Program takes a lot of time to end because of this warning Executor: Issue communicating with driver in heartbeater - scala

I have the standalone spark cluster with one master and four workers which must read the large oracle table and process it. Each node has 30G Ram. In average program time is about 1.7 Hours, but sometimes it takes a lot of time because of this warning:
WARN Executor: Issue communicating with driver in heartbeater
org.apache.spark.rpc.RpcTimeoutException: Futures timed out after [10000 milliseconds]. This timeout is controlled by spark.executor.heartbeatInterval
at org.apache.spark.rpc.RpcTimeout.org$apache$spark$rpc$RpcTimeout$$createRpcTimeoutException(RpcTimeout.scala:47)
at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:62)
at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:58)
at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:38)
at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:76)
at org.apache.spark.rpc.RpcEndpointRef.askSync(RpcEndpointRef.scala:103)
at org.apache.spark.executor.Executor.reportHeartBeat(Executor.scala:996)
at org.apache.spark.executor.Executor.$anonfun$heartbeater$1(Executor.scala:212)
at org.apache.spark.executor.Executor$$Lambda$356/321695195.apply$mcV$sp(Unknown Source)
at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1996)
at org.apache.spark.Heartbeater$$anon$1.run(Heartbeater.scala:46)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.TimeoutException: Futures timed out after [10000 milliseconds]
at scala.concurrent.impl.Promise$DefaultPromise.ready(Promise.scala:259)
at scala.concurrent.impl.Promise$DefaultPromise.result(Promise.scala:263)
at org.apache.spark.util.ThreadUtils$.awaitResult(ThreadUtils.scala:293)
at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:75)
... 14 more
I search and added these options to the spark_submit command.But, still receive the same warning.
--conf spark.sql.broadcastTimeout=3600 --conf spark.rpc.message.maxSize=1024 --conf spark.rpc.askTimeout=600s
Also, I set 28G for driver memory and 24G for executor memory. Moreover, I read this post:
https://stackoverflow.com/a/54038675/6640504
As this comment said, it is not right to increase spark.network.timeout and spark.executor.heartbeatInterval to 10000000 with the same value. I am sure the program takes more time to run with this setting.
Would you please guide me how to solve this problem and improve speed of the program?
Any help is really appreciated.

Related

Spark streaming, kafka broker error, "Failed to get records for spark-executor- .... after polling for 512"

We have a spark streaming application reading data from Kafka.
Data size: 15 Million
Below errors were seen:
java.lang.AssertionError: assertion failed: Failed to get records for spark-executor- after ...polling for 512 at scala.Predef$.assert(Predef.scala:170)
There were more errors seen pertaining to CachedKafkaConsumer
at org.apache.spark.streaming.kafka010.CachedKafkaConsumer.get(CachedKafkaConsumer.scala:74)
at org.apache.spark.streaming.kafka010.KafkaRDD$KafkaRDDIterator.next(KafkaRDD.scala:227)
at org.apache.spark.streaming.kafka010.KafkaRDD$KafkaRDDIterator.next(KafkaRDD.scala:193)
at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:214)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:935)
at org.apache.spark.storage.BlockManager$$anonfun$doPutIterator$1.apply(BlockManager.scala:926)
at org.apache.spark.storage.BlockManager.doPut(BlockManager.scala:866)
at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:926)
at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:670)
at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:330)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:281)
at org.apache.spark.rdd.UnionRDD.compute(UnionRDD.scala:105)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
at org.apache.spark.scheduler.Task.run(Task.scala:86)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
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)
The spark.streaming.kafka.consumer.poll.ms is set to default 512ms and other Kafka stream timeout settings are default.
"request.timeout.ms"
"heartbeat.interval.ms"
"session.timeout.ms"
"max.poll.interval.ms"
Also, the Kafka is being recently updated to 0.10 from 0.8. In 0.8, this behavior was not seen.
No resource issues are seen.
Any pointers?

Out of memory exception or worked node lost during the spark scala job

I am executing a spark-scala job using spark-shell and the problem I am facing is, at the end of the final stage and final mapper like in stage 5 it allocates 50 and completed 49 very quickly and at the 50th it takes 5 minutes and says that out of memory and fails. I am using SPARK_MAJOR_VERSION=2
I am using the below command
spark-shell --master yarn --conf spark.driver.memory=30G --conf spark.executor.memory=40G --conf spark.shuffle.service.enabled=true --conf spark.dynamicAllocation.enabled=false --conf spark.sql.broadcastTimeout=36000 --conf spark.shuffle.compress=true --conf spark.executor.heartbeatInterval=3600s --conf spark.executor.instance=160
In the above configuration I have tried the dynamic allocation to true and started the driver and executor memory from 1GB. I have the overall ram of 6.78TB and 1300 VCores(This is my entire hadoop hardware).
