[Hadoop-common-user] Nor "OOM Java Heap Space" neither "GC OverHead Limit Exeeceded"

On Tue, Jun 16, 2009 at 10:51 AM, akhil1988 wrote:


Hi All,

I am running my mapred program in local mode by setting
mapred.jobtracker.local to local mode so that I can debug my code.
The mapred program is a direct porting of my original sequential code.
There
is no reduce phase.
Basically, I have just put my program in the map class.

My program takes around 1-2 min. in instantiating the data objects which
are
present in the constructor of Map class(it loads some data model files,
therefore it takes some time). After the instantiation part in the
constrcutor of Map class the map function is supposed to process the input
split.

The problem is that the data objects do not get instantiated completely and
in between(whlie it is still in constructor) the program stops giving the
exceptions pasted at bottom.
The program runs fine without mapreduce and does not require more than 2GB
memory, but in mapreduce even after doing export HADOOP_HEAPSIZE=2500(I am
working on machines with 16GB RAM), the program fails. I have also set
HADOOP_OPTS="-server -XX:-UseGCOverheadLimit" as sometimes I was getting GC
Overhead Limit Exceeded exceptions also.

Somebody, please help me with this problem: I have trying to debug it for
the last 3 days, but unsuccessful. Thanks!

java.lang.OutOfMemoryError: Java heap space
at
sun.misc.FloatingDecimal.toJavaFormatString(FloatingDecimal.java:889)
at java.lang.Double.toString(Double.java:179)
at java.text.DigitList.set(DigitList.java:272)
at java.text.DecimalFormat.format(DecimalFormat.java:584)
at java.text.DecimalFormat.format(DecimalFormat.java:507)
at java.text.NumberFormat.format(NumberFormat.java:269)
at
org.apache.hadoop.util.StringUtils.formatPercent(StringUtils.java:110)
at org.apache.hadoop.mapred.JobClient.runJob(JobClient.java:1147)
at LbjTagger.NerTagger.main(NerTagger.java:109)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at

sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at

sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.hadoop.util.RunJar.main(RunJar.java:165)
at org.apache.hadoop.mapred.JobShell.run(JobShell.java:54)
at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:65)
at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:79)
at org.apache.hadoop.mapred.JobShell.main(JobShell.java:68)

09/06/16 12:34:41 WARN mapred.LocalJobRunner: job_local_0001
java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
at
org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:81)
at org.apache.hadoop.mapred.MapRunner.configure(MapRunner.java:34)
at
org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:58)
at
org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:83)
at org.apache.hadoop.mapred.MapTask.run(MapTask.java:328)
at
org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:138)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method)
at

sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
at

sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
at
org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:79)
... 5 more
Caused by: java.lang.ThreadDeath
at java.lang.Thread.stop(Thread.java:715)
at
org.apache.hadoop.mapred.LocalJobRunner.killJob(LocalJobRunner.java:310)
at
org.apache.hadoop.mapred.JobClient$NetworkedJob.killJob(JobClient.java:315)
at org.apache.hadoop.mapred.JobClient.runJob(JobClient.java:1224)
at LbjTagger.NerTagger.main(NerTagger.java:109)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at

sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at

sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.hadoop.util.RunJar.main(RunJar.java:165)
at org.apache.hadoop.mapred.JobShell.run(JobShell.java:54)
at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:65)
at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:79)
at org.apache.hadoop.mapred.JobShell.main(JobShell.java:68)

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Is it possible that your map class is an inner class and not static?

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Thank you Jason for your reply.

