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From Mark Kerzner <mark.kerz...@shmsoft.com>
Subject Re: Memory exception in the mapper
Date Thu, 24 May 2012 02:35:22 GMT
Joey,

my errors closely resembles this
one<http://mail-archives.apache.org/mod_mbox/hadoop-mapreduce-user/201006.mbox/%3CAANLkTikR3DF4ce-tGIPhv9_-EVFOeD_5-T684NF4y6dd@mail.gmail.com%3E>in
the archives. I can now be much more specific with the errors message,
and it is quoted below. I tried -Xmx3096. But I got the same error.

Thank you,
Mark


syslog logs
2012-05-23 20:04:52,349 WARN org.apache.hadoop.util.NativeCodeLoader:
Unable to load native-hadoop library for your platform... using
builtin-java classes where applicable
2012-05-23 20:04:52,519 INFO org.apache.hadoop.metrics.jvm.JvmMetrics:
Initializing JVM Metrics with processName=MAP, sessionId=
2012-05-23 20:04:52,695 INFO org.apache.hadoop.util.ProcessTree: setsid
exited with exit code 0
2012-05-23 20:04:52,699 INFO org.apache.hadoop.mapred.Task:  Using
ResourceCalculatorPlugin :
org.apache.hadoop.util.LinuxResourceCalculatorPlugin@d56b37
2012-05-23 20:04:52,813 INFO org.apache.hadoop.mapred.MapTask: io.sort.mb =
100
2012-05-23 20:04:52,998 INFO org.apache.hadoop.mapred.MapTask: data buffer
= 79691776/99614720
2012-05-23 20:04:52,998 INFO org.apache.hadoop.mapred.MapTask: record
buffer = 262144/327680
2012-05-23 20:04:53,010 WARN
org.apache.hadoop.io.compress.snappy.LoadSnappy: Snappy native library not
loaded
2012-05-23 20:12:29,120 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:12:29,134 INFO org.apache.hadoop.mapred.MapTask: bufstart =
0; bufend = 79542629; bufvoid = 99614720
2012-05-23 20:12:29,134 INFO org.apache.hadoop.mapred.MapTask: kvstart = 0;
kvend = 228; length = 327680
2012-05-23 20:12:31,248 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 0
2012-05-23 20:13:01,862 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:13:01,862 INFO org.apache.hadoop.mapred.MapTask: bufstart =
79542629; bufend = 53863940; bufvoid = 99614720
2012-05-23 20:13:01,862 INFO org.apache.hadoop.mapred.MapTask: kvstart =
228; kvend = 431; length = 327680
2012-05-23 20:13:03,294 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 1
2012-05-23 20:13:48,121 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:13:48,122 INFO org.apache.hadoop.mapred.MapTask: bufstart =
53863940; bufend = 31696780; bufvoid = 99614720
2012-05-23 20:13:48,122 INFO org.apache.hadoop.mapred.MapTask: kvstart =
431; kvend = 861; length = 327680
2012-05-23 20:13:49,818 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 2
2012-05-23 20:15:25,618 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:15:25,618 INFO org.apache.hadoop.mapred.MapTask: bufstart =
31696780; bufend = 10267329; bufvoid = 99614720
2012-05-23 20:15:25,618 INFO org.apache.hadoop.mapred.MapTask: kvstart =
861; kvend = 1462; length = 327680
2012-05-23 20:15:27,068 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 3
2012-05-23 20:15:53,519 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:15:53,519 INFO org.apache.hadoop.mapred.MapTask: bufstart =
10267329; bufend = 85241086; bufvoid = 99614720
2012-05-23 20:15:53,519 INFO org.apache.hadoop.mapred.MapTask: kvstart =
1462; kvend = 1642; length = 327680
2012-05-23 20:15:54,760 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 4
2012-05-23 20:16:26,284 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:16:26,284 INFO org.apache.hadoop.mapred.MapTask: bufstart =
85241086; bufend = 51305930; bufvoid = 99614720
2012-05-23 20:16:26,284 INFO org.apache.hadoop.mapred.MapTask: kvstart =
1642; kvend = 1946; length = 327680
2012-05-23 20:16:27,566 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 5
2012-05-23 20:16:57,046 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:16:57,046 INFO org.apache.hadoop.mapred.MapTask: bufstart =
51305930; bufend = 31353466; bufvoid = 99614720
2012-05-23 20:16:57,046 INFO org.apache.hadoop.mapred.MapTask: kvstart =
1946; kvend = 2263; length = 327680
2012-05-23 20:16:58,076 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 6
2012-05-23 20:17:52,820 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:17:52,820 INFO org.apache.hadoop.mapred.MapTask: bufstart =
31353466; bufend = 10945750; bufvoid = 99614720
2012-05-23 20:17:52,820 INFO org.apache.hadoop.mapred.MapTask: kvstart =
2263; kvend = 2755; length = 327680
2012-05-23 20:17:53,939 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 7
2012-05-23 20:18:19,528 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:18:19,528 INFO org.apache.hadoop.mapred.MapTask: bufstart =
