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Spark Shell

Spark can run in several modes, including YARN client/server, Standalone, Mesos and Local. For this training, we will use local mode. Specifically, you can start the Spark interactive shell by invoking the command below in the terminal to run Spark in the local mode with two threads. Then you will see

> spark-shell --master "local[2]" --driver-memory 6G
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
...
[messages]
...
Spark context available as sc.
scala>

Here you can set --driver-memory according to your local setting. If your setting of driver memory is larger than the VM memory, don't forget to change the VM memory setting first.

In Spark, we call the main entrance of a Spark program the driver and Spark distribute computation to workers to compute. Here in the interactive shell, the Spark shell program is the driver. In above example we set the memory of driver program to 3GB as in local mode driver and worker are together. A driver program can access Spark through a SparkContext object, which represents a connection to a computing cluster. In the above interactive shell, SparkContext is already created for you as variable sc. You can input sc to see its type.

scala> sc
res0: org.apache.spark.SparkContext = org.apache.spark.SparkContext@27896d3b

RDD

Resilient Distributed Dataset (RDD) is Spark's core abstraction for working with data. An RDD is simply a fault-tolerant distributed collection of elements. You can imagine RDD as a large array but you cannot access elements randomly but you can apply the same operations to all elements in the array easily. In Spark, all the work is expressed as either creating new RDDs, transforming existing RDDs, or calling operations on RDDs to compute results. There are two ways to create RDDs: by distributing a collection of objects (e.g., a list or set), or by referencing a dataset in an external storage system, such as a shared filesystem, HDFS, HBase, or any data source offering a Hadoop InputFormat.

Parallelized Collections

For the demo purpose, the simplest way to create an RDD is to take an existing collection (e.g. a Scala Array) in your program and pass it to SparkContext's parallelize() method.

scala> val data = Array(1, 2, 3, 4, 5)
data: Array[Int] = Array(1, 2, 3, 4, 5)

scala> val distData = sc.parallelize(data)
distData: org.apache.spark.rdd.RDD[Int] = ParallelCollectionRDD[0] at parallelize at <console>:23

Once created, the distributed dataset (distData) can be operated in parallel. For example, we can add up the elements by calling distData.reduce((a, b) => a + b). You will see more operations on RDD later on.

External Datasets

A common way for creating RDDs is loading data from external storage. Below you will learn how to load data from a file system. Assuming you have put some data into HDFS as described in the HDFS Basic section. If not, please do that first.

scala> val lines = sc.textFile("input/case.csv")
lines: org.apache.spark.rdd.RDD[String] = README.md MapPartitionsRDD[1] at textFile at <console>:21

Here in the above example, each line of the original file will become an element in the lines RDD.

RDD Operations

RDDs offer two types of operations: transformations and actions:

• Transformations are operations on RDDs that return a new RDD, such as map() and filter().
• Actions are operations that return a result to the driver program or write it to storage, such as first() and count().

Spark treats transformations and actions very differently, so understanding which type of operation you are performing is very important. You can check whether a function is a transformation or an action by looking at its return type: transformations return RDDs, whereas actions return some other data type.

All transformations in Spark are lazy, in that they do not compute the results right away. Instead, they just remember the operations applied to some base dataset (e.g. an Array or a file). The transformations are only computed when an action requires a result to be returned to the driver program. Therefore, the above command of reading in a file has not actually been executed yet. We can force the evaluation of RDDs by calling any actions.

Let's go through some common RDD operations using the healthcare dataset. Recall that in the file case.csv, each line is a 4-field tuple (patient-id, event-id, timestamp, value).

Count

In order to know how large is our raw event sequence data, we can count the number of lines in the input file using count operation, i.e.

scala> lines.count()
res1: Long = 14046

Clearly, count is an action.

Take

You may wonder what the loaded data looks like, you can take a peek at the data. The take(k) will return the first k elements in the RDD. Spark also provides collect() which brings all the elements in the RDD back to the driver program. Note that collect() should only be used when the data is small. Both take and collect are actions.

scala> lines.take(5)
res2: Array[String] = Array(00013D2EFD8E45D1,DIAG78820,1166,1.0, 00013D2EFD8E45D1,DIAGV4501,1166,1.0, 00013D2EFD8E45D1,heartfailure,1166,1.0, 00013D2EFD8E45D1,DIAG2720,1166,1.0, 00013D2EFD8E45D1,DIAG4019,1166,1.0)  

We got the first 5 records in this RDD. However, this is hard to read due to a poor format. We can make it more readable by traversing the array to print each record on its own line.

scala> lines.take(5).foreach(println)
00013D2EFD8E45D1,DIAG78820,1166,1.0
00013D2EFD8E45D1,DIAGV4501,1166,1.0
00013D2EFD8E45D1,heartfailure,1166,1.0
00013D2EFD8E45D1,DIAG2720,1166,1.0
00013D2EFD8E45D1,DIAG4019,1166,1.0

Note that in above 3 code block examples, the RDD lines has been computed (i.e. read in from file) 3 times. We can prevent this by calling lines.cache(), which will cache the RDD in memory to avoid reloading.

scala> lines.take(5).map(_.split(",")).map(_(1)).foreach(println)

Map

The map operation in Spark is similar to that of Hadoop. It's a transformation that transforms each item in the RDD into a new item by applying the provided function. Notice this map will map exactly one element from source to target. For example, suppose we are only interested in knowing IDs of patients, we use map like

scala> lines.map(line => line.split(",")(0))

It is also possible to write a more complex, multiple-lines map function. In this case, curly braces should be used in place of parentheses. For example, we can get both patient-id and event-id as a tuple at the same time.

