NullPointerException when cache DataFrame in Java (Spark1.5.1)
It is not a problem to use JavaRDD.cache() for 200M data (all Objects read form Json Format). But when I try to use DataFrame.cache(), It shown exception in below. My machine can cache 1 G data in Avro format without any problem. 15/10/29 13:26:23 INFO GeneratePredicate: Code generated in 154.531827 ms 15/10/29 13:26:23 INFO GenerateUnsafeProjection: Code generated in 27.832369 ms 15/10/29 13:26:23 ERROR Executor: Exception in task 0.0 in stage 1.0 (TID 1) java.lang.NullPointerException at sun.reflect.GeneratedMethodAccessor11.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke( DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:497) at org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1$$anonfun$apply$2.apply( SQLContext.scala:500) at org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1$$anonfun$apply$2.apply( SQLContext.scala:500) at scala.collection.TraversableLike$$anonfun$map$1.apply( TraversableLike.scala:244) at scala.collection.TraversableLike$$anonfun$map$1.apply( TraversableLike.scala:244) at scala.collection.IndexedSeqOptimized$class.foreach( IndexedSeqOptimized.scala:33) at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108) at scala.collection.TraversableLike$class.map(TraversableLike.scala:244) at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:108) at org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1.apply( SQLContext.scala:500) at org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1.apply( SQLContext.scala:498) at scala.collection.Iterator$$anon$11.next(Iterator.scala:328) at scala.collection.Iterator$$anon$14.hasNext(Iterator.scala:389) at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327) at org.apache.spark.sql.columnar.InMemoryRelation$$anonfun$3$$anon$1.next( InMemoryColumnarTableScan.scala:127) at org.apache.spark.sql.columnar.InMemoryRelation$$anonfun$3$$anon$1.next( InMemoryColumnarTableScan.scala:120) at org.apache.spark.storage.MemoryStore.unrollSafely(MemoryStore.scala:278) at org.apache.spark.CacheManager.putInBlockManager(CacheManager.scala:171) at org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:78) at org.apache.spark.rdd.RDD.iterator(RDD.scala:262) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297) at org.apache.spark.rdd.RDD.iterator(RDD.scala:264) at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38) at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297) at org.apache.spark.rdd.RDD.iterator(RDD.scala:264) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66) at org.apache.spark.scheduler.Task.run(Task.scala:88) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214) at java.util.concurrent.ThreadPoolExecutor.runWorker( ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run( ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) 15/10/29 13:26:23 WARN TaskSetManager: Lost task 0.0 in stage 1.0 (TID 1, localhost): java.lang.NullPointerException at sun.reflect.GeneratedMethodAccessor11.invoke(Unknown Source) Thanks, Jingyu -- This message and its attachments may contain legally privileged or confidential information. It is intended solely for the named addressee. If you are not the addressee indicated in this message or responsible for delivery of the message to the addressee, you may not copy or deliver this message or its attachments to anyone. Rather, you should permanently delete this message and its attachments and kindly notify the sender by reply e-mail. Any content of this message and its attachments which does not relate to the official business of the sending company must be taken not to have been sent or endorsed by that company or any of its related entities. No warranty is made that the e-mail or attachments are free from computer virus or other defect.
Re: NullPointerException when cache DataFrame in Java (Spark1.5.1)
Did you try to cache a DataFrame with just a single row? Do you rows have any columns with null values? Can you post a code snippet here on how you load/generate the dataframe? Does dataframe.rdd.cache work? *Romi Kuntsman*, *Big Data Engineer* http://www.totango.com On Thu, Oct 29, 2015 at 4:33 AM, Zhang, Jingyu wrote: > It is not a problem to use JavaRDD.cache() for 200M data (all Objects read > form Json Format). But when I try to use DataFrame.cache(), It shown > exception in below. > > My machine can cache 1 G data in Avro format without any problem. > > 15/10/29 13:26:23 INFO GeneratePredicate: Code generated in 154.531827 ms > > 15/10/29 13:26:23 INFO GenerateUnsafeProjection: Code generated in > 27.832369 ms > > 15/10/29 13:26:23 ERROR Executor: Exception in task 0.0 in stage 1.0 (TID > 1) > > java.lang.NullPointerException > > at sun.reflect.GeneratedMethodAccessor11.invoke(Unknown Source) > > at sun.reflect.DelegatingMethodAccessorImpl.invoke( > DelegatingMethodAccessorImpl.java:43) > > at java.lang.reflect.Method.invoke(Method.java:497) > > at > org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1$$anonfun$apply$2.apply( > SQLContext.scala:500) > > at > org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1$$anonfun$apply$2.apply( > SQLContext.scala:500) > > at