pandas - collect() or toPandas() on a large DataFrame in pyspark/EMR

Question

I have an EMR cluster of one machine "c3.8xlarge", after reading several resources, I understood that I have to allow decent amount of memory off-heap because I am using pyspark, so I have configured the cluster as follow:

One executor:

• spark.executor.memory 6g
• spark.executor.cores 10
• spark.yarn.executor.memoryOverhead 4096

Driver:

• spark.driver.memory 21g

When I cache() the DataFrame it takes about 3.6GB of memory.

Now when I call collect() or toPandas() on the DataFrame, the process crashes.

I know that I am bringing a large amount of data into the driver, but I think that it is not that large, and I am not able to figure out the reason of the crash.

When I call collect() or toPandas() I get this error:

Py4JJavaError: An error occurred while calling o181.collectToPython.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 5 in stage 6.0 failed 4 times, most recent failure: Lost task 5.3 in stage 6.0 (TID 110, ip-10-0-47-207.prod.eu-west-1.hs.internal, executor 9): ExecutorLostFailure (executor 9 exited caused by one of the running tasks) Reason: Container marked as failed: container_1511879540686_0005_01_000016 on host: ip-10-0-47-207.prod.eu-west-1.hs.internal. Exit status: 137. Diagnostics: Container killed on request. Exit code is 137
Container exited with a non-zero exit code 137
Killed by external signal
Driver stacktrace:
    at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1690)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1678)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1677)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1677)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:855)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:855)
    at scala.Option.foreach(Option.scala:257)
    at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:855)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1905)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1860)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1849)
    at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:671)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2022)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2043)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2062)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2087)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
    at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
    at org.apache.spark.rdd.RDD.collect(RDD.scala:935)
    at org.apache.spark.sql.execution.SparkPlan.executeCollect(SparkPlan.scala:278)
    at org.apache.spark.sql.Dataset$$anonfun$collectToPython$1.apply$mcI$sp(Dataset.scala:2803)
    at org.apache.spark.sql.Dataset$$anonfun$collectToPython$1.apply(Dataset.scala:2800)
    at org.apache.spark.sql.Dataset$$anonfun$collectToPython$1.apply(Dataset.scala:2800)
    at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:65)
    at org.apache.spark.sql.Dataset.withNewExecutionId(Dataset.scala:2823)
    at org.apache.spark.sql.Dataset.collectToPython(Dataset.scala:2800)
    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 py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
    at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
    at py4j.Gateway.invoke(Gateway.java:280)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:214)
    at java.lang.Thread.run(Thread.java:748)

==== Update ====

As @user6910411 suggested, I have tried the solution mentioned here, and in that case I get the following error:

Py4JJavaError: An error occurred while calling z:org.apache.spark.api.python.PythonRDD.collectAndServe.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 7 in stage 2.0 failed 4 times, most recent failure: Lost task 7.3 in stage 2.0 (TID 41, ip-10-0-33-57.prod.eu-west-1.hs.internal, executor 5): ExecutorLostFailure (executor 5 exited caused by one of the running tasks) Reason: Container killed by YARN for exceeding memory limits. 13.5 GB of 12 GB physical memory used. Consider boosting spark.yarn.executor.memoryOverhead.
Driver stacktrace:
    at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1690)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1678)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1677)
    at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
    at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1677)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:855)
    at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:855)
    at scala.Option.foreach(Option.scala:257)
    at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:855)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1905)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1860)
    at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1849)
    at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
    at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:671)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2022)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2043)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2062)
    at org.apache.spark.SparkContext.runJob(SparkContext.scala:2087)
    at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:936)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
    at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
    at org.apache.spark.rdd.RDD.withScope(RDD.scala:362)
    at org.apache.spark.rdd.RDD.collect(RDD.scala:935)
    at org.apache.spark.api.python.PythonRDD$.collectAndServe(PythonRDD.scala:458)
    at org.apache.spark.api.python.PythonRDD.collectAndServe(PythonRDD.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 py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
    at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
    at py4j.Gateway.invoke(Gateway.java:280)
    at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
    at py4j.commands.CallCommand.execute(CallCommand.java:79)
    at py4j.GatewayConnection.run(GatewayConnection.java:214)
    at java.lang.Thread.run(Thread.java:748)

Any hint about what is happening here?

Answer 1

TL;DR I believe you're seriously underestimating memory requirements.

Even assuming that data is fully cached, storage info will show only a fraction of peak memory required for bringing data back to the driver.

• First of all Spark SQL uses compressed columnar storage for caching. Depending on the data distribution and compression algorithm in-memory size can be much smaller than the uncompressed Pandas output, not to mention plain List[Row]. The latter also stores column names, further increasing memory usage.
• Data collection is indirect, with data being stored both on the JVM side and Python side. While JVM memory can be released once data goes through socket, peak memory usage should account for both.

• Plain toPandas implementation collects Rows first, then creates Pandas DataFrame locally. This further increases (possibly doubles) memory usage. Luckily this part is already addressed on master (Spark 2.3), with more direct approach using Arrow serialization (SPARK-13534 - Implement Apache Arrow serializer for Spark DataFrame for use in DataFrame.toPandas).

  For possible solution independent of Apache Arrow you can check Faster and Lower memory implementation toPandas on the Apache Spark Developer List.

Since data is actually pretty large I would consider writing it to Parquet and reading it back directly in Python using PyArrow (Reading and Writing the Apache Parquet Format) completely skipping all the intermediate stages.