[
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 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 spark 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 on 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 vectorized reader off 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 spark 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),
(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 on 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 vectorized reader off 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
>
> 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 spark 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 on 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 vectorized reader off 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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