Details
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Bug
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Status: Resolved
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Minor
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Resolution: Invalid
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2.4.7
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None
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Amazon EMR with AMI version 5.32.0
Description
Hi, we've been experiencing some rows get corrupted while partitioned CSV files were written to Amazon S3. Some records were found broken without any error on Spark. Digging into the root cause, we found out Spark speculation tried to upload a partition being uploaded slowly and ended up uploading only a part of the partition, letting broken data uploaded to S3.
Here're stacktraces we've found. There are two executor involved - A: the first executor which tried to upload the file, but it took much longer than other executor (but still succeeded), which made spark speculation cut in and kick off another executor B. Executor B started to upload the file too, but was interrupted during uploading (killed: another attempt succeeded), and ended up uploading only a part of the whole file. You can see in the log, the file executor A uploaded (8461990 bytes originally) was overwritten by executor B (uploaded only 3145728 bytes).
Executor A:
21/01/28 17:22:21 INFO Executor: Running task 426.0 in stage 45.0 (TID 13201)
21/01/28 17:22:21 INFO ShuffleBlockFetcherIterator: Getting 470 non-empty blocks including 10 local blocks and 460 remote blocks
21/01/28 17:22:21 INFO ShuffleBlockFetcherIterator: Started 46 remote fetches in 18 ms
21/01/28 17:22:21 INFO FileOutputCommitter: File Output Committer Algorithm version is 2
21/01/28 17:22:21 INFO FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: true
21/01/28 17:22:21 INFO DirectFileOutputCommitter: Direct Write: ENABLED
21/01/28 17:22:21 INFO SQLConfCommitterProvider: Using output committer class
21/01/28 17:22:21 INFO INFO CSEMultipartUploadOutputStream: close closed:false s3://{obfuscated}/part-00426-7d5677a9-f740-4db6-9d3c-dc589d75e965-c000.csv
21/01/28 17:22:31 INFO DefaultMultipartUploadDispatcher: Completed multipart upload of 1 parts 8461990 bytes
21/01/28 17:22:31 INFO CSEMultipartUploadOutputStream: Finished uploading {obfuscated}/part-00426-7d5677a9-f740-4db6-9d3c-dc589d75e965-c000.csv. Elapsed seconds: 10.
21/01/28 17:22:31 INFO SparkHadoopMapRedUtil: No need to commit output of task because needsTaskCommit=false: attempt_20210128172219_0045_m_000426_13201
21/01/28 17:22:31 INFO Executor: Finished task 426.0 in stage 45.0 (TID 13201). 8782 bytes result sent to driver
Executor B:
21/01/28 17:22:31 INFO CoarseGrainedExecutorBackend: Got assigned task 13245 21/01/28 17:22:31 INFO Executor: Running task 426.1 in stage 45.0 (TID 13245)
21/01/28 17:22:31 INFO ShuffleBlockFetcherIterator: Getting 470 non-empty blocks including 11 local blocks and 459 remote blocks
21/01/28 17:22:31 INFO ShuffleBlockFetcherIterator: Started 46 remote fetches in 2 ms
21/01/28 17:22:31 INFO FileOutputCommitter: File Output Committer Algorithm version is 2
21/01/28 17:22:31 INFO FileOutputCommitter: FileOutputCommitter skip cleanup _temporary folders under output directory:false, ignore cleanup failures: true
21/01/28 17:22:31 INFO DirectFileOutputCommitter: Direct Write: ENABLED
21/01/28 17:22:31 INFO SQLConfCommitterProvider: Using output committer class org.apache.hadoop.mapreduce.lib.output.DirectFileOutputCommitter
21/01/28 17:22:31 INFO Executor: Executor is trying to kill task 426.1 in stage 45.0 (TID 13245), reason: another attempt succeeded
21/01/28 17:22:31 INFO CSEMultipartUploadOutputStream: close closed:false s3://{obfuscated}/part-00426-7d5677a9-f740-4db6-9d3c-dc589d75e965-c000.csv
21/01/28 17:22:32 INFO DefaultMultipartUploadDispatcher: Completed multipart upload of 1 parts 3145728 bytes
21/01/28 17:22:32 INFO CSEMultipartUploadOutputStream: Finished uploading {obfuscated}/part-00426-7d5677a9-f740-4db6-9d3c-dc589d75e965-c000.csv. Elapsed seconds: 0.
