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HBase, mail # user - Region Servers crashing following: "File does not exist", "Too many open files" exceptions

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Region Servers crashing following: "File does not exist", "Too many open files" exceptions
David Koch 2013-02-10, 01:07

As of lately, we have been having issues with Region Servers crashing in
our cluster. This happens while running Map/Reduce jobs over HBase tables
in particular but also spontaneously when the cluster is seemingly idle.

Restarting the Region Servers or even HBase entirely as well as HDFS and
Map/Reduce services does not fix the problem and jobs will fail during the
next attempt citing "Region not served" exceptions. It is not always the
same nodes that crash.

The log data during the minutes leading up to the crash contain many "File
does not exist /hbase/<table_name>/..." error messages which change to "Too
many open files" messages, finally, there are a few "Failed to renew lease
for DFSClient" messages followed by several "FATAL" messages about HLog not
being able to synch and immediately afterwards a terminal "ABORTING region

You can find an extract of a Region Server log here:

Running "hbase hbck" reveals inconsistencies in some tables, but attempting
a repair with "hbase hbck -repair" stalls due to some regions being in
transition, see here: http://pastebin.com/JAbcQ4cc.

The setup contains 30 machines, 26GB RAM each, the services are managed
using CDH4, so HBase version is 0.92.x. We did not tweak any of the default
configuration settings, however table scans are done with sensible
scan/batch/filter settings.

Data intake is about 100GB/day which are added at a time when no Map/Reduce
jobs are running. Tables have between 100 * 10^6 and 2 * 10^9 rows, with an
average of 10 KVs, about 1kb each. Very few rows exceed 10^6 KV.

What can we do to fix these issues? Are they symptomic of a mal-configured
setup or some critical threshold level being reached? The cluster used to
be stable.

Thank you,