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From Michael Armbrust <mich...@databricks.com>
Subject Re: SparkSQL exception on cached parquet table
Date Thu, 20 Nov 2014 19:59:41 GMT
Can you open a JIRA?

On Thu, Nov 20, 2014 at 10:39 AM, Sadhan Sood <sadhan.sood@gmail.com> wrote:

> I am running on master, pulled yesterday I believe but saw the same issue
> with 1.2.0
>
> On Thu, Nov 20, 2014 at 1:37 PM, Michael Armbrust <michael@databricks.com>
> wrote:
>
>> Which version are you running on again?
>>
>> On Thu, Nov 20, 2014 at 8:17 AM, Sadhan Sood <sadhan.sood@gmail.com>
>> wrote:
>>
>>> Also attaching the parquet file if anyone wants to take a further look.
>>>
>>> On Thu, Nov 20, 2014 at 8:54 AM, Sadhan Sood <sadhan.sood@gmail.com>
>>> wrote:
>>>
>>>> So, I am seeing this issue with spark sql throwing an exception when
>>>> trying to read selective columns from a thrift parquet file and also when
>>>> caching them:
>>>> On some further digging, I was able to narrow it down to at-least one
>>>> particular column type: map<string, set<string>> to be causing
this issue.
>>>> To reproduce this I created a test thrift file with a very basic schema and
>>>> stored some sample data in a parquet file:
>>>>
>>>> Test.thrift
>>>> ===========
>>>> typedef binary SomeId
>>>>
>>>> enum SomeExclusionCause {
>>>>   WHITELIST = 1,
>>>>   HAS_PURCHASE = 2,
>>>> }
>>>>
>>>> struct SampleThriftObject {
>>>>   10: string col_a;
>>>>   20: string col_b;
>>>>   30: string col_c;
>>>>   40: optional map<SomeExclusionCause, set<SomeId>> col_d;
>>>> }
>>>> =============
>>>>
>>>> And loading the data in spark through schemaRDD:
>>>>
>>>> import org.apache.spark.sql.SchemaRDD
>>>> val sqlContext = new org.apache.spark.sql.SQLContext(sc);
>>>> val parquetFile = "/path/to/generated/parquet/file"
>>>> val parquetFileRDD = sqlContext.parquetFile(parquetFile)
>>>> parquetFileRDD.printSchema
>>>> root
>>>>  |-- col_a: string (nullable = true)
>>>>  |-- col_b: string (nullable = true)
>>>>  |-- col_c: string (nullable = true)
>>>>  |-- col_d: map (nullable = true)
>>>>  |    |-- key: string
>>>>  |    |-- value: array (valueContainsNull = true)
>>>>  |    |    |-- element: string (containsNull = false)
>>>>
>>>> parquetFileRDD.registerTempTable("test")
>>>> sqlContext.cacheTable("test")
>>>> sqlContext.sql("select col_a from test").collect() <-- see the
>>>> exception stack here
>>>>
>>>> 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): parquet.io.ParquetDecodingException: Can not read
>>>> value at 0 in block -1 in file file:/tmp/xyz/part-r-00000.parquet
>>>> at
>>>> parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:213)
>>>> at
>>>> parquet.hadoop.ParquetRecordReader.nextKeyValue(ParquetRecordReader.java:204)
>>>> at
>>>> org.apache.spark.rdd.NewHadoopRDD$$anon$1.hasNext(NewHadoopRDD.scala:145)
>>>> at
>>>> org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
>>>> at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
>>>> at scala.collection.Iterator$$anon$14.hasNext(Iterator.scala:388)
>>>> at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:327)
>>>> at scala.collection.Iterator$class.foreach(Iterator.scala:727)
