Operating RDD failed while setting Spark record delimiter with org.apache.hadoop.conf.Configuration

apache-spark, configuration, delimiter, rdd, scala

Solution

You are getting this exception because you are closing over `org.apache.hadoop.conf.Configuration` but it is not `serializable`

Caused by: java.io.NotSerializableException: org.apache.hadoop.conf.Configuration
    at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1183)
    at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1547)
    at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1508)
    at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1431)
    at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1177)
    at java.io.ObjectOutputStream.defaultWriteFields(ObjectOutputStream.java:1547)
    at java.io.ObjectOutputStream.writeSerialData(ObjectOutputStream.java:1508)
    at java.io.ObjectOutputStream.writeOrdinaryObject(ObjectOutputStream.java:1431)
    at java.io.ObjectOutputStream.writeObject0(ObjectOutputStream.java:1177)

You can do two things: 1. Register Configuration with a Kyro serializer OR 2. Just mark your conf variable as `transient` which basically tells Spark not to ship it with the closure.

scala> @transient val conf = new Configuration
conf: org.apache.hadoop.conf.Configuration = Configuration: core-default.xml, core-site.xml, mapred-default.xml, mapred-site.xml

scala> val raw_data = sc.newAPIHadoopFile("../test.txt", classOf[TextInputFormat], classOf[LongWritable], classOf[Text], conf).map(_._2.toString)
14/11/28 00:54:03 INFO MemoryStore: ensureFreeSpace(32937) called with curMem=70594, maxMem=278302556
14/11/28 00:54:03 INFO MemoryStore: Block broadcast_4 stored as values in memory (estimated size 32.2 KB, free 265.3 MB)
raw_data: org.apache.spark.rdd.RDD[String] = MappedRDD[5] at map at <console>:18

scala> val data = raw_data.filter{x => x.split(FIELD_SEP).size >= 3}
data: org.apache.spark.rdd.RDD[String] = FilteredRDD[6] at filter at <console>:22

scala> data.count
14/11/28 00:54:16 INFO FileInputFormat: Total input paths to process : 1
14/11/28 00:54:16 INFO SparkContext: Starting job: count at <console>:25
14/11/28 00:54:16 INFO DAGScheduler: Got job 2 (count at <console>:25) with 1 output partitions (allowLocal=false)
14/11/28 00:54:16 INFO DAGScheduler: Final stage: Stage 2(count at <console>:25)
14/11/28 00:54:16 INFO DAGScheduler: Parents of final stage: List()
14/11/28 00:54:16 INFO DAGScheduler: Missing parents: List()
14/11/28 00:54:16 INFO DAGScheduler: Submitting Stage 2 (FilteredRDD[6] at filter at <console>:22), which has no missing parents
14/11/28 00:54:16 INFO MemoryStore: ensureFreeSpace(4488) called with curMem=103531, maxMem=278302556
14/11/28 00:54:16 INFO MemoryStore: Block broadcast_5 stored as values in memory (estimated size 4.4 KB, free 265.3 MB)
14/11/28 00:54:16 INFO DAGScheduler: Submitting 1 missing tasks from Stage 2 (FilteredRDD[6] at filter at <console>:22)
14/11/28 00:54:16 INFO TaskSchedulerImpl: Adding task set 2.0 with 1 tasks
14/11/28 00:54:16 INFO TaskSetManager: Starting task 0.0 in stage 2.0 (TID 2, localhost, PROCESS_LOCAL, 1223 bytes)
14/11/28 00:54:16 INFO Executor: Running task 0.0 in stage 2.0 (TID 2)
14/11/28 00:54:16 INFO NewHadoopRDD: Input split: file:/Users/ssimanta/spark/test.txt:0+123
14/11/28 00:54:16 INFO Executor: Finished task 0.0 in stage 2.0 (TID 2). 1731 bytes result sent to driver
14/11/28 00:54:16 INFO TaskSetManager: Finished task 0.0 in stage 2.0 (TID 2) in 19 ms on localhost (1/1)
14/11/28 00:54:16 INFO DAGScheduler: Stage 2 (count at <console>:25) finished in 0.019 s
14/11/28 00:54:16 INFO TaskSchedulerImpl: Removed TaskSet 2.0, whose tasks have all completed, from pool 
14/11/28 00:54:16 INFO DAGScheduler: Job 2 finished: count at <console>:25, took 0.025300 s
res5: Long = 1

scala> data.collect
14/11/28 00:55:16 INFO SparkContext: Starting job: collect at <console>:25
14/11/28 00:55:16 INFO DAGScheduler: Got job 3 (collect at <console>:25) with 1 output partitions (allowLocal=false)
14/11/28 00:55:16 INFO DAGScheduler: Final stage: Stage 3(collect at <console>:25)
14/11/28 00:55:16 INFO DAGScheduler: Parents of final stage: List()
14/11/28 00:55:16 INFO DAGScheduler: Missing parents: List()
14/11/28 00:55:16 INFO DAGScheduler: Submitting Stage 3 (FilteredRDD[6] at filter at <console>:22), which has no missing parents
14/11/28 00:55:16 INFO MemoryStore: ensureFreeSpace(4504) called with curMem=108019, maxMem=278302556
14/11/28 00:55:16 INFO MemoryStore: Block broadcast_6 stored as values in memory (estimated size 4.4 KB, free 265.3 MB)
14/11/28 00:55:16 INFO DAGScheduler: Submitting 1 missing tasks from Stage 3 (FilteredRDD[6] at filter at <console>:22)
14/11/28 00:55:16 INFO TaskSchedulerImpl: Adding task set 3.0 with 1 tasks
14/11/28 00:55:16 INFO TaskSetManager: Starting task 0.0 in stage 3.0 (TID 3, localhost, PROCESS_LOCAL, 1223 bytes)
14/11/28 00:55:16 INFO Executor: Running task 0.0 in stage 3.0 (TID 3)
14/11/28 00:55:16 INFO NewHadoopRDD: Input split: file:/Users/ssimanta/spark/test.txt:0+123
14/11/28 00:55:16 INFO Executor: Finished task 0.0 in stage 3.0 (TID 3). 1717 bytes result sent to driver
14/11/28 00:55:16 INFO TaskSetManager: Finished task 0.0 in stage 3.0 (TID 3) in 16 ms on localhost (1/1)
14/11/28 00:55:16 INFO DAGScheduler: Stage 3 (collect at <console>:25) finished in 0.017 s
14/11/28 00:55:16 INFO TaskSchedulerImpl: Removed TaskSet 3.0, whose tasks have all completed, from pool 
14/11/28 00:55:16 INFO DAGScheduler: Job 3 finished: collect at <console>:25, took 0.021439 s
res6: Array[String] = Array(MMMM_|NNNNN_|OOOOO\ |)

Problem

Original source