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Posted to issues@drill.apache.org by "Paul Rogers (JIRA)" <ji...@apache.org> on 2017/05/07 07:00:10 UTC
[jira] [Comment Edited] (DRILL-5470) CSV reader data corruption on
truncated lines
[ https://issues.apache.org/jira/browse/DRILL-5470?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15999712#comment-15999712 ]
Paul Rogers edited comment on DRILL-5470 at 5/7/17 6:59 AM:
------------------------------------------------------------
To illustrate the CSV data corruption, I created a CSV file, test4.csv, of the following form:
{code}
h,u
abc,def
ghi
{code}
Then, I created a simple test using the "cluster fixture" framework:
{code}
@Test
public void readerTest() throws Exception {
FixtureBuilder builder = ClusterFixture.builder()
.maxParallelization(1);
try (ClusterFixture cluster = builder.build();
ClientFixture client = cluster.clientFixture()) {
TextFormatConfig csvFormat = new TextFormatConfig();
csvFormat.fieldDelimiter = ',';
csvFormat.skipFirstLine = false;
csvFormat.extractHeader = true;
cluster.defineWorkspace("dfs", "data", "/tmp/data", "csv", csvFormat);
String sql = "SELECT * FROM `dfs.data`.`csv/test4.csv` LIMIT 10";
client.queryBuilder().sql(sql).printCsv();
}
}
{code}
The results show we've got a problem:
{code}
Exception (no rows returned): org.apache.drill.common.exceptions.UserRemoteException: SYSTEM ERROR:
IllegalArgumentException: length: -3 (expected: >= 0)
{code}
If the last line were:
{code}
efg,
{code}
Then the offset vector should look like this:
{code}
[0, 3, 3]
{code}
Very likely we have an offset vector that looks like this instead:
{code}
[0, 3, 0]
{code}
When we compute the second column of the second row, we should compute:
{code}
length = offset[2] - offset[1] = 3 - 3 = 0
{code}
Instead we get:
{code}
length = offset[2] - offset[1] = 0 - 3 = -3
{code}
Somehow, in the user's scenario, the number are far larger and the value has wrapped around to the bogus length shown.
The summary is that a premature EOF appears to cause the "missing" columns to be skipped; they are not filled with a blank value to "bump" the offset vectors to fill in the last row. Instead, they are left at 0, causing havoc downstream in the query.
was (Author: paul-rogers):
To illustrate the CSV data corruption, I created a CSV file, test4.csv, of the following form:
{code}
h,u
abc,def
ghi
{code}
Then, I created a simple test using the "cluster fixture" framework:
{code}
@Test
public void readerTest() throws Exception {
FixtureBuilder builder = ClusterFixture.builder()
.maxParallelization(1);
try (ClusterFixture cluster = builder.build();
ClientFixture client = cluster.clientFixture()) {
TextFormatConfig csvFormat = new TextFormatConfig();
csvFormat.fieldDelimiter = ',';
csvFormat.skipFirstLine = false;
csvFormat.extractHeader = true;
cluster.defineWorkspace("dfs", "data", "/tmp/data", "csv", csvFormat);
String sql = "SELECT * FROM `dfs.data`.`csv/test4.csv` LIMIT 10";
client.queryBuilder().sql(sql).printCsv();
}
}
{code}
The results show we've got a problem:
{code}
Exception (no rows returned): org.apache.drill.common.exceptions.UserRemoteException: SYSTEM ERROR:
IllegalArgumentException: length: -3 (expected: >= 0)
{code}
If the last line were:
{code}
efg,
{code}
Then the offset vector should look like this:
{code}
\[0, 3, 3]
{code}
Very likely we have an offset vector that looks like this instead:
{code}
\[0, 3, 0]
{code}
When we compute the second column of the second row, we should compute:
{code}
length = offset\[2] - offset\[1] = 3 - 3 = 0
{code}
Instead we get:
{code}
length = offset\[2] - offset\[1] = 0 - 3 = -3
{code}
Somehow, in the user's scenario, the number are far larger and the value has wrapped around to the bogus length shown.
The summary is that a premature EOF appears to cause the "missing" columns to be skipped; they are not filled with a blank value to "bump" the offset vectors to fill in the last row. Instead, they are left at 0, causing havoc downstream in the query.
> CSV reader data corruption on truncated lines
> ---------------------------------------------
>
> Key: DRILL-5470
> URL: https://issues.apache.org/jira/browse/DRILL-5470
> Project: Apache Drill
> Issue Type: Bug
> Components: Server
> Affects Versions: 1.10.0
> Environment: - ubuntu 14.04
> - r3.8xl (32 CPU/240GB Mem)
> - openjdk version "1.8.0_111"
> - drill 1.10.0 with 8656c83b00f8ab09fb6817e4e9943b2211772541 cherry-picked
> Reporter: Nathan Butler
> Assignee: Paul Rogers
>
> 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:
> bq. 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:
> bq. 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:
> {quote}
> 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
> {quote}
> I'm in communication with Paul and will send him the full log file.
> Thanks,
> Nathan
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