10945750; bufend = 81838103; bufvoid = 99614720
2012-05-23 20:18:19,528 INFO org.apache.hadoop.mapred.MapTask: kvstart =
2755; kvend = 2967; length = 327680
2012-05-23 20:18:21,145 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 8
2012-05-23 20:18:52,353 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:18:52,353 INFO org.apache.hadoop.mapred.MapTask: bufstart =
81838103; bufend = 61751422; bufvoid = 99614720
2012-05-23 20:18:52,353 INFO org.apache.hadoop.mapred.MapTask: kvstart =
2967; kvend = 3202; length = 327680
2012-05-23 20:18:53,485 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 9
2012-05-23 20:19:42,993 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:19:42,993 INFO org.apache.hadoop.mapred.MapTask: bufstart =
61751422; bufend = 38440188; bufvoid = 99614720
2012-05-23 20:19:42,993 INFO org.apache.hadoop.mapred.MapTask: kvstart =
3202; kvend = 3628; length = 327680
2012-05-23 20:19:44,346 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 10
2012-05-23 20:20:47,957 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:20:47,957 INFO org.apache.hadoop.mapred.MapTask: bufstart =
38440188; bufend = 18376423; bufvoid = 99614720
2012-05-23 20:20:47,957 INFO org.apache.hadoop.mapred.MapTask: kvstart =
3628; kvend = 4252; length = 327680
2012-05-23 20:20:48,767 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 11
2012-05-23 20:21:19,207 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:21:19,207 INFO org.apache.hadoop.mapred.MapTask: bufstart =
18376423; bufend = 97890160; bufvoid = 99614720
2012-05-23 20:21:19,207 INFO org.apache.hadoop.mapred.MapTask: kvstart =
4252; kvend = 4488; length = 327680
2012-05-23 20:21:20,176 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 12
2012-05-23 20:21:47,395 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:21:47,395 INFO org.apache.hadoop.mapred.MapTask: bufstart =
97890160; bufend = 77234938; bufvoid = 99614720
2012-05-23 20:21:47,395 INFO org.apache.hadoop.mapred.MapTask: kvstart =
4488; kvend = 4771; length = 327680
2012-05-23 20:21:48,383 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 13
2012-05-23 20:22:21,086 INFO org.apache.hadoop.mapred.MapTask: Spilling map
output: buffer full= true
2012-05-23 20:22:21,086 INFO org.apache.hadoop.mapred.MapTask: bufstart =
77234938; bufend = 52962105; bufvoid = 99614720
2012-05-23 20:22:21,086 INFO org.apache.hadoop.mapred.MapTask: kvstart =
4771; kvend = 5203; length = 327680
2012-05-23 20:22:21,641 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 14
2012-05-23 20:22:46,559 INFO org.apache.hadoop.mapred.MapTask: Starting
flush of map output
2012-05-23 20:22:46,615 INFO org.apache.hadoop.mapred.MapTask: Finished
spill 15
2012-05-23 20:22:47,606 INFO org.apache.hadoop.mapred.Merger: Merging 16
sorted segments
2012-05-23 20:22:47,696 INFO org.apache.hadoop.mapred.Merger: Merging 7
intermediate segments out of a total of 16
2012-05-23 20:22:58,083 INFO org.apache.hadoop.mapred.TaskLogsTruncater:
Initializing logs' truncater with mapRetainSize=-1 and reduceRetainSize=-1
2012-05-23 20:22:58,108 FATAL org.apache.hadoop.mapred.Child: Error running
child : java.lang.OutOfMemoryError: Java heap space
    at org.apache.hadoop.mapred.IFile$Reader.readNextBlock(IFile.java:355)
    at org.apache.hadoop.mapred.IFile$Reader.next(IFile.java:417)
    at org.apache.hadoop.mapred.Merger$Segment.next(Merger.java:220)
    at
org.apache.hadoop.mapred.Merger$MergeQueue.adjustPriorityQueue(Merger.java:330)
    at org.apache.hadoop.mapred.Merger$MergeQueue.next(Merger.java:350)
    at org.apache.hadoop.mapred.Merger.writeFile(Merger.java:156)
    at org.apache.hadoop.mapred.Merger$MergeQueue.merge(Merger.java:499)
    at org.apache.hadoop.mapred.Merger$MergeQueue.merge(Merger.java:381)
    at org.apache.hadoop.mapred.Merger.merge(Merger.java:77)
    at
org.apache.hadoop.mapred.MapTask$MapOutputBuffer.mergeParts(MapTask.java:1548)
    at
org.apache.hadoop.mapred.MapTask$MapOutputBuffer.flush(MapTask.java:1180)
    at
org.apache.hadoop.mapred.MapTask$NewOutputCollector.close(MapTask.java:582)
    at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:649)
    at org.apache.hadoop.mapred.MapTask.run(MapTask.java:323)
    at org.apache.hadoop.mapred.Child$4.run(Child.java:270)
    at java.security.AccessController.doPrivileged(Native Method)
    at javax.security.auth.Subject.doAs(Subject.java:396)
    at
org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1177)
    at org.apache.hadoop.mapred.Child.main(Child.java:264)

