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From nagarjuna kanamarlapudi <nagarjuna.kanamarlap...@gmail.com>
Subject Re: Child JVM memory allocation / Usage
Date Wed, 27 Mar 2013 09:51:26 GMT
Hi Hemanth,

Nice to see this. I didnot know about this till now.

But few one more issue.. the dump file did not get created..   The
following are the logs



ttempt_201302211510_81218_m_000000_0:
/data/1/mapred/local/taskTracker/distcache/8776089957260881514_-363500746_715125253/cmp111wcd/user/ims-b/nagarjuna/AddressId_Extractor/Numbers
attempt_201302211510_81218_m_000000_0: java.lang.OutOfMemoryError: Java
heap space
attempt_201302211510_81218_m_000000_0: Dumping heap to ./heapdump.hprof ...
attempt_201302211510_81218_m_000000_0: Heap dump file created [210641441
bytes in 3.778 secs]
attempt_201302211510_81218_m_000000_0: #
attempt_201302211510_81218_m_000000_0: # java.lang.OutOfMemoryError: Java
heap space
attempt_201302211510_81218_m_000000_0: # -XX:OnOutOfMemoryError="./dump.sh"
attempt_201302211510_81218_m_000000_0: #   Executing /bin/sh -c
"./dump.sh"...
attempt_201302211510_81218_m_000000_0: put: File myheapdump.hprof does not
exist.
attempt_201302211510_81218_m_000000_0: log4j:WARN No appenders could be
found for logger (org.apache.hadoop.hdfs.DFSClient).





On Wed, Mar 27, 2013 at 2:29 PM, Hemanth Yamijala <yhemanth@thoughtworks.com
> wrote:

> Couple of things to check:
>
> Does your class com.hadoop.publicationMrPOC.Launcher implement the Tool
> interface ? You can look at an example at (
> http://hadoop.apache.org/docs/r1.0.4/mapred_tutorial.html#Source+Code-N110D0).
> That's what accepts the -D params on command line. Alternatively, you can
> also set the same in the configuration object like this, in your launcher
> code:
>
> Configuration conf = new Configuration()
>
> conf.set("mapred.create.symlink", "yes");
>
> conf.set("mapred.cache.files", "hdfs:///user/hemanty/scripts/copy_dump.sh#copy_dump.sh");
>
> conf.set("mapred.child.java.opts",
>
>   "-Xmx200m -XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath=./heapdump.hprof -XX:OnOutOfMemoryError=./copy_dump.sh");
>
>
> Second, the position of the arguments matters. I think the command should
> be
>
> hadoop jar -Dmapred.create.symlink=yes -Dmapred.cache.files=hdfs:///user/ims-b/dump.sh#dump.sh
> -Dmapred.reduce.child.java.opts='-Xmx2048m -XX:+HeapDumpOnOutOfMemoryError
> -XX:HeapDumpPath=./myheapdump.hprof -XX:OnOutOfMemoryError=./dump.sh'
> com.hadoop.publicationMrPOC.Launcher  Fudan\ Univ
>
> Thanks
> Hemanth
>
>
> On Wed, Mar 27, 2013 at 1:58 PM, nagarjuna kanamarlapudi <
> nagarjuna.kanamarlapudi@gmail.com> wrote:
>
>> Hi Hemanth/Koji,
>>
>> Seems the above script doesn't work for me.  Can u look into the
>> following and suggest what more can I do
>>
>>
>>  hadoop fs -cat /user/ims-b/dump.sh
>> #!/bin/sh
>> hadoop dfs -put myheapdump.hprof /tmp/myheapdump_ims/${PWD//\//_}.hprof
>>
>>
>> hadoop jar LL.jar com.hadoop.publicationMrPOC.Launcher  Fudan\ Univ
>>  -Dmapred.create.symlink=yes
>> -Dmapred.cache.files=hdfs:///user/ims-b/dump.sh#dump.sh
>> -Dmapred.reduce.child.java.opts='-Xmx2048m -XX:+HeapDumpOnOutOfMemoryError
>> -XX:HeapDumpPath=./myheapdump.hprof -XX:OnOutOfMemoryError=./dump.sh'
>>
>>
>> I am not able to see the heap dump at  /tmp/myheapdump_ims
>>
>>
>>
>> Erorr in the mapper :
>>
>> Caused by: java.lang.reflect.InvocationTargetException
>> 	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.ReflectionUtils.setJobConf(ReflectionUtils.java:88)
>> 	... 17 more
>> Caused by: java.lang.OutOfMemoryError: Java heap space
>> 	at java.util.Arrays.copyOf(Arrays.java:2734)
>> 	at java.util.ArrayList.ensureCapacity(ArrayList.java:167)
>> 	at java.util.ArrayList.add(ArrayList.java:351)
>> 	at com.hadoop.publicationMrPOC.PublicationMapper.configure(PublicationMapper.java:59)
>> 	... 22 more
>>
>>
>>
>>
>>
>> On Wed, Mar 27, 2013 at 10:16 AM, Hemanth Yamijala <
>> yhemanth@thoughtworks.com> wrote:
>>
>>> Koji,
>>>
>>> Works beautifully. Thanks a lot. I learnt at least 3 different things
>>> with your script today !
>>>
>>> Hemanth
>>>
>>>
>>> On Tue, Mar 26, 2013 at 9:41 PM, Koji Noguchi <knoguchi@yahoo-inc.com>wrote:
>>>
>>>> Create a dump.sh on hdfs.
>>>>
>>>> $ hadoop dfs -cat /user/knoguchi/dump.sh
>>>> #!/bin/sh
>>>> hadoop dfs -put myheapdump.hprof
>>>> /tmp/myheapdump_knoguchi/${PWD//\//_}.hprof
>>>>
>>>> Run your job with
>>>>
>>>> -Dmapred.create.symlink=yes
>>>> -Dmapred.cache.files=hdfs:///user/knoguchi/dump.sh#dump.sh
>>>> -Dmapred.reduce.child.java.opts='-Xmx2048m
>>>> -XX:+HeapDumpOnOutOfMemoryError
>>>> -XX:HeapDumpPath=./myheapdump.hprof -XX:OnOutOfMemoryError=./dump.sh'
>>>>
>>>> This should create the heap dump on hdfs at /tmp/myheapdump_knoguchi.
>>>>
>>>> Koji
>>>>
>>>>
>>>> On Mar 26, 2013, at 11:53 AM, Hemanth Yamijala wrote:
>>>>
>>>> > Hi,
>>>> >
>>>> > I tried to use the -XX:+HeapDumpOnOutOfMemoryError. Unfortunately,
>>>> like I suspected, the dump goes to the current work directory of the task
>>>> attempt as it executes on the cluster. This directory is cleaned up once
>>>> the task is done. There are options to keep failed task files or task files
>>>> matching a pattern. However, these are NOT retaining the current working
>>>> directory. Hence, there is no option to get this from a cluster AFAIK.
>>>> >
>>>> > You are effectively left with the jmap option on pseudo distributed
>>>> cluster I think.
>>>> >
>>>> > Thanks
>>>> > Hemanth
>>>> >
>>>> >
>>>> > On Tue, Mar 26, 2013 at 11:37 AM, Hemanth Yamijala <
>>>> yhemanth@thoughtworks.com> wrote:
>>>> > If your task is running out of memory, you could add the option
>>>> -XX:+HeapDumpOnOutOfMemoryError
>>>> > to mapred.child.java.opts (along with the heap memory). However, I am
>>>> not sure  where it stores the dump.. You might need to experiment a little
>>>> on it.. Will try and send out the info if I get time to try out.
>>>> >
>>>> >
>>>> > Thanks
>>>> > Hemanth
>>>> >
>>>> >
>>>> > On Tue, Mar 26, 2013 at 10:23 AM, nagarjuna kanamarlapudi <