The table I am reading is 40GB and I am joining 6 tables to that 40GB table, so, overall might be 60GB. so spark is initializing 4 stages for this and in the final stage at the end it is failing. I am using the spark sql to execute SQL.
Below are the errors:
19/04/26 14:29:02 WARN HeartbeatReceiver: Removing executor 2 with no recent heartbeats: 125967 ms exceeds timeout 120000 ms
19/04/26 14:29:02 ERROR YarnScheduler: Lost executor 2 on worker03.some.com: Executor heartbeat timed out after 125967 ms
19/04/26 14:29:02 WARN TaskSetManager: Lost task 5.0 in stage 2.0 (TID 119, worker03.some.com, executor 2): ExecutorLostFailure (executor 2 exited caused by one of the running tasks) Reason: Executor heartbeat timed out after 125967 ms
19/04/26 14:29:02 WARN HeartbeatReceiver: Removing executor 1 with no recent heartbeats: 126225 ms exceeds timeout 120000 ms
19/04/26 14:29:02 ERROR YarnScheduler: Lost executor 1 on ncednhpwrka0008.devhadoop.charter.com: Executor heartbeat timed out after 126225 ms
19/04/26 14:29:02 WARN YarnSchedulerBackend$YarnSchedulerEndpoint: Container marked as failed: container_e1223_1556277056929_0976_01_000003 on host: worker03.some.com. Exit status: 52. Diagnostics: Exception from container-launch.
Container id: container_e1223_1556277056929_0976_01_000003
Exit code: 52
Shell output: main : command provided 1
main : run as user is svc-bd-xdladmrw-dev
main : requested yarn user is svc-bd-xdladmrw-dev
Getting exit code file...
Creating script paths...
Writing pid file...
Writing to tmp file /data/00/yarn/local/nmPrivate/application_1556277056929_0976/container_e1223_1556277056929_0976_01_000003/container_e1223_1556277056929_0976_01_000003.pid.tmp
Writing to cgroup task files...
Creating local dirs...
Launching container...
Getting exit code file...
Creating script paths...
Container exited with a non-zero exit code 52. Last 4096 bytes of stderr :
0 in stage 2.0 (TID 119)
19/04/26 14:27:37 INFO HadoopRDD: Input split: hdfs://datadev/data/dev/HIVE_SCHEMA/somedb.db/sbscr_usge_cycl_key_xref/000000_0_copy_2:0+6623042
19/04/26 14:27:37 INFO OrcRawRecordMerger: min key = null, max key = null
19/04/26 14:27:37 INFO ReaderImpl: Reading ORC rows from hdfs://datadev/data/dev/HIVE_SCHEMA/somedb.db/sbscr_usge_cycl_key_xref/000000_0_copy_2 with {include: [true, true, true], offset: 0, length: 9223372036854775807}
19/04/26 14:29:00 ERROR Executor: Exception in task 5.0 in stage 2.0 (TID 119)
java.lang.OutOfMemoryError
at java.io.ByteArrayOutputStream.hugeCapacity(ByteArrayOutputStream.java:123)
at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:117)
at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:153)
at net.jpountz.lz4.LZ4BlockOutputStream.flushBufferedData(LZ4BlockOutputStream.java:205)
at net.jpountz.lz4.LZ4BlockOutputStream.write(LZ4BlockOutputStream.java:158)
at java.io.DataOutputStream.write(DataOutputStream.java:107)
at org.apache.spark.sql.catalyst.expressions.UnsafeRow.writeToStream(UnsafeRow.java:554)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:237)
at org.apache.spark.sql.execution.SparkPlan$$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:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
19/04/26 14:29:00 ERROR SparkUncaughtExceptionHandler: Uncaught exception in thread Thread[Executor task launch worker for task 119,5,main]
java.lang.OutOfMemoryError
at java.io.ByteArrayOutputStream.hugeCapacity(ByteArrayOutputStream.java:123)
at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:117)
at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:153)
at net.jpountz.lz4.LZ4BlockOutputStream.flushBufferedData(LZ4BlockOutputStream.java:205)
at net.jpountz.lz4.LZ4BlockOutputStream.write(LZ4BlockOutputStream.java:158)
at java.io.DataOutputStream.write(DataOutputStream.java:107)
at org.apache.spark.sql.catalyst.expressions.UnsafeRow.writeToStream(UnsafeRow.java:554)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:237)
at org.apache.spark.sql.execution.SparkPlan$$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:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
19/04/26 14:29:00 INFO DiskBlockManager: Shutdown hook called
19/04/26 14:29:00 INFO ShutdownHookManager: Shutdown hook called
19/04/26 14:29:02 ERROR YarnScheduler: Lost executor 2 on worker03.some.com: Container marked as failed: container_e1223_1556277056929_0976_01_000003 on host: worker03.some.com. Exit status: 52. Diagnostics: Exception from container-launch.
