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https://issues.apache.org/jira/browse/SPARK-17634?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15513673#comment-15513673
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Thomas Powell edited comment on SPARK-17634 at 9/22/16 4:35 PM:
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I also ran this on a row limited version of this dataset. The first 22 tasks 
completed immediately (since there was no data to process). The final task 
recorded 13MB of shuffle read, (out of ~300MB of shuffle write in the previous 
stage), at which point it then stalled.


was (Author: iamthomaspowell):
I also ran this on a row limited version of this dataset. The first 22 tasks 
completed immediately (since there was no data to process). The final task 
recorded 32MB of shuffle read, (out of ~300MB of shuffle write in the previous 
stage), at which point it then stalled.

> Spark job hangs when using dapply
> ---------------------------------
>
>                 Key: SPARK-17634
>                 URL: https://issues.apache.org/jira/browse/SPARK-17634
>             Project: Spark
>          Issue Type: Bug
>          Components: SparkR
>    Affects Versions: 2.0.0
>            Reporter: Thomas Powell
>            Priority: Critical
>
> I'm running into an issue when using dapply on yarn. I have a data frame 
> backed by files in parquet with around 200 files that is around 2GB. When I 
> load this in with the new partition coalescing it ends up having around 20 
> partitions so each one roughly 100MB. The data frame itself has 4 columns of 
> integers and doubles. If I run a count over this things work fine.
> However, if I add a {{dapply}} in between the read and the {{count}} that 
> just uses an identity function the tasks hang and make no progress. Both the 
> R and Java processes are running on the Spark nodes and are listening on the 
> {{SPARKR_WORKER_PORT}}.
> {{result <- dapply(df, function(x){x}, SparkR::schema(df))}}
> I took a jstack of the Java process and see that it is just listening on the 
> socket but never seems to make any progress. The R process is harder to debug 
> what it is doing.
> {code}
> Thread 112823: (state = IN_NATIVE)
>  - java.net.SocketInputStream.socketRead0(java.io.FileDescriptor, byte[], 
> int, int, int) @bci=0 (Interpreted frame)
>  - java.net.SocketInputStream.socketRead(java.io.FileDescriptor, byte[], int, 
> int, int) @bci=8, line=116 (Interpreted frame)
>  - java.net.SocketInputStream.read(byte[], int, int, int) @bci=79, line=170 
> (Interpreted frame)
>  - java.net.SocketInputStream.read(byte[], int, int) @bci=11, line=141 
> (Interpreted frame)
>  - java.io.BufferedInputStream.fill() @bci=214, line=246 (Interpreted frame)
>  - java.io.BufferedInputStream.read() @bci=12, line=265 (Compiled frame)
>  - java.io.DataInputStream.readInt() @bci=4, line=387 (Compiled frame)
>  - org.apache.spark.api.r.RRunner.org$apache$spark$api$r$RRunner$$read() 
> @bci=4, line=212 (Interpreted frame)
>  - 
> org.apache.spark.api.r.RRunner$$anon$1.<init>(org.apache.spark.api.r.RRunner) 
> @bci=25, line=96 (Interpreted frame)
>  - org.apache.spark.api.r.RRunner.compute(scala.collection.Iterator, int) 
> @bci=109, line=87 (Interpreted frame)
>  - 
> org.apache.spark.sql.execution.r.MapPartitionsRWrapper.apply(scala.collection.Iterator)
>  @bci=322, line=59 (Interpreted frame)
>  - 
> org.apache.spark.sql.execution.r.MapPartitionsRWrapper.apply(java.lang.Object)
>  @bci=5, line=29 (Interpreted frame)
>  - 
> org.apache.spark.sql.execution.MapPartitionsExec$$anonfun$6.apply(scala.collection.Iterator)
>  @bci=59, line=178 (Interpreted frame)
>  - 
> org.apache.spark.sql.execution.MapPartitionsExec$$anonfun$6.apply(java.lang.Object)
>  @bci=5, line=175 (Interpreted frame)
>  - 
> org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$24.apply(org.apache.spark.TaskContext,
>  int, scala.collection.Iterator) @bci=8, line=784 (Interpreted frame)
>  - 
> org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$24.apply(java.lang.Object,
>  java.lang.Object, java.lang.Object) @bci=13, line=784 (Interpreted frame)
>  - org.apache.spark.rdd.MapPartitionsRDD.compute(org.apache.spark.Partition, 
> org.apache.spark.TaskContext) @bci=27, line=38 (Interpreted frame)
>  - 
> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(org.apache.spark.Partition, 
> org.apache.spark.TaskContext) @bci=26, line=319 (Interpreted frame)
>  - org.apache.spark.rdd.RDD.iterator(org.apache.spark.Partition, 
> org.apache.spark.TaskContext) @bci=33, line=283 (Interpreted frame)
>  - org.apache.spark.rdd.MapPartitionsRDD.compute(org.apache.spark.Partition, 
> org.apache.spark.TaskContext) @bci=24, line=38 (Interpreted frame)
>  - 
> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(org.apache.spark.Partition, 
> org.apache.spark.TaskContext) @bci=26, line=319 (Interpreted frame)
>  - org.apache.spark.rdd.RDD.iterator(org.apache.spark.Partition, 
> org.apache.spark.TaskContext) @bci=33, line=283 (Interpreted frame)
>  - org.apache.spark.rdd.MapPartitionsRDD.compute(org.apache.spark.Partition, 
> org.apache.spark.TaskContext) @bci=24, line=38 (Interpreted frame)
>  - 
> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(org.apache.spark.Partition, 
> org.apache.spark.TaskContext) @bci=26, line=319 (Interpreted frame)
>  - org.apache.spark.rdd.RDD.iterator(org.apache.spark.Partition, 
> org.apache.spark.TaskContext) @bci=33, line=283 (Interpreted frame)
>  - 
> org.apache.spark.scheduler.ShuffleMapTask.runTask(org.apache.spark.TaskContext)
>  @bci=168, line=79 (Interpreted frame)
>  - 
> org.apache.spark.scheduler.ShuffleMapTask.runTask(org.apache.spark.TaskContext)
>  @bci=2, line=47 (Interpreted frame)
>  - org.apache.spark.scheduler.Task.run(long, int, 
> org.apache.spark.metrics.MetricsSystem) @bci=82, line=85 (Interpreted frame)
>  - org.apache.spark.executor.Executor$TaskRunner.run() @bci=374, line=274 
> (Interpreted frame)
>  - 
> java.util.concurrent.ThreadPoolExecutor.runWorker(java.util.concurrent.ThreadPoolExecutor$Worker)
>  @bci=95, line=1142 (Interpreted frame)
>  - java.util.concurrent.ThreadPoolExecutor$Worker.run() @bci=5, line=617 
> (Interpreted frame)
>  - java.lang.Thread.run() @bci=11, line=745 (Interpreted frame)
> {code}
> Any recommendations on how best to debug? Nothing appears in the logs since 
> the processes don't actually fail. The executors themselves have 4GB of 
> memory which should be more than enough.
> My feeling is this could be something around serialization?



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