Python 在本地模式下使用PySpark读取文件时发生OutOfMemoryError
我有十几个gpg加密文件，其中包含我想用PySpark分析的数据。我的策略是将解密函数作为平面映射应用于每个文件，然后在记录级别继续处理：Python 在本地模式下使用PySpark读取文件时发生OutOfMemoryError,python,apache-spark,pyspark,Python,Apache Spark,Pyspark,我有十几个gpg加密文件，其中包含我想用PySpark分析的数据。我的策略是将解密函数作为平面映射应用于每个文件，然后在记录级别继续处理： def read_fun_generator(filename): with gpg_open(filename[0].split(':')[-1], 'r') as f: for line in f: yield line.strip() gpg_files = sc.wholeTextFiles(/pat
def read_fun_generator(filename):
with gpg_open(filename[0].split(':')[-1], 'r') as f:
for line in f:
yield line.strip()
gpg_files = sc.wholeTextFiles(/path/to/files/*.gpg)
rdd_from_gpg = gpg_files.flatMap(read_fun_generator).map(lambda x: x.split('|'))
rdd_from_gpg.count() # <-- For example...
15/06/10 11:03:30 INFO SparkContext: Running Spark version 1.3.1
15/06/10 11:03:31 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
15/06/10 11:03:31 INFO SecurityManager: Changing view acls to: santon
15/06/10 11:03:31 INFO SecurityManager: Changing modify acls to: santon
15/06/10 11:03:31 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(santon); users with modify permissions: Set(santon)
15/06/10 11:03:31 INFO Slf4jLogger: Slf4jLogger started
15/06/10 11:03:31 INFO Remoting: Starting remoting
15/06/10 11:03:32 INFO Remoting: Remoting started; listening on addresses :[akka.tcp://sparkDriver@localhost:44347]
15/06/10 11:03:32 INFO Utils: Successfully started service 'sparkDriver' on port 44347.
15/06/10 11:03:32 INFO SparkEnv: Registering MapOutputTracker
15/06/10 11:03:32 INFO SparkEnv: Registering BlockManagerMaster
15/06/10 11:03:32 INFO DiskBlockManager: Created local directory at /tmp/spark-24dc8f0a-a89a-44f8-bb95-cd5514e5bf0c/blockmgr-85b6f082-ff5a-4a0e-b48a-1ec62715dda0
15/06/10 11:03:32 INFO MemoryStore: MemoryStore started with capacity 265.4 MB
15/06/10 11:03:32 INFO HttpFileServer: HTTP File server directory is /tmp/spark-7b2172ed-d658-4e11-bbc1-600697f3255e/httpd-5423f8bc-ec43-48c5-9367-87214dad54f4
15/06/10 11:03:32 INFO HttpServer: Starting HTTP Server
15/06/10 11:03:32 INFO Server: jetty-8.y.z-SNAPSHOT
15/06/10 11:03:32 INFO AbstractConnector: Started SocketConnector@0.0.0.0:50366
15/06/10 11:03:32 INFO Utils: Successfully started service 'HTTP file server' on port 50366.
15/06/10 11:03:32 INFO SparkEnv: Registering OutputCommitCoordinator
15/06/10 11:03:32 INFO Server: jetty-8.y.z-SNAPSHOT
15/06/10 11:03:32 INFO AbstractConnector: Started SelectChannelConnector@0.0.0.0:4040
15/06/10 11:03:32 INFO Utils: Successfully started service 'SparkUI' on port 4040.
