【发布时间】:2018-08-17 11:57:21
【问题描述】:
作为背景知识,我正在尝试在 Spark 中实现 Kaplan-Meier。特别是,我假设我有一个数据框/集,其中 Double 列表示为 Data 和 Int 列名为 censorFlag (0 值如果被审查,1 如果没有,更喜欢这个Boolean 类型)。
例子:
val df = Seq((1.0, 1), (2.3, 0), (4.5, 1), (0.8, 1), (0.7, 0), (4.0, 1), (0.8, 1)).toDF("data", "censorFlag").as[(Double, Int)]
现在我需要计算一个列 wins 来计算每个 data 值的实例。我使用以下代码实现了这一点:
val distDF = df.withColumn("wins", sum(col("censorFlag")).over(Window.partitionBy("data").orderBy("data")))
当我需要计算一个称为 atRisk 的数量时,问题就来了,对于 data 的每个值,大于或等于它的 data 点的数量(累积过滤计数,如果你会的)。
以下代码有效:
// We perform the counts per value of "bins". This is an array of doubles
val bins = df.select(col("data").as("dataBins")).distinct().sort("dataBins").as[Double].collect
val atRiskCounts = bins.map(x => (x, df.filter(col("data").geq(x)).count)).toSeq.toDF("data", "atRisk")
// this works:
atRiskCounts.show
但是,用例涉及从列data 派生bins 本身,我宁愿将其保留为单列数据集(或最坏的 RDD),但肯定不是本地数组。但这不起作用:
// Here, 'bins' rightfully come from the data itself.
val bins = df.select(col("data").as("dataBins")).distinct().as[Double]
val atRiskCounts = bins.map(x => (x, df.filter(col("data").geq(x)).count)).toSeq.toDF("data", "atRisk")
// This doesn't work -- NullPointerException
atRiskCounts.show
这也不是:
// Manually creating the bins and then parallelizing them.
val bins = Seq(0.7, 0.8, 1.0, 3.0).toDS
val atRiskCounts = bins.map(x => (x, df.filter(col("data").geq(x)).count)).toDF("data", "atRisk")
// Also fails with a NullPointerException
atRiskCounts.show
另一种确实有效但从并行化角度来看也不令人满意的方法是使用Window:
// Do the counts in one fell swoop using a giant window per value.
val atRiskCounts = df.withColumn("atRisk", count("censorFlag").over(Window.orderBy("data").rowsBetween(0, Window.unboundedFollowing))).groupBy("data").agg(first("atRisk").as("atRisk"))
// Works, BUT, we get a "WARN WindowExec: No Partition Defined for Window operation! Moving all data to a single partition, this can cause serious performance degradation."
atRiskCounts.show
最后一个解决方案没有用,因为它最终将我的数据洗牌到单个分区(在这种情况下,我不妨选择选项 1 工作)。
成功的方法很好,只是箱子不平行,如果可能的话,我真的很想保留这些东西。我查看了 groupBy 聚合、pivot 类型的聚合,但似乎没有任何意义。
我的问题是:有没有办法以分布式方式计算 atRisk 列?另外,为什么我在失败的解决方案中得到NullPointerException?
编辑每条评论:
我最初并没有发布NullPointerException,因为它似乎没有包含任何有用的内容。我会注意,这是通过自制软件在我的 Macbook Pro 上安装的 Spark(Spark 版本 2.2.1,独立 localhost 模式)。
18/03/12 11:41:00 ERROR ExecutorClassLoader: Failed to check existence of class <root>.package on REPL class server at spark://10.37.109.111:53360/classes
java.net.URISyntaxException: Illegal character in path at index 36: spark://10.37.109.111:53360/classes/<root>/package.class
at java.net.URI$Parser.fail(URI.java:2848)
at java.net.URI$Parser.checkChars(URI.java:3021)
at java.net.URI$Parser.parseHierarchical(URI.java:3105)
at java.net.URI$Parser.parse(URI.java:3053)
at java.net.URI.<init>(URI.java:588)
at org.apache.spark.rpc.netty.NettyRpcEnv.openChannel(NettyRpcEnv.scala:327)
at org.apache.spark.repl.ExecutorClassLoader.org$apache$spark$repl$ExecutorClassLoader$$getClassFileInputStreamFromSparkRPC(ExecutorClassLoader.scala:90)
at org.apache.spark.repl.ExecutorClassLoader$$anonfun$1.apply(ExecutorClassLoader.scala:57)
at org.apache.spark.repl.ExecutorClassLoader$$anonfun$1.apply(ExecutorClassLoader.scala:57)
at org.apache.spark.repl.ExecutorClassLoader.findClassLocally(ExecutorClassLoader.scala:162)
at org.apache.spark.repl.ExecutorClassLoader.findClass(ExecutorClassLoader.scala:80)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
. . . .
