your own aggregations.
2. Filter input earlier in the program rather than
later.
3. Go to this afternoon’s talk!
30

Degree of Parallelism
> input = sc.textFile("s3n://log-files/2014/*.log.gz") #matches thousands
of files
> input.getNumPartitions()
35154
> lines = input.filter(lambda line: line.startswith("2014-10-17 08:")) #
selective
> lines.getNumPartitions()
35154
> lines = lines.coalesce(5).cache() # We coalesce the lines RDD before
caching
> lines.getNumPartitions()
5
>>> lines.count() # occurs on coalesced RDD 31

Degree of Parallelism
If you have a huge number of mostly idle tasks (e.g.
10’s of thousands), then it’s often good to coalesce.
If you are not using all slots in your cluster,
repartition can increase parallelism.
32

Choice of Serializer
Serialization is sometimes a bottleneck when
shuffling and caching data. Using the Kryo
serializer is often faster.
val conf = new SparkConf()
conf.set("spark.serializer",
"org.apache.spark.serializer.KryoSerializer")
// Be strict about class registration
conf.set("spark.kryo.registrationRequired", "true")
conf.registerKryoClasses(Array(classOf[MyClass],
classOf[MyOtherClass])) 33

Cache Format
By default Spark will cache() data using
MEMORY_ONLY level, deserialized JVM objects
MEMORY_ONLY_SER can help cut down on
GC
MEMORY_AND_DISK can avoid expensive
recompuations
34

Hardware
Spark scales horizontally, so more is better
Disk/Memory/Network balance depends on
workload: CPU intensive ML jobs vs IO intensive
ETL jobs
Good to keep executor heap size to 64GB or less
(can run multiple on each node)
35

Other Performance Tweaks
Switching to LZF compression can improve shuffle
performance (sacrifices some robustness for
massive shuffles):
conf.set(“spark.io.compression.codec”, “lzf”)
Turn on speculative execution to help prevent
stragglers
conf.set(“spark.speculation”, “true”)
36

Other Performance Tweaks
Make sure to give Spark as many disks as possible
to allow striping shuffle output
SPARK_LOCAL_DIRS in Mesos/Standalone
In YARN mode, inherits YARN’s local directories
37

38
One Weird Trick for Great
Performance

Use Higher Level API’s!
DataFrame APIs for core processing
Works across Scala, Java, Python and R
Spark ML for machine learning
Spark SQL for structured query processing
39

40
See also
Chapter 8: Tuning and
Debugging Spark.

Come to Spark Summit 2015!
41
June 15-17 in San
Francisco

Other Spark Happenings Today
Spark team “Ask Us Anything” at 2:20 in 211 B
Tips for writing better Spark programs at 4:00 in
230C
I’ll be around Databricks booth after this
42

Internals of the RDD Interface
45
1) List of partitions
2) Set of dependencies on parent RDDs
3) Function to compute a partition, given parents
4) Optional partitioning info for k/v RDDs (Partitioner)
RDD
Partition
1
Partition
2
Partition
3

Example: Hadoop RDD
46
Partitions = 1 per HDFS block
Dependencies = None
compute(partition) = read corresponding HDFS block
Partitioner = None
> rdd =
spark.hadoopFile(“hdfs://click_logs/”)

Example: Filtered RDD
47
Partitions = parent partitions
Dependencies = a single parent
compute(partition) = call parent.compute(partition) and filter
Partitioner = parent partitioner
> filtered = rdd.filter(lambda x: x contains
“ERROR”)

Example: Joined RDD
48
Partitions = number chosen by user or heuristics
Dependencies = ShuffleDependency on two or more
parents
compute(partition) = read and join data from all parents
Partitioner = HashPartitioner(# partitions)

49
A More Complex DAG
Joined RDD
Partition
1
Partition
2
Partition
3
Filtered
RDDPartition
1
Partition
2
Mapped
RDDPartition
1
Partition
2
Hadoop
RDDPartition
1
Partition
2
JDBC RDD
Partition
1
Partition
2
Filtered
RDDPartition
1
Partition
2
Partition
3
.count()

50
A More Complex DAG
Stage 3
Task 1
Task 2
Task 3
Stage 2
Task 1
Task 2
Stage 1
Task 1
Task 2
Shuffle
Read
Shuffle
Write

51
RDD
Partition
1
Partition
2
Partition
3
Parent
Partition
1
Partition
2
Partition
3
Narrow and Wide Transformations
RDD
Partition
1
Partition
2
Partition
3
Parent 1
Partition
1
Partition
2
Parent 2
Partition
1
Partition
2
FilteredRDD JoinedRDD

Tuning and Debugging in Apache Spark

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