Hi,

When you implement code that starts memory-storing value copies for
every record (even if of just a single key), things are going to break
in big-data-land. Practically, post-partitioning, the # of values for
a given key can be huge given the source data, so you cannot hold it
all in and then write in one go. You'd probably need to write out
something continuously if you really really want to do this, or use an
alternative form of key-value storage where updates can be made
incrementally (Apache HBase is such a store, as one example).

This has been discussed before IIRC, and if the goal were to store the
outputs onto a file then its better to just directly serialize them
with a file opened instead of keeping it in a data structure and
serializing it at the end. The caveats that'd apply if you were to
open your own file from a task are described at
http://wiki.apache.org/hadoop/FAQ#Can_I_write_create.2BAC8-write-to_hdfs_files_directly_from_map.2BAC8-reduce_tasks.3F.

On Fri, Mar 8, 2013 at 4:35 AM, Christian Schneider
<[EMAIL PROTECTED]> wrote:
> I had a look to the stacktrace and it says the problem is at the reducer:
> userSet.add(iterator.next().toString());
>
> Error: Java heap space
> attempt_201303072200_0016_r_000002_0: WARN : mapreduce.Counters - Group
> org.apache.hadoop.mapred.Task$Counter is deprecated. Use
> org.apache.hadoop.mapreduce.TaskCounter instead
> attempt_201303072200_0016_r_000002_0: WARN :
> org.apache.hadoop.conf.Configuration - session.id is deprecated. Instead,
> use dfs.metrics.session-id
> attempt_201303072200_0016_r_000002_0: WARN :
> org.apache.hadoop.conf.Configuration - slave.host.name is deprecated.
> Instead, use dfs.datanode.hostname
> attempt_201303072200_0016_r_000002_0: FATAL: org.apache.hadoop.mapred.Child
> - Error running child : java.lang.OutOfMemoryError: Java heap space
> attempt_201303072200_0016_r_000002_0: at
> java.util.Arrays.copyOfRange(Arrays.java:3209)
> attempt_201303072200_0016_r_000002_0: at
> java.lang.String.<init>(String.java:215)
> attempt_201303072200_0016_r_000002_0: at
> java.nio.HeapCharBuffer.toString(HeapCharBuffer.java:542)
> attempt_201303072200_0016_r_000002_0: at
> java.nio.CharBuffer.toString(CharBuffer.java:1157)
> attempt_201303072200_0016_r_000002_0: at
> org.apache.hadoop.io.Text.decode(Text.java:394)
> attempt_201303072200_0016_r_000002_0: at
> org.apache.hadoop.io.Text.decode(Text.java:371)
> attempt_201303072200_0016_r_000002_0: at
> org.apache.hadoop.io.Text.toString(Text.java:273)
> attempt_201303072200_0016_r_000002_0: at
> com.myCompany.UserToAppReducer.reduce(RankingReducer.java:21)
> attempt_201303072200_0016_r_000002_0: at
> com.myCompany.UserToAppReducer.reduce(RankingReducer.java:1)
> attempt_201303072200_0016_r_000002_0: at
> org.apache.hadoop.mapreduce.Reducer.run(Reducer.java:164)
> attempt_201303072200_0016_r_000002_0: at
> org.apache.hadoop.mapred.ReduceTask.runNewReducer(ReduceTask.java:610)
> attempt_201303072200_0016_r_000002_0: at
> org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:444)
> attempt_201303072200_0016_r_000002_0: at
> org.apache.hadoop.mapred.Child$4.run(Child.java:268)
> attempt_201303072200_0016_r_000002_0: at
> java.security.AccessController.doPrivileged(Native Method)
> attempt_201303072200_0016_r_000002_0: at
> javax.security.auth.Subject.doAs(Subject.java:396)
> attempt_201303072200_0016_r_000002_0: at
> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1408)
> attempt_201303072200_0016_r_000002_0: at
> org.apache.hadoop.mapred.Child.main(Child.java:262)
>
> But how to solve this?
>
>
> 2013/3/7 Christian Schneider <[EMAIL PROTECTED]>
>>
>> Hi,
>> during the Reduce phase or afterwards (i don't really know how to debug
>> it) I get a heap out of Memory Exception.
>>
>> I guess this is because the value of the reduce task (a Custom Writable)
>> holds a List with a lot of user ids.
>> The Setup is quite simple. This are the related classes I used:
>>
>> //----
Harsh J

As always, what Harsh said :)

Looking at your reducer code, it appears that you are trying to compute the distinct set of user IDs for a given reduce key. Rather than computing this by holding the set in memory, use a secondary sort of the reduce values, then while iterating over the reduce values, look for changes of user id. Whenever it changes, write out the key and the newly found value.

