从临时 table 请求数据时，Spark 查询中的内存泄漏导致错误
Memory leak in Spark query causes error when requesting data from the temporary table
首先，我在 scala 代码中将数据添加到 tempTable：
resultIndexed.show(490, false)
resultIndexed.registerTempTable("pivoted")
然后读入python（导入省略）：
%spark.pyspark
import bkzep
import numpy as np
from bokeh.io import output_notebook, show
from bokeh.plotting import figure
from bokeh.models import ColumnDataSource
from bokeh.layouts import gridplot
from pyspark.sql.functions import col, coalesce, lit, monotonically_increasing_id
from pyspark.sql import DataFrame
from pyspark.sql.functions import *
output_notebook(notebook_type='zeppelin')
%pyspark
from pyspark.sql.functions import *
def plot_summaries(sensor, dfName):
df = sqlContext.table(dfName)
pdf = df.toPandas()
#sample = pdf.sample(50)
source = ColumnDataSource(pdf)
#print(pdf)
TOOLTIPS = [
("month", "@month"),
("day", "@day"),
("hour", "@hour"),
("min", "@{min}{0.3f}"),
("avg", "@{avg}{0.3f}"),
("max", "@{max}{0.3f}"),
("median", "@{median}{0.3f}"),
("stddev", "@{stddev}{0.3f}"),
]
TOOLTIPS2 = [
("month", "@month"),
("day", "@day"),
("count", "@{count}{0.3f}"),
]
fig = figure(title="Hourly summaries of '{}'".format(sensor), tooltips=TOOLTIPS)
#fig.line(x='id', y='avg', source=source, color="orange")
#fig.line(x='id', y='min', source=source, color="green")
#fig.line(x='id', y='max', source=source, color="red")
fig.line(x='id', y='median', source=source, color="blue")
#fig.line(x='id', y='stddev', source=source, color="aquamarine")
#fig2 = figure(title="Hourly summaries of '{}' counters".format(sensor), tooltips=TOOLTIPS2)
#fig2.line(x='id', y='count', source=source, color="orange")
show(gridplot([fig], ncols=1, plot_width=1000, plot_height=400))
#show(fig)
sensors = [
"Water_Level_Sensor_stddev",
"Water_Level_Sensor_mean"
]
%pyspark
from pyspark.sql.functions import *
keyCol = "month_day_hour"
#for sensor in sensors:
plot_summaries("Water_Level_Sensor_stddev", "pivoted")
然后我在执行过程中得到了错误：
/spark/python/lib/pyspark.zip/pyspark/sql/pandas/conversion.py:134: UserWarning: toPandas attempted Arrow optimization because 'spark.sql.execution.arrow.pyspark.enabled' is set to true, but has reached the error below and can not continue. Note that 'spark.sql.execution.arrow.pyspark.fallback.enabled' does not have an effect on failures in the middle of computation.
An error occurred while calling o117.getResult.
: org.apache.spark.SparkException: Exception thrown in awaitResult:
at org.apache.spark.util.ThreadUtils$.awaitResult(ThreadUtils.scala:302)
at org.apache.spark.security.SocketAuthServer.getResult(SocketAuthServer.scala:88)
at org.apache.spark.security.SocketAuthServer.getResult(SocketAuthServer.scala:84)
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:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 1157.0 failed 4 times, most recent failure: Lost task 0.3 in stage 1157.0 (TID 81153, 10.244.1.26, executor 12): org.apache.spark.util.TaskCompletionListenerException: Memory was leaked by query. Memory leaked: (671744)
Allocator(toBatchIterator) 0/671744/671744/9223372036854775807 (res/actual/peak/limit)
Previous exception in task: sun.misc.Unsafe or java.nio.DirectByteBuffer.<init>(long, int) not available
io.netty.util.internal.PlatformDependent.directBuffer(PlatformDependent.java:490)
io.netty.buffer.NettyArrowBuf.getDirectBuffer(NettyArrowBuf.java:243)
io.netty.buffer.NettyArrowBuf.nioBuffer(NettyArrowBuf.java:233)
io.netty.buffer.ArrowBuf.nioBuffer(ArrowBuf.java:245)
org.apache.arrow.vector.ipc.message.ArrowRecordBatch.computeBodyLength(ArrowRecordBatch.java:222)
org.apache.arrow.vector.ipc.message.MessageSerializer.serialize(MessageSerializer.java:240)
org.apache.arrow.vector.ipc.message.MessageSerializer.serialize(MessageSerializer.java:226)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.$anonfun$next(ArrowConverters.scala:118)
scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.next(ArrowConverters.scala:121)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.next(ArrowConverters.scala:97)
scala.collection.Iterator.foreach(Iterator.scala:941)
scala.collection.Iterator.foreach$(Iterator.scala:941)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.foreach(ArrowConverters.scala:97)
scala.collection.generic.Growable.$plus$plus$eq(Growable.scala:62)
scala.collection.generic.Growable.$plus$plus$eq$(Growable.scala:53)
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:105)
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:49)