15/06/10 11:03:32 INFO SparkUI: Started SparkUI at localhost:4040
15/06/10 11:03:32 INFO Executor: Starting executor ID <driver> on host localhost
15/06/10 11:03:32 INFO AkkaUtils: Connecting to HeartbeatReceiver: akka.tcp://sparkDriver@localhost:44347/user/HeartbeatReceiver
15/06/10 11:03:33 INFO NettyBlockTransferService: Server created on 46730
15/06/10 11:03:33 INFO BlockManagerMaster: Trying to register BlockManager
15/06/10 11:03:33 INFO BlockManagerMasterActor: Registering block manager localhost:46730 with 265.4 MB RAM, BlockManagerId(<driver>, localhost, 46730)
15/06/10 11:03:33 INFO BlockManagerMaster: Registered BlockManager
15/06/10 11:05:19 INFO MemoryStore: ensureFreeSpace(215726) called with curMem=0, maxMem=278302556
15/06/10 11:05:19 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 210.7 KB, free 265.2 MB)
15/06/10 11:05:19 INFO MemoryStore: ensureFreeSpace(31533) called with curMem=215726, maxMem=278302556
15/06/10 11:05:19 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 30.8 KB, free 265.2 MB)
15/06/10 11:05:19 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on localhost:46730 (size: 30.8 KB, free: 265.4 MB)
15/06/10 11:05:19 INFO BlockManagerMaster: Updated info of block broadcast_0_piece0
15/06/10 11:05:19 INFO SparkContext: Created broadcast 0 from wholeTextFiles at NativeMethodAccessorImpl.java:-2
15/06/10 11:05:22 INFO FileInputFormat: Total input paths to process : 16
15/06/10 11:05:22 INFO FileInputFormat: Total input paths to process : 16
15/06/10 11:05:22 INFO CombineFileInputFormat: DEBUG: Terminated node allocation with : CompletedNodes: 1, size left: 71665121
15/06/10 11:05:22 INFO SparkContext: Starting job: count at <timed exec>:2
15/06/10 11:05:22 INFO DAGScheduler: Got job 0 (count at <timed exec>:2) with 2 output partitions (allowLocal=false)
15/06/10 11:05:22 INFO DAGScheduler: Final stage: Stage 0(count at <timed exec>:2)
15/06/10 11:05:22 INFO DAGScheduler: Parents of final stage: List()
15/06/10 11:05:22 INFO DAGScheduler: Missing parents: List()
15/06/10 11:05:22 INFO DAGScheduler: Submitting Stage 0 (PythonRDD[1] at count at <timed exec>:2), which has no missing parents
15/06/10 11:05:23 INFO MemoryStore: ensureFreeSpace(6264) called with curMem=247259, maxMem=278302556
15/06/10 11:05:23 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 6.1 KB, free 265.2 MB)
15/06/10 11:05:23 INFO MemoryStore: ensureFreeSpace(4589) called with curMem=253523, maxMem=278302556
15/06/10 11:05:23 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 4.5 KB, free 265.2 MB)
15/06/10 11:05:23 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on localhost:46730 (size: 4.5 KB, free: 265.4 MB)
15/06/10 11:05:23 INFO BlockManagerMaster: Updated info of block broadcast_1_piece0
15/06/10 11:05:23 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:839
15/06/10 11:05:23 INFO DAGScheduler: Submitting 2 missing tasks from Stage 0 (PythonRDD[1] at count at <timed exec>:2)
15/06/10 11:05:23 INFO TaskSchedulerImpl: Adding task set 0.0 with 2 tasks
15/06/10 11:05:23 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, PROCESS_LOCAL, 1903 bytes)
15/06/10 11:05:23 INFO TaskSetManager: Starting task 1.0 in stage 0.0 (TID 1, localhost, PROCESS_LOCAL, 3085 bytes)
15/06/10 11:05:23 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
15/06/10 11:05:23 INFO Executor: Running task 1.0 in stage 0.0 (TID 1)
15/06/10 11:05:26 INFO WholeTextFileRDD: Input split: Paths:[gpg_files]
15/06/10 11:05:40 ERROR Utils: Uncaught exception in thread stdout writer for /anaconda/python/bin/python
java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOfRange(Arrays.java:2694)
at java.lang.String.<init>(String.java:203)
at java.nio.HeapCharBuffer.toString(HeapCharBuffer.java:561)
at java.nio.CharBuffer.toString(CharBuffer.java:1201)
at org.apache.hadoop.io.Text.decode(Text.java:405)
at org.apache.hadoop.io.Text.decode(Text.java:382)
at org.apache.hadoop.io.Text.toString(Text.java:280)
at org.apache.spark.input.WholeTextFileRecordReader.nextKeyValue(WholeTextFileRecordReader.scala:86)
at org.apache.hadoop.mapreduce.lib.input.CombineFileRecordReader.nextKeyValue(CombineFileRecordReader.java:69)
at org.apache.spark.rdd.NewHadoopRDD$$anon$1.hasNext(NewHadoopRDD.scala:143)
at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at org.apache.spark.InterruptibleIterator.foreach(InterruptibleIterator.scala:28)
at org.apache.spark.api.python.PythonRDD$.writeIteratorToStream(PythonRDD.scala:421)
at org.apache.spark.api.python.PythonRDD$WriterThread$$anonfun$run$1.apply(PythonRDD.scala:243)
at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1618)
at org.apache.spark.api.python.PythonRDD$WriterThread.run(PythonRDD.scala:205)
Exception in thread "stdout writer for /anaconda/python/bin/python" java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOfRange(Arrays.java:2694)
at java.lang.String.<init>(String.java:203)
at java.nio.HeapCharBuffer.toString(HeapCharBuffer.java:561)
at java.nio.CharBuffer.toString(CharBuffer.java:1201)
at org.apache.hadoop.io.Text.decode(Text.java:405)
at org.apache.hadoop.io.Text.decode(Text.java:382)
at org.apache.hadoop.io.Text.toString(Text.java:280)
at org.apache.spark.input.WholeTextFileRecordReader.nextKeyValue(WholeTextFileRecordReader.scala:86)
at org.apache.hadoop.mapreduce.lib.input.CombineFileRecordReader.nextKeyValue(CombineFileRecordReader.java:69)
at org.apache.spark.rdd.NewHadoopRDD$$anon$1.hasNext(NewHadoopRDD.scala:143)
at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at org.apache.spark.InterruptibleIterator.foreach(InterruptibleIterator.scala:28)
at org.apache.spark.api.python.PythonRDD$.writeIteratorToStream(PythonRDD.scala:421)
at org.apache.spark.api.python.PythonRDD$WriterThread$$anonfun$run$1.apply(PythonRDD.scala:243)
at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1618)
at org.apache.spark.api.python.PythonRDD$WriterThread.run(PythonRDD.scala:205)
