Inconsistencies in Hbase table (hbase hbck)

[#1]

Hi guys,

I am using HDP cluster (HDP-2.5.0.0) with Hbase version 1.1.2 and Phoenix 4.7.0 and couple days ago we experienced major crash resulting in inconsistency in one of our tables (1.5TB) (+2 index tables as we are using phoenix). I have run hbase hbck and found following results (snippet bellow):

---- Table 'SR_ACTIVITIES': overlap groups
There are 0 overlap groups with 0 overlapping regions
ERROR: Found inconsistency in table SR_ACTIVITIES
---- Table 'hbase:meta': region split map
:	[ { meta => hbase:meta,,1.1588230740, hdfs => hdfs://pcluster/apps/hbase/data/data/hbase/meta/1588230740, deployed => hbase-hdp206.lan,16020,1512001442898;hbase:meta,,1.1588230740, replicaId => 0 }, ]
null:
---- Table 'hbase:meta': overlap groups
There are 0 overlap groups with 0 overlapping regions
2017-12-02 00:32:56,453 INFO  [main] util.HBaseFsck: Computing mapping of all store files
................................................................................................................................................................
2017-12-02 00:32:57,075 INFO  [main] util.HBaseFsck: Validating mapping using HDFS state
ERROR: Found lingering reference file hdfs://pcluster/apps/hbase/data/data/default/SR_ACTIVITIES/3bb33b5f4fba26a9f56dec1aedd402c9/0/e59e308a41194bb5b8299c84b0818dca.d143c81eb14ac29cd4e92681fde8cd7a
ERROR: Found lingering reference file hdfs://pcluster/apps/hbase/data/data/default/SR_ACTIVITIES_INDEX_1/436271a35b6a313ac5fa69db4795e73b/0/d39348bde5134b12b0c79b8382f79a78.18ff59ef5cd0d918247f1419625020ab
ERROR: Found lingering reference file hdfs://pcluster/apps/hbase/data/data/default/SR_ACTIVITIES_INDEX_1/e97a62ccee7217b9492de2efabfcfd3c/0/ad9129b0813a4f4892c51688140f4a03.2594d95578b8946187267112cc0d4098
ERROR: Found lingering reference file hdfs://pcluster/apps/hbase/data/data/default/SR_ACTIVITIES/3bb33b5f4fba26a9f56dec1aedd402c9/0/2705dd256c0e49a39152d7958c074e17.d143c81eb14ac29cd4e92681fde8cd7a
ERROR: Found lingering reference file hdfs://pcluster/apps/hbase/data/data/default/SR_ACTIVITIES_INDEX_1/0eceec2ec0e6e2d732f2b7a028fee2c7/0/6de9e548483e4550adee0c8ed51c7ddc.9695332dd4db41f2f4b98a5da0966eed
ERROR: Found lingering reference file hdfs://pcluster/apps/hbase/data/data/default/SR_ACTIVITIES/f5b32587753648b53b78261887361758/0/2826951b5325407e9027a1c005d5ee93.623d2dc65245bf6360c79a184e527705
ERROR: Found lingering reference file hdfs://pcluster/apps/hbase/data/data/default/SR_ACTIVITIES_INDEX_1/0eceec2ec0e6e2d732f2b7a028fee2c7/0/8f85f60216254247aa2c7c66e29b4d76.9695332dd4db41f2f4b98a5da0966eed
ERROR: Found lingering reference file hdfs://pcluster/apps/hbase/data/data/default/SR_ACTIVITIES_INDEX_1/b688d235f38a437c0454e1b20a9e9e5e/0/36bc175dd8914291a915ea54ab0170d0.394b35ad4f3db41e06aae8d768837098
ERROR: Found lingering reference file hdfs://pcluster/apps/hbase/data/data/default/SR_ACTIVITIES_INDEX_1/436271a35b6a313ac5fa69db4795e73b/0/d9a7948e713b4053b337b8002846a26d.18ff59ef5cd0d918247f1419625020ab
ERROR: Found lingering reference file hdfs://pcluster/apps/hbase/data/data/default/SR_ACTIVITIES_INDEX_1/436271a35b6a313ac5fa69db4795e73b/0/36cc3329b3f14b429d762c9d6b87dc5f.18ff59ef5cd0d918247f1419625020ab
ERROR: Found lingering reference file hdfs://pcluster/apps/hbase/data/data/default/SR_ACTIVITIES/f5b32587753648b53b78261887361758/0/fb8679074112418d9ca9db4b7e506e37.623d2dc65245bf6360c79a184e527705