scala.collection.TraversableOnce.to(TraversableOnce.scala:315)
scala.collection.TraversableOnce.to$(TraversableOnce.scala:313)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.to(ArrowConverters.scala:97)
scala.collection.TraversableOnce.toBuffer(TraversableOnce.scala:307)
scala.collection.TraversableOnce.toBuffer$(TraversableOnce.scala:307)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.toBuffer(ArrowConverters.scala:97)
scala.collection.TraversableOnce.toArray(TraversableOnce.scala:294)
scala.collection.TraversableOnce.toArray$(TraversableOnce.scala:288)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.toArray(ArrowConverters.scala:97)
org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3562)
org.apache.spark.SparkContext.$anonfun$runJob(SparkContext.scala:2193)
org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
org.apache.spark.scheduler.Task.run(Task.scala:127)
org.apache.spark.executor.Executor$TaskRunner.$anonfun$run(Executor.scala:446)
org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449)
java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
java.base/java.lang.Thread.run(Unknown Source)
at org.apache.spark.TaskContextImpl.invokeListeners(TaskContextImpl.scala:145)
at org.apache.spark.TaskContextImpl.markTaskCompleted(TaskContextImpl.scala:124)
at org.apache.spark.scheduler.Task.run(Task.scala:137)
at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run(Executor.scala:446)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2059)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage(DAGScheduler.scala:2008)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$adapted(DAGScheduler.scala:2007)
at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2007)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed(DAGScheduler.scala:973)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$adapted(DAGScheduler.scala:973)
at scala.Option.foreach(Option.scala:407)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:973)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2239)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2188)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2177)
at org.apache.spark.util.EventLoop$$anon.run(EventLoop.scala:49)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:775)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2099)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2194)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3560)
at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3564)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython$adapted(Dataset.scala:3541)
at org.apache.spark.sql.Dataset.$anonfun$withAction(Dataset.scala:3618)
at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId(SQLExecution.scala:100)
at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:160)
at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId(SQLExecution.scala:87)
at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:764)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:64)
at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3616)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3541)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython$adapted(Dataset.scala:3540)
at org.apache.spark.security.SocketAuthServer$.$anonfun$serveToStream(SocketAuthServer.scala:130)
at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.security.SocketAuthServer$.$anonfun$serveToStream(SocketAuthServer.scala:132)
at org.apache.spark.security.SocketAuthServer$.$anonfun$serveToStream$adapted(SocketAuthServer.scala:127)
at org.apache.spark.security.SocketFuncServer.handleConnection(SocketAuthServer.scala:104)
at org.apache.spark.security.SocketFuncServer.handleConnection(SocketAuthServer.scala:98)
at org.apache.spark.security.SocketAuthServer$$anon.$anonfun$run(SocketAuthServer.scala:60)
at scala.util.Try$.apply(Try.scala:213)
at org.apache.spark.security.SocketAuthServer$$anon.run(SocketAuthServer.scala:60)
Caused by: org.apache.spark.util.TaskCompletionListenerException: Memory was leaked by query. Memory leaked: (671744)
Allocator(toBatchIterator) 0/671744/671744/9223372036854775807 (res/actual/peak/limit)
Previous exception in task: sun.misc.Unsafe or java.nio.DirectByteBuffer.<init>(long, int) not available
io.netty.util.internal.PlatformDependent.directBuffer(PlatformDependent.java:490)
io.netty.buffer.NettyArrowBuf.getDirectBuffer(NettyArrowBuf.java:243)
io.netty.buffer.NettyArrowBuf.nioBuffer(NettyArrowBuf.java:233)
