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Upserts, Deletes And Incremental Processing on Big Data.
https://hudi.apache.org/
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[SUPPORT] Async cleaner OOM when serializing cleaner plan #11248

Open noahtaite opened 4 months ago

noahtaite commented 4 months ago

Describe the problem you faced

We've had a Hudi pipeline running for about a year without cleaner enabled for ~150 tables. After enabling cleaning, all but one of my tables ran the cleaning operation successfully, but this table fails consistently with an OutOfMemory error when serializing the cleaning plan.

Table dimensions in storage:

Async cleaner job:

spark-submit --master yarn --deploy-mode cluster --class org.apache.hudi.utilities.HoodieCleaner --jars /usr/lib/hudi/hudi-utilities-bundle.jar,/usr/lib/hudi/hudi-spark-bundle.jar /usr/lib/hudi/hudi-utilities-bundle.jar --target-base-path s3://bucket/table.all_hudi/ --hoodie-conf hoodie.cleaner.policy=KEEP_LATEST_COMMITS --hoodie-conf hoodie.cleaner.commits.retained=30 --hoodie-conf hoodie.cleaner.parallelism=640 --hoodie-conf hoodie.keep.min.commits=40 --hoodie-conf hoodie.keep.max.commits=50 --spark-master yarn

Cluster configs:

spark.driver.memory 219695M
spark.executor.cores    32
spark.executor.memory   218880M
spark.executor.memoryOverheadFactor 0.1
spark.executor.instances    10

Spark History Server:

image

After this completes, the job almost immediately fails, with the stacktrace below being logged to the driver.

Ganglia shows my nodes being under-utilized, with memory maxing out around 1/4 of the total allocated memory: image

To Reproduce

Steps to reproduce the behavior:

  1. Generate similar dimensioned table with many updates, causing a large cleaner plan.
  2. Run cleaner async
  3. OOM after trying to serialize cleaner plan.

Expected behavior

Clean, or at least use all the driver memory before OOMing

Environment Description

Additional context

Larger tables with more partitions were able to generate the cleaning plan fine, which we thought was strange.

We also tried reducing the size of the plan by retaining more commits (60 retained) but still received the same error.

Note that I also tried running cleaner synchronously with my ingestion job but also received driver OOM errors.

