[DRILL-5470] Offset vector data corruption with CSV data

• Type: Bug
• Status: Closed
• Priority: Critical
• Resolution: Fixed
• Affects Version/s: 1.10.0
• Component/s: Server

Environment

• ubuntu 14.04
• r3.8xl (32 CPU/240GB Mem)
• openjdk version "1.8.0_111"
• drill 1.10.0 with 8656c83b00f8ab09fb6817e4e9943b2211772541 cherry-picked

• Assignee: Paul Rogers
• Reporter: Nathan Butler
• Reviewer: Rahul Kumar Challapalli
• Created: 03/May/17 18:18
• Updated: 11/Oct/19 11:26
• Resolved: 11/Oct/19 11:26

Description

Per the mailing list discussion and Rahul's and Paul's suggestion I'm filing this Jira issue. Drill seems to be running out of memory when doing an External Sort. Per Zelaine's suggestion I enabled sort.external.disable_managed in drill-override.conf and in the sqlline session. This caused the query to run for longer but it still would fail with the same message.

Per Paul's suggestion, I enabled debug logging for the org.apache.drill.exec.physical.impl.xsort.managed package and re-ran the query.

Here's the initial DEBUG line for ExternalSortBatch for our query:

2017-05-03 12:02:56,095 [26f600f1-17b3-d649-51be-2ca0c9bf7606:frag:2:15] DEBUG o.a.d.e.p.i.x.m.ExternalSortBatch - Config: memory limit = 10737418240, spill file size = 268435456, spill batch size = 8388608, merge limit = 2147483647, merge batch size = 16777216

And here's the last DEBUG line before the stack trace:

2017-05-03 12:37:44,249 [26f600f1-17b3-d649-51be-2ca0c9bf7606:frag:2:4] DEBUG o.a.d.e.p.i.x.m.ExternalSortBatch - Available memory: 10737418240, buffer memory = 10719535268, merge memory = 10707140978

And the stacktrace:

2017-05-03 12:38:02,927 [26f600f1-17b3-d649-51be-2ca0c9bf7606:frag:2:6] INFO o.a.d.e.p.i.x.m.ExternalSortBatch - User Error Occurred: External Sort encountered an error while spilling to disk (Un
able to allocate buffer of size 268435456 due to memory limit. Current allocation: 10579849472)
org.apache.drill.common.exceptions.UserException: RESOURCE ERROR: External Sort encountered an error while spilling to disk

[Error Id: 5d53c677-0cd9-4c01-a664-c02089670a1c ]
at org.apache.drill.common.exceptions.UserException$Builder.build(UserException.java:544) ~[drill-common-1.10.0.jar:1.10.0]
at org.apache.drill.exec.physical.impl.xsort.managed.ExternalSortBatch.doMergeAndSpill(ExternalSortBatch.java:1447) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.physical.impl.xsort.managed.ExternalSortBatch.mergeAndSpill(ExternalSortBatch.java:1376) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.physical.impl.xsort.managed.ExternalSortBatch.spillFromMemory(ExternalSortBatch.java:1339) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.physical.impl.xsort.managed.ExternalSortBatch.processBatch(ExternalSortBatch.java:831) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.physical.impl.xsort.managed.ExternalSortBatch.loadBatch(ExternalSortBatch.java:618) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.physical.impl.xsort.managed.ExternalSortBatch.load(ExternalSortBatch.java:660) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.physical.impl.xsort.managed.ExternalSortBatch.innerNext(ExternalSortBatch.java:559) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.record.AbstractRecordBatch.next(AbstractRecordBatch.java:162) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.record.AbstractRecordBatch.next(AbstractRecordBatch.java:119) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.record.AbstractRecordBatch.next(AbstractRecordBatch.java:109) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.physical.impl.aggregate.StreamingAggBatch.innerNext(StreamingAggBatch.java:137) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.record.AbstractRecordBatch.next(AbstractRecordBatch.java:162) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.physical.impl.BaseRootExec.next(BaseRootExec.java:104) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.physical.impl.partitionsender.PartitionSenderRootExec.innerNext(PartitionSenderRootExec.java:144) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.physical.impl.BaseRootExec.next(BaseRootExec.java:94) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.work.fragment.FragmentExecutor$1.run(FragmentExecutor.java:232) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.work.fragment.FragmentExecutor$1.run(FragmentExecutor.java:226) [drill-java-exec-1.10.0.jar:1.10.0]
at java.security.AccessController.doPrivileged(Native Method) [na:1.8.0_111]
at javax.security.auth.Subject.doAs(Subject.java:422) [na:1.8.0_111]
at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1657) [hadoop-common-2.7.1.jar:na]
at org.apache.drill.exec.work.fragment.FragmentExecutor.run(FragmentExecutor.java:226) [drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.common.SelfCleaningRunnable.run(SelfCleaningRunnable.java:38) [drill-common-1.10.0.jar:1.10.0]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_111]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_111]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_111]
Caused by: org.apache.drill.exec.exception.OutOfMemoryException: Unable to allocate buffer of size 268435456 due to memory limit. Current allocation: 10579849472
at org.apache.drill.exec.memory.BaseAllocator.buffer(BaseAllocator.java:220) ~[drill-memory-base-1.10.0.jar:1.10.0]
at org.apache.drill.exec.memory.BaseAllocator.buffer(BaseAllocator.java:195) ~[drill-memory-base-1.10.0.jar:1.10.0]
at org.apache.drill.exec.vector.VarCharVector.reAlloc(VarCharVector.java:425) ~[vector-1.10.0.jar:1.10.0]
at org.apache.drill.exec.vector.VarCharVector.copyFromSafe(VarCharVector.java:278) ~[vector-1.10.0.jar:1.10.0]
at org.apache.drill.exec.vector.NullableVarCharVector.copyFromSafe(NullableVarCharVector.java:379) ~[vector-1.10.0.jar:1.10.0]
at org.apache.drill.exec.test.generated.PriorityQueueCopierGen140.doCopy(PriorityQueueCopierTemplate.java:22) ~[na:na]
at org.apache.drill.exec.test.generated.PriorityQueueCopierGen140.next(PriorityQueueCopierTemplate.java:76) ~[na:na]
at org.apache.drill.exec.physical.impl.xsort.managed.CopierHolder$BatchMerger.next(CopierHolder.java:234) ~[drill-java-exec-1.10.0.jar:1.10.0]
at org.apache.drill.exec.physical.impl.xsort.managed.ExternalSortBatch.doMergeAndSpill(ExternalSortBatch.java:1408) [drill-java-exec-1.10.0.jar:1.10.0]
... 24 common frames omitted

I'm in communication with Paul and will send him the full log file.

Thanks,
Nathan

Issue Links

• is related to: DRILL-5451 Query on csv file w/ header fails with an exception when non existing column is requested if file is over 4096 lines long
• is related to: DRILL-5590 Drill return IndexOutOfBoundsException when a (Text) file > 4096 rows
• relates to: DRILL-5590 Drill return IndexOutOfBoundsException when a (Text) file > 4096 rows