io.netty.buffer.ArrowBuf.nioBuffer(ArrowBuf.java:245)
org.apache.arrow.vector.ipc.message.ArrowRecordBatch.computeBodyLength(ArrowRecordBatch.java:222)
org.apache.arrow.vector.ipc.message.MessageSerializer.serialize(MessageSerializer.java:240)
org.apache.arrow.vector.ipc.message.MessageSerializer.serialize(MessageSerializer.java:226)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.$anonfun$next(ArrowConverters.scala:118)
scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.next(ArrowConverters.scala:121)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.next(ArrowConverters.scala:97)
scala.collection.Iterator.foreach(Iterator.scala:941)
scala.collection.Iterator.foreach$(Iterator.scala:941)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.foreach(ArrowConverters.scala:97)
scala.collection.generic.Growable.$plus$plus$eq(Growable.scala:62)
scala.collection.generic.Growable.$plus$plus$eq$(Growable.scala:53)
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:105)
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:49)
scala.collection.TraversableOnce.to(TraversableOnce.scala:315)
scala.collection.TraversableOnce.to$(TraversableOnce.scala:313)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.to(ArrowConverters.scala:97)
scala.collection.TraversableOnce.toBuffer(TraversableOnce.scala:307)
scala.collection.TraversableOnce.toBuffer$(TraversableOnce.scala:307)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.toBuffer(ArrowConverters.scala:97)
scala.collection.TraversableOnce.toArray(TraversableOnce.scala:294)
scala.collection.TraversableOnce.toArray$(TraversableOnce.scala:288)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.toArray(ArrowConverters.scala:97)
org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3562)
org.apache.spark.SparkContext.$anonfun$runJob(SparkContext.scala:2193)
org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
org.apache.spark.scheduler.Task.run(Task.scala:127)
org.apache.spark.executor.Executor$TaskRunner.$anonfun$run(Executor.scala:446)
org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449)
java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
java.lang.Thread.run(Unknown Source)
at org.apache.spark.TaskContextImpl.invokeListeners(TaskContextImpl.scala:145)
at org.apache.spark.TaskContextImpl.markTaskCompleted(TaskContextImpl.scala:124)
at org.apache.spark.scheduler.Task.run(Task.scala:137)
at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run(Executor.scala:446)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
warnings.warn(msg)
---------------------------------------------------------------------------
Py4JJavaError Traceback (most recent call last)
<ipython-input-127-51c79da6d64b> in <module>
4
5 #for sensor in sensors:
----> 6 plot_summaries("Water_Level_Sensor_stddev", "pivoted")
<ipython-input-124-70e98889279f> in plot_summaries(sensor, dfName)
5 df = sqlContext.table(dfName)
6
----> 7 pdf = df.toPandas()
8 #.select("*") \
9 #.orderBy("index") \
/spark/python/lib/pyspark.zip/pyspark/sql/pandas/conversion.py in toPandas(self)
106 # Rename columns to avoid duplicated column names.
107 tmp_column_names = ['col_{}'.format(i) for i in range(len(self.columns))]
--> 108 batches = self.toDF(*tmp_column_names)._collect_as_arrow()
109 if len(batches) > 0:
110 table = pyarrow.Table.from_batches(batches)
/spark/python/lib/pyspark.zip/pyspark/sql/pandas/conversion.py in _collect_as_arrow(self)
242 finally:
243 # Join serving thread and raise any exceptions from collectAsArrowToPython
--> 244 jsocket_auth_server.getResult()
245
246 # Separate RecordBatches from batch order indices in results
/spark/python/lib/py4j-0.10.9-src.zip/py4j/java_gateway.py in __call__(self, *args)
1303 answer = self.gateway_client.send_command(command)
1304 return_value = get_return_value(
-> 1305 answer, self.gateway_client, self.target_id, self.name)
1306
1307 for temp_arg in temp_args:
/spark/python/lib/pyspark.zip/pyspark/sql/utils.py in deco(*a, **kw)
126 def deco(*a, **kw):
127 try:
--> 128 return f(*a, **kw)
129 except py4j.protocol.Py4JJavaError as e:
130 converted = convert_exception(e.java_exception)
/spark/python/lib/py4j-0.10.9-src.zip/py4j/protocol.py in get_return_value(answer, gateway_client, target_id, name)
326 raise Py4JJavaError(
327 "An error occurred while calling {0}{1}{2}.\n".
--> 328 format(target_id, ".", name), value)
329 else:
330 raise Py4JError(
Py4JJavaError: An error occurred while calling o117.getResult.
