Luis Felipe Sant Ana created SPARK-19711:
--------------------------------------------
Summary: Bug in gapply function
Key: SPARK-19711
URL: https://issues.apache.org/jira/browse/SPARK-19711
Project: Spark
Issue Type: Bug
Components: SparkR
Affects Versions: 2.1.0
Environment: Using Databricks plataform.
Reporter: Luis Felipe Sant Ana
I have a dataframe in SparkR like
CNPJ PID DATA N
1 10140281000131 10000000000021 2015-04-23 1
2 10140281000131 10000000000021 2015-04-27 1
3 10140281000131 10000000000021 2015-04-02 1
4 10140281000131 10000000000021 2015-11-10 1
5 10140281000131 10000000000021 2016-11-14 1
6 10140281000131 10000000000021 2015-04-03 1
And, I want to group by columns CNPJ and PID using gapply() function, filling
in the column DATA with date
The code:
schema <- structType(structField("CNPJ", "string"),
structField("PID", "string"),
structField("DATA", "date"),
structField("N", "double"))
result <- gapply(
ds_filtered,
c("CNPJ", "PID"),
function(key, x) {
dts <- data.frame(key, DATA = seq(min(as.Date(x$DATA)), as.Date(e_date),
"days"))
colnames(dts)[c(1, 2)] <- c("CNPJ", "PID")
y <- data.frame(key, DATA = as.Date(x$DATA), N = x$N)
colnames(y)[c(1, 2)] <- c("CNPJ", "PID")
y <- dplyr::left_join(dts,
y,
by = c("CNPJ", "PID", "DATA"))
y[is.na(y$N), 4] <- 0
data.frame(CNPJ = as.character(y$CNPJ),
PID = as.character(y$PID),
DATA = y$DATA,
N = y$N)
},
schema)
Error:
Error in handleErrors(returnStatus, conn) :
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in
stage 92.0 failed 4 times, most recent failure: Lost task 0.3 in stage 92.0
(TID 7032, 10.93.243.111, executor 0): org.apache.spark.SparkException: R
computation failed with
Error in writeType(con, serdeType) :
Unsupported type for serialization factor
Calls: outputResult ... serializeRow -> writeList -> writeObject -> writeType
Execution halted
at org.apache.spark.api.r.RRunner.compute(RRunner.scala:108)
at
org.apache.spark.sql.execution.FlatMapGroupsInRExec$$anonfun$12.apply(objects.scala:404)
at
org.apache.spark.sql.execution.FlatMapGroupsInRExec$$anonfun$12.apply(objects.scala:386)
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$25.apply(RDD.scala:826)
at
org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at
org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at
org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:323)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:287)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
at org.apache.spark.scheduler.Task.run(Task.scala:99)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:322)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Driver stacktrace:
at
org.apache.spark.scheduler.DAGScheduler.org$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$1.run(EventLoop.scala:48)
at
org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:628)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1918)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1931)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:1944)
at
org.apache.spark.sql.execution.SparkPlan.executeTake(SparkPlan.scala:333)
at
org.apache.spark.sql.execution.CollectLimitExec.executeCollect(limit.scala:38)
at
org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collectFromPlan(Dataset.scala:2784)
at
org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2354)
at
org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2354)
at org.apache.spark.sql.Dataset$$anonfun$59.apply(Dataset.scala:2768)
at
org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:57)
at org.apache.spark.sql.Dataset.withAction(Dataset.scala:2767)
at org.apache.spark.sql.Dataset.collect(Dataset.scala:2354)
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.lang.Thread.run(Thread.java:745)
Caused by: org.apache.spark.SparkException: R computation failed with
Error in writeType(con, serdeType) :
Unsupported type for serialization factor
Calls: outputResult ... serializeRow -> writeList -> writeObject -> writeType
Execution halted
at org.apache.spark.api.r.RRunner.compute(RRunner.scala:108)
at
org.apache.spark.sql.execution.FlatMapGroupsInRExec$$anonfun$12.apply(objects.scala:404)
at
org.apache.spark.sql.execution.FlatMapGroupsInRExec$$anonfun$12.apply(objects.scala:386)
at org.apache.spark.rdd.RDD$$an
With gapplyCollect() function this work.
Thank you!
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