Stacktrace

24/05/15 19:01:31 ERROR HoodieCleaner: Fail to run cleaning for s3://bucket/table.all_hudi/
java.lang.OutOfMemoryError: null
    at java.io.ByteArrayOutputStream.hugeCapacity(ByteArrayOutputStream.java:123) ~[?:1.8.0_412]
    at java.io.ByteArrayOutputStream.grow(ByteArrayOutputStream.java:117) ~[?:1.8.0_412]
    at java.io.ByteArrayOutputStream.ensureCapacity(ByteArrayOutputStream.java:93) ~[?:1.8.0_412]
    at java.io.ByteArrayOutputStream.write(ByteArrayOutputStream.java:153) ~[?:1.8.0_412]
    at org.apache.avro.io.DirectBinaryEncoder.writeFixed(DirectBinaryEncoder.java:124) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.io.BinaryEncoder.writeString(BinaryEncoder.java:57) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.io.Encoder.writeString(Encoder.java:130) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.writeString(GenericDatumWriter.java:392) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.specific.SpecificDatumWriter.writeString(SpecificDatumWriter.java:76) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.writeWithoutConversion(GenericDatumWriter.java:165) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:95) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.writeWithoutConversion(GenericDatumWriter.java:159) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.specific.SpecificDatumWriter.writeField(SpecificDatumWriter.java:108) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.writeRecord(GenericDatumWriter.java:234) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.specific.SpecificDatumWriter.writeRecord(SpecificDatumWriter.java:92) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.writeWithoutConversion(GenericDatumWriter.java:145) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:95) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.writeArray(GenericDatumWriter.java:288) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.writeWithoutConversion(GenericDatumWriter.java:151) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:95) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.writeMap(GenericDatumWriter.java:347) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.writeWithoutConversion(GenericDatumWriter.java:154) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:95) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.writeWithoutConversion(GenericDatumWriter.java:159) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.specific.SpecificDatumWriter.writeField(SpecificDatumWriter.java:108) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.writeRecord(GenericDatumWriter.java:234) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.specific.SpecificDatumWriter.writeRecord(SpecificDatumWriter.java:92) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.writeWithoutConversion(GenericDatumWriter.java:145) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:95) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.generic.GenericDatumWriter.write(GenericDatumWriter.java:82) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.avro.file.DataFileWriter.append(DataFileWriter.java:314) ~[avro-1.11.1.jar:1.11.1]
    at org.apache.hudi.common.table.timeline.TimelineMetadataUtils.serializeAvroMetadata(TimelineMetadataUtils.java:159) ~[__app__.jar:0.13.1-amzn-0]
    at org.apache.hudi.common.table.timeline.TimelineMetadataUtils.serializeCleanerPlan(TimelineMetadataUtils.java:114) ~[__app__.jar:0.13.1-amzn-0]
    at org.apache.hudi.table.action.clean.CleanPlanActionExecutor.requestClean(CleanPlanActionExecutor.java:158) ~[__app__.jar:0.13.1-amzn-0]
    at org.apache.hudi.table.action.clean.CleanPlanActionExecutor.execute(CleanPlanActionExecutor.java:176) ~[__app__.jar:0.13.1-amzn-0]
    at org.apache.hudi.table.HoodieSparkCopyOnWriteTable.scheduleCleaning(HoodieSparkCopyOnWriteTable.java:198) ~[__app__.jar:0.13.1-amzn-0]
    at org.apache.hudi.client.BaseHoodieTableServiceClient.scheduleTableServiceInternal(BaseHoodieTableServiceClient.java:433) ~[__app__.jar:0.13.1-amzn-0]
    at org.apache.hudi.client.BaseHoodieTableServiceClient.clean(BaseHoodieTableServiceClient.java:546) ~[__app__.jar:0.13.1-amzn-0]
    at org.apache.hudi.client.BaseHoodieWriteClient.clean(BaseHoodieWriteClient.java:766) ~[__app__.jar:0.13.1-amzn-0]
    at org.apache.hudi.client.BaseHoodieWriteClient.clean(BaseHoodieWriteClient.java:738) ~[__app__.jar:0.13.1-amzn-0]
    at org.apache.hudi.client.BaseHoodieWriteClient.clean(BaseHoodieWriteClient.java:770) ~[__app__.jar:0.13.1-amzn-0]
    at org.apache.hudi.utilities.HoodieCleaner.run(HoodieCleaner.java:69) ~[__app__.jar:0.13.1-amzn-0]
    at org.apache.hudi.utilities.HoodieCleaner.main(HoodieCleaner.java:111) ~[__app__.jar:0.13.1-amzn-0]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_412]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:1.8.0_412]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_412]
    at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_412]
    at org.apache.spark.deploy.yarn.ApplicationMaster$$anon$2.run(ApplicationMaster.scala:760) ~[spark-yarn_2.12-3.4.0-amzn-0.jar:3.4.0-amzn-0]

Seems the error is happening at org.apache.hudi.common.table.timeline.TimelineMetadataUtils.serializeCleanerPlan(TimelineMetadataUtils.java:114) ~[app.jar:0.13.1-amzn-0]

Looking for assistance in properly configuring the memory settings for this. Thanks so much!

xushiyan commented 4 months ago

briefly chatted in office hour: this is likely caused by clean planning loading archived commits which is about 500 mb each on storage, since the clean never run before. the active timeline only has about 70-80 commits.

noahtaite commented 4 months ago

Is this related? https://stackoverflow.com/questions/53462161/java-lang-outofmemoryerror-when-plenty-of-memory-left-94gb-200gb-xmx

I've tried changing my offHeap memory, memory overhead, and instance size but the job driver to OOM at 12GB of memory usage.

nsivabalan commented 2 weeks ago

can we try settting hoodie.cleaner.commits.retained to say 1000. and then get few data cleaned up. and then try 500. and after few runs, 300. and after few runs, 100.

essentially reducing the amount of data to clean on every batch. looks like we are trying to clean pretty much most of past history in 1 shot.