: org.apache.spark.SparkException: Exception thrown in awaitResult:
at org.apache.spark.util.ThreadUtils$.awaitResult(ThreadUtils.scala:302)
at org.apache.spark.security.SocketAuthServer.getResult(SocketAuthServer.scala:88)
at org.apache.spark.security.SocketAuthServer.getResult(SocketAuthServer.scala:84)
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:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 1157.0 failed 4 times, most recent failure: Lost task 0.3 in stage 1157.0 (TID 81153, 10.244.1.26, executor 12): org.apache.spark.util.TaskCompletionListenerException: Memory was leaked by query. Memory leaked: (671744)
Allocator(toBatchIterator) 0/671744/671744/9223372036854775807 (res/actual/peak/limit)
Previous exception in task: sun.misc.Unsafe or java.nio.DirectByteBuffer.<init>(long, int) not available
io.netty.util.internal.PlatformDependent.directBuffer(PlatformDependent.java:490)
io.netty.buffer.NettyArrowBuf.getDirectBuffer(NettyArrowBuf.java:243)
io.netty.buffer.NettyArrowBuf.nioBuffer(NettyArrowBuf.java:233)
io.netty.buffer.ArrowBuf.nioBuffer(ArrowBuf.java:245)
org.apache.arrow.vector.ipc.message.ArrowRecordBatch.computeBodyLength(ArrowRecordBatch.java:222)
org.apache.arrow.vector.ipc.message.MessageSerializer.serialize(MessageSerializer.java:240)
org.apache.arrow.vector.ipc.message.MessageSerializer.serialize(MessageSerializer.java:226)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.$anonfun$next(ArrowConverters.scala:118)
scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.next(ArrowConverters.scala:121)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.next(ArrowConverters.scala:97)
scala.collection.Iterator.foreach(Iterator.scala:941)
scala.collection.Iterator.foreach$(Iterator.scala:941)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.foreach(ArrowConverters.scala:97)
scala.collection.generic.Growable.$plus$plus$eq(Growable.scala:62)
scala.collection.generic.Growable.$plus$plus$eq$(Growable.scala:53)
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:105)
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:49)
scala.collection.TraversableOnce.to(TraversableOnce.scala:315)
scala.collection.TraversableOnce.to$(TraversableOnce.scala:313)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.to(ArrowConverters.scala:97)
scala.collection.TraversableOnce.toBuffer(TraversableOnce.scala:307)
scala.collection.TraversableOnce.toBuffer$(TraversableOnce.scala:307)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.toBuffer(ArrowConverters.scala:97)
scala.collection.TraversableOnce.toArray(TraversableOnce.scala:294)
scala.collection.TraversableOnce.toArray$(TraversableOnce.scala:288)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.toArray(ArrowConverters.scala:97)
org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3562)
org.apache.spark.SparkContext.$anonfun$runJob(SparkContext.scala:2193)
org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
org.apache.spark.scheduler.Task.run(Task.scala:127)
org.apache.spark.executor.Executor$TaskRunner.$anonfun$run(Executor.scala:446)
org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449)
java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
java.base/java.lang.Thread.run(Unknown Source)
at org.apache.spark.TaskContextImpl.invokeListeners(TaskContextImpl.scala:145)
at org.apache.spark.TaskContextImpl.markTaskCompleted(TaskContextImpl.scala:124)
at org.apache.spark.scheduler.Task.run(Task.scala:137)
at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run(Executor.scala:446)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2059)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage(DAGScheduler.scala:2008)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$adapted(DAGScheduler.scala:2007)
at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2007)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed(DAGScheduler.scala:973)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$adapted(DAGScheduler.scala:973)
at scala.Option.foreach(Option.scala:407)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:973)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2239)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2188)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2177)
at org.apache.spark.util.EventLoop$$anon.run(EventLoop.scala:49)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:775)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2099)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2194)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3560)
at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3564)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython$adapted(Dataset.scala:3541)
at org.apache.spark.sql.Dataset.$anonfun$withAction(Dataset.scala:3618)
at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId(SQLExecution.scala:100)
at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:160)
