I find it easier to run jobs via MRUnit (http://mrunit.apache.org, TDD) first, or via LocalJobRunner, for debug purposes.
On Sat, Jul 28, 2012 at 5:53 AM, Sriram Ramachandrasekaran <sri.ram...@gmail.com> wrote: > hello harsh, > thanks for your investigations. while we were debugging, I saw the exact > thing. As you pointed out, we suspected it to be a problem. So, we set the > job conf object directly on Gora's query object. > It goes something like this, > query.setConf..(job.getConfig..()) > > And, then I saw that it was not getting into creating a new object at > getOrCreate(). > > OTOH, i've not tried the job.xml thing. I should give it a try n I shall > keep the loop posted. > > I would also like to hear about standard practices for debugging distributed > MR tasks. > > ----- > reply from a hh device. Pl excuse typos n lack of formatting. > > On 28 Jul 2012 03:30, "Harsh J" <ha...@cloudera.com> wrote: >> >> Hi Sriram, >> >> I suspect the following in Gora to somehow be causing this issue: >> >> IOUtils source: >> >> http://svn.apache.org/viewvc/gora/trunk/gora-core/src/main/java/org/apache/gora/util/IOUtils.java?view=markup >> QueryBase source: >> >> http://svn.apache.org/viewvc/gora/trunk/gora-core/src/main/java/org/apache/gora/query/impl/QueryBase.java?view=markup >> >> Notice that IOUtils.deserialize(…) calls expect a proper Configuration >> object. If not passed (i.e., if null), they call the following. >> >> 68 private static Configuration getOrCreateConf(Configuration conf) >> { >> 69 if(conf == null) { >> 70 if(IOUtils.conf == null) { >> 71 IOUtils.conf = new Configuration(); >> 72 } >> 73 } >> 74 return conf != null ? conf : IOUtils.conf; >> 75 } >> >> Now QueryBase, has in its readFields method, some >> IOUtils.deserialize(…) calls, that seem to pass a null for the >> configuration object. The IOUtils.deserialize(…) method hence calls >> this above method, and initializes a whole new Configuration object, >> as the passed conf object is null. >> >> If it does that, it would not be loading the "job.xml" file contents, >> which is the job's config file (thats something the map task's config >> set alone loads, and not a file thats loaded by default). So hence, >> custom serializers will disappear the moment it begins using this new >> Configuration object. >> >> This is what you'll want to investigate and fix or notify the Gora >> devs about (why QueryBase#readFields uses a null object, and if it can >> reuse some set conf object). As a cheap hack fix, maybe doing the >> following will make it work in an MR environment? >> >> IOUtils.conf = new Configuration(); >> IOUtils.conf.addResource("job.xml"); >> >> I haven't tried the above, but let us know how we can be of further >> assistance. An ideal fix would be to only use the MapTask's provided >> Configuration object everywhere, somehow, and never re-create one. >> >> P.s. If you want a thread ref link to share with other devs over Gora, >> here it is: http://search-hadoop.com/m/BXZA4dTUFC >> >> On Fri, Jul 27, 2012 at 1:24 PM, Sriram Ramachandrasekaran >> <sri.ram...@gmail.com> wrote: >> > Hello, >> > I have an MR job that talks to HBase. I use Gora to talk to HBase. Gora >> > also >> > provides couple of classes which can be extended to write Mappers and >> > Reducers, if the mappers need input from an HBase store and Reducers >> > need to >> > write it out to an HBase store. This is the reason why I use Gora. >> > >> > Now, when I run my MR job, I get an exception as below. >> > (https://issues.apache.org/jira/browse/HADOOP-3093) >> > java.lang.RuntimeException: java.io.IOException: >> > java.lang.NullPointerException >> > at >> > >> > org.apache.gora.mapreduce.GoraInputFormat.setConf(GoraInputFormat.java:115) >> > at >> > org.apache.hadoop.util.ReflectionUtils.setConf(ReflectionUtils.java:62) >> > at >> > >> > org.apache.hadoop.util.ReflectionUtils.newInstance(ReflectionUtils.java:117) >> > at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:723) >> > at org.apache.hadoop.mapred.MapTask.run(MapTask.java:370) >> > at org.apache.hadoop.mapred.Child$4.run(Child.java:255) >> > at java.security.AccessController.doPrivileged(Native Method) >> > at javax.security.auth.Subject.doAs(Subject.java:415) >> > at >> > >> > org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1093) >> > at org.apache.hadoop.mapred.Child.main(Child.java:249) >> > Caused by: java.io.IOException: java.lang.NullPointerException >> > at org.apache.gora.util.IOUtils.loadFromConf(IOUtils.java:483) >> > at >> > >> > org.apache.gora.mapreduce.GoraInputFormat.getQuery(GoraInputFormat.java:125) >> > at >> > >> > org.apache.gora.mapreduce.GoraInputFormat.setConf(GoraInputFormat.java:112) >> > ... 9 more >> > Caused by: java.lang.NullPointerException >> > at >> > >> > org.apache.hadoop.io.serializer.SerializationFactory.getDeserializer(SerializationFactory.java:77) >> > at org.apache.gora.util.IOUtils.deserialize(IOUtils.java:205) >> > at org.apache.gora.query.impl.QueryBase.readFields(QueryBase.java:234) >> > at >> > >> > org.apache.hadoop.io.serializer.WritableSerialization$WritableDeserializer.deserialize(WritableSerialization.java:67) >> > at >> > >> > org.apache.hadoop.io.serializer.WritableSerialization$WritableDeserializer.deserialize(WritableSerialization.java:40) >> > at >> > >> > org.apache.hadoop.io.DefaultStringifier.fromString(DefaultStringifier.java:75) >> > at >> > org.apache.hadoop.io.DefaultStringifier.load(DefaultStringifier.java:133) >> > at org.apache.gora.util.IOUtils.loadFromConf(IOUtils.java:480) >> > ... 11 more >> > >> > I tried the following things to work through this issue. >> > 0. The stack trace indicates that, when setting up a new Mapper, it is >> > unable to deserialize something. (I could not get to understand where it >> > fails). >> > 1. I looked around the forums and realized that serialization options >> > are >> > not getting passed, so, I tried setting up, io.serializations config on >> > the >> > job. >> > 1.1. I am not setting up the "io.serializations" myself, I use >> > GoraMapReduceUtils.setIOSerializations() to do it. I verified that, the >> > confs are getting proper serializers. >> > 2. I verified in the job xml to see if these confs have got through, >> > they >> > were. But, it failed again. >> > 3. I tried starting the hadoop job runner with debug options turned on >> > and >> > in suspend mode, -XDebug suspend=y and I also set the VM options for >> > mapred >> > child tasks, via the mapred.child.java.opts to see if I can debug the VM >> > that gets spawned newly. Although I get a message on my stdout saying, >> > opening port X and waiting, when I try to attach a remote debugger on >> > that >> > port, it does not work. >> > >> > I understand that, when SerializationFactory tries to deSerialize >> > 'something', it does not find an appropriate unmarshaller and so it >> > fails. >> > But, I would like to know a way to find that 'something' and I would >> > like to >> > get some idea on how (pseudo) distributed MR jobs should be generally >> > debugged. I tried searching, did not find anything useful. >> > >> > Any help/pointers would be greatly useful. >> > >> > Thanks! >> > >> > -- >> > It's just about how deep your longing is! >> > >> >> >> >> -- >> Harsh J -- Harsh J
