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From "Hadoop QA (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (HBASE-16754) Regions failing compaction due to referencing non-existent store file
Date Sat, 15 Oct 2016 03:20:20 GMT

    [ https://issues.apache.org/jira/browse/HBASE-16754?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15577247#comment-15577247
] 

Hadoop QA commented on HBASE-16754:
-----------------------------------

| (x) *{color:red}-1 overall{color}* |
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|| Vote || Subsystem || Runtime || Comment ||
| {color:blue}0{color} | {color:blue} reexec {color} | {color:blue} 2m 14s {color} | {color:blue}
Docker mode activated. {color} |
| {color:green}+1{color} | {color:green} @author {color} | {color:green} 0m 0s {color} | {color:green}
The patch does not contain any @author tags. {color} |
| {color:green}+1{color} | {color:green} test4tests {color} | {color:green} 0m 0s {color}
| {color:green} The patch appears to include 1 new or modified test files. {color} |
| {color:green}+1{color} | {color:green} mvninstall {color} | {color:green} 4m 47s {color}
| {color:green} master passed {color} |
| {color:green}+1{color} | {color:green} compile {color} | {color:green} 0m 44s {color} |
{color:green} master passed {color} |
| {color:green}+1{color} | {color:green} checkstyle {color} | {color:green} 0m 54s {color}
| {color:green} master passed {color} |
| {color:green}+1{color} | {color:green} mvneclipse {color} | {color:green} 0m 17s {color}
| {color:green} master passed {color} |
| {color:green}+1{color} | {color:green} findbugs {color} | {color:green} 2m 8s {color} |
{color:green} master passed {color} |
| {color:green}+1{color} | {color:green} javadoc {color} | {color:green} 0m 34s {color} |
{color:green} master passed {color} |
| {color:green}+1{color} | {color:green} mvninstall {color} | {color:green} 0m 56s {color}
| {color:green} the patch passed {color} |
| {color:green}+1{color} | {color:green} compile {color} | {color:green} 0m 49s {color} |
{color:green} the patch passed {color} |
| {color:green}+1{color} | {color:green} javac {color} | {color:green} 0m 49s {color} | {color:green}
the patch passed {color} |
| {color:green}+1{color} | {color:green} checkstyle {color} | {color:green} 0m 50s {color}
| {color:green} the patch passed {color} |
| {color:green}+1{color} | {color:green} mvneclipse {color} | {color:green} 0m 19s {color}
| {color:green} the patch passed {color} |
| {color:green}+1{color} | {color:green} whitespace {color} | {color:green} 0m 0s {color}
| {color:green} The patch has no whitespace issues. {color} |
| {color:green}+1{color} | {color:green} hadoopcheck {color} | {color:green} 34m 15s {color}
| {color:green} Patch does not cause any errors with Hadoop 2.4.0 2.4.1 2.5.0 2.5.1 2.5.2
2.6.1 2.6.2 2.6.3 2.7.1. {color} |
| {color:green}+1{color} | {color:green} hbaseprotoc {color} | {color:green} 0m 14s {color}
| {color:green} the patch passed {color} |
| {color:green}+1{color} | {color:green} findbugs {color} | {color:green} 2m 32s {color} |
{color:green} the patch passed {color} |
| {color:green}+1{color} | {color:green} javadoc {color} | {color:green} 0m 33s {color} |
{color:green} the patch passed {color} |
| {color:red}-1{color} | {color:red} unit {color} | {color:red} 123m 20s {color} | {color:red}
hbase-server in the patch failed. {color} |
| {color:green}+1{color} | {color:green} asflicense {color} | {color:green} 0m 20s {color}
| {color:green} The patch does not generate ASF License warnings. {color} |
| {color:black}{color} | {color:black} {color} | {color:black} 176m 30s {color} | {color:black}
{color} |
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|| Reason || Tests ||
| Timed out junit tests | org.apache.hadoop.hbase.snapshot.TestSnapshotClientRetries |
|   | org.apache.hadoop.hbase.snapshot.TestRestoreFlushSnapshotFromClient |
|   | org.apache.hadoop.hbase.client.TestHCM |
|   | org.apache.hadoop.hbase.snapshot.TestMobFlushSnapshotFromClient |
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|| Subsystem || Report/Notes ||
| Docker | Client=1.11.2 Server=1.11.2 Image:yetus/hbase:7bda515 |
| JIRA Patch URL | https://issues.apache.org/jira/secure/attachment/12833476/HBASE-16754.001.patch
|
| JIRA Issue | HBASE-16754 |
| Optional Tests |  asflicense  javac  javadoc  unit  findbugs  hadoopcheck  hbaseanti  checkstyle
 compile  |
| uname | Linux 5c55ca34ce37 3.13.0-92-generic #139-Ubuntu SMP Tue Jun 28 20:42:26 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux |
| Build tool | maven |
| Personality | /home/jenkins/jenkins-slave/workspace/PreCommit-HBASE-Build/component/dev-support/hbase-personality.sh
|
| git revision | master / b972839 |
| Default Java | 1.8.0_101 |
| findbugs | v3.0.0 |
| unit | https://builds.apache.org/job/PreCommit-HBASE-Build/4031/artifact/patchprocess/patch-unit-hbase-server.txt
|
| unit test logs |  https://builds.apache.org/job/PreCommit-HBASE-Build/4031/artifact/patchprocess/patch-unit-hbase-server.txt
|
|  Test Results | https://builds.apache.org/job/PreCommit-HBASE-Build/4031/testReport/ |
| modules | C: hbase-server U: hbase-server |
| Console output | https://builds.apache.org/job/PreCommit-HBASE-Build/4031/console |
| Powered by | Apache Yetus 0.3.0   http://yetus.apache.org |