Container id: container_e1223_1556277056929_0976_01_000003
Exit code: 52
Shell output: main : command provided 1
main : run as user is svc-bd-xdladmrw-dev
main : requested yarn user is svc-bd-xdladmrw-dev
Getting exit code file...
Creating script paths...
Writing pid file...
Writing to tmp file /data/00/yarn/local/nmPrivate/application_1556277056929_0976/container_e1223_1556277056929_0976_01_000003/container_e1223_1556277056929_0976_01_000003.pid.tmp
Writing to cgroup task files...
Creating local dirs...
Launching container...
Getting exit code file...
Creating script paths...
Container exited with a non-zero exit code 52. Last 4096 bytes of stderr :
0 in stage 2.0 (TID 119)
19/04/26 14:27:37 INFO HadoopRDD: Input split: hdfs://datadev/data/dev/HIVE_SCHEMA/somedb.db/sbscr_usge_cycl_key_xref/000000_0_copy_2:0+6623042
19/04/26 14:27:37 INFO OrcRawRecordMerger: min key = null, max key = null
19/04/26 14:27:37 INFO ReaderImpl: Reading ORC rows from hdfs://datadev/data/dev/HIVE_SCHEMA/somedb.db/sbscr_usge_cycl_key_xref/000000_0_copy_2 with {include: [true, true, true], offset: 0, length: 9223372036854775807}
19/04/26 14:29:00 ERROR Executor: Exception in task 5.0 in stage 2.0 (TID 119)
java.lang.OutOfMemoryError
at java.io.ByteArrayOutputStream.hugeCapacity(ByteArrayOutputStream.java:123)
at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:117)
at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:153)
at net.jpountz.lz4.LZ4BlockOutputStream.flushBufferedData(LZ4BlockOutputStream.java:205)
at net.jpountz.lz4.LZ4BlockOutputStream.write(LZ4BlockOutputStream.java:158)
at java.io.DataOutputStream.write(DataOutputStream.java:107)
at org.apache.spark.sql.catalyst.expressions.UnsafeRow.writeToStream(UnsafeRow.java:554)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:237)
at org.apache.spark.sql.execution.SparkPlan$$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:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
19/04/26 14:29:00 ERROR SparkUncaughtExceptionHandler: Uncaught exception in thread Thread[Executor task launch worker for task 119,5,main]
java.lang.OutOfMemoryError
at java.io.ByteArrayOutputStream.hugeCapacity(ByteArrayOutputStream.java:123)
at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:117)
at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93)
at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:153)
at net.jpountz.lz4.LZ4BlockOutputStream.flushBufferedData(LZ4BlockOutputStream.java:205)
at net.jpountz.lz4.LZ4BlockOutputStream.write(LZ4BlockOutputStream.java:158)
at java.io.DataOutputStream.write(DataOutputStream.java:107)
at org.apache.spark.sql.catalyst.expressions.UnsafeRow.writeToStream(UnsafeRow.java:554)
at org.apache.spark.sql.execution.SparkPlan$$anonfun$2.apply(SparkPlan.scala:237)
at org.apache.spark.sql.execution.SparkPlan$$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:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)
19/04/26 14:29:00 INFO DiskBlockManager: Shutdown hook called
19/04/26 14:29:00 INFO ShutdownHookManager: Shutdown hook called
Can anyone let me know if I am doing anything wrong here, like the memory allocation or something?, please suggest any alternatives to complete this job without getting the our of memory exception or worker node lost error. Any help or info is greatly appreciated.