2017-12-02 00:32:57,078 INFO  [main] zookeeper.RecoverableZooKeeper: Process identifier=hbase Fsck connecting to ZooKeeper ensemble=master-hdp202.lan:2181,master-hdp201.lan:2181,master-hdp203.lan:2181
2017-12-02 00:32:57,078 INFO  [main] zookeeper.ZooKeeper: Initiating client connection, connectString=master-hdp202.lan:2181,master-hdp201.lan:2181,master-hdp203.lan:2181 sessionTimeout=90000 watcher=org.apache.hadoop.hbase.zookeeper.PendingWatcher@1c12f3ee
2017-12-02 00:32:57,157 INFO  [main-SendThread(master-hdp202.lan:2181)] zookeeper.ClientCnxn: Opening socket connection to server master-hdp202.lan/10.14.0.102:2181. Will not attempt to authenticate using SASL (unknown error)
2017-12-02 00:32:57,158 INFO  [main-SendThread(master-hdp202.lan:2181)] zookeeper.ClientCnxn: Socket connection established to master-hdp202.lan/10.14.0.102:2181, initiating session
2017-12-02 00:32:57,159 INFO  [main-SendThread(master-hdp202.lan:2181)] zookeeper.ClientCnxn: Session establishment complete on server master-hdp202.lan/10.14.0.102:2181, sessionid = 0x25aae5ddf40428e, negotiated timeout = 90000
2017-12-02 00:32:57,190 INFO  [main] zookeeper.ZooKeeper: Session: 0x25aae5ddf40428e closed
2017-12-02 00:32:57,190 INFO  [main-EventThread] zookeeper.ClientCnxn: EventThread shut down
2017-12-02 00:32:57,190 INFO  [main] zookeeper.RecoverableZooKeeper: Process identifier=hbase Fsck connecting to ZooKeeper ensemble=master-hdp202.lan:2181,master-hdp201.lan:2181,master-hdp203.lan:2181
2017-12-02 00:32:57,190 INFO  [main] zookeeper.ZooKeeper: Initiating client connection, connectString=master-hdp202.lan:2181,master-hdp201.lan:2181,master-hdp203.lan:2181 sessionTimeout=90000 watcher=org.apache.hadoop.hbase.zookeeper.PendingWatcher@47c64cfe
2017-12-02 00:32:57,192 INFO  [main-SendThread(master-hdp203.lan:2181)] zookeeper.ClientCnxn: Opening socket connection to server master-hdp203.lan/10.14.0.103:2181. Will not attempt to authenticate using SASL (unknown error)
2017-12-02 00:32:57,193 INFO  [main-SendThread(master-hdp203.lan:2181)] zookeeper.ClientCnxn: Socket connection established to master-hdp203.lan/10.14.0.103:2181, initiating session
2017-12-02 00:32:57,196 INFO  [main-SendThread(master-hdp203.lan:2181)] zookeeper.ClientCnxn: Session establishment complete on server master-hdp203.lan/10.14.0.103:2181, sessionid = 0x35aae5dde234249, negotiated timeout = 90000
2017-12-02 00:32:57,206 INFO  [main] zookeeper.ZooKeeper: Session: 0x35aae5dde234249 closed
2017-12-02 00:32:57,206 INFO  [main-EventThread] zookeeper.ClientCnxn: EventThread shut down
2017-12-02 00:32:57,516 INFO  [main] util.HBaseFsck: Finishing hbck
Summary:
Table SR_ACTIVITIES is okay.
    Number of regions: 445
    Deployed on:  hbase-hdp201.lan,16020,1512001916143 hbase-hdp202.lan,16020,1512002519632 hbase-hdp203.lan,16020,1512001180484 hbase-hdp204.lan,16020,1512001283591 hbase-hdp205.lan,16020,1512001554528 hbase-hdp206.lan,16020,1512001442898
Table hbase:meta is okay.
    Number of regions: 1
    Deployed on:  hbase-hdp206.lan,16020,1512001442898
15 inconsistencies detected.
Status: INCONSISTENT
2017-12-02 00:32:57,516 INFO  [main] client.ConnectionManager$HConnectionImplementation: Closing master protocol: MasterService
2017-12-02 00:32:57,516 INFO  [main] client.ConnectionManager$HConnectionImplementation: Closing zookeeper sessionid=0x15ba5e122b09ebb
2017-12-02 00:32:57,517 INFO  [main] zookeeper.ZooKeeper: Session: 0x15ba5e122b09ebb closed
2017-12-02 00:32:57,517 INFO  [main-EventThread] zookeeper.ClientCnxn: EventThread shut down