My Map class is an inner class and it is a static class. Here is the
structure of my code.

public class NerTagger {

public static class Map extends MapReduceBase implements
Mapper<LongWritable, Text, Text, Text>{
private Text word = new Text();
private static NETaggerLevel1 tagger1 = new
NETaggerLevel1();
private static NETaggerLevel2 tagger2 = new
NETaggerLevel2();

Map(){
System.out.println("HI2\n");

Parameters.readConfigAndLoadExternalData("Config/allLayer1.config");
System.out.println("HI3\n");

Parameters.forceNewSentenceOnLineBreaks=Boolean.parseBoolean("true");

System.out.println("loading the tagger");

tagger1=(NETaggerLevel1)Classifier.binaryRead(Parameters.pathToModelFile+".level1");
System.out.println("HI5\n");

tagger2=(NETaggerLevel2)Classifier.binaryRead(Parameters.pathToModelFile+".level2");
System.out.println("Done- loading the tagger");
}

public void map(LongWritable key, Text value,
OutputCollector<Text, Text> output, Reporter reporter ) throws IOException
{
String inputline = value.toString();

/* Processing of the input pair is done here */
}


public static void main(String [] args) throws Exception {
JobConf conf = new JobConf(NerTagger.class);
conf.setJobName("NerTagger");

conf.setOutputKeyClass(Text.class);
conf.setOutputValueClass(IntWritable.class);

conf.setMapperClass(Map.class);
conf.setNumReduceTasks(0);

conf.setInputFormat(TextInputFormat.class);
conf.setOutputFormat(TextOutputFormat.class);

conf.set("mapred.job.tracker", "local");
conf.set("fs.default.name", "file:///");

DistributedCache.addCacheFile(new
URI("/home/akhil1988/Ner/OriginalNer/Data/"), conf);
DistributedCache.addCacheFile(new
URI("/home/akhil1988/Ner/OriginalNer/Config/"), conf);
DistributedCache.createSymlink(conf);


conf.set("mapred.child.java.opts","-Xmx4096m");

FileInputFormat.setInputPaths(conf, new Path(args[0]));
FileOutputFormat.setOutputPath(conf, new Path(args[1]));

System.out.println("HI1\n");

JobClient.runJob(conf);
}

Jason, when the program executes HI1 and HI2 are printed but it does not
reaches HI3. In the statement
Parameters.readConfigAndLoadExternalData("Config/allLayer1.config"); it is
able to access Config/allLayer1.config file (as while executing this
statement, it prints some messages like which data it is loading, etc.)
but it gets stuck there(while loading some classifier) and never reaches
HI3.

This program runs fine when executed normally(without mapreduce).

Thanks, Akhil




jason hadoop wrote:

On Tue, Jun 16, 2009 at 8:32 PM, akhil1988 wrote:


One more thing, finally it terminates there (after some time) by giving the
final Exception:

java.io.IOException: Job failed!
at org.apache.hadoop.mapred.JobClient.runJob(JobClient.java:1217)
at LbjTagger.NerTagger.main(NerTagger.java:109)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at

sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at

sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at org.apache.hadoop.util.RunJar.main(RunJar.java:165)
at org.apache.hadoop.mapred.JobShell.run(JobShell.java:54)
at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:65)
at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:79)
at org.apache.hadoop.mapred.JobShell.main(JobShell.java:68)


akhil1988 wrote:
which
getting
org.apache.hadoop.mapred.JobClient.runJob(JobClient.java:1147)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:81)
org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:83)
org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:138)
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:79)
org.apache.hadoop.mapred.LocalJobRunner.killJob(LocalJobRunner.java:310)
org.apache.hadoop.mapred.JobClient$NetworkedJob.killJob(JobClient.java:315)
org.apache.hadoop.mapred.JobClient.runJob(JobClient.java:1224)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
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Something is happening inside of your (Parameters.
readConfigAndLoadExternalData("Config/allLayer1.config");)
code, and the framework is killing the job for not heartbeating for 600
seconds

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On Wed, Jun 17, 2009 at 6:56 AM, akhil1988 wrote:


Thanks Jason.

I went inside the code of the statement and found out that it eventually
makes some binaryRead function call to read a binary file and there it
strucks.