Thanks!
at the end of the final stage and final mapper like in stage 5 it allocates 50 and completed 49 very quickly and at the 50th it takes 5 minutes and says that out of memory and fails.
The table I am reading is 40GB and I am joining 6 tables to that 40GB table
It sounds like a skewed data to me, most of the keys used for joining are in one partition. So instead spreading the work among multiple executors, Spark uses just one and overloads it. It affects both memory consumption and performance.
There are a few ways to deal with it:
Skewed dataset join in Spark?
How to repartition a dataframe in Spark scala on a skewed column?

Spark streaming error: Issue communicating with driver in heartbeater

I'm experimenting an issue with heartbeating when I running my Spark Streaming app.
I know the meaning of heartbeating, I have tried to increase its value in "spark.executor.heartbeatInterval", but the issue it still remaing.
My config is:
4 executors
4 cores per executor
6GB RAM per executor
Spark streaming time window: 30s
Each batch takes between 2s and 28s to complete
In the logs I can see how, suddenly, executors start to log "Issue communicating with driver in heartbeater" and when the it happen X times, the executor shutdown (as the spark doc says).
In the logs I can't see any exception (such as OOM or something about GC). Simply, some time (some hours after starting), heartbeater fails.
I have read about to repartition data to try to solve the issue, but I can't because it is a Kafka Direct appication and each partition is partial ordered so I don't do repartition anytime.
This is the trace I can see:
2018/12/16 13:44:26:317 WARN org.apache.spark.executor.Executor: Issue communicating with driver in heartbeater
org.apache.spark.rpc.RpcTimeoutException: Futures timed out after [10 seconds]. This timeout is controlled by spark.executor.heartbeatInterval
at org.apache.spark.rpc.RpcTimeout.org$apache$spark$rpc$RpcTimeout$$createRpcTimeoutException(RpcTimeout.scala:47)
at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:62)
at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:58)
at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:36)
at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:76)
at org.apache.spark.rpc.RpcEndpointRef.askSync(RpcEndpointRef.scala:92)
at org.apache.spark.executor.Executor.org$apache$spark$executor$Executor$$reportHeartBeat(Executor.scala:785)
at org.apache.spark.executor.Executor$$anon$2$$anonfun$run$1.apply$mcV$sp(Executor.scala:814)
at org.apache.spark.executor.Executor$$anon$2$$anonfun$run$1.apply(Executor.scala:814)
at org.apache.spark.executor.Executor$$anon$2$$anonfun$run$1.apply(Executor.scala:814)
at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1988)
at org.apache.spark.executor.Executor$$anon$2.run(Executor.scala:814)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.TimeoutException: Futures timed out after [10 seconds]
at scala.concurrent.impl.Promise$DefaultPromise.ready(Promise.scala:219)
at scala.concurrent.impl.Promise$DefaultPromise.result(Promise.scala:223)
at org.apache.spark.util.ThreadUtils$.awaitResult(ThreadUtils.scala:201)
at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:75)
... 14 more

How to investigate failing dataproc worker processes?

I'm running a PySpark job and Im having trouble determining the cause of failure on worker processes.