>>>> at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
>>>> at
>>>> scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:48)
>>>> at
>>>> scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:103)
>>>> at
>>>> scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:47)
>>>> at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:273)
>>>> at scala.collection.AbstractIterator.to(Iterator.scala:1157)
>>>> at
>>>> scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:265)
>>>> at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1157)
>>>> at
>>>> scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:252)
>>>> at scala.collection.AbstractIterator.toArray(Iterator.scala:1157)
>>>> at org.apache.spark.rdd.RDD$$anonfun$16.apply(RDD.scala:780)
>>>> at org.apache.spark.rdd.RDD$$anonfun$16.apply(RDD.scala:780)
>>>> at
>>>> org.apache.spark.SparkContext$$anonfun$runJob$3.apply(SparkContext.scala:1223)
>>>> at
>>>> org.apache.spark.SparkContext$$anonfun$runJob$3.apply(SparkContext.scala:1223)
>>>> at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:61)
>>>> at org.apache.spark.scheduler.Task.run(Task.scala:56)
>>>> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:195)
>>>> 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)
>>>>
>>>> Caused by: java.lang.ArrayIndexOutOfBoundsException: -1
>>>> at java.util.ArrayList.elementData(ArrayList.java:418)
>>>> at java.util.ArrayList.get(ArrayList.java:431)
>>>> at parquet.io.GroupColumnIO.getLast(GroupColumnIO.java:95)
>>>> at parquet.io.GroupColumnIO.getLast(GroupColumnIO.java:95)
>>>> at parquet.io.PrimitiveColumnIO.getLast(PrimitiveColumnIO.java:80)
>>>> at parquet.io.PrimitiveColumnIO.isLast(PrimitiveColumnIO.java:74)
>>>> at
>>>> parquet.io.RecordReaderImplementation.<init>(RecordReaderImplementation.java:282)
>>>> at parquet.io.MessageColumnIO$1.visit(MessageColumnIO.java:131)
>>>> at parquet.io.MessageColumnIO$1.visit(MessageColumnIO.java:96)
>>>> at
>>>> parquet.filter2.compat.FilterCompat$NoOpFilter.accept(FilterCompat.java:136)
>>>> at parquet.io.MessageColumnIO.getRecordReader(MessageColumnIO.java:96)
>>>> at
>>>> parquet.hadoop.InternalParquetRecordReader.checkRead(InternalParquetRecordReader.java:126)
>>>> at
>>>> parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:193)
>>>> ... 27 more
>>>>
>>>> If you take out the col_d from the thrift file, the problem goes away.
>>>> The problem also shows up when trying to read the particular column without
>>>> caching the table first. The same file can be dumped/read using
>>>> parquet-tools just fine. Here is the file dump using parquet-tools:
>>>>
>>>> row group 0
>>>> --------------------------------------------------------------------------------
>>>> col_a:           BINARY UNCOMPRESSED DO:0 FPO:4 SZ:89/89/1.00 VC:9 ENC [more]...
>>>> col_b:           BINARY UNCOMPRESSED DO:0 FPO:93 SZ:89/89/1.00 VC:9 EN [more]...
>>>> col_c:           BINARY UNCOMPRESSED DO:0 FPO:182 SZ:89/89/1.00 VC:9 E [more]...
>>>> col_d:
>>>> .map:
>>>> ..key:           BINARY UNCOMPRESSED DO:0 FPO:271 SZ:29/29/1.00 VC:9 E [more]...
>>>> ..value:
>>>> ...value_tuple:  BINARY UNCOMPRESSED DO:0 FPO:300 SZ:29/29/1.00 VC:9 E [more]...