Your output will change from this:

  key, [value 1, value2, ... valueN]

to this:

  key, value1
  key, value2
       ...
  key, valueN

Whether this is suitable for your follow-on processing is the next question, but this approach will scale to whatever data you can throw at it.

Paul
On 8 March 2013 10:57, Harsh J <[EMAIL PROTECTED]> wrote:
> Hi,
>
> When you implement code that starts memory-storing value copies for
> every record (even if of just a single key), things are going to break
> in big-data-land. Practically, post-partitioning, the # of values for
> a given key can be huge given the source data, so you cannot hold it
> all in and then write in one go. You'd probably need to write out
> something continuously if you really really want to do this, or use an
> alternative form of key-value storage where updates can be made
> incrementally (Apache HBase is such a store, as one example).
>
> This has been discussed before IIRC, and if the goal were to store the
> outputs onto a file then its better to just directly serialize them
> with a file opened instead of keeping it in a data structure and
> serializing it at the end. The caveats that'd apply if you were to
> open your own file from a task are described at
> http://wiki.apache.org/hadoop/FAQ#Can_I_write_create.2BAC8-write-to_hdfs_files_directly_from_map.2BAC8-reduce_tasks.3F.
>
> On Fri, Mar 8, 2013 at 4:35 AM, Christian Schneider
> <[EMAIL PROTECTED]> wrote:
> > I had a look to the stacktrace and it says the problem is at the reducer:
> > userSet.add(iterator.next().toString());
> >
> > Error: Java heap space
> > attempt_201303072200_0016_r_000002_0: WARN : mapreduce.Counters - Group
> > org.apache.hadoop.mapred.Task$Counter is deprecated. Use
> > org.apache.hadoop.mapreduce.TaskCounter instead
> > attempt_201303072200_0016_r_000002_0: WARN :
> > org.apache.hadoop.conf.Configuration - session.id is deprecated. Instead,
> > use dfs.metrics.session-id
> > attempt_201303072200_0016_r_000002_0: WARN :
> > org.apache.hadoop.conf.Configuration - slave.host.name is deprecated.
> > Instead, use dfs.datanode.hostname
> > attempt_201303072200_0016_r_000002_0: FATAL: org.apache.hadoop.mapred.Child
> > - Error running child : java.lang.OutOfMemoryError: Java heap space
> > attempt_201303072200_0016_r_000002_0: at
> > java.util.Arrays.copyOfRange(Arrays.java:3209)
> > attempt_201303072200_0016_r_000002_0: at
> > java.lang.String.<init>(String.java:215)
> > attempt_201303072200_0016_r_000002_0: at
> > java.nio.HeapCharBuffer.toString(HeapCharBuffer.java:542)
> > attempt_201303072200_0016_r_000002_0: at
> > java.nio.CharBuffer.toString(CharBuffer.java:1157)
> > attempt_201303072200_0016_r_000002_0: at
> > org.apache.hadoop.io.Text.decode(Text.java:394)
> > attempt_201303072200_0016_r_000002_0: at
> > org.apache.hadoop.io.Text.decode(Text.java:371)
> > attempt_201303072200_0016_r_000002_0: at
> > org.apache.hadoop.io.Text.toString(Text.java:273)
> > attempt_201303072200_0016_r_000002_0: at
> > com.myCompany.UserToAppReducer.reduce(RankingReducer.java:21)
> > attempt_201303072200_0016_r_000002_0: at
> > com.myCompany.UserToAppReducer.reduce(RankingReducer.java:1)
> > attempt_201303072200_0016_r_000002_0: at
> > org.apache.hadoop.mapreduce.Reducer.run(Reducer.java:164)
> > attempt_201303072200_0016_r_000002_0: at
> > org.apache.hadoop.mapred.ReduceTask.runNewReducer(ReduceTask.java:610)
> > attempt_201303072200_0016_r_000002_0: at
> > org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:444)
> > attempt_201303072200_0016_r_000002_0: at
> > org.apache.hadoop.mapred.Child$4.run(Child.java:268)

"A potential problem could be, that a reduce is going to write files >600MB and our mapred.child.java.opts is set to ~380MB."