at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId(SQLExecution.scala:87)
at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:764)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:64)
at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3616)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3541)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython$adapted(Dataset.scala:3540)
at org.apache.spark.security.SocketAuthServer$.$anonfun$serveToStream(SocketAuthServer.scala:130)
at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.security.SocketAuthServer$.$anonfun$serveToStream(SocketAuthServer.scala:132)
at org.apache.spark.security.SocketAuthServer$.$anonfun$serveToStream$adapted(SocketAuthServer.scala:127)
at org.apache.spark.security.SocketFuncServer.handleConnection(SocketAuthServer.scala:104)
at org.apache.spark.security.SocketFuncServer.handleConnection(SocketAuthServer.scala:98)
at org.apache.spark.security.SocketAuthServer$$anon.$anonfun$run(SocketAuthServer.scala:60)
at scala.util.Try$.apply(Try.scala:213)
at org.apache.spark.security.SocketAuthServer$$anon.run(SocketAuthServer.scala:60)
Caused by: org.apache.spark.util.TaskCompletionListenerException: Memory was leaked by query. Memory leaked: (671744)
Allocator(toBatchIterator) 0/671744/671744/9223372036854775807 (res/actual/peak/limit)
如何避免？
不过重启Spark解释器后问题终于解决了
首先，我在 scala 代码中将数据添加到 tempTable：
resultIndexed.show(490, false)
resultIndexed.registerTempTable("pivoted")
然后读入python（导入省略）：
%spark.pyspark
import bkzep
import numpy as np
from bokeh.io import output_notebook, show
from bokeh.plotting import figure
from bokeh.models import ColumnDataSource
from bokeh.layouts import gridplot
from pyspark.sql.functions import col, coalesce, lit, monotonically_increasing_id
from pyspark.sql import DataFrame
from pyspark.sql.functions import *
output_notebook(notebook_type='zeppelin')
%pyspark
from pyspark.sql.functions import *
def plot_summaries(sensor, dfName):
df = sqlContext.table(dfName)
pdf = df.toPandas()
#sample = pdf.sample(50)
source = ColumnDataSource(pdf)
#print(pdf)
TOOLTIPS = [
("month", "@month"),
("day", "@day"),
("hour", "@hour"),
("min", "@{min}{0.3f}"),
("avg", "@{avg}{0.3f}"),
("max", "@{max}{0.3f}"),
("median", "@{median}{0.3f}"),
("stddev", "@{stddev}{0.3f}"),
]
TOOLTIPS2 = [
("month", "@month"),
("day", "@day"),
("count", "@{count}{0.3f}"),
]
fig = figure(title="Hourly summaries of '{}'".format(sensor), tooltips=TOOLTIPS)
#fig.line(x='id', y='avg', source=source, color="orange")
#fig.line(x='id', y='min', source=source, color="green")
#fig.line(x='id', y='max', source=source, color="red")
fig.line(x='id', y='median', source=source, color="blue")
#fig.line(x='id', y='stddev', source=source, color="aquamarine")
#fig2 = figure(title="Hourly summaries of '{}' counters".format(sensor), tooltips=TOOLTIPS2)
#fig2.line(x='id', y='count', source=source, color="orange")
show(gridplot([fig], ncols=1, plot_width=1000, plot_height=400))
#show(fig)
sensors = [
"Water_Level_Sensor_stddev",
"Water_Level_Sensor_mean"
]
%pyspark
from pyspark.sql.functions import *
keyCol = "month_day_hour"
#for sensor in sensors:
plot_summaries("Water_Level_Sensor_stddev", "pivoted")
然后我在执行过程中得到了错误：
/spark/python/lib/pyspark.zip/pyspark/sql/pandas/conversion.py:134: UserWarning: toPandas attempted Arrow optimization because 'spark.sql.execution.arrow.pyspark.enabled' is set to true, but has reached the error below and can not continue. Note that 'spark.sql.execution.arrow.pyspark.fallback.enabled' does not have an effect on failures in the middle of computation.
An error occurred while calling o117.getResult.
: org.apache.spark.SparkException: Exception thrown in awaitResult:
at org.apache.spark.util.ThreadUtils$.awaitResult(ThreadUtils.scala:302)
at org.apache.spark.security.SocketAuthServer.getResult(SocketAuthServer.scala:88)
at org.apache.spark.security.SocketAuthServer.getResult(SocketAuthServer.scala:84)
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:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 1157.0 failed 4 times, most recent failure: Lost task 0.3 in stage 1157.0 (TID 81153, 10.244.1.26, executor 12): org.apache.spark.util.TaskCompletionListenerException: Memory was leaked by query. Memory leaked: (671744)
Allocator(toBatchIterator) 0/671744/671744/9223372036854775807 (res/actual/peak/limit)
Previous exception in task: sun.misc.Unsafe or java.nio.DirectByteBuffer.<init>(long, int) not available
io.netty.util.internal.PlatformDependent.directBuffer(PlatformDependent.java:490)
io.netty.buffer.NettyArrowBuf.getDirectBuffer(NettyArrowBuf.java:243)
io.netty.buffer.NettyArrowBuf.nioBuffer(NettyArrowBuf.java:233)
io.netty.buffer.ArrowBuf.nioBuffer(ArrowBuf.java:245)
org.apache.arrow.vector.ipc.message.ArrowRecordBatch.computeBodyLength(ArrowRecordBatch.java:222)
org.apache.arrow.vector.ipc.message.MessageSerializer.serialize(MessageSerializer.java:240)