This message was automatically generated.



> Regions failing compaction due to referencing non-existent store file
> ---------------------------------------------------------------------
>
>                 Key: HBASE-16754
>                 URL: https://issues.apache.org/jira/browse/HBASE-16754
>             Project: HBase
>          Issue Type: Bug
>    Affects Versions: 1.2.3
>            Reporter: Gary Helmling
>            Assignee: Gary Helmling
>            Priority: Blocker
>             Fix For: 1.3.0
>
>         Attachments: HBASE-16754.001.patch
>
>
> Running a mixed read write workload on a recent build off branch-1.3, we are seeing compactions
occasionally fail with errors like the following (actual filenames replaced with placeholders):
> {noformat}
> 16/09/27 16:57:28 ERROR regionserver.CompactSplitThread: Compaction selection failed
Store = XXX, pri = 116
> java.io.FileNotFoundException: File does not exist: hdfs://.../hbase/data/ns/table/region/cf/XXfilenameXX
>         at org.apache.hadoop.hdfs.DistributedFileSystem$22.doCall(DistributedFileSystem.java:1309)
>         at org.apache.hadoop.hdfs.DistributedFileSystem$22.doCall(DistributedFileSystem.java:1301)
>         at org.apache.hadoop.fs.FileSystemLinkResolver.resolve(FileSystemLinkResolver.java:81)
>         at org.apache.hadoop.hdfs.DistributedFileSystem.getFileStatus(DistributedFileSystem.java:1317)
>         at org.apache.hadoop.fs.FilterFileSystem.getFileStatus(FilterFileSystem.java:421)
 
>         at org.apache.hadoop.hbase.regionserver.StoreFileInfo.getReferencedFileStatus(StoreFileInfo.java:342)
>         at org.apache.hadoop.hbase.regionserver.StoreFileInfo.getFileStatus(StoreFileInfo.java:355)
 
>         at org.apache.hadoop.hbase.regionserver.StoreFileInfo.getModificationTime(StoreFileInfo.java:360)
>         at org.apache.hadoop.hbase.regionserver.StoreFile.getModificationTimeStamp(StoreFile.java:321)
 
>         at org.apache.hadoop.hbase.regionserver.StoreUtils.getLowestTimestamp(StoreUtils.java:63)
>         at org.apache.hadoop.hbase.regionserver.compactions.RatioBasedCompactionPolicy.shouldPerformMajorCompaction(RatioBasedCompactionPolicy.java:63)
>         at org.apache.hadoop.hbase.regionserver.compactions.SortedCompactionPolicy.selectCompaction(SortedCompactionPolicy.java:82)
 