While my job is running I started noticing stack traces in the job output such as:
16/04/10 03:24:21 WARN org.apache.spark.scheduler.cluster.YarnSchedulerBackend$YarnSchedulerEndpoint: Container marked as failed: container_1460240417530_0021_01_000003 on host: cluster-2-w-0.c.my-project.internal. Exit status: -100. Diagnostics: Container released on a *lost* node
[Stage 0:=================================> (19 + 13) / 32]16/04/10 03:26:21 WARN org.apache.spark.rpc.netty.NettyRpcEndpointRef: Error sending message [message = RemoveExecutor(2,Container marked as failed: container_1460240417530_0021_01_000003 on host: cluster-2-w-0.c.my-project.internal. Exit status: -100. Diagnostics: Container released on a *lost* node)] in 1 attempts
org.apache.spark.rpc.RpcTimeoutException: Futures timed out after [120 seconds]. This timeout is controlled by spark.rpc.askTimeout
at org.apache.spark.rpc.RpcTimeout.org$apache$spark$rpc$RpcTimeout$$createRpcTimeoutException(RpcTimeout.scala:48)
at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:63)
at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:59)
at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:33)
at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:76)
at org.apache.spark.rpc.RpcEndpointRef.askWithRetry(RpcEndpointRef.scala:101)
at org.apache.spark.rpc.RpcEndpointRef.askWithRetry(RpcEndpointRef.scala:77)
at org.apache.spark.scheduler.cluster.CoarseGrainedSchedulerBackend.removeExecutor(CoarseGrainedSchedulerBackend.scala:359)
at org.apache.spark.scheduler.cluster.YarnSchedulerBackend$YarnSchedulerEndpoint$$anonfun$receive$1.applyOrElse(YarnSchedulerBackend.scala:176)
at org.apache.spark.rpc.netty.Inbox$$anonfun$process$1.apply$mcV$sp(Inbox.scala:116)
at org.apache.spark.rpc.netty.Inbox.safelyCall(Inbox.scala:204)
at org.apache.spark.rpc.netty.Inbox.process(Inbox.scala:100)
at org.apache.spark.rpc.netty.Dispatcher$MessageLoop.run(Dispatcher.scala:215)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.TimeoutException: Futures timed out after [120 seconds]
at scala.concurrent.impl.Promise$DefaultPromise.ready(Promise.scala:219)
at scala.concurrent.impl.Promise$DefaultPromise.result(Promise.scala:223)
at scala.concurrent.Await$$anonfun$result$1.apply(package.scala:107)
at scala.concurrent.BlockContext$DefaultBlockContext$.blockOn(BlockContext.scala:53)
at scala.concurrent.Await$.result(package.scala:107)
at org.apache.spark.rpc.RpcTimeout.awaitResult(RpcTimeout.scala:75)
... 11 more
16/04/10 03:26:40 WARN org.apache.spark.rpc.netty.NettyRpcEndpointRef: Error sending message [message = RequestExecutors(23,0,Map())] in 1 attempts
org.apache.spark.rpc.RpcTimeoutException: Cannot receive any reply in 120 seconds. This timeout is controlled by spark.rpc.askTimeout
at org.apache.spark.rpc.RpcTimeout.org$apache$spark$rpc$RpcTimeout$$createRpcTimeoutException(RpcTimeout.scala:48)
at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:63)
at org.apache.spark.rpc.RpcTimeout$$anonfun$addMessageIfTimeout$1.applyOrElse(RpcTimeout.scala:59)
at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:33)
at scala.util.Failure$$anonfun$recover$1.apply(Try.scala:185)
at scala.util.Try$.apply(Try.scala:161)
at scala.util.Failure.recover(Try.scala:185)
at scala.concurrent.Future$$anonfun$recover$1.apply(Future.scala:324)
at scala.concurrent.Future$$anonfun$recover$1.apply(Future.scala:324)
at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:32)
at org.spark-project.guava.util.concurrent.MoreExecutors$SameThreadExecutorService.execute(MoreExecutors.java:293)
at scala.concurrent.impl.ExecutionContextImpl$$anon$1.execute(ExecutionContextImpl.scala:133)
at scala.concurrent.impl.CallbackRunnable.executeWithValue(Promise.scala:40)
at scala.concurrent.impl.Promise$DefaultPromise.tryComplete(Promise.scala:248)
at scala.concurrent.Promise$class.complete(Promise.scala:55)
at scala.concurrent.impl.Promise$DefaultPromise.complete(Promise.scala:153)
at scala.concurrent.Future$$anonfun$map$1.apply(Future.scala:235)
at scala.concurrent.Future$$anonfun$map$1.apply(Future.scala:235)
at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:32)
at scala.concurrent.Future$InternalCallbackExecutor$Batch$$anonfun$run$1.processBatch$1(Future.scala:643)
at scala.concurrent.Future$InternalCallbackExecutor$Batch$$anonfun$run$1.apply$mcV$sp(Future.scala:658)
at scala.concurrent.Future$InternalCallbackExecutor$Batch$$anonfun$run$1.apply(Future.scala:635)
at scala.concurrent.Future$InternalCallbackExecutor$Batch$$anonfun$run$1.apply(Future.scala:635)
at scala.concurrent.BlockContext$.withBlockContext(BlockContext.scala:72)
at scala.concurrent.Future$InternalCallbackExecutor$Batch.run(Future.scala:634)
at scala.concurrent.Future$InternalCallbackExecutor$.scala$concurrent$Future$InternalCallbackExecutor$$unbatchedExecute(Future.scala:694)
at scala.concurrent.Future$InternalCallbackExecutor$.execute(Future.scala:685)
at scala.concurrent.impl.CallbackRunnable.executeWithValue(Promise.scala:40)
at scala.concurrent.impl.Promise$DefaultPromise.tryComplete(Promise.scala:248)
at scala.concurrent.Promise$class.tryFailure(Promise.scala:112)
at scala.concurrent.impl.Promise$DefaultPromise.tryFailure(Promise.scala:153)
at org.apache.spark.rpc.netty.NettyRpcEnv$$anon$1.run(NettyRpcEnv.scala:241)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.concurrent.TimeoutException: Cannot receive any reply in 120 seconds
at org.apache.spark.rpc.netty.NettyRpcEnv$$anon$1.run(NettyRpcEnv.scala:242)
... 7 more
[Stage 0:=================================> (19 + 13) / 32]
Ill also notice the overall CPU usage of the cluster slowly drop as worker nodes fail. These nodes seem to permanently fail and do not re-join the cluster:
I'm using preemtible machines but when I check the status of these machines they are still running and have not been preempted. So I'm guessing its something wrong on the worker:
It could be because of the heavy workload in the workers. Try to increase spark.network.timeout (default 120) to a bigger number.