scala.collection.TraversableLike$$anonfun$map$1.apply( > TraversableLike.scala:244) > > at scala.collection.TraversableLike$$anonfun$map$1.apply( > TraversableLike.scala:244) > > at scala.collection.IndexedSeqOptimized$class.foreach( > IndexedSeqOptimized.scala:33) > > at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108) > > at scala.collection.TraversableLike$class.map(TraversableLike.scala:244) > > at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:108) > > at org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1.apply( > SQLContext.scala:500) > > at org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1.apply( > SQLContext.scala:498) > > at scala.collection.Iterator$$anon$11.next(Iterator.scala:328) > > at scala.collection.Iterator$$anon$14.hasNext(Iterator.scala:389) > > at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327) > > at org.apache.spark.sql.columnar.InMemoryRelation$$anonfun$3$$anon$1.next( > InMemoryColumnarTableScan.scala:127) > > at org.apache.spark.sql.columnar.InMemoryRelation$$anonfun$3$$anon$1.next( > InMemoryColumnarTableScan.scala:120) > > at org.apache.spark.storage.MemoryStore.unrollSafely(MemoryStore.scala:278 > ) > > at org.apache.spark.CacheManager.putInBlockManager(CacheManager.scala:171) > > at org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:78) > > at org.apache.spark.rdd.RDD.iterator(RDD.scala:262) > > at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38 > ) > > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297) > > at org.apache.spark.rdd.RDD.iterator(RDD.scala:264) > > at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38 > ) > > at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297) > > at org.apache.spark.rdd.RDD.iterator(RDD.scala:264) > > at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66) > > at org.apache.spark.scheduler.Task.run(Task.scala:88) > > at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214) > > at java.util.concurrent.ThreadPoolExecutor.runWorker( > ThreadPoolExecutor.java:1142) > > at java.util.concurrent.ThreadPoolExecutor$Worker.run( > ThreadPoolExecutor.java:617) > > at java.lang.Thread.run(Thread.java:745) > > 15/10/29 13:26:23 WARN TaskSetManager: Lost task 0.0 in stage 1.0 (TID 1, > localhost): java.lang.NullPointerException > > at sun.reflect.GeneratedMethodAccessor11.invoke(Unknown Source) > > > Thanks, > > > Jingyu > > This message and its attachments may contain legally privileged or > confidential information. It is intended solely for the named addressee. If > you are not the addressee indicated in this message or responsible for > delivery of the message to the addressee, you may not copy or deliver this > message or its attachments to anyone. Rather, you should permanently delete > this message and its attachments and kindly notify the sender by reply > e-mail. Any content of this message and its attachments which does not > relate to the official business of the sending company must be taken not to > have been sent or endorsed by that company or any of its related entities. > No warranty is made that the e-mail or attachments are free from computer > virus or other defect.
Re: NullPointerException when cache DataFrame in Java (Spark1.5.1)
Thanks Romi,
I resize the dataset to 7MB, however, the code show NullPointerException
exception as well.
Did you try to cache a DataFrame with just a single row?
Yes, I tried. But, Same problem.
.
Do you rows have any columns with null values?
No, I had filter out null values before cache the dataframe.
Can you post a code snippet here on how you load/generate the dataframe?
Sure, Here is the working code 1:
JavaRDD pixels = pixelsStr.map(new PixelGenerator()).cache();
System.out.println(pixels.count()); // 3000-4000 rows
Working code 2:
JavaRDD pixels = pixelsStr.map(new PixelGenerator());
DataFrame schemaPixel = sqlContext.createDataFrame(pixels, PixelObject.class
);
DataFrame totalDF1 =
schemaPixel.select(schemaPixel.col("domain")).filter("'domain'
is not null").limit(500);
System.out.println(totalDF1.count());
BUT, after change limit(500) to limit(1000). The code report
NullPointerException.
JavaRDD pixels = pixelsStr.map(new PixelGenerator());
DataFrame schemaPixel = sqlContext.createDataFrame(pixels, PixelObject.class
);
DataFrame totalDF =
schemaPixel.select(schemaPixel.col("domain")).filter("'domain'
is not null").limit(*1000*);
System.out.println(totalDF.count()); // problem at this line
15/10/29 18:56:28 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks
have all completed, from pool
15/10/29 18:56:28 INFO TaskSchedulerImpl: Cancelling stage 0
15/10/29 18:56:28 INFO DAGScheduler: ShuffleMapStage 0 (count at
X.java:113) failed in 3.764 s
15/10/29 18:56:28 INFO DAGScheduler: Job 0 failed: count at XXX.java:113,
took 3.862207 s
org.apache.spark.SparkException: Job aborted due to stage failure: Task 0
in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage
0.0 (TID 0, localhost): java.lang.NullPointerException
at sun.reflect.GeneratedMethodAccessor7.invoke(Unknown Source)
Does dataframe.rdd.cache work?
