[NUTCH-2395] Cannot run job worker! - error while running multiple crawling jobs in parallel

• Type: Bug
• Status: Closed
• Priority: Major
• Resolution: Auto Closed
• Affects Version/s: 2.3.1
• Fix Version/s: 2.5
• Component/s: generator, nutch server

Environment

Ubuntu 16.04 64-bit
Oracle Java 8 64-bit
Nutch 2.3.1 (standalone deployment)
MongoDB 3.4

• Assignee: Unassigned
• Reporter: Vyacheslav Pascarel
• Created: 26/Jun/17 14:57
• Updated: 19/Jan/20 12:25
• Resolved: 13/Oct/19 22:35

Description

Cannot run job worker! - error while running multiple crawling jobs in parallel

Ubuntu 16.04 64-bit
Oracle Java 8 64-bit
Nutch 2.3.1 (standalone deployment)
MongoDB 3.4

My application is trying to execute multiple Nutch jobs in parallel using Nutch REST services. The application injects a seed URL and then repeats GENERATE/FETCH/PARSE/UPDATEDB sequence requested number of times to emulated continuous crawling (each step in the sequence is executed upon successful competition of the previous step then the whole sequence is repeated again). Here is a brief description of the jobs:

• Number of parallel jobs: 7
• Each job has unique crawl id and MongoDB collection
• Seed URL for all jobs: http://www.cnn.com
• Regex URL filters for all jobs:
  • "-^.{1000,}$" - exclude very long URLs
  • "+." - include the rest

The jobs are started as expected but at some point some of them fail with "Cannot run job worker!" error. For more details see job status and hadoop.log lines below.

In debugger during crash I noticed that a single instance of SelectorEntryComparator (definition is nested in GeneratorJob) is shared across multiple reducer tasks. The class is inherited from org.apache.hadoop.io.WritableComparator which has a few members unprotected for concurrent usage. At some point multiple threads may access those members in WritableComparator.compare call. I modified SelectorEntryComparator and it seems solved the problem but I am not sure if the change is appropriate and/or sufficient (covers GENERATE only?)

Original code:

public static class SelectorEntryComparator extends WritableComparator {
    public SelectorEntryComparator() {
      super(SelectorEntry.class, true);
    }
}

Modified code:

public static class SelectorEntryComparator extends WritableComparator {
    public SelectorEntryComparator() {
      super(SelectorEntry.class, true);
    }
    
    @Override
    synchronized public int compare(byte[] b1, int s1, int l1, byte[] b2, int s2, int l2) {
    	return super.compare(b1, s1, l1, b2, s2, l2);
    }    
}

Example of failed job status:

{
"id" : "parallel_0-65ff2f1b-382e-4eb2-a813-a0370b84d5b6-GENERATE-1961495833",
"type" : "GENERATE",
"confId" : "65ff2f1b-382e-4eb2-a813-a0370b84d5b6",
"args" : { "topN" : "100" },
"result" : null,
"state" : "FAILED",
"msg" : "ERROR: java.lang.RuntimeException: job failed: name=[parallel_0]generate: 1498059912-1448058551, jobid=job_local1142434549_0036",
"crawlId" : "parallel_0"
}

Lines from hadoop.log

2017-06-21 11:45:13,021 WARN  mapred.LocalJobRunner - job_local1142434549_0036
java.lang.Exception: java.lang.RuntimeException: java.io.EOFException
                at org.apache.hadoop.mapred.LocalJobRunner$Job.runTasks(LocalJobRunner.java:462)
                at org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:529)
Caused by: java.lang.RuntimeException: java.io.EOFException
                at org.apache.hadoop.io.WritableComparator.compare(WritableComparator.java:164)
                at org.apache.hadoop.mapreduce.task.ReduceContextImpl.nextKeyValue(ReduceContextImpl.java:158)
                at org.apache.hadoop.mapreduce.task.ReduceContextImpl.nextKey(ReduceContextImpl.java:121)
                at org.apache.hadoop.mapreduce.lib.reduce.WrappedReducer$Context.nextKey(WrappedReducer.java:302)
                at org.apache.hadoop.mapreduce.Reducer.run(Reducer.java:170)
                at org.apache.hadoop.mapred.ReduceTask.runNewReducer(ReduceTask.java:627)
                at org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:389)
                at org.apache.hadoop.mapred.LocalJobRunner$Job$ReduceTaskRunnable.run(LocalJobRunner.java:319)
                at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
                at java.util.concurrent.FutureTask.run(FutureTask.java:266)
                at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
                at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
                at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.EOFException
                at java.io.DataInputStream.readFully(DataInputStream.java:197)
                at org.apache.hadoop.io.Text.readString(Text.java:466)
                at org.apache.hadoop.io.Text.readString(Text.java:457)
                at org.apache.nutch.crawl.GeneratorJob$SelectorEntry.readFields(GeneratorJob.java:92)
                at org.apache.hadoop.io.WritableComparator.compare(WritableComparator.java:158)
                ... 12 more
2017-06-21 11:45:13,058 WARN  mapred.LocalJobRunner - job_local1976432650_0038
java.lang.Exception: java.lang.RuntimeException: java.io.EOFException
                at org.apache.hadoop.mapred.LocalJobRunner$Job.runTasks(LocalJobRunner.java:462)
                at org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:522)
Caused by: java.lang.RuntimeException: java.io.EOFException
                at org.apache.hadoop.io.WritableComparator.compare(WritableComparator.java:164)
                at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.compare(MapTask.java:1245)
                at org.apache.hadoop.util.QuickSort.sortInternal(QuickSort.java:99)
                at org.apache.hadoop.util.QuickSort.sortInternal(QuickSort.java:126)
                at org.apache.hadoop.util.QuickSort.sort(QuickSort.java:63)
                at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.sortAndSpill(MapTask.java:1575)
                at org.apache.hadoop.mapred.MapTask$MapOutputBuffer.flush(MapTask.java:1462)
                at org.apache.hadoop.mapred.MapTask$NewOutputCollector.close(MapTask.java:700)
                at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:770)
                at org.apache.hadoop.mapred.MapTask.run(MapTask.java:340)
                at org.apache.hadoop.mapred.LocalJobRunner$Job$MapTaskRunnable.run(LocalJobRunner.java:243)
                at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
                at java.util.concurrent.FutureTask.run(FutureTask.java:266)
                at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
                at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
                at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.EOFException
                at java.io.DataInputStream.readByte(DataInputStream.java:267)
                at org.apache.hadoop.io.WritableUtils.readVLong(WritableUtils.java:308)
                at org.apache.hadoop.io.WritableUtils.readVIntInRange(WritableUtils.java:348)
                at org.apache.hadoop.io.Text.readString(Text.java:464)
                at org.apache.hadoop.io.Text.readString(Text.java:457)
                at org.apache.nutch.crawl.GeneratorJob$SelectorEntry.readFields(GeneratorJob.java:92)
                at org.apache.hadoop.io.WritableComparator.compare(WritableComparator.java:158)
                ... 15 more

2017-06-21 11:45:13,372 ERROR impl.JobWorker - Cannot run job worker!
java.lang.RuntimeException: job failed: name=[parallel_0]generate: 1498059912-1448058551, jobid=job_local1142434549_0036
                at org.apache.nutch.util.NutchJob.waitForCompletion(NutchJob.java:120)
                at org.apache.nutch.crawl.GeneratorJob.run(GeneratorJob.java:227)
                at org.apache.nutch.api.impl.JobWorker.run(JobWorker.java:64)
                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)

Issue Links

• links to: GitHub Pull Request #197