I have snapshot from morning before crash, but when I was trying just to copy to another hfs, I am getting FileNotFoundException:

2017-11-30 13:19:54,438 INFO  [main] mapreduce.Job: Task Id : attempt_1493215799486_47105_m_000006_2, Status : FAILED
Error: java.io.FileNotFoundException: Unable to open link: org.apache.hadoop.hbase.io.HFileLink locations=[hdfs://pcluster/apps/hbase/data/data/default/SR_ACTIVITIES/623d2dc65245bf6360c79a184e527705/0/fb8679074112418d9ca9db4b7e506e37, hdfs://pcluster/apps/hbase/data/.tmp/data/default/SR_ACTIVITIES/623d2dc65245bf6360c79a184e527705/0/fb8679074112418d9ca9db4b7e506e37, hdfs://pcluster/apps/hbase/data/mobdir/data/default/SR_ACTIVITIES/623d2dc65245bf6360c79a184e527705/0/fb8679074112418d9ca9db4b7e506e37, hdfs://pcluster/apps/hbase/data/archive/data/default/SR_ACTIVITIES/623d2dc65245bf6360c79a184e527705/0/fb8679074112418d9ca9db4b7e506e37]
        at org.apache.hadoop.hbase.io.FileLink.getFileStatus(FileLink.java:390)
        at org.apache.hadoop.hbase.snapshot.ExportSnapshot$ExportMapper.getSourceFileStatus(ExportSnapshot.java:472)
        at org.apache.hadoop.hbase.snapshot.ExportSnapshot$ExportMapper.copyFile(ExportSnapshot.java:255)
        at org.apache.hadoop.hbase.snapshot.ExportSnapshot$ExportMapper.map(ExportSnapshot.java:197)
        at org.apache.hadoop.hbase.snapshot.ExportSnapshot$ExportMapper.map(ExportSnapshot.java:123)
        at org.apache.hadoop.mapreduce.Mapper.run(Mapper.java:146)
        at org.apache.hadoop.mapred.MapTask.runNewMapper(MapTask.java:787)
        at org.apache.hadoop.mapred.MapTask.run(MapTask.java:341)
        at org.apache.hadoop.mapred.YarnChild$2.run(YarnChild.java:168)
        at java.security.AccessController.doPrivileged(Native Method)
        at javax.security.auth.Subject.doAs(Subject.java:422)
        at org.apache.hadoop.security.UserGroupInformation.doAs(UserGroupInformation.java:1724)
        at org.apache.hadoop.mapred.YarnChild.main(YarnChild.java:162)

However, I am able to find that file but in another region:

[hdfs@hbase-hdp201 ~]$ hdfs dfs -find /apps/hbase -name fb8679074112418d9ca9db4b7e506e37 -print
/apps/hbase/data/data/default/SR_ACTIVITIES/f5b32587753648b53b78261887361758/0/fb8679074112418d9ca9db4b7e506e37
[hdfs@hbase-hdp201 ~]$

I believe this is somehow related to region splitting, and I believe that manually moving those file or using hbck can help, but can you help me to find right and secure direction ?

Thanks in advance!

Robert

[#2]

@Robert Jonczy To fix the issue, could you please try running hbck tool with -repair option