15/06/10 11:05:47 INFO PythonRDD: Times: total = 24140, boot = 2860, init = 664, finish = 20616
15/06/10 11:05:47 INFO Executor: Finished task 1.0 in stage 0.0 (TID 1). 1873 bytes result sent to driver
15/06/10 11:05:47 INFO TaskSetManager: Finished task 1.0 in stage 0.0 (TID 1) in 24251 ms on localhost (1/2)
15/06/10 11:03:30信息SparkContext:运行Spark版本1.3.1
15/06/10 11:03:31警告NativeCodeLoader:无法为您的平台加载本机hadoop库。。。在适用的情况下使用内置java类
15/06/10 11:03:31信息安全管理器：将视图ACL更改为：santon
15/06/10 11:03:31信息安全管理器：将修改ACL更改为：santon
15/06/10 11:03:31信息安全管理器：安全管理器：身份验证已禁用；ui ACL被禁用；具有查看权限的用户：Set（santon）；具有修改权限的用户：设置（santon）
15/06/10 11:03:31信息Slf4jLogger:Slf4jLogger已启动
15/06/10 11:03:31信息远程处理：开始远程处理
15/06/10 11:03:32信息远程处理：远程处理已启动；收听地址：[阿克卡。tcp://sparkDriver@本地主机：44347]
15/06/10 11:03:32信息实用程序：已在端口44347上成功启动服务“sparkDriver”。
15/06/10 11:03:32信息SparkEnv:正在注册MapOutputRacker
15/06/10 11:03:32信息SparkEnv:正在注册BlockManagerMaster
15/06/10 11:03:32信息DiskBlockManager:已在/tmp/spark-24dc8f0a-a89a-44f8-bb95-cd5514e5bf0c/blockmgr-85b6f082-ff5a-4a0e-b48a-1ec62715dda0处创建本地目录
15/06/10 11:03:32信息MemoryStore:MemoryStore以265.4 MB的容量启动
15/06/10 11:03:32信息HttpFileServer:HTTP文件服务器目录是/tmp/spark-7b2172d-d658-4e11-bbc1-600697f3255e/httpd-5423f8bc-ec43-48c5-9367-87214dad54f4
15/06/10 11:03:32信息HttpServer:正在启动HTTP服务器
15/06/10 11:03:32信息服务器：jetty-8.y.z-SNAPSHOT
15/06/10 11:03:32信息摘要连接器：已启动SocketConnector@0.0.0.0:50366
15/06/10 11:03:32信息实用程序：已在端口50366上成功启动服务“HTTP文件服务器”。
15/06/10 11:03:32信息SparkEnv:正在注册OutputCommitCoordinator
15/06/10 11:03:32信息服务器：jetty-8.y.z-SNAPSHOT
15/06/10 11:03:32信息摘要连接器：已启动SelectChannelConnector@0.0.0.0:4040
15/06/10 11:03:32信息实用程序：已成功启动端口4040上的服务“SparkUI”。
15/06/10 11:03:32信息SparkUI:在本地主机上启动SparkUI:4040
15/06/10 11:03:32信息执行器：正在启动主机localhost上的执行器ID
15/06/10 11:03:32信息AkkaUtils:连接到HeartbeatReceiver:akka。tcp://sparkDriver@localhost:44347/user/HeartbeatReceiver
15/06/10 11:03:33信息NettyBlockTransferService:服务器已在46730上创建
15/06/10 11:03:33信息BlockManager管理员：正在尝试注册BlockManager
15/06/10 11:03:33信息BlockManagerMasterActor:正在使用265.4 MB RAM注册块管理器localhost:46730，BlockManagerId（，localhost，46730）
15/06/10 11:03:33信息BlockManager管理员：注册BlockManager
2010年6月15日11:05:19信息内存存储：使用curMem=0、maxMem=278302556调用EnsureRefreeSpace（215726）
15/06/10 11:05:19信息内存存储：块广播0存储为内存中的值（估计大小210.7KB，可用容量265.2MB）
15/06/10 11:05:19信息内存存储：使用curMem=215726、maxMem=278302556调用EnsureRefreeSpace（31533）
15/06/10 11:05:19信息内存存储：块广播0块存储为内存中的字节（估计大小30.8 KB，可用空间265.2 MB）
15/06/10 11:05:19信息块管理信息：在本地主机上的内存中添加了广播片段0:46730（大小：30.8 KB，可用：265.4 MB）
15/06/10 11:05:19信息区块管理器管理员：区块广播的更新信息
15/06/10 11:05:19信息SparkContext:已从NativeMethodAccessorImpl.java中的Wholetext文件创建广播0:-2
15/06/10 11:05:22信息文件InputFormat:要处理的总输入路径：16
15/06/10 11:05:22信息文件InputFormat:要处理的总输入路径：16
2010年6月15日11:05:22信息组合输入格式：调试：终止的节点分配：CompletedNodes:1，左侧大小：71665121
15/06/10 11:05:22信息SparkContext:开始作业：计数时间：2
15/06/10 11:05:22信息调度程序：获取了具有2个输出分区的作业0（计数：2）（allowLocal=false）
2010年6月15日11:05:22信息调度程序：最终阶段：阶段0（计数时间：2）
