Tuning Spark

Data Serialization (#data-serialization)

Memory Tuning (#memory-tuning)
Memory Management Overview (#memory-management-overview)
Determining Memory Consumption (#determining-memory-consumption)
Tuning Data Structures (#tuning-data-structures)
Serialized RDD Storage (#serialized-rdd-storage)
Garbage Collection Tuning (#garbage-collection-tuning)
Other Considerations (#other-considerations)
Level of Parallelism (#level-of-parallelism)
Parallel Listing on Input Paths (#parallel-listing-on-input-paths)
Memory Usage of Reduce Tasks (#memory-usage-of-reduce-tasks)
Broadcasting Large Variables (#broadcasting-large-variables)
Data Locality (#data-locality)
Summary (#summary)

Because of the in-memory nature of most Spark computations, Spark programs can be
bottlenecked by any resource in the cluster: CPU, network bandwidth, or memory. Most
often, if the data fits in memory, the bottleneck is network bandwidth, but sometimes, you
also need to do some tuning, such as storing RDDs in serialized form (rdd-programming-
guide.html#rdd-persistence), to decrease memory usage. This guide will cover two main
topics: data serialization, which is crucial for good network performance and can also
reduce memory use, and memory tuning. We also sketch several smaller topics.

Data Serialization
Serialization plays an important role in the performance of any distributed application.
Formats that are slow to serialize objects into, or consume a large number of bytes, will
greatly slow down the computation. Often, this will be the first thing you should tune to
optimize a Spark application. Spark aims to strike a balance between convenience
(allowing you to work with any Java type in your operations) and performance. It provides
two serialization libraries:

Java serialization (https://docs.oracle.com/javase/8/docs/api/java/io/Serializable.html):

By default, Spark serializes objects using Java’s ObjectOutputStream framework, and
 can work with any class you create that implements java.io.Serializable
(https://docs.oracle.com/javase/8/docs/api/java/io/Serializable.html). You can also
control the performance of your serialization more closely by extending
java.io.Externalizable
(https://docs.oracle.com/javase/8/docs/api/java/io/Externalizable.html). Java
serialization is flexible but often quite slow, and leads to large serialized formats for
many classes.
Kryo serialization (https://github.com/EsotericSoftware/kryo): Spark can also use the
Kryo library (version 4) to serialize objects more quickly. Kryo is significantly faster and
more compact than Java serialization (often as much as 10x), but does not support all
Serializable types and requires you to register the classes you’ll use in the program
in advance for best performance.

You can switch to using Kryo by initializing your job with a SparkConf
(configuration.html#spark-properties) and calling
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer").
This setting configures the serializer used for not only shuffling data between worker nodes
but also when serializing RDDs to disk. The only reason Kryo is not the default is because of
the custom registration requirement, but we recommend trying it in any network-intensive
application. Since Spark 2.0.0, we internally use Kryo serializer when shuffling RDDs with
simple types, arrays of simple types, or string type.

Spark automatically includes Kryo serializers for the many commonly-used core Scala
classes covered in the AllScalaRegistrar from the Twitter chill
(https://github.com/twitter/chill) library.

To register your own custom classes with Kryo, use the registerKryoClasses method.

val conf = new SparkConf().setMaster(...).setAppName(...)

conf.registerKryoClasses(Array(classOf[MyClass1], classOf[MyClass2]))
val sc = new SparkContext(conf)

The Kryo documentation (https://github.com/EsotericSoftware/kryo) describes more

advanced registration options, such as adding custom serialization code.

If your objects are large, you may also need to increase the spark.kryoserializer.buffer
config (configuration.html#compression-and-serialization). This value needs to be large
enough to hold the largest object you will serialize.

Finally, if you don’t register your custom classes, Kryo will still work, but it will have to store
the full class name with each object, which is wasteful.
Memory Tuning
There are three considerations in tuning memory usage: the amount of memory used by
your objects (you may want your entire dataset to fit in memory), the cost of accessing
those objects, and the overhead of garbage collection (if you have high turnover in terms
of objects).