18/03/12 11:41:00 ERROR ExecutorClassLoader: Failed to check existence of class <root>.scala on REPL class server at spark://10.37.109.111:53360/classes
java.net.URISyntaxException: Illegal character in path at index 36: spark://10.37.109.111:53360/classes/<root>/scala.class
at java.net.URI$Parser.fail(URI.java:2848)
at java.net.URI$Parser.checkChars(URI.java:3021)
at java.net.URI$Parser.parseHierarchical(URI.java:3105)
at java.net.URI$Parser.parse(URI.java:3053)
at java.net.URI.<init>(URI.java:588)
at org.apache.spark.rpc.netty.NettyRpcEnv.openChannel(NettyRpcEnv.scala:327)
at org.apache.spark.repl.ExecutorClassLoader.org$apache$spark$repl$ExecutorClassLoader$$getClassFileInputStreamFromSparkRPC(ExecutorClassLoader.scala:90)
at org.apache.spark.repl.ExecutorClassLoader$$anonfun$1.apply(ExecutorClassLoader.scala:57)
at org.apache.spark.repl.ExecutorClassLoader$$anonfun$1.apply(ExecutorClassLoader.scala:57)
at org.apache.spark.repl.ExecutorClassLoader.findClassLocally(ExecutorClassLoader.scala:162)
at org.apache.spark.repl.ExecutorClassLoader.findClass(ExecutorClassLoader.scala:80)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
. . .
18/03/12 11:41:00 ERROR ExecutorClassLoader: Failed to check existence of class <root>.org on REPL class server at spark://10.37.109.111:53360/classes
java.net.URISyntaxException: Illegal character in path at index 36: spark://10.37.109.111:53360/classes/<root>/org.class
at java.net.URI$Parser.fail(URI.java:2848)
at java.net.URI$Parser.checkChars(URI.java:3021)
at java.net.URI$Parser.parseHierarchical(URI.java:3105)
at java.net.URI$Parser.parse(URI.java:3053)
at java.net.URI.<init>(URI.java:588)
at org.apache.spark.rpc.netty.NettyRpcEnv.openChannel(NettyRpcEnv.scala:327)
at org.apache.spark.repl.ExecutorClassLoader.org$apache$spark$repl$ExecutorClassLoader$$getClassFileInputStreamFromSparkRPC(ExecutorClassLoader.scala:90)
at org.apache.spark.repl.ExecutorClassLoader$$anonfun$1.apply(ExecutorClassLoader.scala:57)
at org.apache.spark.repl.ExecutorClassLoader$$anonfun$1.apply(ExecutorClassLoader.scala:57)
at org.apache.spark.repl.ExecutorClassLoader.findClassLocally(ExecutorClassLoader.scala:162)
at org.apache.spark.repl.ExecutorClassLoader.findClass(ExecutorClassLoader.scala:80)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
. . .