If that is not resolving the error, most likely causes are garbage collection. Try to run a memory profile with the following options.
-verbose:gc -XX:+PrintGCDetails -XX:+PrintGCTimeStamps -XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath=/tmp/ -XX:+CMSClassUnloadingEnabled

memory error in standalone spark cluster as "shutting down JVM since 'akka.jvm-exit-on-fatal-error' is enabled for ActorSystem[Remote]"

I got the following memory error in my standalone spark cluster, after 140 iterations of my code. How shall I run my code without memory fault?
I am having 7 nodes with 8GB RAM out of which 6GB is allocated to all the workers. The master is also having 8GB RAM.
[error] application - Remote calculator (Actor[akka.tcp://Remote#127.0.0.1:44545/remote/akka.tcp/NotebookServer#127.0.0.1:50778/user/$c/$a#872469007]) has been terminated !!!!!
[info] application - View notebook 'kamaruddin/PSOAANN_BreastCancer_optimized.snb', presentation: 'None'
[info] application - Closing websockets for kernel 6c8e8090-cbeb-430e-9d45-5710ce60b984
Uncaught error from thread [Remote-akka.actor.default-dispatcher-6] shutting down JVM since 'akka.jvm-exit-on-fatal-error' is enabled for ActorSystem[Remote]
Exception in thread "Thread-36" java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.jar.Attributes.read(Attributes.java:394)
at java.util.jar.Manifest.read(Manifest.java:199)
at java.util.jar.Manifest.<init>(Manifest.java:69)
at java.util.jar.JarFile.getManifestFromReference(JarFile.java:186)
at java.util.jar.JarFile.getManifest(JarFile.java:167)
at sun.misc.URLClassPath$JarLoader$2.getManifest(URLClassPath.java:779)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:416)
at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
at org.apache.spark.repl.SparkIMain$ReadEvalPrint.bindError(SparkIMain.scala:1041)
at org.apache.spark.repl.SparkIMain$Request.loadAndRun(SparkIMain.scala:1347)
at org.apache.spark.repl.SparkIMain.loadAndRunReq$1(SparkIMain.scala:840)
at org.apache.spark.repl.SparkIMain.interpret(SparkIMain.scala:871)
at org.apache.spark.repl.SparkIMain.interpret(SparkIMain.scala:819)
at notebook.kernel.Repl$$anonfun$3.apply(Repl.scala:173)
at notebook.kernel.Repl$$anonfun$3.apply(Repl.scala:173)
at scala.util.DynamicVariable.withValue(DynamicVariable.scala:57)
at scala.Console$.withOut(Console.scala:126)
at notebook.kernel.Repl.evaluate(Repl.scala:172)
at notebook.client.ReplCalculator$$anonfun$10$$anon$1$$anonfun$24.apply(ReplCalculator.scala:364)
at notebook.client.ReplCalculator$$anonfun$10$$anon$1$$anonfun$24.apply(ReplCalculator.scala:361)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.liftedTree1$1(Future.scala:24)
at scala.concurrent.impl.Future$PromiseCompletingRunnable.run(Future.scala:24)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(AbstractDispatcher.scala:397)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
Uncaught error from thread [Remote-akka.remote.default-remote-dispatcher-445] shutting down JVM since 'akka.jvm-exit-on-fatal-error' is enabled for ActorSystem[Remote]
java.lang.OutOfMemoryError: GC overhead limit exceeded
java.lang.OutOfMemoryError: GC overhead limit exceeded
at java.util.Arrays.copyOf(Arrays.java:2367)
at java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:130)
at java.lang.AbstractStringBuilder.ensureCapacityInternal(AbstractStringBuilder.java:114)
at java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:535)
at java.lang.StringBuffer.append(StringBuffer.java:322)
at java.io.StringWriter.write(StringWriter.java:94)
