Question

感谢大家的帮助！我对Spark非常陌生，一直在使用Databricks（运行时版本5.0，包括Apache Spark 2.4.0，Scala 2.11）。

我一直在尝试使用spark-xml（2.11.0.5.0）加载一些XML文件，并遇到以下sparkException：

org.apache.spark.SparkException: Job aborted due to stage failure: 
Task 5 in stage 0.0 failed 4 times, most recent failure: Lost task 
5.3 in stage 0.0 (TID 17, 10.106.234.32, executor 0): 
java.lang.NullPointerException

at scala.collection.immutable.StringOps$.apply$extension(StringOps.scala:37)
at com.databricks.spark.xml.XmlRecordReader.readUntilStartElement(XmlInputFormat.scala:156)
at com.databricks.spark.xml.XmlRecordReader.next(XmlInputFormat.scala:131)
at com.databricks.spark.xml.XmlRecordReader.nextKeyValue(XmlInputFormat.scala:119)
at org.apache.spark.rdd.NewHadoopRDD$$anon$1.hasNext(NewHadoopRDD.scala:236)
at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:37)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIteratorForCodegenStage1.agg_doAggregateWithoutKey_0$(Unknown Source)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIteratorForCodegenStage1.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$11$$anon$1.hasNext(WholeStageCodegenExec.scala:619)
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
at org.apache.spark.shuffle.sort.BypassMergeSortShuffleWriter.write(BypassMergeSortShuffleWriter.java:125)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:99)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:55)
at org.apache.spark.scheduler.Task.run(Task.scala:124)
at org.apache.spark.executor.Executor$TaskRunner$$anonfun$11.apply(Executor.scala:459)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1401)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:465)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

奇怪的是，在使用完全相同的集群配置前一天加载文件没有问题：

Databricks运行时版本：5.0（包括Apache Spark 2.4.0，Scala 2.11）
驱动程序和工作程序类型：i3.xlarge-30.5 GB内存，4核，1 DBU

每个未压缩的XML文件的大小在70M到130M之间，其中有8个。我希望将它们加载到一个数据集中。

我获得了以下数据，并将其上传到Databricks：

wget ftp://ftp.nlm.nih.gov/nlmdata/sample/medline/*.gz
gunzip *.gz

代码如下：

import com.databricks.spark.xml._
import org.apache.spark.sql.{Dataset, SparkSession}
import org.apache.hadoop.conf.Configuration
import org.apache.hadoop.io.{Text, LongWritable}


def loadMedline(spark: SparkSession, path: String) = {
  import spark.implicits._

  /* conf: org.apache.hadoop.conf.Configuration = Configuration: 
   * core-default.xml, core-site.xml, mapred-default.xml, 
   * mapred-site.xml, yarn-default.xml, yarn-site.xml, 
   * hdfs-default.xml, hdfs-site.xml
   */

  @transient val conf = new Configuration()
  conf.set(XmlInputFormat.START_TAG_KEY, "<MedlineCitation>")
  conf.set(XmlInputFormat.END_TAG_KEY, "</MedlineCitation>")

  /* sc: org.apache.spark.SparkContext */
  val sc = spark.sparkContext

  /* records: org.apache.spark.rdd.RDD[(org.apache.hadoop.io.LongWritable, org.apache.hadoop.io.Text)] = 
   * dbfs:/FileStore/tables/ch7_medline/ NewHadoopRDD[0] at newAPIHadoopFile at command-2335143412865645:1
   */

  val records = sc.newAPIHadoopFile(path, classOf[XmlInputFormat],
    classOf[LongWritable], classOf[Text])

  /* returns: org.apache.spark.sql.Dataset[String] = [value: string] */
  records.map(line => line._2.toString).toDS()
}

/* medlineRaw: org.apache.spark.sql.Dataset[String] = [value: string] */
val medlineRaw = loadMedline(spark, "dbfs:/FileStore/tables/ch7_medline/")

medlineRaw.count()   // <--- got the error here

再次非常感谢您！环顾了一段时间，但仍然无法正常工作。

由于阶段故障，Spark Job中止了：使用spark-xml加载xml文件时，java.lang.NullPointerException

0 个答案: