Thanks Michael, opened this https://issues.apache.org/jira/browse/SPARK-4520
On Thu, Nov 20, 2014 at 2:59 PM, Michael Armbrust <mich...@databricks.com> wrote: > Can you open a JIRA? > > On Thu, Nov 20, 2014 at 10:39 AM, Sadhan Sood <sadhan.s...@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 <mich...@databricks.com >> > wrote: >> >>> Which version are you running on again? >>> >>> On Thu, Nov 20, 2014 at 8:17 AM, Sadhan Sood <sadhan.s...@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.s...@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.s...@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....@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.s...@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....@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 >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> --------------------------------------------------------------------- >>>> To unsubscribe, e-mail: user-unsubscr...@spark.apache.org >>>> For additional commands, e-mail: user-h...@spark.apache.org >>>> >>> >>> >> >