scala> lines.map{line =>
  val s = line.split(",")
  (s(0), s(1))
}

Filter

As indicated by its name, filter can transform an RDD to another RDD by keeping only elements that satisfy the filtering condition. For example, we want to count the number of events collected for a particular patient to verify amount of the data from that patient. We can use a filter function.

scala> lines.filter(line => line.contains("00013D2EFD8E45D1")).count()
res4: Long = 200

Distinct

distinct is a transformation that transforms a RDD to another by eliminating duplications. We can use that to count the number of distinct patients. In order to do this, we first extract the patient ID from each line. We use the map() function as described above. In this example, we transform each line into the corresponding patient ID by extracting only the first column. We then eliminate duplicate IDs by the distinct() function.

scala> lines.map(line => line.split(",")(0)).distinct().count()
res5: Long = 100

Group

Sometimes, you will need to group the input events according to patient-id to put everything about each patient together. For example, in order to extract index date for predictive modeling, you may first group input data by patient then handle each patient seperately in parallel. We can see each element in RDD is a (Key, Value) pair (patient-id, iterable[event]).

> val patientIdEventPair = lines.map{line =>
  val patientId = line.split(",")(0)
  (patientId, line)
}
> val groupedPatientData = patientIdEventPair.groupByKey
> groupedPatientData.take(1)
res1: Array[(String, Iterable[String])] = Array((0102353632C5E0D0,CompactBuffer(0102353632C5E0D0,DIAG29181,562,1.0, 0102353632C5E0D0,DIAG29212,562,1.0, 0102353632C5E0D0,DIAG34590,562,1.0, 0102353632C5E0D0,DIAG30000,562,1.0, 0102353632C5E0D0,DIAG2920,562,1.0, 0102353632C5E0D0,DIAG412,562,1.0, 0102353632C5E0D0,DIAG28800,562,1.0, 0102353632C5E0D0,DIAG30391,562,1.0, 0102353632C5E0D0,DIAGRG894,562,1.0, 0102353632C5E0D0,PAYMENT,562,6000.0, 0102353632C5E0D0,DIAG5781,570,1.0, 0102353632C5E0D0,DIAG53010,570,1.0, 0102353632C5E0D0,DIAGE8490,570,1.0, 0102353632C5E0D0,DIAG27651,570,1.0, 0102353632C5E0D0,DIAG78559,570,1.0, 0102353632C5E0D0,DIAG56210,570,1.0, 0102353632C5E0D0,DIAG5856,570,1.0, 0102353632C5E0D0,heartfailure,570,1.0, 0102353632C5E0D0,DIAG5070,570,1.0, 0102353632C5E0D0,DIAGRG346,570,1.0,...
....

Reduce By Key

reduceByKey transforms an RDD[(K, V)] into RDD[(K, List[V])] (like what groupByKey does) and then apply reduce function on List[V] to get final output RDD[(K, V)]. Please be careful that we intentionally denote V as return type of reduce which should be same as input type of the list element. Suppose now we want to calculate the total payment by each patient. A payment record in the dataset is in the form of (patient-id, PAYMENT, timestamp, value).

val payment_events = lines.filter(line => line.contains("PAYMENT"))
val payments = payment_events.map{ x =>
                                   val s = x.split(",")
                                   (s(0), s(3).toFloat)
                                 }
val paymentPerPatient = payments.reduceByKey(_+_)

The payment_events RDD returned by filter contains those records associated with payment. Each item is then transformed to a key-value pair (patient-id, payment) with map. Because each patient can have multiple payments, we need to use reduceByKey to sum up the payments for each patient. Here in this example, patient-id will be served as the key, and payment will be the value to sum up for each patient. The figure below shows the process of reduceByKey in our example

Sort

We can then find the top-3 patients with the highest payment by using sortBy first.

scala> paymentPerPatient.sortBy(_._2, false).take(3).foreach(println)

and output is

(0085B4F55FFA358D,139880.0)
(019E4729585EF3DD,108980.0)
(01AC552BE839AB2B,108530.0)

Again in sortBy we use the _ placeholder, so that _._2 is an anonymous function that returns the second element of a tuple, which is the total payment a patient. The second parameter of sortBy controls the order of sorting. In above example, false means decreasing order.

scala> val maxPaymentPerPatient = payments.reduceByKey(math.max)

scala> val drugFrequency = lines.filter(_.contains("DRUG")).
                                 map{ x =>
                                   val s = x.split(",")
                                   (s(1), 1)
                                 }.reduceByKey(_+_)

Statistics

Now we have total payment information of patients, we can run some basic statistics. For RDD consists of numeric values, Spark provides some useful statistical primitives.

scala> val payment_values = paymentPerPatient.map(payment => payment._2).cache()
scala> payment_values.max()
res6: Float = 139880.0

scala> payment_values.min()
res7: Float = 3910.0

scala> payment_values.sum()
res8: Double = 2842480.0

scala> payment_values.mean()
res9: Double = 28424.8  

scala> payment_values.stdev()
res10: Double = 26337.091771112468

Set Operation

RDDs support many of the set operations, such as union and intersection, even when the RDDs themselves are not properly sets. For example, we can combine the two files by the union function. Please notice that union here is not strictly identical to union operation in mathematics as Spark will not remove duplications.

scala> val linesControl = sc.textFile("input/control.csv")
scala> lines.union(linesControl).count() 
res11: Long = 31144 

scala> val lines = sc.textFile("input/")

scala> val drugCase = sc.textFile("input/case.csv").
                     filter(_.contains("DRUG")).
                     map(_.split(",")(1)).
                     distinct()
scala> val drugControl = sc.textFile("input/control.csv").
                     filter(_.contains("DRUG")).  
                     map(_.split(",")(1)).
                     distinct()
scala> drugCase.intersection(drugControl).count()
res: Long = 396

Further Reading

For the complete list of RDD operations, please see the Spark Programming Guide.

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