>>>> nagarjuna.kanamarlapudi@gmail.com> wrote:
>>>> > Hi hemanth,
>>>> >
>>>> > This sounds interesting, will out try out that on the pseudo cluster.
>>>>  But the real problem for me is, the cluster is being maintained by third
>>>> party. I only have have a edge node through which I can submit the jobs.
>>>> >
>>>> > Is there any other way of getting the dump instead of physically
>>>> going to that machine and  checking out.
>>>> >
>>>> >
>>>> >
>>>> > On Tue, Mar 26, 2013 at 10:12 AM, Hemanth Yamijala <
>>>> yhemanth@thoughtworks.com> wrote:
>>>> > Hi,
>>>> >
>>>> > One option to find what could be taking the memory is to use jmap on
>>>> the running task. The steps I followed are:
>>>> >
>>>> > - I ran a sleep job (which comes in the examples jar of the
>>>> distribution - effectively does nothing in the mapper / reducer).
>>>> > - From the JobTracker UI looked at a map task attempt ID.
>>>> > - Then on the machine where the map task is running, got the PID of
>>>> the running task - ps -ef | grep <task attempt id>
>>>> > - On the same machine executed jmap -histo <pid>
>>>> >
>>>> > This will give you an idea of the count of objects allocated and
>>>> size. Jmap also has options to get a dump, that will contain more
>>>> information, but this should help to get you started with debugging.
>>>> >
>>>> > For my sleep job task - I saw allocations worth roughly 130 MB.
>>>> >
>>>> > Thanks
>>>> > hemanth
>>>> >
>>>> >
>>>> >
>>>> >
>>>> > On Mon, Mar 25, 2013 at 6:43 PM, Nagarjuna Kanamarlapudi <
>>>> nagarjuna.kanamarlapudi@gmail.com> wrote:
>>>> > I have a lookup file which I need in the mapper. So I am trying to
>>>> read the whole file and load it into list in the mapper.
>>>> >
>>>> >
>>>> > For each and every record Iook in this file which I got from
>>>> distributed cache.
>>>> >
>>>> > —
>>>> > Sent from iPhone
>>>> >
>>>> >
>>>> > On Mon, Mar 25, 2013 at 6:39 PM, Hemanth Yamijala <
>>>> yhemanth@thoughtworks.com> wrote:
>>>> >
>>>> > Hmm. How are you loading the file into memory ? Is it some sort of
>>>> memory mapping etc ? Are they being read as records ? Some details of the
>>>> app will help
>>>> >
>>>> >
>>>> > On Mon, Mar 25, 2013 at 2:14 PM, nagarjuna kanamarlapudi <
>>>> nagarjuna.kanamarlapudi@gmail.com> wrote:
>>>> > Hi Hemanth,
>>>> >
>>>> > I tried out your suggestion loading 420 MB file into memory. It threw
>>>> java heap space error.
>>>> >
>>>> > I am not sure where this 1.6 GB of configured heap went to ?
>>>> >
>>>> >
>>>> > On Mon, Mar 25, 2013 at 12:01 PM, Hemanth Yamijala <
>>>> yhemanth@thoughtworks.com> wrote:
>>>> > Hi,
>>>> >
>>>> > The free memory might be low, just because GC hasn't reclaimed what
>>>> it can. Can you just try reading in the data you want to read and see if
>>>> that works ?
>>>> >
>>>> > Thanks
>>>> > Hemanth
>>>> >
>>>> >
>>>> > On Mon, Mar 25, 2013 at 10:32 AM, nagarjuna kanamarlapudi <
>>>> nagarjuna.kanamarlapudi@gmail.com> wrote:
>>>> > io.sort.mb = 256 MB
>>>> >
>>>> >
>>>> > On Monday, March 25, 2013, Harsh J wrote:
>>>> > The MapTask may consume some memory of its own as well. What is your
>>>> > io.sort.mb (MR1) or mapreduce.task.io.sort.mb (MR2) set to?
>>>> >
>>>> > On Sun, Mar 24, 2013 at 3:40 PM, nagarjuna kanamarlapudi
>>>> > <nagarjuna.kanamarlapudi@gmail.com> wrote:
>>>> > > Hi,
>>>> > >
>>>> > > I configured  my child jvm heap to 2 GB. So, I thought I could
>>>> really read
>>>> > > 1.5GB of data and store it in memory (mapper/reducer).
>>>> > >
>>>> > > I wanted to confirm the same and wrote the following piece of code
>>>> in the
>>>> > > configure method of mapper.
>>>> > >
>>>> > > @Override
>>>> > >
>>>> > > public void configure(JobConf job) {
>>>> > >
>>>> > > System.out.println("FREE MEMORY -- "
>>>> > >
>>>> > > + Runtime.getRuntime().freeMemory());
>>>> > >
>>>> > > System.out.println("MAX MEMORY ---" +
>>>> Runtime.getRuntime().maxMemory());
>>>> > >
>>>> > > }
>>>> > >
>>>> > >
>>>> > > Surprisingly the output was
>>>> > >
>>>> > >
>>>> > > FREE MEMORY -- 341854864  = 320 MB
>>>> > > MAX MEMORY ---1908932608  = 1.9 GB
>>>> > >
>>>> > >
>>>> > > I am just wondering what processes are taking up that extra 1.6GB
>>>> of heap
>>>> > > which I configured for the child jvm heap.
>>>> > >
>>>> > >
>>>> > > Appreciate in helping me understand the scenario.
>>>> > >
>>>> > >
>>>> > >
>>>> > > Regards
>>>> > >
>>>> > > Nagarjuna K
>>>> > >
>>>> > >
>>>> > >
>>>> >
>>>> >
>>>> >
>>>> > --
>>>> > Harsh J
>>>> >
>>>> >
>>>> > --
>>>> > Sent from iPhone
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>> >
>>>>
>>>>
>>>
>>
>

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