By default, Java objects are fast to access, but can easily consume a factor of 2-5x more
space than the “raw” data inside their fields. This is due to several reasons:

Each distinct Java object has an “object header”, which is about 16 bytes and contains
information such as a pointer to its class. For an object with very little data in it (say
one Int field), this can be bigger than the data.
Java Strings have about 40 bytes of overhead over the raw string data (since they
store it in an array of Chars and keep extra data such as the length), and store each
character as two bytes due to String’s internal usage of UTF-16 encoding. Thus a 10-
character string can easily consume 60 bytes.
Common collection classes, such as HashMap and LinkedList, use linked data
structures, where there is a “wrapper” object for each entry (e.g. Map.Entry). This
object not only has a header, but also pointers (typically 8 bytes each) to the next
object in the list.
Collections of primitive types often store them as “boxed” objects such as
java.lang.Integer. O
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Memory Management x.
Overview
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Memory usage in Spark largelym falls under one of two categories: execution and storage.
Execution memory refers to l) that used for computation in shuffles, joins, sorts and
aggregations, while storage memory refers to that used for caching and propagating
internal data across the cluster. In Spark, execution and storage share a unified region (M).
When no execution memory is used, storage can acquire all the available memory and vice
versa. Execution may evict storage if necessary, but only until total storage memory usage
falls under a certain threshold (R). In other words, R describes a subregion within M where
cached blocks are never evicted. Storage may not evict execution due to complexities in
implementation.

This design ensures several desirable properties. First, applications that do not use
caching can use the entire space for execution, obviating unnecessary disk spills. Second,
applications that do use caching can reserve a minimum storage space (R) where their
data blocks are immune to being evicted. Lastly, this approach provides reasonable out-
of-the-box performance for a variety of workloads without requiring user expertise of how
memory is divided internally.

Although there are two relevant configurations, the typical user should not need to adjust
them as the default values are applicable to most workloads:

spark.memory.fraction expresses the size of M as a fraction of the (JVM heap space

- 300MiB) (default 0.6). The rest of the space (40%) is reserved for user data
structures, internal metadata in Spark, and safeguarding against OOM errors in the
case of sparse and unusually large records.
spark.memory.storageFraction expresses the size of R as a fraction of M (default 0.5).
R is the storage space within M where cached blocks immune to being evicted by
execution.

The value of spark.memory.fraction should be set in order to fit this amount of heap
space comfortably within the JVM’s old or “tenured” generation. See the discussion of
advanced GC tuning below for details.

Determining Memory Consumption

The best way to size the amount of memory consumption a dataset will require is to create
an RDD, put it into cache, and look at the “Storage” page in the web UI. The page will tell
you how much memory the RDD is occupying.

To estimate the memory consumption of a particular object, use SizeEstimator’s

estimate method. This is useful for experimenting with different data layouts to trim
memory usage, as well as determining the amount of space a broadcast variable will
occupy on each executor heap.

Tuning Data Structures

The first way to reduce memory consumption is to avoid the Java features that add
overhead, such as pointer-based data structures and wrapper objects. There are several
ways to do this:
 1. Design your data structures to prefer arrays of objects, and primitive types, instead of
the standard Java or Scala collection classes (e.g. HashMap). The fastutil
(http://fastutil.di.unimi.it) library provides convenient collection classes for primitive
types that are compatible with the Java standard library.
2. Avoid nested structures with a lot of small objects and pointers when possible.
3. Consider using numeric IDs or enumeration objects instead of strings for keys.
4. If you have less than 32 GiB of RAM, set the JVM flag -XX:+UseCompressedOops to
make pointers be four bytes instead of eight. You can add these options in
spark-env.sh (configuration.html#environment-variables).

Serialized RDD Storage

When your objects are still too large to efficiently store despite this tuning, a much simpler
way to reduce memory usage is to store them in serialized form, using the serialized
StorageLevels in the RDD persistence API (rdd-programming-guide.html#rdd-
persistence), such as MEMORY_ONLY_SER. Spark will then store each RDD partition as one
large byte array. The only downside of storing data in serialized form is slower access
times, due to having to deserialize each object on the fly. We highly recommend using Kryo
(#data-serialization) if you want to cache data in serialized form, as it leads to much
smaller sizes than Java serialization (and certainly than raw Java objects).

Garbage Collection Tuning

JVM garbage collection can be a problem when you have large “churn” in terms of the
RDDs stored by your program. (It is usually not a problem in programs that just read an
RDD once and then run many operations on it.) When Java needs to evict old objects to
make room for new ones, it will need to trace through all your Java objects and find the
unused ones. The main point to remember here is that the cost of garbage collection is
proportional to the number of Java objects, so using data structures with fewer objects
(e.g. an array of Ints instead of a LinkedList) greatly lowers this cost. An even better
method is to persist objects in serialized form, as described above: now there will be only
one object (a byte array) per RDD partition. Before trying other techniques, the first thing
to try if GC is a problem is to use serialized caching (#serialized-rdd-storage).

