Given the following code which just reads from s3, then saves files to s3
----------------------------
val inputFileName: String = "s3n://input/file/path"
val outputFileName: String = "s3n://output/file/path"
val conf = new
SparkConf().setAppName(this.getClass.getName).setMaster("local[4]")
val sparkContext = new SparkContext(conf)
// Problems here: executors thread locked
sparkContext.textFile(inputFileName).saveAsTextFile(outputFileName)
// But this one works
sparkContext.textFile(inputFileName).count()
----------------------------
It blocks without showing any exceptions or errors. jstack shows that
all executors are locked. The thread dump is in end of this post.
I am using spark-1.4.0 on my PC which has 4 CPU cores.
There are 21 parquet files in the input directory, 500KB / file.
In addition, if we change the last action to a non IO bounded one, for
example, count(). It works.
It seems that S3 read and write in the same stage makes executors deadlocked.
I encountered the same problem when using DataFrame load/save
operations, jira created:
https://issues.apache.org/jira/browse/SPARK-8869
"Executor task launch worker-3" #69 daemon prio=5 os_prio=0
tid=0x00007f7bd4036800 nid=0x1296 in Object.wait()
[0x00007f7c1099a000]
java.lang.Thread.State: WAITING (on object monitor)
at java.lang.Object.wait(Native Method)
at
org.apache.commons.httpclient.MultiThreadedHttpConnectionManager.doGetConnection(MultiThreadedHttpConnectionManager.java:518)
- *locked* <0x00000000e56745b8> (a
org.apache.commons.httpclient.MultiThreadedHttpConnectionManager$ConnectionPool)
at
org.apache.commons.httpclient.MultiThreadedHttpConnectionManager.getConnectionWithTimeout(MultiThreadedHttpConnectionManager.java:416)
at
org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:153)
at
org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397)
at
org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:323)
at
org.jets3t.service.impl.rest.httpclient.RestS3Service.performRequest(RestS3Service.java:342)
at
org.jets3t.service.impl.rest.httpclient.RestS3Service.performRestHead(RestS3Service.java:718)
at
org.jets3t.service.impl.rest.httpclient.RestS3Service.getObjectImpl(RestS3Service.java:1599)
at
org.jets3t.service.impl.rest.httpclient.RestS3Service.getObjectDetailsImpl(RestS3Service.java:1535)
at org.jets3t.service.S3Service.getObjectDetails(S3Service.java:1987)
at org.jets3t.service.S3Service.getObjectDetails(S3Service.java:1332)
at
org.apache.hadoop.fs.s3native.Jets3tNativeFileSystemStore.retrieveMetadata(Jets3tNativeFileSystemStore.java:111)
at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at
org.apache.hadoop.io.retry.RetryInvocationHandler.invokeMethod(RetryInvocationHandler.java:186)
at
org.apache.hadoop.io.retry.RetryInvocationHandler.invoke(RetryInvocationHandler.java:102)
at org.apache.hadoop.fs.s3native.$Proxy15.retrieveMetadata(Unknown
Source)
at
org.apache.hadoop.fs.s3native.NativeS3FileSystem.getFileStatus(NativeS3FileSystem.java:414)
at org.apache.hadoop.fs.FileSystem.exists(FileSystem.java:1397)
at
org.apache.hadoop.fs.s3native.NativeS3FileSystem.create(NativeS3FileSystem.java:341)
at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:905)
at org.apache.hadoop.fs.FileSystem.create(FileSystem.java:798)
at
org.apache.hadoop.mapred.TextOutputFormat.getRecordWriter(TextOutputFormat.java:123)
at org.apache.spark.SparkHadoopWriter.open(SparkHadoopWriter.scala:90)
at
org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopDataset$1$$anonfun$13.apply(PairRDDFunctions.scala:1104)
at
org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopDataset$1$$anonfun$13.apply(PairRDDFunctions.scala:1095)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:63)
at org.apache.spark.scheduler.Task.run(Task.scala:70)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:213)
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)
--
Hao Ren
Data Engineer @ leboncoin
Paris, France