org.apache.arrow.vector.ipc.message.MessageSerializer.serialize(MessageSerializer.java:226)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.$anonfun$next(ArrowConverters.scala:118)
scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.next(ArrowConverters.scala:121)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.next(ArrowConverters.scala:97)
scala.collection.Iterator.foreach(Iterator.scala:941)
scala.collection.Iterator.foreach$(Iterator.scala:941)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.foreach(ArrowConverters.scala:97)
scala.collection.generic.Growable.$plus$plus$eq(Growable.scala:62)
scala.collection.generic.Growable.$plus$plus$eq$(Growable.scala:53)
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:105)
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:49)
scala.collection.TraversableOnce.to(TraversableOnce.scala:315)
scala.collection.TraversableOnce.to$(TraversableOnce.scala:313)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.to(ArrowConverters.scala:97)
scala.collection.TraversableOnce.toBuffer(TraversableOnce.scala:307)
scala.collection.TraversableOnce.toBuffer$(TraversableOnce.scala:307)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.toBuffer(ArrowConverters.scala:97)
scala.collection.TraversableOnce.toArray(TraversableOnce.scala:294)
scala.collection.TraversableOnce.toArray$(TraversableOnce.scala:288)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.toArray(ArrowConverters.scala:97)
org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3562)
org.apache.spark.SparkContext.$anonfun$runJob(SparkContext.scala:2193)
org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
org.apache.spark.scheduler.Task.run(Task.scala:127)
org.apache.spark.executor.Executor$TaskRunner.$anonfun$run(Executor.scala:446)
org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449)
java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
java.base/java.lang.Thread.run(Unknown Source)
at org.apache.spark.TaskContextImpl.invokeListeners(TaskContextImpl.scala:145)
at org.apache.spark.TaskContextImpl.markTaskCompleted(TaskContextImpl.scala:124)
at org.apache.spark.scheduler.Task.run(Task.scala:137)
at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run(Executor.scala:446)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2059)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage(DAGScheduler.scala:2008)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$adapted(DAGScheduler.scala:2007)
at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2007)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed(DAGScheduler.scala:973)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$adapted(DAGScheduler.scala:973)
at scala.Option.foreach(Option.scala:407)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:973)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2239)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2188)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2177)
at org.apache.spark.util.EventLoop$$anon.run(EventLoop.scala:49)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:775)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2099)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2194)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3560)
at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3564)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython$adapted(Dataset.scala:3541)
at org.apache.spark.sql.Dataset.$anonfun$withAction(Dataset.scala:3618)
at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId(SQLExecution.scala:100)
at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:160)
at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId(SQLExecution.scala:87)
at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:764)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:64)
at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3616)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3541)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython$adapted(Dataset.scala:3540)
at org.apache.spark.security.SocketAuthServer$.$anonfun$serveToStream(SocketAuthServer.scala:130)
at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.security.SocketAuthServer$.$anonfun$serveToStream(SocketAuthServer.scala:132)
at org.apache.spark.security.SocketAuthServer$.$anonfun$serveToStream$adapted(SocketAuthServer.scala:127)
at org.apache.spark.security.SocketFuncServer.handleConnection(SocketAuthServer.scala:104)
at org.apache.spark.security.SocketFuncServer.handleConnection(SocketAuthServer.scala:98)
at org.apache.spark.security.SocketAuthServer$$anon.$anonfun$run(SocketAuthServer.scala:60)
at scala.util.Try$.apply(Try.scala:213)
at org.apache.spark.security.SocketAuthServer$$anon.run(SocketAuthServer.scala:60)
Caused by: org.apache.spark.util.TaskCompletionListenerException: Memory was leaked by query. Memory leaked: (671744)