>>>>
>>>>     col_a TV=9 RL=0 DL=1
>>>>     ----------------------------------------------------------------------------
>>>>     page 0:  DLE:RLE RLE:BIT_PACKED VLE:PLAIN SZ:60 VC:9
>>>>
>>>>     col_b TV=9 RL=0 DL=1
>>>>     ----------------------------------------------------------------------------
>>>>     page 0:  DLE:RLE RLE:BIT_PACKED VLE:PLAIN SZ:60 VC:9
>>>>
>>>>     col_c TV=9 RL=0 DL=1
>>>>     ----------------------------------------------------------------------------
>>>>     page 0:  DLE:RLE RLE:BIT_PACKED VLE:PLAIN SZ:60 VC:9
>>>>
>>>>     col_d.map.key TV=9 RL=1 DL=2
>>>>     ----------------------------------------------------------------------------
>>>>     page 0:  DLE:RLE RLE:RLE VLE:PLAIN SZ:12 VC:9
>>>>
>>>>     col_d.map.value.value_tuple TV=9 RL=2 DL=4
>>>>     ----------------------------------------------------------------------------
>>>>     page 0:  DLE:RLE RLE:RLE VLE:PLAIN SZ:12 VC:9
>>>>
>>>> BINARY col_a
>>>> --------------------------------------------------------------------------------
>>>> *** row group 1 of 1, values 1 to 9 ***
>>>> value 1: R:1 D:1 V:a1
>>>> value 2: R:1 D:1 V:a2
>>>> value 3: R:1 D:1 V:a3
>>>> value 4: R:1 D:1 V:a4
>>>> value 5: R:1 D:1 V:a5
>>>> value 6: R:1 D:1 V:a6
>>>> value 7: R:1 D:1 V:a7
>>>> value 8: R:1 D:1 V:a8
>>>> value 9: R:1 D:1 V:a9
>>>>
>>>> BINARY col_b
>>>> --------------------------------------------------------------------------------
>>>> *** row group 1 of 1, values 1 to 9 ***
>>>> value 1: R:1 D:1 V:b1
>>>> value 2: R:1 D:1 V:b2
>>>> value 3: R:1 D:1 V:b3
>>>> value 4: R:1 D:1 V:b4
>>>> value 5: R:1 D:1 V:b5
>>>> value 6: R:1 D:1 V:b6
>>>> value 7: R:1 D:1 V:b7
>>>> value 8: R:1 D:1 V:b8
>>>> value 9: R:1 D:1 V:b9
>>>>
>>>> BINARY col_c
>>>> --------------------------------------------------------------------------------
>>>> *** row group 1 of 1, values 1 to 9 ***
>>>> value 1: R:1 D:1 V:c1
>>>> value 2: R:1 D:1 V:c2
>>>> value 3: R:1 D:1 V:c3
>>>> value 4: R:1 D:1 V:c4
>>>> value 5: R:1 D:1 V:c5
>>>> value 6: R:1 D:1 V:c6
>>>> value 7: R:1 D:1 V:c7
>>>> value 8: R:1 D:1 V:c8
>>>> value 9: R:1 D:1 V:c9
>>>>
>>>> BINARY col_d.map.key
>>>> --------------------------------------------------------------------------------
>>>> *** row group 1 of 1, values 1 to 9 ***
>>>> value 1: R:0 D:0 V:<null>
>>>> value 2: R:0 D:0 V:<null>
>>>> value 3: R:0 D:0 V:<null>
>>>> value 4: R:0 D:0 V:<null>
>>>> value 5: R:0 D:0 V:<null>
>>>> value 6: R:0 D:0 V:<null>
>>>> value 7: R:0 D:0 V:<null>
>>>> value 8: R:0 D:0 V:<null>
>>>> value 9: R:0 D:0 V:<null>
>>>>
>>>> BINARY col_d.map.value.value_tuple
>>>> --------------------------------------------------------------------------------
>>>> *** row group 1 of 1, values 1 to 9 ***
>>>> value 1: R:0 D:0 V:<null>
>>>> value 2: R:0 D:0 V:<null>
>>>> value 3: R:0 D:0 V:<null>
>>>> value 4: R:0 D:0 V:<null>
>>>> value 5: R:0 D:0 V:<null>
>>>> value 6: R:0 D:0 V:<null>
>>>> value 7: R:0 D:0 V:<null>
>>>> value 8: R:0 D:0 V:<null>
>>>> value 9: R:0 D:0 V:<null>
>>>>
>>>>
>>>> I am happy to provide more information but any help is appreciated.