at com.fasterxml.jackson.core.json.WriterBasedJsonGenerator._flushBuffer(WriterBasedJsonGenerator.java:1879)
at com.fasterxml.jackson.core.json.WriterBasedJsonGenerator._writeString(WriterBasedJsonGenerator.java:916)
at com.fasterxml.jackson.core.json.WriterBasedJsonGenerator._writeFieldName(WriterBasedJsonGenerator.java:213)
at com.fasterxml.jackson.core.json.WriterBasedJsonGenerator.writeFieldName(WriterBasedJsonGenerator.java:104)
at play.api.libs.json.JsValueSerializer$$anonfun$serialize$2.apply(JsValue.scala:319)
at play.api.libs.json.JsValueSerializer$$anonfun$serialize$2.apply(JsValue.scala:318)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:47)
at play.api.libs.json.JsValueSerializer.serialize(JsValue.scala:318)
at play.api.libs.json.JsValueSerializer$$anonfun$serialize$1.apply(JsValue.scala:312)
at play.api.libs.json.JsValueSerializer$$anonfun$serialize$1.apply(JsValue.scala:311)
at scala.collection.immutable.List.foreach(List.scala:318)
at play.api.libs.json.JsValueSerializer.serialize(JsValue.scala:311)
at play.api.libs.json.JsValueSerializer$$anonfun$serialize$2.apply(JsValue.scala:320)
at play.api.libs.json.JsValueSerializer$$anonfun$serialize$2.apply(JsValue.scala:318)
at scala.collection.immutable.List.foreach(List.scala:318)
at play.api.libs.json.JsValueSerializer.serialize(JsValue.scala:318)
at play.api.libs.json.JsValueSerializer.serialize(JsValue.scala:302)
at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:128)
at com.fasterxml.jackson.databind.ObjectMapper.writeValue(ObjectMapper.java:1902)
at play.api.libs.json.JacksonJson$.generateFromJsValue(JsValue.scala:494)
at play.api.libs.json.Json$.stringify(Json.scala:51)
at play.api.libs.json.JsValue$class.toString(JsValue.scala:80)
at play.api.libs.json.JsObject.toString(JsValue.scala:166)
at java.util.Formatter$FormatSpecifier.printString(Formatter.java:2838)
at java.util.Formatter$FormatSpecifier.print(Formatter.java:2718)
Uncaught error from thread [Remote-akka.remote.default-remote-dispatcher-446] shutting down JVM since 'akka.jvm-exit-on-fatal-error' is enabled for ActorSystem[Remote]
java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "appclient-receive-and-reply-threadpool-0" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "appclient-receive-and-reply-threadpool-2" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "appclient-receive-and-reply-threadpool-4" java.lang.OutOfMemoryError: GC overhead limit exceeded
Exception in thread "appclient-receive-and-reply-threadpool-6" java.lang.OutOfMemoryError: GC overhead limit exceeded
[error] application - Process exited with an error: 255 (Exit value: 255)
org.apache.commons.exec.ExecuteException: Process exited with an error: 255 (Exit value: 255)
at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
at org.apache.commons.exec.DefaultExecutor.access$200(DefaultExecutor.java:48)
at org.apache.commons.exec.DefaultExecutor$1.run(DefaultExecutor.java:200)
at java.lang.Thread.run(Thread.java:745)
Maybe you can try to use checkpointing.
Data checkpointing - Saving of the generated RDDs to reliable storage.
This is necessary in some stateful transformations that combine data
across multiple batches. In such transformations, the generated RDDs
depend on RDDs of previous batches, which causes the length of the
dependency chain to keep increasing with time. To avoid such unbounded
increases in recovery time (proportional to dependency chain),
intermediate RDDs of stateful transformations are periodically
checkpointed to reliable storage (e.g. HDFS) to cut off the dependency
chain