15/06/10 11:05:22信息：最后阶段的家长：列表（）
15/06/10 11:05:22信息调度程序：缺少家长：列表（）
2010年6月15日11:05:22信息调度程序：正在提交阶段0（PythonRDD[1]，计数为：2），该阶段没有丢失的父级
2010年6月15日11:05:23信息内存存储：使用curMem=247259、maxMem=278302556调用EnsureRefreeSpace（6264）
15/06/10 11:05:23信息内存存储：块广播存储为内存中的值（估计大小为6.1 KB，可用容量为265.2 MB）
2010年6月15日11:05:23信息内存存储：使用curMem=253523、maxMem=278302556调用EnsureRefreeSpace（4589）
15/06/10 11:05:23信息内存存储：块广播\u 1\u片段0以字节形式存储在内存中（估计大小4.5 KB，可用空间265.2 MB）
15/06/10 11:05:23信息块管理信息：在本地主机上的内存中添加了广播片段0:46730（大小：4.5 KB，可用：265.4 MB）
15/06/10 11:05:23信息区块管理器管理员：区块广播的更新信息\u 1\u 0
15/06/10 11:05:23信息SparkContext:从DAGScheduler的广播创建了广播1。scala:839
15/06/10 11:05:23信息调度程序：从阶段0提交2个缺少的任务（PythonRDD[1]计数时间：2）
15/06/10 11:05:23信息TaskSchedulerImpl:添加包含2个任务的任务集0.0
15/06/10 11:05:23信息任务集管理器：在阶段0.0中启动任务0.0（TID 0，本地主机，进程\本地，1903字节）
15/06/10 11:05:23信息任务集管理器：在阶段0.0中启动任务1.0（TID 1，本地主机，进程\u本地，3085字节）
2010年6月15日11:05:23信息执行者：在阶段0.0（TID 0）中运行任务0.0
2010年6月15日11:05:23信息执行者：在阶段0.0（TID 1）中运行任务1.0
15/06/10 11:05:26信息WholeTextFileRDD:输入拆分：路径：[gpg_文件]
15/06/10 11:05:40错误Utils:线程stdout writer for/anaconda/python/bin/python中出现未捕获异常
java.lang.OutOfMemoryError:java堆空间
在java.util.Array
15/06/10 11:03:30 INFO SparkContext: Running Spark version 1.3.1
15/06/10 11:03:31 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
15/06/10 11:03:31 INFO SecurityManager: Changing view acls to: santon
15/06/10 11:03:31 INFO SecurityManager: Changing modify acls to: santon
15/06/10 11:03:31 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(santon); users with modify permissions: Set(santon)
15/06/10 11:03:31 INFO Slf4jLogger: Slf4jLogger started
15/06/10 11:03:31 INFO Remoting: Starting remoting
15/06/10 11:03:32 INFO Remoting: Remoting started; listening on addresses :[akka.tcp://sparkDriver@localhost:44347]
15/06/10 11:03:32 INFO Utils: Successfully started service 'sparkDriver' on port 44347.
15/06/10 11:03:32 INFO SparkEnv: Registering MapOutputTracker
15/06/10 11:03:32 INFO SparkEnv: Registering BlockManagerMaster
15/06/10 11:03:32 INFO DiskBlockManager: Created local directory at /tmp/spark-24dc8f0a-a89a-44f8-bb95-cd5514e5bf0c/blockmgr-85b6f082-ff5a-4a0e-b48a-1ec62715dda0
15/06/10 11:03:32 INFO MemoryStore: MemoryStore started with capacity 265.4 MB
15/06/10 11:03:32 INFO HttpFileServer: HTTP File server directory is /tmp/spark-7b2172ed-d658-4e11-bbc1-600697f3255e/httpd-5423f8bc-ec43-48c5-9367-87214dad54f4
15/06/10 11:03:32 INFO HttpServer: Starting HTTP Server
15/06/10 11:03:32 INFO Server: jetty-8.y.z-SNAPSHOT
15/06/10 11:03:32 INFO AbstractConnector: Started SocketConnector@0.0.0.0:50366
15/06/10 11:03:32 INFO Utils: Successfully started service 'HTTP file server' on port 50366.
15/06/10 11:03:32 INFO SparkEnv: Registering OutputCommitCoordinator
15/06/10 11:03:32 INFO Server: jetty-8.y.z-SNAPSHOT
15/06/10 11:03:32 INFO AbstractConnector: Started SelectChannelConnector@0.0.0.0:4040
15/06/10 11:03:32 INFO Utils: Successfully started service 'SparkUI' on port 4040.