On Wed, May 23, 2012 at 2:47 PM, Joey Krabacher <jkrabacher@gmail.com>wrote:

> My experience with this sort of problem tells me one of two things and
> maybe both:
>
> 1. there are some optimizations to the code that can be made (variable
> re-creation inside of loops, etc.)
> 2. something has gone horribly wrong with the logic in the mapper.
>
> To troubleshoot I would output some log entries at specific points in the
> mapper (be careful not to log every execution of the mapper because this
> could cause major issues with the disk filling up and that sort of thing.)
>
> Hope that helps.
>
> /* Joey */
>
> On Wed, May 23, 2012 at 2:16 PM, Mark Kerzner <mark.kerzner@shmsoft.com
> >wrote:
>
> > Hi, all,
> >
> > I got the exception below in the mapper. I already have my global Hadoop
> > heap at 5 GB, but is there a specific other setting? Or maybe I should
> > troubleshoot for memory?
> >
> > But the same application works in the IDE.
> >
> > Thank you!
> >
> > Mark
> >
> > *stderr logs*
> >
> > Exception in thread "Thread for syncLogs" java.lang.OutOfMemoryError:
> > Java heap space
> >        at
> java.io.BufferedOutputStream.<init>(BufferedOutputStream.java:76)
> >        at
> java.io.BufferedOutputStream.<init>(BufferedOutputStream.java:59)
> >        at
> > org.apache.hadoop.mapred.TaskLog.writeToIndexFile(TaskLog.java:292)
> >        at org.apache.hadoop.mapred.TaskLog.syncLogs(TaskLog.java:365)
> >        at org.apache.hadoop.mapred.Child$3.run(Child.java:157)
> > Exception in thread "communication thread" java.lang.OutOfMemoryError:
> > Java heap space
> >
> > Exception: java.lang.OutOfMemoryError thrown from the
> > UncaughtExceptionHandler in thread "communication thread"
> >
>

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