Isn't the minimum heap normally 512MB?

Why not just increase your child heap size, assuming you have enough memory on the box...
On Mar 8, 2013, at 4:57 AM, Harsh J <[EMAIL PROTECTED]> wrote:

> Hi,
>
> When you implement code that starts memory-storing value copies for
> every record (even if of just a single key), things are going to break
> in big-data-land. Practically, post-partitioning, the # of values for
> a given key can be huge given the source data, so you cannot hold it
> all in and then write in one go. You'd probably need to write out
> something continuously if you really really want to do this, or use an
> alternative form of key-value storage where updates can be made
> incrementally (Apache HBase is such a store, as one example).
>
> This has been discussed before IIRC, and if the goal were to store the
> outputs onto a file then its better to just directly serialize them
> with a file opened instead of keeping it in a data structure and
> serializing it at the end. The caveats that'd apply if you were to
> open your own file from a task are described at
> http://wiki.apache.org/hadoop/FAQ#Can_I_write_create.2BAC8-write-to_hdfs_files_directly_from_map.2BAC8-reduce_tasks.3F.
>
> On Fri, Mar 8, 2013 at 4:35 AM, Christian Schneider
> <[EMAIL PROTECTED]> wrote:
>> I had a look to the stacktrace and it says the problem is at the reducer:
>> userSet.add(iterator.next().toString());
>>
>> Error: Java heap space
>> attempt_201303072200_0016_r_000002_0: WARN : mapreduce.Counters - Group
>> org.apache.hadoop.mapred.Task$Counter is deprecated. Use
>> org.apache.hadoop.mapreduce.TaskCounter instead
>> attempt_201303072200_0016_r_000002_0: WARN :
>> org.apache.hadoop.conf.Configuration - session.id is deprecated. Instead,
>> use dfs.metrics.session-id
>> attempt_201303072200_0016_r_000002_0: WARN :
>> org.apache.hadoop.conf.Configuration - slave.host.name is deprecated.
>> Instead, use dfs.datanode.hostname
>> attempt_201303072200_0016_r_000002_0: FATAL: org.apache.hadoop.mapred.Child
>> - Error running child : java.lang.OutOfMemoryError: Java heap space
>> attempt_201303072200_0016_r_000002_0: at
>> java.util.Arrays.copyOfRange(Arrays.java:3209)
>> attempt_201303072200_0016_r_000002_0: at
>> java.lang.String.<init>(String.java:215)
>> attempt_201303072200_0016_r_000002_0: at
>> java.nio.HeapCharBuffer.toString(HeapCharBuffer.java:542)
>> attempt_201303072200_0016_r_000002_0: at
>> java.nio.CharBuffer.toString(CharBuffer.java:1157)
>> attempt_201303072200_0016_r_000002_0: at
>> org.apache.hadoop.io.Text.decode(Text.java:394)
>> attempt_201303072200_0016_r_000002_0: at
>> org.apache.hadoop.io.Text.decode(Text.java:371)
>> attempt_201303072200_0016_r_000002_0: at
>> org.apache.hadoop.io.Text.toString(Text.java:273)
>> attempt_201303072200_0016_r_000002_0: at
>> com.myCompany.UserToAppReducer.reduce(RankingReducer.java:21)
>> attempt_201303072200_0016_r_000002_0: at
>> com.myCompany.UserToAppReducer.reduce(RankingReducer.java:1)
>> attempt_201303072200_0016_r_000002_0: at
>> org.apache.hadoop.mapreduce.Reducer.run(Reducer.java:164)
>> attempt_201303072200_0016_r_000002_0: at
>> org.apache.hadoop.mapred.ReduceTask.runNewReducer(ReduceTask.java:610)
>> attempt_201303072200_0016_r_000002_0: at
>> org.apache.hadoop.mapred.ReduceTask.run(ReduceTask.java:444)
>> attempt_201303072200_0016_r_000002_0: at
>> org.apache.hadoop.mapred.Child$4.run(Child.java:268)
>> attempt_201303072200_0016_r_000002_0: at
>> java.security.AccessController.doPrivileged(Native Method)
>> attempt_201303072200_0016_r_000002_0: at
>> javax.security.auth.Subject.doAs(Subject.java:396)
>> attempt_201303072200_0016_r_000002_0: at
>> org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1408)
>> attempt_201303072200_0016_r_000002_0: at
>> org.apache.hadoop.mapred.Child.main(Child.java:262)
>>