15/06/10 11:03:32 INFO SparkUI: Started SparkUI at localhost:4040
15/06/10 11:03:32 INFO Executor: Starting executor ID <driver> on host localhost
15/06/10 11:03:32 INFO AkkaUtils: Connecting to HeartbeatReceiver: akka.tcp://sparkDriver@localhost:44347/user/HeartbeatReceiver
15/06/10 11:03:33 INFO NettyBlockTransferService: Server created on 46730
15/06/10 11:03:33 INFO BlockManagerMaster: Trying to register BlockManager
15/06/10 11:03:33 INFO BlockManagerMasterActor: Registering block manager localhost:46730 with 265.4 MB RAM, BlockManagerId(<driver>, localhost, 46730)
15/06/10 11:03:33 INFO BlockManagerMaster: Registered BlockManager
15/06/10 11:05:19 INFO MemoryStore: ensureFreeSpace(215726) called with curMem=0, maxMem=278302556
15/06/10 11:05:19 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 210.7 KB, free 265.2 MB)
15/06/10 11:05:19 INFO MemoryStore: ensureFreeSpace(31533) called with curMem=215726, maxMem=278302556
15/06/10 11:05:19 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 30.8 KB, free 265.2 MB)
15/06/10 11:05:19 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on localhost:46730 (size: 30.8 KB, free: 265.4 MB)
15/06/10 11:05:19 INFO BlockManagerMaster: Updated info of block broadcast_0_piece0
15/06/10 11:05:19 INFO SparkContext: Created broadcast 0 from wholeTextFiles at NativeMethodAccessorImpl.java:-2
15/06/10 11:05:22 INFO FileInputFormat: Total input paths to process : 16
15/06/10 11:05:22 INFO FileInputFormat: Total input paths to process : 16
15/06/10 11:05:22 INFO CombineFileInputFormat: DEBUG: Terminated node allocation with : CompletedNodes: 1, size left: 71665121
15/06/10 11:05:22 INFO SparkContext: Starting job: count at <timed exec>:2
15/06/10 11:05:22 INFO DAGScheduler: Got job 0 (count at <timed exec>:2) with 2 output partitions (allowLocal=false)
15/06/10 11:05:22 INFO DAGScheduler: Final stage: Stage 0(count at <timed exec>:2)
15/06/10 11:05:22 INFO DAGScheduler: Parents of final stage: List()
15/06/10 11:05:22 INFO DAGScheduler: Missing parents: List()
15/06/10 11:05:22 INFO DAGScheduler: Submitting Stage 0 (PythonRDD[1] at count at <timed exec>:2), which has no missing parents
15/06/10 11:05:23 INFO MemoryStore: ensureFreeSpace(6264) called with curMem=247259, maxMem=278302556
15/06/10 11:05:23 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 6.1 KB, free 265.2 MB)
15/06/10 11:05:23 INFO MemoryStore: ensureFreeSpace(4589) called with curMem=253523, maxMem=278302556
15/06/10 11:05:23 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 4.5 KB, free 265.2 MB)
15/06/10 11:05:23 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on localhost:46730 (size: 4.5 KB, free: 265.4 MB)
15/06/10 11:05:23 INFO BlockManagerMaster: Updated info of block broadcast_1_piece0
15/06/10 11:05:23 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:839
15/06/10 11:05:23 INFO DAGScheduler: Submitting 2 missing tasks from Stage 0 (PythonRDD[1] at count at <timed exec>:2)
15/06/10 11:05:23 INFO TaskSchedulerImpl: Adding task set 0.0 with 2 tasks
15/06/10 11:05:23 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, PROCESS_LOCAL, 1903 bytes)
15/06/10 11:05:23 INFO TaskSetManager: Starting task 1.0 in stage 0.0 (TID 1, localhost, PROCESS_LOCAL, 3085 bytes)
15/06/10 11:05:23 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