GC can also be a problem due to interference between your tasks’ working memory (the
amount of space needed to run the task) and the RDDs cached on your nodes. We will
discuss how to control the space allocated to the RDD cache to mitigate this.

Measuring the Impact of GC

The first step in GC tuning is to collect statistics on how frequently garbage collection
occurs and the amount of time spent GC. This can be done by adding
-verbose:gc -XX:+PrintGCDetails -XX:+PrintGCTimeStamps to the Java options. (See
the configuration guide (configuration.html#Dynamically-Loading-Spark-Properties) for
info on passing Java options to Spark jobs.) Next time your Spark job is run, you will see
messages printed in the worker’s logs each time a garbage collection occurs. Note these
logs will be on your cluster’s worker nodes (in the stdout files in their work directories), not
on your driver program.

Advanced GC Tuning

To further tune garbage collection, we first need to understand some basic information
about memory management in the JVM:

Java Heap space is divided in to two regions Young and Old. The Young generation is
meant to hold short-lived objects while the Old generation is intended for objects
with longer lifetimes.

The Young generation is further divided into three regions [Eden, Survivor1, Survivor2].

A simplified description of the garbage collection procedure: When Eden is full, a

minor GC is run on Eden and objects that are alive from Eden and Survivor1 are copied
to Survivor2. The Survivor regions are swapped. If an object is old enough or Survivor2
is full, it is moved to Old. Finally, when Old is close to full, a full GC is invoked.

The goal of GC tuning in Spark is to ensure that only long-lived RDDs are stored in the Old
generation and that the Young generation is sufficiently sized to store short-lived objects.
This will help avoid full GCs to collect temporary objects created during task execution.
Some steps which may be useful are:

Check if there are too many garbage collections by collecting GC stats. If a full GC is
invoked multiple times before a task completes, it means that there isn’t enough
memory available for executing tasks.

If there are too many minor collections but not many major GCs, allocating more
memory for Eden would help. You can set the size of the Eden to be an over-estimate
of how much memory each task will need. If the size of Eden is determined to be E,
then you can set the size of the Young generation using the option -Xmn=4/3*E. (The
scaling up by 4/3 is to account for space used by survivor regions as well.)

In the GC stats that are printed, if the OldGen is close to being full, reduce the amount
of memory used for caching by lowering spark.memory.fraction; it is better to cache
fewer objects than to slow down task execution. Alternatively, consider decreasing the
size of the Young generation. This means lowering -Xmn if you’ve set it as above. If not,
 try changing the value of the JVM’s NewRatio parameter. Many JVMs default this to 2,
meaning that the Old generation occupies 2/3 of the heap. It should be large enough
such that this fraction exceeds spark.memory.fraction.

Try the G1GC garbage collector with -XX:+UseG1GC. It can improve performance in
some situations where garbage collection is a bottleneck. Note that with large
executor heap sizes, it may be important to increase the G1 region size
(http://www.oracle.com/technetwork/articles/java/g1gc-1984535.html) with
-XX:G1HeapRegionSize.

As an example, if your task is reading data from HDFS, the amount of memory used by
the task can be estimated using the size of the data block read from HDFS. Note that
the size of a decompressed block is often 2 or 3 times the size of the block. So if we
wish to have 3 or 4 tasks’ worth of working space, and the HDFS block size is 128 MiB,
we can estimate the size of Eden to be 4*3*128MiB.

Monitor how the frequency and time taken by garbage collection changes with the
new settings.

Our experience suggests that the effect of GC tuning depends on your application and the
amount of memory available. There are many more tuning options
(https://docs.oracle.com/javase/8/docs/technotes/guides/vm/gctuning/index.html)
described online, but at a high level, managing how frequently full GC takes place can help
in reducing the overhead.

GC tuning flags for executors can be specified by setting

spark.executor.defaultJavaOptions or spark.executor.extraJavaOptions in a job’s
configuration.