>>>>
>>>>
>>>> On Sun, Nov 16, 2014 at 7:40 PM, Sadhan Sood <sadhan.sood@gmail.com>
>>>> wrote:
>>>>
>>>>> Hi Cheng,
>>>>>
>>>>> I tried reading the parquet file(on which we were getting the
>>>>> exception) through parquet-tools and it is able to dump the file and
I can
>>>>> read the metadata, etc. I also loaded the file through hive table and
can
>>>>> run a table scan query on it as well. Let me know if I can do more to
help
>>>>> resolve the problem, I'll run it through a debugger and see if I can
get
>>>>> more information on it in the meantime.
>>>>>
>>>>> Thanks,
>>>>> Sadhan
>>>>>
>>>>> On Sun, Nov 16, 2014 at 4:35 AM, Cheng Lian <lian.cs.zju@gmail.com>
>>>>> wrote:
>>>>>
>>>>>>  (Forgot to cc user mail list)
>>>>>>
>>>>>>
>>>>>> On 11/16/14 4:59 PM, Cheng Lian wrote:
>>>>>>
>>>>>> Hey Sadhan,
>>>>>>
>>>>>>  Thanks for the additional information, this is helpful. Seems that
>>>>>> some Parquet internal contract was broken, but I'm not sure whether
it's
>>>>>> caused by Spark SQL or Parquet, or even maybe the Parquet file itself
was
>>>>>> damaged somehow. I'm investigating this. In the meanwhile, would
you mind
>>>>>> to help to narrow down the problem by trying to scan exactly the
same
>>>>>> Parquet file with some other systems (e.g. Hive or Impala)? If other
>>>>>> systems work, then there must be something wrong with Spark SQL.
>>>>>>
>>>>>>  Cheng
>>>>>>
>>>>>> On Sun, Nov 16, 2014 at 1:19 PM, Sadhan Sood <sadhan.sood@gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Cheng,
>>>>>>>
>>>>>>>  Thanks for your response. Here is the stack trace from yarn
logs:
>>>>>>>
>>>>>>>  Caused by: java.lang.ArrayIndexOutOfBoundsException: -1
>>>>>>>         at java.util.ArrayList.elementData(ArrayList.java:418)
>>>>>>>         at java.util.ArrayList.get(ArrayList.java:431)
>>>>>>>         at parquet.io.GroupColumnIO.getLast(GroupColumnIO.java:95)
>>>>>>>         at parquet.io.GroupColumnIO.getLast(GroupColumnIO.java:95)
>>>>>>>         at parquet.io.PrimitiveColumnIO.getLast(PrimitiveColumnIO.java:80)
>>>>>>>         at parquet.io.PrimitiveColumnIO.isLast(PrimitiveColumnIO.java:74)
>>>>>>>         at parquet.io.RecordReaderImplementation.<init>(RecordReaderImplementation.java:282)
>>>>>>>         at parquet.io.MessageColumnIO$1.visit(MessageColumnIO.java:131)
>>>>>>>         at parquet.io.MessageColumnIO$1.visit(MessageColumnIO.java:96)
>>>>>>>         at parquet.filter2.compat.FilterCompat$NoOpFilter.accept(FilterCompat.java:136)
>>>>>>>         at parquet.io.MessageColumnIO.getRecordReader(MessageColumnIO.java:96)
>>>>>>>         at parquet.hadoop.InternalParquetRecordReader.checkRead(InternalParquetRecordReader.java:126)
>>>>>>>         at parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:193)
>>>>>>>         ... 26 more
>>>>>>>
>>>>>>>
>>>>>>> On Sat, Nov 15, 2014 at 9:28 AM, Cheng Lian <lian.cs.zju@gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>>  Hi Sadhan,
>>>>>>>>
>>>>>>>> Could you please provide the stack trace of the
>>>>>>>> ArrayIndexOutOfBoundsException (if any)? The reason why the
first
>>>>>>>> query succeeds is that Spark SQL doesn’t bother reading
all data from the
>>>>>>>> table to give COUNT(*). In the second case, however, the
whole
>>>>>>>> table is asked to be cached lazily via the cacheTable call,
thus
>>>>>>>> it’s scanned to build the in-memory columnar cache. Then
thing went wrong
>>>>>>>> while scanning this LZO compressed Parquet file. But unfortunately
the
>>>>>>>> stack trace at hand doesn’t indicate the root cause.