No, I tried but same exception.
Thanks,
Jingyu
On 29 October 2015 at 17:38, Romi Kuntsman wrote:
> Did you try to cache a DataFrame with just a single row?
> Do you rows have any columns with null values?
> Can you post a code snippet here on how you load/generate the dataframe?
> Does dataframe.rdd.cache work?
>
> *Romi Kuntsman*, *Big Data Engineer*
> http://www.totango.com
>
> On Thu, Oct 29, 2015 at 4:33 AM, Zhang, Jingyu
> wrote:
>
>> It is not a problem to use JavaRDD.cache() for 200M data (all Objects
>> read form Json Format). But when I try to use DataFrame.cache(), It shown
>> exception in below.
>>
>> My machine can cache 1 G data in Avro format without any problem.
>>
>> 15/10/29 13:26:23 INFO GeneratePredicate: Code generated in 154.531827 ms
>>
>> 15/10/29 13:26:23 INFO GenerateUnsafeProjection: Code generated in
>> 27.832369 ms
>>
>> 15/10/29 13:26:23 ERROR Executor: Exception in task 0.0 in stage 1.0 (TID
>> 1)
>>
>> java.lang.NullPointerException
>>
>> at sun.reflect.GeneratedMethodAccessor11.invoke(Unknown Source)
>>
>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(
>> DelegatingMethodAccessorImpl.java:43)
>>
>> at java.lang.reflect.Method.invoke(Method.java:497)
>>
>> at
>> org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1$$anonfun$apply$2.apply(
>> SQLContext.scala:500)
>>
>> at
>> org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1$$anonfun$apply$2.apply(
>> SQLContext.scala:500)
>>
>> at scala.collection.TraversableLike$$anonfun$map$1.apply(
>> TraversableLike.scala:244)
>>
>> at scala.collection.TraversableLike$$anonfun$map$1.apply(
>> TraversableLike.scala:244)
>>
>> at scala.collection.IndexedSeqOptimized$class.foreach(
>> IndexedSeqOptimized.scala:33)
>>
>> at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
>>
>> at scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
>>
>> at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:108)
>>
>> at org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1.apply(
>> SQLContext.scala:500)
>>
>> at org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1.apply(
>> SQLContext.scala:498)
>>
>> at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
>>
>> at scala.collection.Iterator$$anon$14.hasNext(Iterator.scala:389)
>>
>> at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
>>
>> at org.apache.spark.sql.columnar.InMemoryRelation$$anonfun$3$$anon$1.next(
>> InMemoryColumnarTableScan.scala:127)
>>
>> at org.apache.spark.sql.columnar.InMemoryRelation$$anonfun$3$$anon$1.next(
>> InMemoryColumnarTableScan.scala:120)
>>
>> at org.apache.spark.storage.MemoryStore.unrollSafely(
>> MemoryStore.scala:278)
>>
>> at org.apache.spark.CacheManager.putInBlockManager(CacheManager.scala:171
>> )
>>
>> at org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:78)
>>
>> at org.apache.spark.rdd.RDD.iterator(RDD.scala:262)
>>
>> at org.apache.spark.rdd.MapPartitionsRDD.compute(
>> MapPartitionsRDD.scala:38)
>>
>> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:297)
>>
>> at org.apache.
Re: NullPointerException when cache DataFrame in Java (Spark1.5.1)
>
> BUT, after change limit(500) to limit(1000). The code report
> NullPointerException.
>
I had a similar situation, and the problem was with a certain record.
Try to find which records are returned when you limit to 1000 but not
returned when you limit to 500.
Could it be a NPE thrown from PixelObject?
Are you running spark with master=local, so it's running inside your IDE
and you can see the errors from the driver and worker?
*Romi Kuntsman*, *Big Data Engineer*
http://www.totango.com
On Thu, Oct 29, 2015 at 10:04 AM, Zhang, Jingyu
wrote:
> Thanks Romi,
>
> I resize the dataset to 7MB, however, the code show NullPointerException
> exception as well.
>
> Did you try to cache a DataFrame with just a single row?
>
> Yes, I tried. But, Same problem.
> .
> Do you rows have any columns with null values?
>
> No, I had filter out null values before cache the dataframe.
>
> Can you post a code snippet here on how you load/generate the dataframe?