21/01/28 17:22:32 ERROR Utils: Aborting task com.univocity.parsers.common.TextWritingException: Error writing row. Internal state when error was thrown: recordCount=18449, recordData=[
Unknown macro: {obfuscated}
] at com.univocity.parsers.common.AbstractWriter.throwExceptionAndClose(AbstractWriter.java:935) at com.univocity.parsers.common.AbstractWriter.writeRow(AbstractWriter.java:714) at org.apache.spark.sql.execution.datasources.csv.UnivocityGenerator.write(UnivocityGenerator.scala:84) at org.apache.spark.sql.execution.datasources.csv.CsvOutputWriter.write(CSVFileFormat.scala:181) at org.apache.spark.sql.execution.datasources.SingleDirectoryDataWriter.write(FileFormatDataWriter.scala:137) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask$3.apply(FileFormatWriter.scala:245) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask$3.apply(FileFormatWriter.scala:242) at org.apache.spark.util.Utils$.tryWithSafeFinallyAndFailureCallbacks(Utils.scala:1439) at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:248) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:170) at org.apache.spark.sql.execution.datasources.FileFormatWriter$$anonfun$write$1.apply(FileFormatWriter.scala:169) at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90) at org.apache.spark.scheduler.Task.run(Task.scala:123) at org.apache.spark.executor.Executor$TaskRunner$$anonfun$10.apply(Executor.scala:408) at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1405) at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:414) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Caused by: com.univocity.parsers.common.TextWritingException: Error writing row. Internal state when error was thrown: recordCount=18449, recordCharacters={obfuscated} at com.univocity.parsers.common.AbstractWriter.throwExceptionAndClose(AbstractWriter.java:920) at com.univocity.parsers.common.AbstractWriter.internalWriteRow(AbstractWriter.java:829) at com.univocity.parsers.common.AbstractWriter.writeRow(AbstractWriter.java:712) ... 17 more Caused by: java.io.InterruptedIOException at java.io.PipedInputStream.awaitSpace(PipedInputStream.java:275) at java.io.PipedInputStream.receive(PipedInputStream.java:231) at java.io.PipedOutputStream.write(PipedOutputStream.java:149) at com.amazon.ws.emr.hadoop.fs.cse.CSEMultipartUploadOutputStream.write(CSEMultipartUploadOutputStream.java:242) at org.apache.hadoop.fs.FSDataOutputStream$PositionCache.write(FSDataOutputStream.java:60) at java.io.DataOutputStream.write(DataOutputStream.java:107) at sun.nio.cs.StreamEncoder.writeBytes(StreamEncoder.java:221) at sun.nio.cs.StreamEncoder.implWrite(StreamEncoder.java:282) at sun.nio.cs.StreamEncoder.write(StreamEncoder.java:125) at java.io.OutputStreamWriter.write(OutputStreamWriter.java:207) at com.univocity.parsers.common.input.WriterCharAppender.writeCharsAndReset(WriterCharAppender.java:153) at com.univocity.parsers.common.AbstractWriter.internalWriteRow(AbstractWriter.java:826) ... 18 more
21/01/28 17:22:32 INFO DirectFileOutputCommitter: Nothing to clean up on abort since there are no temporary files written
21/01/28 17:22:32 ERROR FileFormatWriter: Job job_20210128172219_0045 aborted.
21/01/28 17:22:32 INFO Executor: Executor interrupted and killed task 426.1 in stage 45.0 (TID 13245), reason: another attempt succeeded
We'll be bypassing this problem by setting speculation off, however ideally it seems that either speculation should be disabled in this stage (writing to S3).