15/06/10 11:05:23 INFO Executor: Running task 1.0 in stage 0.0 (TID 1)
15/06/10 11:05:26 INFO WholeTextFileRDD: Input split: Paths:[gpg_files]
15/06/10 11:05:40 ERROR Utils: Uncaught exception in thread stdout writer for /anaconda/python/bin/python
java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOfRange(Arrays.java:2694)
at java.lang.String.<init>(String.java:203)
at java.nio.HeapCharBuffer.toString(HeapCharBuffer.java:561)
at java.nio.CharBuffer.toString(CharBuffer.java:1201)
at org.apache.hadoop.io.Text.decode(Text.java:405)
at org.apache.hadoop.io.Text.decode(Text.java:382)
at org.apache.hadoop.io.Text.toString(Text.java:280)
at org.apache.spark.input.WholeTextFileRecordReader.nextKeyValue(WholeTextFileRecordReader.scala:86)
at org.apache.hadoop.mapreduce.lib.input.CombineFileRecordReader.nextKeyValue(CombineFileRecordReader.java:69)
at org.apache.spark.rdd.NewHadoopRDD$$anon$1.hasNext(NewHadoopRDD.scala:143)
at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at org.apache.spark.InterruptibleIterator.foreach(InterruptibleIterator.scala:28)
at org.apache.spark.api.python.PythonRDD$.writeIteratorToStream(PythonRDD.scala:421)
at org.apache.spark.api.python.PythonRDD$WriterThread$$anonfun$run$1.apply(PythonRDD.scala:243)
at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1618)
at org.apache.spark.api.python.PythonRDD$WriterThread.run(PythonRDD.scala:205)
Exception in thread "stdout writer for /anaconda/python/bin/python" java.lang.OutOfMemoryError: Java heap space
at java.util.Arrays.copyOfRange(Arrays.java:2694)
at java.lang.String.<init>(String.java:203)
at java.nio.HeapCharBuffer.toString(HeapCharBuffer.java:561)
at java.nio.CharBuffer.toString(CharBuffer.java:1201)
at org.apache.hadoop.io.Text.decode(Text.java:405)
at org.apache.hadoop.io.Text.decode(Text.java:382)
at org.apache.hadoop.io.Text.toString(Text.java:280)
at org.apache.spark.input.WholeTextFileRecordReader.nextKeyValue(WholeTextFileRecordReader.scala:86)
at org.apache.hadoop.mapreduce.lib.input.CombineFileRecordReader.nextKeyValue(CombineFileRecordReader.java:69)
at org.apache.spark.rdd.NewHadoopRDD$$anon$1.hasNext(NewHadoopRDD.scala:143)
at org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at org.apache.spark.InterruptibleIterator.foreach(InterruptibleIterator.scala:28)
at org.apache.spark.api.python.PythonRDD$.writeIteratorToStream(PythonRDD.scala:421)
at org.apache.spark.api.python.PythonRDD$WriterThread$$anonfun$run$1.apply(PythonRDD.scala:243)
at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1618)
at org.apache.spark.api.python.PythonRDD$WriterThread.run(PythonRDD.scala:205)
15/06/10 11:05:47 INFO PythonRDD: Times: total = 24140, boot = 2860, init = 664, finish = 20616
15/06/10 11:05:47 INFO Executor: Finished task 1.0 in stage 0.0 (TID 1). 1873 bytes result sent to driver
15/06/10 11:05:47 INFO TaskSetManager: Finished task 1.0 in stage 0.0 (TID 1) in 24251 ms on localhost (1/2)
def read_fun_generator(filename):
with gpg_open(filename.split(':')[-1], 'r') as f:
for line in f:
yield line.strip()
gpg_filelist = glob.glob("/path/to/files/*.gpg")
# generate RDD with file name per record
gpg_files = sc.parallelize(gpg_filelist)
rdd_from_gpg = gpg_files.flatMap(read_fun_generator).map(lambda x: x.split('|'))
rdd_from_gpg.count() # <-- For example...