Other Considerations
Level of Parallelism
Clusters will not be fully utilized unless you set the level of parallelism for each operation
high enough. Spark automatically sets the number of “map” tasks to run on each file
according to its size (though you can control it through optional parameters to
SparkContext.textFile, etc), and for distributed “reduce” operations, such as groupByKey
and reduceByKey, it uses the largest parent RDD’s number of partitions. You can pass the
level of parallelism as a second argument (see the spark.PairRDDFunctions
(api/scala/org/apache/spark/rdd/PairRDDFunctions.html) documentation), or set the
config property spark.default.parallelism to change the default. In general, we
recommend 2-3 tasks per CPU core in your cluster.
Parallel Listing on Input Paths

Sometimes you may also need to increase directory listing parallelism when job input has
large number of directories, otherwise the process could take a very long time, especially
when against object store like S3. If your job works on RDD with Hadoop input formats (e.g.,
via SparkContext.sequenceFile), the parallelism is controlled via
spark.hadoop.mapreduce.input.fileinputformat.list-status.num-threads
(https://hadoop.apache.org/docs/current/hadoop-mapreduce-client/hadoop-
mapreduce-client-core/mapred-default.xml) (currently default is 1).

For Spark SQL with file-based data sources, you can tune
spark.sql.sources.parallelPartitionDiscovery.threshold and
spark.sql.sources.parallelPartitionDiscovery.parallelism to improve listing
parallelism. Please refer to Spark SQL performance tuning guide (sql-performance-
tuning.html) for more details.

Memory Usage of Reduce Tasks

Sometimes, you will get an OutOfMemoryError not because your RDDs don’t fit in memory,
but because the working set of one of your tasks, such as one of the reduce tasks in
groupByKey, was too large. Spark’s shuffle operations (sortByKey, groupByKey,
reduceByKey, join, etc) build a hash table within each task to perform the grouping, which
can often be large. The simplest fix here is to increase the level of parallelism, so that each
task’s input set is smaller. Spark can efficiently support tasks as short as 200 ms, because
it reuses one executor JVM across many tasks and it has a low task launching cost, so you
can safely increase the level of parallelism to more than the number of cores in your
clusters.

Broadcasting Large Variables

Using the broadcast functionality (rdd-programming-guide.html#broadcast-variables)

available in SparkContext can greatly reduce the size of each serialized task, and the cost
of launching a job over a cluster. If your tasks use any large object from the driver program
inside of them (e.g. a static lookup table), consider turning it into a broadcast variable.
Spark prints the serialized size of each task on the master, so you can look at that to
decide whether your tasks are too large; in general, tasks larger than about 20 KiB are
probably worth optimizing.
Data Locality
Data locality can have a major impact on the performance of Spark jobs. If data and the
code that operates on it are together, then computation tends to be fast. But if code and
data are separated, one must move to the other. Typically, it is faster to ship serialized
code from place to place than a chunk of data because code size is much smaller than
data. Spark builds its scheduling around this general principle of data locality.

Data locality is how close data is to the code processing it. There are several levels of
locality based on the data’s current location. In order from closest to farthest:

PROCESS_LOCAL data is in the same JVM as the running code. This is the best locality
possible.
NODE_LOCAL data is on the same node. Examples might be in HDFS on the same node,
or in another executor on the same node. This is a little slower than PROCESS_LOCAL
because the data has to travel between processes.
NO_PREF data is accessed equally quickly from anywhere and has no locality
preference.
RACK_LOCAL data is on the same rack of servers. Data is on a different server on the
same rack so needs to be sent over the network, typically through a single switch.
ANY data is elsewhere on the network and not in the same rack.

Spark prefers to schedule all tasks at the best locality level, but this is not always possible.
In situations where there is no unprocessed data on any idle executor, Spark switches to
lower locality levels. There are two options: a) wait until a busy CPU frees up to start a task
on data on the same server, or b) immediately start a new task in a farther away place that
requires moving data there.

What Spark typically does is wait a bit in the hopes that a busy CPU frees up. Once that
timeout expires, it starts moving the data from far away to the free CPU. The wait timeout
for fallback between each level can be configured individually or all together in one
parameter; see the spark.locality parameters on the configuration page
(configuration.html#scheduling) for details. You should increase these settings if your
tasks are long and see poor locality, but the default usually works well.

Summary
This has been a short guide to point out the main concerns you should know about when
tuning a Spark application – most importantly, data serialization and memory tuning. For
most programs, switching to Kryo serialization and persisting data in serialized form will
solve most common performance issues. Feel free to ask on the Spark mailing list
(https://spark.apache.org/community.html) about other tuning best practices.