18/03/12 11:41:00 ERROR ExecutorClassLoader: Failed to check existence of class <root>.java on REPL class server at spark://10.37.109.111:53360/classes
java.net.URISyntaxException: Illegal character in path at index 36: spark://10.37.109.111:53360/classes/<root>/java.class
at java.net.URI$Parser.fail(URI.java:2848)
at java.net.URI$Parser.checkChars(URI.java:3021)
at java.net.URI$Parser.parseHierarchical(URI.java:3105)
at java.net.URI$Parser.parse(URI.java:3053)
at java.net.URI.<init>(URI.java:588)
at org.apache.spark.rpc.netty.NettyRpcEnv.openChannel(NettyRpcEnv.scala:327)
at org.apache.spark.repl.ExecutorClassLoader.org$apache$spark$repl$ExecutorClassLoader$$getClassFileInputStreamFromSparkRPC(ExecutorClassLoader.scala:90)
at org.apache.spark.repl.ExecutorClassLoader$$anonfun$1.apply(ExecutorClassLoader.scala:57)
at org.apache.spark.repl.ExecutorClassLoader$$anonfun$1.apply(ExecutorClassLoader.scala:57)
at org.apache.spark.repl.ExecutorClassLoader.findClassLocally(ExecutorClassLoader.scala:162)
at org.apache.spark.repl.ExecutorClassLoader.findClass(ExecutorClassLoader.scala:80)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
. . .
18/03/12 11:41:00 ERROR Executor: Exception in task 0.0 in stage 55.0 (TID 432)
java.lang.NullPointerException
at org.apache.spark.sql.Dataset.<init>(Dataset.scala:171)
at org.apache.spark.sql.Dataset$.apply(Dataset.scala:62)
at org.apache.spark.sql.Dataset.withTypedPlan(Dataset.scala:2889)
at org.apache.spark.sql.Dataset.filter(Dataset.scala:1301)
at $line124.$read$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$anonfun$1.apply(<console>:33)
at $line124.$read$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$anonfun$1.apply(<console>:33)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:395)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:234)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:228)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:108)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:338)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
18/03/12 11:41:00 WARN TaskSetManager: Lost task 0.0 in stage 55.0 (TID 432, localhost, executor driver): java.lang.NullPointerException
at org.apache.spark.sql.Dataset.<init>(Dataset.scala:171)
at org.apache.spark.sql.Dataset$.apply(Dataset.scala:62)
at org.apache.spark.sql.Dataset.withTypedPlan(Dataset.scala:2889)
at org.apache.spark.sql.Dataset.filter(Dataset.scala:1301)
at $line124.$read$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$anonfun$1.apply(<console>:33)
at $line124.$read$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$iw$$anonfun$1.apply(<console>:33)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:395)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:234)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:228)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:108)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:338)
18/03/12 11:41:00 ERROR TaskSetManager: Task 0 in stage 55.0 failed 1 times; aborting job
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 55.0 failed 1 times, most recent failure: Lost task 0.0 in stage 55.0 (TID 432, localhost, executor driver): java.lang.NullPointerException
at org.apache.spark.sql.Dataset.<init>(Dataset.scala:171)
at org.apache.spark.sql.Dataset$.apply(Dataset.scala:62)
at org.apache.spark.sql.Dataset.withTypedPlan(Dataset.scala:2889)
at org.apache.spark.sql.Dataset.filter(Dataset.scala:1301)
at $anonfun$1.apply(<console>:33)
at $anonfun$1.apply(<console>:33)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:395)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:234)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:228)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:108)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:338)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1517)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1505)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1504)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
... 50 elided
Caused by: java.lang.NullPointerException
at org.apache.spark.sql.Dataset.<init>(Dataset.scala:171)
at org.apache.spark.sql.Dataset$.apply(Dataset.scala:62)
at org.apache.spark.sql.Dataset.withTypedPlan(Dataset.scala:2889)
at org.apache.spark.sql.Dataset.filter(Dataset.scala:1301)
at $anonfun$1.apply(<console>:33)
at $anonfun$1.apply(<console>:33)
at org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown Source)
at org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:395)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:234)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:228)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:827)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:108)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:338)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:748)
我的最佳猜测是 df("data").geq(x).count 行可能是 barfs 的部分,因为并非每个节点都可能有 x 并因此是空指针?
【问题讨论】:
-
你能发布
NullPointerException的堆栈跟踪吗?我没有立即发现任何东西(并不是说其他人不会),但堆栈跟踪可能有助于缩小范围。
标签: scala apache-spark spark-dataframe rdd