[
https://issues.apache.org/jira/browse/SPARK-19299?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel
]
Franklyn Dsouza updated SPARK-19299:
------------------------------------
Description:
The problem we're seeing is that if a null occurs in a no-nullable field and is
written down to parquet the resulting file gets corrupted and can not be read
back correctly.
One way that this can occur is when a long value in python is too big to fit
into a sql LongType it gets cast to null.
We're also seeing that the behaviour is different depending on whether or not
the vectorized reader is enabled.
Here's an example in PySpark
{code}
from datetime import datetime
from pyspark.sql import types
data = [
(1, 6),
(2, 7),
(3, 2 ** 64), # value overflows sql LongType
(4, 8),
(5, 9)
]
schema = types.StructType([
types.StructField("index", types.LongType(), False),
types.StructField("long", types.LongType(), False),
])
df = sc.sql.createDataFrame(data, schema)
df.collect()
df.write.parquet("corrupt_parquet")
df_parquet = sqlCtx.read.parquet("corrupt_parquet/*.parquet")
df_parquet.collect()
{code}
with the vectorized reader enabled this causes
{code}
In [2]: df.collect()
Out[2]:
[Row(index=1, long=6),
Row(index=2, long=7),
Row(index=3, long=None),
Row(index=4, long=8),
Row(index=5, long=9)]
In [3]: df_parquet.collect()
Out[3]:
[Row(index=1, long=6),
Row(index=2, long=7),
Row(index=3, long=8),
Row(index=4, long=9),
Row(index=5, long=5)]
{code}
as you can see reading the data back from disk causes data to get shifted up
and between columns.
with the vectorized reader disabled we are completely unable to read the file.
{code}
Py4JJavaError: An error occurred while calling o143.collectToPython.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in
stage 3.0 failed 1 times, most recent failure: Lost task 0.0 in stage 3.0 (TID
3, localhost): org.apache.parquet.io.ParquetDecodingException: Can not read
value at 4 in block 0 in file
file:/Users/franklyndsouza/dev/starscream/corrupt/part-r-00000-4fa5aee8-2138-4e0c-b6d8-22a418d90fd3.snappy.parquet
at
org.apache.parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:228)
at
org.apache.parquet.hadoop.ParquetRecordReader.nextKeyValue(ParquetRecordReader.java:201)
at
org.apache.spark.sql.execution.datasources.RecordReaderIterator.hasNext(RecordReaderIterator.scala:39)
at
org.apache.spark.sql.execution.datasources.FileScanRDD$$anon$1.hasNext(FileScanRDD.scala:91)
at
org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown
Source)
at
org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at
org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:370)
at
org.apache.spark.sql.execution.SparkPlan$$anonfun$4.apply(SparkPlan.scala:246)
at
org.apache.spark.sql.execution.SparkPlan$$anonfun$4.apply(SparkPlan.scala:240)
at
org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$24.apply(RDD.scala:803)
at
org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$24.apply(RDD.scala:803)
at
org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
at org.apache.spark.scheduler.Task.run(Task.scala:86)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
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: org.apache.parquet.io.ParquetDecodingException: Can't read value in
column [long] INT64 at value 5 out of 5, 5 out of 5 in currentPage. repetition
level: 0, definition level: 0
at
org.apache.parquet.column.impl.ColumnReaderImpl.readValue(ColumnReaderImpl.java:462)
at
org.apache.parquet.column.impl.ColumnReaderImpl.writeCurrentValueToConverter(ColumnReaderImpl.java:364)
at
org.apache.parquet.io.RecordReaderImplementation.read(RecordReaderImplementation.java:405)
at
org.apache.parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:209)
... 19 more
Caused by: org.apache.parquet.io.ParquetDecodingException: could not read long
at
org.apache.parquet.column.values.plain.PlainValuesReader$LongPlainValuesReader.readLong(PlainValuesReader.java:131)
at
org.apache.parquet.column.impl.ColumnReaderImpl$2$4.read(ColumnReaderImpl.java:258)
at
org.apache.parquet.column.impl.ColumnReaderImpl.readValue(ColumnReaderImpl.java:458)
... 22 more
Caused by: java.io.EOFException
at
org.apache.parquet.bytes.LittleEndianDataInputStream.readFully(LittleEndianDataInputStream.java:90)
at
org.apache.parquet.bytes.LittleEndianDataInputStream.readLong(LittleEndianDataInputStream.java:377)
at
org.apache.parquet.column.values.plain.PlainValuesReader$LongPlainValuesReader.readLong(PlainValuesReader.java:129)
{code}
was:
The problem we're seeing is that if a null occurs in a no-nullable field and is
written down to parquet the resulting file gets corrupt and can not be read
back correctly.
One way that this can occur is when a long value in python is too big to fit
into a sql LongType it gets cast to null.
We're also seeing that the behaviour is different depending on whether or not
the vectorized reader is enabled.