Allocator(toBatchIterator) 0/671744/671744/9223372036854775807 (res/actual/peak/limit)
Previous exception in task: sun.misc.Unsafe or java.nio.DirectByteBuffer.<init>(long, int) not available
io.netty.util.internal.PlatformDependent.directBuffer(PlatformDependent.java:490)
io.netty.buffer.NettyArrowBuf.getDirectBuffer(NettyArrowBuf.java:243)
io.netty.buffer.NettyArrowBuf.nioBuffer(NettyArrowBuf.java:233)
io.netty.buffer.ArrowBuf.nioBuffer(ArrowBuf.java:245)
org.apache.arrow.vector.ipc.message.ArrowRecordBatch.computeBodyLength(ArrowRecordBatch.java:222)
org.apache.arrow.vector.ipc.message.MessageSerializer.serialize(MessageSerializer.java:240)
org.apache.arrow.vector.ipc.message.MessageSerializer.serialize(MessageSerializer.java:226)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.$anonfun$next(ArrowConverters.scala:118)
scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.next(ArrowConverters.scala:121)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.next(ArrowConverters.scala:97)
scala.collection.Iterator.foreach(Iterator.scala:941)
scala.collection.Iterator.foreach$(Iterator.scala:941)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.foreach(ArrowConverters.scala:97)
scala.collection.generic.Growable.$plus$plus$eq(Growable.scala:62)
scala.collection.generic.Growable.$plus$plus$eq$(Growable.scala:53)
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:105)
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:49)
scala.collection.TraversableOnce.to(TraversableOnce.scala:315)
scala.collection.TraversableOnce.to$(TraversableOnce.scala:313)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.to(ArrowConverters.scala:97)
scala.collection.TraversableOnce.toBuffer(TraversableOnce.scala:307)
scala.collection.TraversableOnce.toBuffer$(TraversableOnce.scala:307)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.toBuffer(ArrowConverters.scala:97)
scala.collection.TraversableOnce.toArray(TraversableOnce.scala:294)
scala.collection.TraversableOnce.toArray$(TraversableOnce.scala:288)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.toArray(ArrowConverters.scala:97)
org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3562)
org.apache.spark.SparkContext.$anonfun$runJob(SparkContext.scala:2193)
org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
org.apache.spark.scheduler.Task.run(Task.scala:127)
org.apache.spark.executor.Executor$TaskRunner.$anonfun$run(Executor.scala:446)
org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449)
java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
java.lang.Thread.run(Unknown Source)
at org.apache.spark.TaskContextImpl.invokeListeners(TaskContextImpl.scala:145)
at org.apache.spark.TaskContextImpl.markTaskCompleted(TaskContextImpl.scala:124)
at org.apache.spark.scheduler.Task.run(Task.scala:137)
at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run(Executor.scala:446)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449)
at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)
warnings.warn(msg)
---------------------------------------------------------------------------
Py4JJavaError Traceback (most recent call last)
<ipython-input-127-51c79da6d64b> in <module>
4
5 #for sensor in sensors:
----> 6 plot_summaries("Water_Level_Sensor_stddev", "pivoted")
<ipython-input-124-70e98889279f> in plot_summaries(sensor, dfName)
5 df = sqlContext.table(dfName)
6
----> 7 pdf = df.toPandas()
8 #.select("*") \
9 #.orderBy("index") \
/spark/python/lib/pyspark.zip/pyspark/sql/pandas/conversion.py in toPandas(self)
106 # Rename columns to avoid duplicated column names.
107 tmp_column_names = ['col_{}'.format(i) for i in range(len(self.columns))]
--> 108 batches = self.toDF(*tmp_column_names)._collect_as_arrow()
109 if len(batches) > 0:
110 table = pyarrow.Table.from_batches(batches)
/spark/python/lib/pyspark.zip/pyspark/sql/pandas/conversion.py in _collect_as_arrow(self)
242 finally:
243 # Join serving thread and raise any exceptions from collectAsArrowToPython
--> 244 jsocket_auth_server.getResult()
245
246 # Separate RecordBatches from batch order indices in results
/spark/python/lib/py4j-0.10.9-src.zip/py4j/java_gateway.py in __call__(self, *args)
1303 answer = self.gateway_client.send_command(command)
1304 return_value = get_return_value(
-> 1305 answer, self.gateway_client, self.target_id, self.name)
1306
1307 for temp_arg in temp_args:
/spark/python/lib/pyspark.zip/pyspark/sql/utils.py in deco(*a, **kw)
126 def deco(*a, **kw):
127 try:
--> 128 return f(*a, **kw)
129 except py4j.protocol.Py4JJavaError as e:
130 converted = convert_exception(e.java_exception)
/spark/python/lib/py4j-0.10.9-src.zip/py4j/protocol.py in get_return_value(answer, gateway_client, target_id, name)
326 raise Py4JJavaError(
327 "An error occurred while calling {0}{1}{2}.\n".
--> 328 format(target_id, ".", name), value)
329 else:
330 raise Py4JError(
Py4JJavaError: An error occurred while calling o117.getResult.