>         at org.apache.hadoop.hbase.regionserver.DefaultStoreEngine$DefaultCompactionContext.select(DefaultStoreEngine.java:107)
 
>         at org.apache.hadoop.hbase.regionserver.HStore.requestCompaction(HStore.java:1644)
>         at org.apache.hadoop.hbase.regionserver.CompactSplitThread.selectCompaction(CompactSplitThread.java:373)
>         at org.apache.hadoop.hbase.regionserver.CompactSplitThread.access$100(CompactSplitThread.java:59)
>         at org.apache.hadoop.hbase.regionserver.CompactSplitThread$CompactionRunner.doCompaction(CompactSplitThread.java:498)
>         at org.apache.hadoop.hbase.regionserver.CompactSplitThread$CompactionRunner.run(CompactSplitThread.java:568)
>         at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>         at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>         at java.lang.Thread.run(Thread.java:745)
> 16/09/27 17:01:31 ERROR regionserver.CompactSplitThread: Compaction selection failed
Store = XXX, pri = 115
> java.io.FileNotFoundException: File does not exist: hdfs://.../hbase/data/ns/table/region/cf/XXfilenameXX
>         at org.apache.hadoop.hdfs.DistributedFileSystem$22.doCall(DistributedFileSystem.java:1309)
>         at org.apache.hadoop.hdfs.DistributedFileSystem$22.doCall(DistributedFileSystem.java:1301)
>         at org.apache.hadoop.fs.FileSystemLinkResolver.resolve(FileSystemLinkResolver.java:81)
>         at org.apache.hadoop.hdfs.DistributedFileSystem.getFileStatus(DistributedFileSystem.java:1317)
>         at org.apache.hadoop.fs.FilterFileSystem.getFileStatus(FilterFileSystem.java:421)
 
>         at org.apache.hadoop.hbase.regionserver.StoreFileInfo.getReferencedFileStatus(StoreFileInfo.java:342)
>         at org.apache.hadoop.hbase.regionserver.StoreFileInfo.getFileStatus(StoreFileInfo.java:355)
 
>         at org.apache.hadoop.hbase.regionserver.StoreFileInfo.getModificationTime(StoreFileInfo.java:360)
>         at org.apache.hadoop.hbase.regionserver.StoreFile.getModificationTimeStamp(StoreFile.java:321)
 
>         at org.apache.hadoop.hbase.regionserver.StoreUtils.getLowestTimestamp(StoreUtils.java:63)
>         at org.apache.hadoop.hbase.regionserver.compactions.RatioBasedCompactionPolicy.shouldPerformMajorCompaction(RatioBasedCompactionPolicy.java:63)
>         at org.apache.hadoop.hbase.regionserver.compactions.SortedCompactionPolicy.selectCompaction(SortedCompactionPolicy.java:82)
 
>         at org.apache.hadoop.hbase.regionserver.DefaultStoreEngine$DefaultCompactionContext.select(DefaultStoreEngine.java:107)
 
>         at org.apache.hadoop.hbase.regionserver.HStore.requestCompaction(HStore.java:1644)
>         at org.apache.hadoop.hbase.regionserver.CompactSplitThread.selectCompaction(CompactSplitThread.java:373)
>         at org.apache.hadoop.hbase.regionserver.CompactSplitThread.access$100(CompactSplitThread.java:59)
>         at org.apache.hadoop.hbase.regionserver.CompactSplitThread$CompactionRunner.doCompaction(CompactSplitThread.java:498)
>         at org.apache.hadoop.hbase.regionserver.CompactSplitThread$CompactionRunner.run(CompactSplitThread.java:568)
>         at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
>         at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
>         at java.lang.Thread.run(Thread.java:745)
> {noformat}
> It looks like we somehow deleted the underlying store file from HDFS (probably after
it was compacted away), after the path was loaded into the list of store files for the region.
> For two cases of this that I looked into, in both cases the region in question was previously
hosted by a regionserver that stalled, then aborted after its zk session expired.  In both
cases it looked like a compaction was also in progress.  So it's possible that the compacted
files are being deleted from HDFS by the stalled regionserver before it aborts, but after
the region has been opened by a new regionserver.  That's speculation though and needs to
be substantiated.



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