Very high CPU usage on data nodes because of FSDataset.checkDataDir() on every 
connect
--------------------------------------------------------------------------------------

                 Key: HADOOP-1170
                 URL: https://issues.apache.org/jira/browse/HADOOP-1170
             Project: Hadoop
          Issue Type: Bug
          Components: dfs
    Affects Versions: 0.11.2
            Reporter: Igor Bolotin


While investigating performance issues in our Hadoop DFS/MapReduce cluster I 
saw very high CPU usage by DataNode processes.

Stack trace showed following on most of the data nodes:
"[EMAIL PROTECTED]" daemon prio=1 tid=0x00002aaacb5b7bd0 nid=0x5940 runnable 
[0x000000004166a000..0x000000004166ac00]
        at java.io.UnixFileSystem.checkAccess(Native Method)
        at java.io.File.canRead(File.java:660)
        at org.apache.hadoop.util.DiskChecker.checkDir(DiskChecker.java:34)
        at 
org.apache.hadoop.dfs.FSDataset$FSDir.checkDirTree(FSDataset.java:164)
        at 
org.apache.hadoop.dfs.FSDataset$FSDir.checkDirTree(FSDataset.java:168)
        at 
org.apache.hadoop.dfs.FSDataset$FSDir.checkDirTree(FSDataset.java:168)
        at 
org.apache.hadoop.dfs.FSDataset$FSDir.checkDirTree(FSDataset.java:168)
        at 
org.apache.hadoop.dfs.FSDataset$FSDir.checkDirTree(FSDataset.java:168)
        at 
org.apache.hadoop.dfs.FSDataset$FSDir.checkDirTree(FSDataset.java:168)
        at 
org.apache.hadoop.dfs.FSDataset$FSDir.checkDirTree(FSDataset.java:168)
        at 
org.apache.hadoop.dfs.FSDataset$FSDir.checkDirTree(FSDataset.java:168)
        at 
org.apache.hadoop.dfs.FSDataset$FSDir.checkDirTree(FSDataset.java:168)
        at 
org.apache.hadoop.dfs.FSDataset$FSDir.checkDirTree(FSDataset.java:168)
        at 
org.apache.hadoop.dfs.FSDataset$FSDir.checkDirTree(FSDataset.java:168)
        at 
org.apache.hadoop.dfs.FSDataset$FSDir.checkDirTree(FSDataset.java:168)
        at 
org.apache.hadoop.dfs.FSDataset$FSDir.checkDirTree(FSDataset.java:168)
        at 
org.apache.hadoop.dfs.FSDataset$FSDir.checkDirTree(FSDataset.java:168)
        at 
org.apache.hadoop.dfs.FSDataset$FSVolume.checkDirs(FSDataset.java:258)
        at 
org.apache.hadoop.dfs.FSDataset$FSVolumeSet.checkDirs(FSDataset.java:339)
        - locked <0x00002aaab6fb8960> (a 
org.apache.hadoop.dfs.FSDataset$FSVolumeSet)
        at org.apache.hadoop.dfs.FSDataset.checkDataDir(FSDataset.java:544)
        at 
org.apache.hadoop.dfs.DataNode$DataXceiveServer.run(DataNode.java:535)
        at java.lang.Thread.run(Thread.java:595)

I understand that it would take a while to check the entire data directory - as 
we have some 180,000 blocks/files in there. But what really bothers me that 
from the code I see that this check is executed for every client connection to 
the DataNode - which also means for every task executed in the cluster. Once I 
commented out the check and restarted datanodes - the performance went up and 
CPU usage went down to reasonable level.


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