Yes. Disk spill can be a huge performance hit, with smaller partitions you may avoid this and possibly complete your job faster. I hope you don't get OOM.

On Sat, 18 Jan 2020 at 10:06, Arwin Tio <arwin.tio@hotmail.com> wrote:
Okay! I didn't realize you can pump those partition numbers up that high. 15000 partitions still failed. I am trying 30000 partitions now. There is still some disk spill but it is not that high.

Thanks,

Arwin


From: Chris Teoh <chris.teoh@gmail.com>
Sent: January 17, 2020 7:32 PM
To: Arwin Tio <arwin.tio@hotmail.com>
Cc: user @spark <user@spark.apache.org>
Subject: Re: Spark Executor OOMs when writing Parquet
 
You also have disk spill which is a performance hit.

Try multiplying the number of partitions by about 20x - 40x and see if you can eliminate shuffle spill.

On Fri, 17 Jan 2020, 10:37 pm Arwin Tio, <arwin.tio@hotmail.com> wrote:
Yes, mostly memory spills though (36.9 TiB memory, 895 GiB disk). I was under the impression that memory spill is OK?


(If you're wondering, this is EMR).


From: Chris Teoh <chris.teoh@gmail.com>
Sent: January 17, 2020 10:30 AM
To: Arwin Tio <arwin.tio@hotmail.com>
Cc: user @spark <user@spark.apache.org>
Subject: Re: Spark Executor OOMs when writing Parquet
 
Sounds like you don't have enough partitions. Try and repartition to 14496 partitions. Are your stages experiencing shuffle spill?

On Fri, 17 Jan 2020, 10:12 pm Arwin Tio, <arwin.tio@hotmail.com> wrote:
Hello,

I have a fairly straightforward Spark job that converts CSV to Parquet:

```
Dataset<Row> df = spark.read(...)

df
  .repartition(5000)
  .write()
  .format("parquet")
  .parquet("s3://mypath/...);
```

For context, there are about 5 billion rows, each with 2000 columns. The entire dataset is about 1 TB (compressed).

The error looks like this:

```
  20/01/16 13:08:55 WARN TaskSetManager: Lost task 265.0 in stage 2.0 (TID 24300, ip-172-24-107-37.us-west-2.compute.internal, executor 13): org.apache.spark.SparkException: Task failed while writing rows.
        at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:257)
        at org.apache.spark.sql.execution.datasources.FileFormatWriter$$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:1360)
        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: java.lang.OutOfMemoryError
        at sun.misc.Unsafe.allocateMemory(Native Method)
        at java.nio.DirectByteBuffer.<init>(DirectByteBuffer.java:127)
        at java.nio.ByteBuffer.allocateDirect(ByteBuffer.java:311)
        at org.apache.parquet.hadoop.codec.SnappyCompressor.setInput(SnappyCompressor.java:97)
        at org.apache.parquet.hadoop.codec.NonBlockedCompressorStream.write(NonBlockedCompressorStream.java:48)
        at org.apache.parquet.bytes.CapacityByteArrayOutputStream.writeToOutput(CapacityByteArrayOutputStream.java:227)
        at org.apache.parquet.bytes.CapacityByteArrayOutputStream.writeTo(CapacityByteArrayOutputStream.java:247)
        at org.apache.parquet.bytes.BytesInput$CapacityBAOSBytesInput.writeAllTo(BytesInput.java:405)
        at org.apache.parquet.bytes.BytesInput$SequenceBytesIn.writeAllTo(BytesInput.java:296)
        at org.apache.parquet.hadoop.CodecFactory$HeapBytesCompressor.compress(CodecFactory.java:164)
        at org.apache.parquet.hadoop.ColumnChunkPageWriteStore$ColumnChunkPageWriter.writePage(ColumnChunkPageWriteStore.java:95)
        at org.apache.parquet.column.impl.ColumnWriterV1.writePage(ColumnWriterV1.java:147)
        at org.apache.parquet.column.impl.ColumnWriterV1.accountForValueWritten(ColumnWriterV1.java:106)
        at org.apache.parquet.column.impl.ColumnWriterV1.writeNull(ColumnWriterV1.java:170)
        at org.apache.parquet.io.MessageColumnIO$MessageColumnIORecordConsumer.writeNull(MessageColumnIO.java:347)
        at org.apache.parquet.io.MessageColumnIO$MessageColumnIORecordConsumer.writeNullForMissingFieldsAtCurrentLevel(MessageColumnIO.java:337)
        at org.apache.parquet.io.MessageColumnIO$MessageColumnIORecordConsumer.endMessage(MessageColumnIO.java:299)
        at org.apache.spark.sql.execution.datasources.parquet.ParquetWriteSupport.consumeMessage(ParquetWriteSupport.scala:424)
        at org.apache.spark.sql.execution.datasources.parquet.ParquetWriteSupport.write(ParquetWriteSupport.scala:113)
        at org.apache.spark.sql.execution.datasources.parquet.ParquetWriteSupport.write(ParquetWriteSupport.scala:50)
        at org.apache.parquet.hadoop.InternalParquetRecordWriter.write(InternalParquetRecordWriter.java:128)
        at org.apache.parquet.hadoop.ParquetRecordWriter.write(ParquetRecordWriter.java:182)
        at org.apache.parquet.hadoop.ParquetRecordWriter.write(ParquetRecordWriter.java:44)
        at org.apache.spark.sql.execution.datasources.parquet.ParquetOutputWriter.write(ParquetOutputWriter.scala:40)
        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:1394)
        at org.apache.spark.sql.execution.datasources.FileFormatWriter$.org$apache$spark$sql$execution$datasources$FileFormatWriter$$executeTask(FileFormatWriter.scala:248)
        ... 10 more
```

Can anybody give me some pointers on how to tune Spark to avoid this? I am using giant machines (r5d.12xlarge) with 384GB of memory. My executors have about 350GB of memory (-Xmx350000m). Could it be that my heap is too large?

Another issue I found was https://issues.apache.org/jira/browse/PARQUET-222, which seems to suggest that too many columns could be a problem. I don't want to throw any columns though.

One more question, why does saving as Parquet create 4 different stages in Spark? You can see in the picture that there are 4 different stages, all at "save at LoglineParquetGenerator.java:241". I am not sure how to interpret these stages:


Thanks,

Arwin


--
Chris