>
> Sure, Here is the working code 1:
>
> JavaRDD pixels = pixelsStr.map(new PixelGenerator()).cache();
>
> System.out.println(pixels.count()); // 3000-4000 rows
>
> Working code 2:
>
> JavaRDD pixels = pixelsStr.map(new PixelGenerator());
>
> DataFrame schemaPixel = sqlContext.createDataFrame(pixels, PixelObject.
> class);
>
> DataFrame totalDF1 =
> schemaPixel.select(schemaPixel.col("domain")).filter("'domain'
> is not null").limit(500);
>
> System.out.println(totalDF1.count());
>
>
> BUT, after change limit(500) to limit(1000). The code report
> NullPointerException.
>
>
> JavaRDD pixels = pixelsStr.map(new PixelGenerator());
>
> DataFrame schemaPixel = sqlContext.createDataFrame(pixels, PixelObject.
> class);
>
> DataFrame totalDF =
> schemaPixel.select(schemaPixel.col("domain")).filter("'domain'
> is not null").limit(*1000*);
>
> System.out.println(totalDF.count()); // problem at this line
>
> 15/10/29 18:56:28 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks
> have all completed, from pool
>
> 15/10/29 18:56:28 INFO TaskSchedulerImpl: Cancelling stage 0
>
> 15/10/29 18:56:28 INFO DAGScheduler: ShuffleMapStage 0 (count at
> X.java:113) failed in 3.764 s
>
> 15/10/29 18:56:28 INFO DAGScheduler: Job 0 failed: count at XXX.java:113,
> took 3.862207 s
>
> org.apache.spark.SparkException: Job aborted due to stage failure: Task 0
> in stage 0.0 failed 1 times, most recent failure: Lost task 0.0 in stage
> 0.0 (TID 0, localhost): java.lang.NullPointerException
>
> at sun.reflect.GeneratedMethodAccessor7.invoke(Unknown Source)
> Does dataframe.rdd.cache work?
>
> No, I tried but same exception.
>
> Thanks,
>
> Jingyu
>
> On 29 October 2015 at 17:38, Romi Kuntsman wrote:
>
>> Did you try to cache a DataFrame with just a single row?
>> Do you rows have any columns with null values?
>> Can you post a code snippet here on how you load/generate the dataframe?
>> Does dataframe.rdd.cache work?
>>
>> *Romi Kuntsman*, *Big Data Engineer*
>> http://www.totango.com
>>
>> On Thu, Oct 29, 2015 at 4:33 AM, Zhang, Jingyu
>> wrote:
>>
>>> It is not a problem to use JavaRDD.cache() for 200M data (all Objects
>>> read form Json Format). But when I try to use DataFrame.cache(), It shown
>>> exception in below.
>>>
>>> My machine can cache 1 G data in Avro format without any problem.
>>>
>>> 15/10/29 13:26:23 INFO GeneratePredicate: Code generated in 154.531827 ms
>>>
>>> 15/10/29 13:26:23 INFO GenerateUnsafeProjection: Code generated in
>>> 27.832369 ms
>>>
>>> 15/10/29 13:26:23 ERROR Executor: Exception in task 0.0 in stage 1.0
>>> (TID 1)
>>>
>>> java.lang.NullPointerException
>>>
>>> at sun.reflect.GeneratedMethodAccessor11.invoke(Unknown Source)
>>>
>>> at sun.reflect.DelegatingMethodAccessorImpl.invoke(
>>> DelegatingMethodAccessorImpl.java:43)
>>>
>>> at java.lang.reflect.Method.invoke(Method.java:497)
>>>
>>> at
>>> org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1$$anonfun$apply$2.apply(
>>> SQLContext.scala:500)
>>>
>>> at
>>> org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1$$anonfun$apply$2.apply(
>>> SQLContext.scala:500)
>>>
>>> at scala.collection.TraversableLike$$anonfun$map$1.apply(
>>> TraversableLike.scala:244)
>>>
>>> at scala.collection.TraversableLike$$anonfun$map$1.apply(
>>> TraversableLike.scala:244)
>>>
>>> at scala.collection.IndexedSeqOptimized$class.foreach(
>>> IndexedSeqOptimized.scala:33)
>>>
>>> at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
>>>
>>> at scala.collection.TraversableLike$class.map(TraversableLike.scala:244)
>>>
>>> at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:108)
>>>
>>> at org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1.apply(
>>> SQLContext.scala:500)
>>>
>>> at org.apache.spark.sql.SQLContext$$anonfun$9$$anonfun$apply$1.apply(
>>> SQLContext.scala:498)
>>>
>>> at scala.collection.Iterator$$anon$11.next(Iterator.scala:328)
>>>
>>> at scala.collection.Iterator$$anon$14.hasNext(Iterator.scala:389)
>>>
>>> at scala.collection.Iterator$$anon$11.hasNext