>>>>>>>>
>>>>>>>> Cheng
>>>>>>>>
>>>>>>>> On 11/15/14 5:28 AM, Sadhan Sood wrote:
>>>>>>>>
>>>>>>>> While testing SparkSQL on a bunch of parquet files (basically
used
>>>>>>>> to be a partition for one of our hive tables), I encountered
this error:
>>>>>>>>
>>>>>>>>  import org.apache.spark.sql.SchemaRDD
>>>>>>>> import org.apache.hadoop.fs.FileSystem;
>>>>>>>> import org.apache.hadoop.conf.Configuration;
>>>>>>>> import org.apache.hadoop.fs.Path;
>>>>>>>>
>>>>>>>>  val sqlContext = new org.apache.spark.sql.SQLContext(sc)
>>>>>>>>
>>>>>>>>  val parquetFileRDD = sqlContext.parquetFile(parquetFile)
>>>>>>>> parquetFileRDD.registerTempTable("xyz_20141109")
>>>>>>>> sqlContext.sql("SELECT count(*)  FROM xyz_20141109").collect()
<--
>>>>>>>> works fine
>>>>>>>> sqlContext.cacheTable("xyz_20141109")
>>>>>>>> sqlContext.sql("SELECT count(*)  FROM xyz_20141109").collect()
<--
>>>>>>>> fails with an exception
>>>>>>>>
>>>>>>>>   parquet.io.ParquetDecodingException: Can not read value
at 0 in
>>>>>>>> block -1 in file
>>>>>>>> hdfs://xxxxxxxx::9000/event_logs/xyz/20141109/part-00009359b87ae-a949-3ded-ac3e-3a6bda3a4f3a-r-00009.lzo.parquet
>>>>>>>>
>>>>>>>>         at
>>>>>>>> parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:213)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> parquet.hadoop.ParquetRecordReader.nextKeyValue(ParquetRecordReader.java:204)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.rdd.NewHadoopRDD$anon$1.hasNext(NewHadoopRDD.scala:145)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.InterruptibleIterator.hasNext(InterruptibleIterator.scala:39)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> scala.collection.Iterator$anon$11.hasNext(Iterator.scala:327)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> scala.collection.Iterator$anon$14.hasNext(Iterator.scala:388)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.sql.columnar.InMemoryRelation$anonfun$3$anon$1.hasNext(InMemoryColumnarTableScan.scala:136)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.storage.MemoryStore.unrollSafely(MemoryStore.scala:248)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.CacheManager.putInBlockManager(CacheManager.scala:163)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.CacheManager.getOrCompute(CacheManager.scala:70)
>>>>>>>>
>>>>>>>>         at org.apache.spark.rdd.RDD.iterator(RDD.scala:228)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
>>>>>>>>
>>>>>>>>         at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
>>>>>>>>
>>>>>>>>         at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:35)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:263)
>>>>>>>>
>>>>>>>>         at org.apache.spark.rdd.RDD.iterator(RDD.scala:230)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:68)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
>>>>>>>>
>>>>>>>>         at org.apache.spark.scheduler.Task.run(Task.scala:56)
>>>>>>>>
>>>>>>>>         at
>>>>>>>> org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:195)
>>>>>>>>
>>>>>>>>         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)
>>>>>>>>
>>>>>>>> Caused by: java.lang.ArrayIndexOutOfBoundsException
>>>>>>>>
>>>>>>>>   ​
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>> ---------------------------------------------------------------------
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>>> For additional commands, e-mail: user-help@spark.apache.org
>>>
>>
>>
>

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