Here's an example in PySpark
{code}
from datetime import datetime
from pyspark.sql import types
data = [
(1, 6),
(2, 7),
(3, 2 ** 64), # value overflows sql LongType
(4, 8),
(5, 9)
]
schema = types.StructType([
types.StructField("index", types.LongType(), False),
types.StructField("long", types.LongType(), False),
])
df = sc.sql.createDataFrame(data, schema)
df.collect()
df.write.parquet("corrupt_parquet")
df_parquet = sqlCtx.read.parquet("corrupt_parquet/*.parquet")
df_parquet.collect()
{code}
with the vectorized reader enabled this causes
{code}
In [2]: df.collect()
Out[2]:
[Row(index=1, long=6),
Row(index=2, long=7),
Row(index=3, long=None),
Row(index=4, long=8),
Row(index=5, long=9)]
In [3]: df_parquet.collect()
Out[3]:
[Row(index=1, long=6),
Row(index=2, long=7),
Row(index=3, long=8),
Row(index=4, long=9),
Row(index=5, long=5)]
{code}
as you can see reading the data back from disk causes data to get shifted up
and between columns.
with the vectorized reader disabled we are completely unable to read the file.
{code}
Py4JJavaError: An error occurred while calling o143.collectToPython.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in
stage 3.0 failed 1 times, most recent failure: Lost task 0.0 in stage 3.0 (TID
3, localhost): org.apache.parquet.io.ParquetDecodingException: Can not read
value at 4 in block 0 in file
file:/Users/franklyndsouza/dev/starscream/corrupt/part-r-00000-4fa5aee8-2138-4e0c-b6d8-22a418d90fd3.snappy.parquet
at
org.apache.parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:228)
at
org.apache.parquet.hadoop.ParquetRecordReader.nextKeyValue(ParquetRecordReader.java:201)
at
org.apache.spark.sql.execution.datasources.RecordReaderIterator.hasNext(RecordReaderIterator.scala:39)
at
org.apache.spark.sql.execution.datasources.FileScanRDD$$anon$1.hasNext(FileScanRDD.scala:91)
at
org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown
Source)
at
org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
at
org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:370)
at
org.apache.spark.sql.execution.SparkPlan$$anonfun$4.apply(SparkPlan.scala:246)
at
org.apache.spark.sql.execution.SparkPlan$$anonfun$4.apply(SparkPlan.scala:240)
at
org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$24.apply(RDD.scala:803)
at
org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$24.apply(RDD.scala:803)
at
org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
at org.apache.spark.scheduler.Task.run(Task.scala:86)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.apache.parquet.io.ParquetDecodingException: Can't read value in
column [long] INT64 at value 5 out of 5, 5 out of 5 in currentPage. repetition
level: 0, definition level: 0
at
org.apache.parquet.column.impl.ColumnReaderImpl.readValue(ColumnReaderImpl.java:462)
at
org.apache.parquet.column.impl.ColumnReaderImpl.writeCurrentValueToConverter(ColumnReaderImpl.java:364)
at
org.apache.parquet.io.RecordReaderImplementation.read(RecordReaderImplementation.java:405)
at
org.apache.parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:209)
... 19 more
Caused by: org.apache.parquet.io.ParquetDecodingException: could not read long
at
org.apache.parquet.column.values.plain.PlainValuesReader$LongPlainValuesReader.readLong(PlainValuesReader.java:131)
at
org.apache.parquet.column.impl.ColumnReaderImpl$2$4.read(ColumnReaderImpl.java:258)
at
org.apache.parquet.column.impl.ColumnReaderImpl.readValue(ColumnReaderImpl.java:458)
... 22 more
Caused by: java.io.EOFException
at
org.apache.parquet.bytes.LittleEndianDataInputStream.readFully(LittleEndianDataInputStream.java:90)
at
org.apache.parquet.bytes.LittleEndianDataInputStream.readLong(LittleEndianDataInputStream.java:377)
at
org.apache.parquet.column.values.plain.PlainValuesReader$LongPlainValuesReader.readLong(PlainValuesReader.java:129)
{code}
> Nulls in non nullable columns causes data corruption in parquet
> ---------------------------------------------------------------
>
> Key: SPARK-19299
> URL: https://issues.apache.org/jira/browse/SPARK-19299
> Project: Spark
> Issue Type: Bug
> Components: PySpark, Spark Core
> Affects Versions: 1.6.0, 2.0.0, 2.0.1, 2.0.2, 2.1.0
> Reporter: Franklyn Dsouza
> Priority: Critical
>
> The problem we're seeing is that if a null occurs in a no-nullable field and
> is written down to parquet the resulting file gets corrupted and can not be
> read back correctly.
> One way that this can occur is when a long value in python is too big to fit
> into a sql LongType it gets cast to null.
> We're also seeing that the behaviour is different depending on whether or not
> the vectorized reader is enabled.
