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Posted to issues@spark.apache.org by "Felix Cheung (JIRA)" <ji...@apache.org> on 2018/01/21 20:45:00 UTC
[jira] [Commented] (SPARK-20307) SparkR: pass on setHandleInvalid
to spark.mllib functions that use StringIndexer
[ https://issues.apache.org/jira/browse/SPARK-20307?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16333663#comment-16333663 ]
Felix Cheung commented on SPARK-20307:
--------------------------------------
for SPARK-20307 and SPARK-21381, do you think you can write up example on how to use them and also a mention in the R programming guide?
> SparkR: pass on setHandleInvalid to spark.mllib functions that use StringIndexer
> --------------------------------------------------------------------------------
>
> Key: SPARK-20307
> URL: https://issues.apache.org/jira/browse/SPARK-20307
> Project: Spark
> Issue Type: Improvement
> Components: SparkR
> Affects Versions: 2.1.0
> Reporter: Anne Rutten
> Assignee: Miao Wang
> Priority: Minor
> Fix For: 2.3.0
>
>
> when training a model in SparkR with string variables (tested with spark.randomForest, but i assume is valid for all spark.xx functions that apply a StringIndexer under the hood), testing on a new dataset with factor levels that are not in the training set will throw an "Unseen label" error.
> I think this can be solved if there's a method to pass setHandleInvalid on to the StringIndexers when calling spark.randomForest.
> code snippet:
> {code}
> # (i've run this in Zeppelin which already has SparkR and the context loaded)
> #library(SparkR)
> #sparkR.session(master = "local[*]")
> data = data.frame(clicked = base::sample(c(0,1),100,replace=TRUE),
> someString = base::sample(c("this", "that"), 100, replace=TRUE), stringsAsFactors=FALSE)
> trainidxs = base::sample(nrow(data), nrow(data)*0.7)
> traindf = as.DataFrame(data[trainidxs,])
> testdf = as.DataFrame(rbind(data[-trainidxs,],c(0,"the other")))
> rf = spark.randomForest(traindf, clicked~., type="classification",
> maxDepth=10,
> maxBins=41,
> numTrees = 100)
> predictions = predict(rf, testdf)
> SparkR::collect(predictions)
> {code}
> stack trace:
> {quote}
> Error in handleErrors(returnStatus, conn): org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 607.0 failed 1 times, most recent failure: Lost task 0.0 in stage 607.0 (TID 1581, localhost, executor driver): org.apache.spark.SparkException: Failed to execute user defined function($anonfun$4: (string) => double)
> at org.apache.spark.sql.catalyst.expressions.GeneratedClass$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:377)
> at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:231)
> at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:225)
> at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:826)
> at org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$25.apply(RDD.scala:826)
> at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
> at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
> at org.apache.spark.scheduler.Task.run(Task.scala:99)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:282)
> 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:745)
> Caused by: org.apache.spark.SparkException: Unseen label: the other.
> at org.apache.spark.ml.feature.StringIndexerModel$$anonfun$4.apply(StringIndexer.scala:170)
> at org.apache.spark.ml.feature.StringIndexerModel$$anonfun$4.apply(StringIndexer.scala:166)
> ... 16 more
> Driver stacktrace:
> at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1435)
> at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1423)
> at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1422)
> at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
> at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
> at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1422)
> at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
> at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:802)
> at scala.Option.foreach(Option.scala:257)
> at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:802)
> at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1650)
> at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1605)
> at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1594)
> at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
> at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:628)
> at org.apache.spark.SparkContext.runJob(SparkContext.scala:1918)
> at org.apache.spark.SparkContext.runJob(SparkContext.scala:1931)
> at org.apache.spark.SparkContext.runJob(SparkContext.scala:1944)
> at org.apache.spark.SparkContext.runJob(SparkContext.scala:1958)
> at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:935)
> at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
> at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
> at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
> at org.apache.spark.rdd.RDD.collect(RDD.scala:934)
> at org.apache.spark.sql.execution.SparkPlan.executeCollect(SparkPlan.scala:275)
> at org.apache.spark.sql.Dataset$$anonfun$org$apache$spark$sql$Dataset$$execute$1$1.apply(Dataset.scala:2371)
> at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57)
> at org.apache.spark.sql.Dataset.withNewExecutionId(Dataset.scala:2765)
> at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$execute$1(Dataset.scala:2370)
> at org.apache.spark.sql.Dataset$$anonfun$org$apache$spark$sql$Dataset$$collect$1.apply(Dataset.scala:2375)
> at org.apache.spark.sql.Dataset$$anonfun$org$apache$spark$sql$Dataset$$collect$1.apply(Dataset.scala:2375)
> at org.apache.spark.sql.Dataset.withCallback(Dataset.scala:2778)
> at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collect(Dataset.scala:2375)
> at org.apache.spark.sql.Dataset.collect(Dataset.scala:2351)
> at org.apache.spark.sql.api.r.SQLUtils$.dfToCols(SQLUtils.scala:208)
> at org.apache.spark.sql.api.r.SQLUtils.dfToCols(SQLUtils.scala)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498)
> at org.apache.spark.api.r.RBackendHandler.handleMethodCall(RBackendHandler.scala:167)
> at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:108)
> at org.apache.spark.api.r.RBackendHandler.channelRead0(RBackendHandler.scala:40)
> at io.netty.channel.SimpleChannelInboundHandler.channelRead(SimpleChannelInboundHandler.java:105)
> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:367)
> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:353)
> at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:346)
> at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:266)
> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:367)
> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:353)
> at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:346)
> at io.netty.handler.codec.MessageToMessageDecoder.channelRead(MessageToMessageDecoder.java:102)
> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:367)
> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:353)
> at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:346)
> at io.netty.handler.codec.ByteToMessageDecoder.fireChannelRead(ByteToMessageDecoder.java:293)
> at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:267)
> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:367)
> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:353)
> at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:346)
> at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1294)
> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:367)
> at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:353)
> at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:911)
> at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:131)
> at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:652)
> at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:575)
> at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:489)
> at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:451)
> at io.netty.util.concurrent.SingleThreadEventExecutor$2.run(SingleThreadEventExecutor.java:140)
> at io.netty.util.concurrent.DefaultThreadFactory$DefaultRunnableDecorator.run(DefaultThreadFactory.java:144)
> at java
> {quote}
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