: org.apache.spark.SparkException: Exception thrown in awaitResult:
at org.apache.spark.util.ThreadUtils$.awaitResult(ThreadUtils.scala:302)
at org.apache.spark.security.SocketAuthServer.getResult(SocketAuthServer.scala:88)
at org.apache.spark.security.SocketAuthServer.getResult(SocketAuthServer.scala:84)
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:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:238)
at java.lang.Thread.run(Thread.java:748)
Caused by: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 1157.0 failed 4 times, most recent failure: Lost task 0.3 in stage 1157.0 (TID 81153, 10.244.1.26, executor 12): org.apache.spark.util.TaskCompletionListenerException: Memory was leaked by query. Memory leaked: (671744)
Allocator(toBatchIterator) 0/671744/671744/9223372036854775807 (res/actual/peak/limit)
Previous exception in task: sun.misc.Unsafe or java.nio.DirectByteBuffer.<init>(long, int) not available
io.netty.util.internal.PlatformDependent.directBuffer(PlatformDependent.java:490)
io.netty.buffer.NettyArrowBuf.getDirectBuffer(NettyArrowBuf.java:243)
io.netty.buffer.NettyArrowBuf.nioBuffer(NettyArrowBuf.java:233)
io.netty.buffer.ArrowBuf.nioBuffer(ArrowBuf.java:245)
org.apache.arrow.vector.ipc.message.ArrowRecordBatch.computeBodyLength(ArrowRecordBatch.java:222)
org.apache.arrow.vector.ipc.message.MessageSerializer.serialize(MessageSerializer.java:240)
org.apache.arrow.vector.ipc.message.MessageSerializer.serialize(MessageSerializer.java:226)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.$anonfun$next(ArrowConverters.scala:118)
scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.next(ArrowConverters.scala:121)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.next(ArrowConverters.scala:97)
scala.collection.Iterator.foreach(Iterator.scala:941)
scala.collection.Iterator.foreach$(Iterator.scala:941)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.foreach(ArrowConverters.scala:97)
scala.collection.generic.Growable.$plus$plus$eq(Growable.scala:62)
scala.collection.generic.Growable.$plus$plus$eq$(Growable.scala:53)
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:105)
scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:49)
scala.collection.TraversableOnce.to(TraversableOnce.scala:315)
scala.collection.TraversableOnce.to$(TraversableOnce.scala:313)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.to(ArrowConverters.scala:97)
scala.collection.TraversableOnce.toBuffer(TraversableOnce.scala:307)
scala.collection.TraversableOnce.toBuffer$(TraversableOnce.scala:307)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.toBuffer(ArrowConverters.scala:97)
scala.collection.TraversableOnce.toArray(TraversableOnce.scala:294)
scala.collection.TraversableOnce.toArray$(TraversableOnce.scala:288)
org.apache.spark.sql.execution.arrow.ArrowConverters$$anon.toArray(ArrowConverters.scala:97)
org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3562)
org.apache.spark.SparkContext.$anonfun$runJob(SparkContext.scala:2193)
org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)
org.apache.spark.scheduler.Task.run(Task.scala:127)
org.apache.spark.executor.Executor$TaskRunner.$anonfun$run(Executor.scala:446)
org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449)
java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
java.base/java.lang.Thread.run(Unknown Source)
at org.apache.spark.TaskContextImpl.invokeListeners(TaskContextImpl.scala:145)
at org.apache.spark.TaskContextImpl.markTaskCompleted(TaskContextImpl.scala:124)
at org.apache.spark.scheduler.Task.run(Task.scala:137)
at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run(Executor.scala:446)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:449)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2059)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage(DAGScheduler.scala:2008)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$adapted(DAGScheduler.scala:2007)
at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2007)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed(DAGScheduler.scala:973)
at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$adapted(DAGScheduler.scala:973)
at scala.Option.foreach(Option.scala:407)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:973)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2239)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2188)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2177)
at org.apache.spark.util.EventLoop$$anon.run(EventLoop.scala:49)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:775)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2099)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2194)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3560)
at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3564)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython$adapted(Dataset.scala:3541)
at org.apache.spark.sql.Dataset.$anonfun$withAction(Dataset.scala:3618)
at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId(SQLExecution.scala:100)
at org.apache.spark.sql.execution.SQLExecution$.withSQLConfPropagated(SQLExecution.scala:160)
at org.apache.spark.sql.execution.SQLExecution$.$anonfun$withNewExecutionId(SQLExecution.scala:87)
at org.apache.spark.sql.SparkSession.withActive(SparkSession.scala:764)
at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:64)
at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3616)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython(Dataset.scala:3541)
at org.apache.spark.sql.Dataset.$anonfun$collectAsArrowToPython$adapted(Dataset.scala:3540)
at org.apache.spark.security.SocketAuthServer$.$anonfun$serveToStream(SocketAuthServer.scala:130)
at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1377)
at org.apache.spark.security.SocketAuthServer$.$anonfun$serveToStream(SocketAuthServer.scala:132)
at org.apache.spark.security.SocketAuthServer$.$anonfun$serveToStream$adapted(SocketAuthServer.scala:127)
at org.apache.spark.security.SocketFuncServer.handleConnection(SocketAuthServer.scala:104)
at org.apache.spark.security.SocketFuncServer.handleConnection(SocketAuthServer.scala:98)
at org.apache.spark.security.SocketAuthServer$$anon.$anonfun$run(SocketAuthServer.scala:60)
at scala.util.Try$.apply(Try.scala:213)
at org.apache.spark.security.SocketAuthServer$$anon.run(SocketAuthServer.scala:60)
Caused by: org.apache.spark.util.TaskCompletionListenerException: Memory was leaked by query. Memory leaked: (671744)
Allocator(toBatchIterator) 0/671744/671744/9223372036854775807 (res/actual/peak/limit)
如何避免？
不过重启Spark解释器后问题终于解决了