Might want to see if Nagles algorithm is cause. See the tcpNoDelay options
in hadoop RPC. I ran into a similar issue a while back

On Thu, May 14, 2009 at 5:44 PM, Jim Kellerman (JIRA) <[email protected]>wrote:

>
>    [
> https://issues.apache.org/jira/browse/HBASE-1177?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=12709648#action_12709648]
>
> Jim Kellerman commented on HBASE-1177:
> --------------------------------------
>
> When I did not deploy a region server on the same machine as the namenode
> and master, I got much better times:
>
> {code}
> When run on node hosting region that is not the same as namenode or master:
>
> Read 1 row with 7 columns 100 times in 113ms
> Read 1 row with 8 columns 100 times in 4057ms
> Read 1 row with 1000 columns 100 times in 10570ms
>
> When run on node not hosting region and is not namenode or master:
>
> Read 1 row with 7 columns 100 times in 109ms
> Read 1 row with 8 columns 100 times in 121ms
> Read 1 row with 1000 columns 100 times in 8838ms
> {code}
>
> So running an application on the same server as the namenode. master and
> region server definately slows things down.
>
> There is basically no difference in the test where we read 1 row with 7
> columns.
>
> Why the read 1 row with 8 columns or the read 1 row with 1000 columns is
> still slower if the application is run on a different machine than the one
> hosting the region, is still a mystery.
>
> Will continue investigation.......
>
> > Delay when client is located on the same node as the regionserver
> > -----------------------------------------------------------------
> >
> >                 Key: HBASE-1177
> >                 URL: https://issues.apache.org/jira/browse/HBASE-1177
> >             Project: Hadoop HBase
> >          Issue Type: Bug
> >    Affects Versions: 0.19.0
> >         Environment: Linux 2.6.25 x86_64
> >            Reporter: Jonathan Gray
> >            Assignee: Jim Kellerman
> >            Priority: Blocker
> >             Fix For: 0.20.0
> >
> >         Attachments: ReadDelayTest.java
> >
> >
> > During testing of HBASE-80, we uncovered a strange 40ms delay for random
> reads.  We ran a series of tests and found that it only happens when the
> client is on the same node as the RS and for a certain range of payloads
> (not specifically related to number of columns or size of them, only total
> payload).  It appears to be precisely 40ms every time.
> > Unsure if this is particular to our architecture, but it does happen on
> all nodes we've tried.  Issue completely goes away with very large payloads
> or moving the client.
> > Will post a test program tomorrow if anyone can test on a different
> architecture.
> > Making a blocker for 0.20.  Since this happens when you have an MR task
> running local to the RS, and this is what we try to do, might also consider
> making this a blocker for 0.19.1.
>
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