> Here's an example in PySpark
> {code}
> from datetime import datetime
> from pyspark.sql import types
> data = [
> (1, 6),
> (2, 7),
> (3, 2 ** 64), # value overflows sql LongType
> (4, 8),
> (5, 9)
> ]
> schema = types.StructType([
> types.StructField("index", types.LongType(), False),
> types.StructField("long", types.LongType(), False),
> ])
> df = sc.sql.createDataFrame(data, schema)
> df.collect()
> df.write.parquet("corrupt_parquet")
> df_parquet = sqlCtx.read.parquet("corrupt_parquet/*.parquet")
> df_parquet.collect()
> {code}
> with the vectorized reader enabled this causes
> {code}
> In [2]: df.collect()
> Out[2]:
> [Row(index=1, long=6),
> Row(index=2, long=7),
> Row(index=3, long=None),
> Row(index=4, long=8),
> Row(index=5, long=9)]
> In [3]: df_parquet.collect()
> Out[3]:
> [Row(index=1, long=6),
> Row(index=2, long=7),
> Row(index=3, long=8),
> Row(index=4, long=9),
> Row(index=5, long=5)]
> {code}
> as you can see reading the data back from disk causes data to get shifted up
> and between columns.
> with the vectorized reader disabled we are completely unable to read the file.
> {code}
> Py4JJavaError: An error occurred while calling o143.collectToPython.
> : org.apache.spark.SparkException: Job aborted due to stage failure: Task 0
> in stage 3.0 failed 1 times, most recent failure: Lost task 0.0 in stage 3.0
> (TID 3, localhost): org.apache.parquet.io.ParquetDecodingException: Can not
> read value at 4 in block 0 in file
> file:/Users/franklyndsouza/dev/starscream/corrupt/part-r-00000-4fa5aee8-2138-4e0c-b6d8-22a418d90fd3.snappy.parquet
> at
> org.apache.parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:228)
> at
> org.apache.parquet.hadoop.ParquetRecordReader.nextKeyValue(ParquetRecordReader.java:201)
> at
> org.apache.spark.sql.execution.datasources.RecordReaderIterator.hasNext(RecordReaderIterator.scala:39)
> at
> org.apache.spark.sql.execution.datasources.FileScanRDD$$anon$1.hasNext(FileScanRDD.scala:91)
> at
> org.apache.spark.sql.catalyst.expressions.GeneratedClass$GeneratedIterator.processNext(Unknown
> Source)
> at
> org.apache.spark.sql.execution.BufferedRowIterator.hasNext(BufferedRowIterator.java:43)
> at
> org.apache.spark.sql.execution.WholeStageCodegenExec$$anonfun$8$$anon$1.hasNext(WholeStageCodegenExec.scala:370)
> at
> org.apache.spark.sql.execution.SparkPlan$$anonfun$4.apply(SparkPlan.scala:246)
> at
> org.apache.spark.sql.execution.SparkPlan$$anonfun$4.apply(SparkPlan.scala:240)
> at
> org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$24.apply(RDD.scala:803)
> at
> org.apache.spark.rdd.RDD$$anonfun$mapPartitionsInternal$1$$anonfun$apply$24.apply(RDD.scala:803)
> at
> org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
> at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:319)
> at org.apache.spark.rdd.RDD.iterator(RDD.scala:283)
> at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:70)
> at org.apache.spark.scheduler.Task.run(Task.scala:86)
> at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:274)
> at
> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
> at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
> at java.lang.Thread.run(Thread.java:745)
> Caused by: org.apache.parquet.io.ParquetDecodingException: Can't read value
> in column [long] INT64 at value 5 out of 5, 5 out of 5 in currentPage.
> repetition level: 0, definition level: 0
> at
> org.apache.parquet.column.impl.ColumnReaderImpl.readValue(ColumnReaderImpl.java:462)
> at
> org.apache.parquet.column.impl.ColumnReaderImpl.writeCurrentValueToConverter(ColumnReaderImpl.java:364)
> at
> org.apache.parquet.io.RecordReaderImplementation.read(RecordReaderImplementation.java:405)
> at
> org.apache.parquet.hadoop.InternalParquetRecordReader.nextKeyValue(InternalParquetRecordReader.java:209)
> ... 19 more
> Caused by: org.apache.parquet.io.ParquetDecodingException: could not read long
> at
> org.apache.parquet.column.values.plain.PlainValuesReader$LongPlainValuesReader.readLong(PlainValuesReader.java:131)
> at
> org.apache.parquet.column.impl.ColumnReaderImpl$2$4.read(ColumnReaderImpl.java:258)
> at
> org.apache.parquet.column.impl.ColumnReaderImpl.readValue(ColumnReaderImpl.java:458)
> ... 22 more
> Caused by: java.io.EOFException
> at
> org.apache.parquet.bytes.LittleEndianDataInputStream.readFully(LittleEndianDataInputStream.java:90)
> at
> org.apache.parquet.bytes.LittleEndianDataInputStream.readLong(LittleEndianDataInputStream.java:377)
> at
> org.apache.parquet.column.values.plain.PlainValuesReader$LongPlainValuesReader.readLong(PlainValuesReader.java:129)
> {code}
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