Do you know whether there is any problem in giving a binary file for
addition to the distributed cache.
In the statement DistributedCache.addCacheFile(new
URI("/home/akhil1988/Ner/OriginalNer/Data/"), conf); Data is a directory
which contains some text as well as some binary files. In the statement
Parameters.readConfigAndLoadExternalData("Config/allLayer1.config"); I can
see(in the output messages) that it is able to read the text files but it
gets struck at the binary files.

So, I think here the problem is: it is not able to read the binary files
which either have not been transferred to the cache or a binary file cannot
be read.

Do you know the solution to this?

Thanks,
Akhil


jason hadoop wrote:
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
tagger1=(NETaggerLevel1)Classifier.binaryRead(Parameters.pathToModelFile+".level1");
tagger2=(NETaggerLevel2)Classifier.binaryRead(Parameters.pathToModelFile+".level2");
tagger");
*/
Path(args[0]));
it
etc.)
giving
it
sun.misc.FloatingDecimal.toJavaFormatString(FloatingDecimal.java:889)
Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:81)
org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:83)
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:79)
org.apache.hadoop.mapred.JobClient$NetworkedJob.killJob(JobClient.java:315)
Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
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I have only ever used the distributed cache to add files, including binary
files such as shared libraries.
It looks like you are adding a directory.

The DistributedCache is not generally used for passing data, but for
passing
file names.
The files must be stored in a shared file system (hdfs for simplicity)
already.

The distributed cache makes the names available to the tasks, and the the
files are extracted from hdfs and stored in the task local work area on
each
task tracker node.
It looks like you may be storing the contents of your files in the
distributed cache.

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Hi Jason!

Thanks for going with me to solve my problem.

To restate things and make it more easier to understand: I am working in
local mode in the directory which contains the job jar and also the Config
and Data directories.

I just removed the following three statements from my code:
The program executes till the same point as before now also and
terminates. That means the above three statements are of no use while
working in local mode. In local mode, the working directory for the
map&reduce tasks becomes the current woking direcotry in which you started
the hadoop command to execute the job.

Since I have removed the DistributedCache.add..... statements there should
be no issue whether I am giving a file name or a directory name as
argument to it. Now it seems to me that there is some problem in reading
the binary file using binaryRead.

Please let me know if I am going wrong anywhere.

Thanks,
Akhil





jason hadoop wrote:

On Thu, Jun 18, 2009 at 1:45 PM, akhil1988 wrote:


Hi Jason!

I finally found out that there was some problem in reserving the HEAPSIZE
which I have resolved now. Actually we cannot change the HADOOP_HEAPSIZE
using export from our user account, after we have started the Hadoop. It
has
to changed by the root.

I have a user account on the cluster and I was trying to change the
Hadoop_heapsize from my user account using 'export' which had no effect.
So I had to request my cluster administrator to increase the
HADOOP_HEAPSIZE
in hadoop-env.sh and then restart hadoop. Now the program is running
absolutely fine. Thanks for your help.

One thing that I would like to ask you is that can we use DistributerCache
for transferring directories to the local cache of the tasks?

Thanks,
Akhil



akhil1988 wrote:
the
eventually
directory
files
Method)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
tagger1=(NETaggerLevel1)Classifier.binaryRead(Parameters.pathToModelFile+".level1");
tagger2=(NETaggerLevel2)Classifier.binaryRead(Parameters.pathToModelFile+".level2");
[email protected]>
more
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
org.apache.hadoop.mapred.JobShell.run(JobShell.java:54)
org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:81)
org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:83)
org.apache.hadoop.mapred.LocalJobRunner$Job.run(LocalJobRunner.java:138)
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:79)
org.apache.hadoop.mapred.LocalJobRunner.killJob(LocalJobRunner.java:310)
org.apache.hadoop.mapred.JobClient$NetworkedJob.killJob(JobClient.java:315)
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
org.apache.hadoop.mapred.JobShell.run(JobShell.java:54)
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