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Date: Wed, 1 May 2013 12:57:39 +0530
Message-ID: 
 <CAAT7MkpH6JM-781erP9s3_cyTwABBs3uDK=h8pdsXogMVU8gPQ@mail.gmail.com>
Subject: Re: Poor HBase map-reduce scan performance
From: ramkrishna vasudevan <ramkrishna.s.vasudevan@gmail.com>
To: user@hbase.apache.org
Cc: lars hofhansl <larsh@apache.org>
Content-Type: multipart/alternative; boundary=20cf3074b9d6888dee04dba30d5a

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Content-Type: text/plain; charset=ISO-8859-1

This happens when your java process is running in debug mode and
suspend='Y' option is selected.

Regards
Ram


On Wed, May 1, 2013 at 12:55 PM, Naidu MS
<sanyasinaidu.malla433@gmail.com>wrote:

> Hi i have two questions regarding hdfs and jps utility
>
> I am new to Hadoop and started leraning hadoop from the past week
>
> 1.when ever i start start-all.sh and jps in console it showing the
> processes started
>
> *naidu@naidu:~/work/hadoop-1.0.4/bin$ jps*
> *22283 NameNode*
> *23516 TaskTracker*
> *26711 Jps*
> *22541 DataNode*
> *23255 JobTracker*
> *22813 SecondaryNameNode*
> *Could not synchronize with target*
>
> But along with the list of process stared it always showing *" Could not
> synchronize with target" *in the jps output. What is meant by "Could not
> synchronize with target"?  Can some one explain why this is happening?
>
>
> 2.Is it possible to format namenode multiple  times? When i enter the
>  namenode -format command, it not formatting the name node and showing the
> following ouput.
>
> *naidu@naidu:~/work/hadoop-1.0.4/bin$ hadoop namenode -format*
> *Warning: $HADOOP_HOME is deprecated.*
> *
> *
> *13/05/01 12:08:04 INFO namenode.NameNode: STARTUP_MSG: *
> */*************************************************************
> *STARTUP_MSG: Starting NameNode*
> *STARTUP_MSG:   host = naidu/127.0.0.1*
> *STARTUP_MSG:   args = [-format]*
> *STARTUP_MSG:   version = 1.0.4*
> *STARTUP_MSG:   build =
> https://svn.apache.org/repos/asf/hadoop/common/branches/branch-1.0 -r
> 1393290; compiled by 'hortonfo' on Wed Oct  3 05:13:58 UTC 2012*
> *************************************************************/*
> *Re-format filesystem in /home/naidu/dfs/namenode ? (Y or N) y*
> *Format aborted in /home/naidu/dfs/namenode*
> *13/05/01 12:08:05 INFO namenode.NameNode: SHUTDOWN_MSG: *
> */*************************************************************
> *SHUTDOWN_MSG: Shutting down NameNode at naidu/127.0.0.1*
> *
> *
> *************************************************************/*
>
> Can someone help me in understanding this? Why is it not possible to format
> name node multiple times?
>
>
> On Wed, May 1, 2013 at 12:22 PM, Matt Corgan <mcorgan@hotpads.com> wrote:
>
> > Not that it's a long-term solution, but try major-compacting before
> running
> > the benchmark.  If the LSM tree is CPU bound in merging HFiles/KeyValues
> > through the PriorityQueue, then reducing to a single file per region
> should
> > help.  The merging of HFiles during a scan is not heavily optimized yet.
> >
> >
> > On Tue, Apr 30, 2013 at 11:21 PM, lars hofhansl <larsh@apache.org>
> wrote:
> >
> > > If you can, try 0.94.4+; it should significantly reduce the amount of
> > > bytes copied around in RAM during scanning, especially if you have wide
> > > rows and/or large key portions. That in turns makes scans scale better
> > > across cores, since RAM is shared resource between cores (much like
> > disk).
> > >
> > >
> > > It's not hard to build the latest HBase against Cloudera's version of
> > > Hadoop. I can send along a simple patch to pom.xml to do that.
> > >
> > > -- Lars
> > >
> > >
> > >
> > > ________________________________
> > >  From: Bryan Keller <bryanck@gmail.com>
> > > To: user@hbase.apache.org
> > > Sent: Tuesday, April 30, 2013 11:02 PM
> > > Subject: Re: Poor HBase map-reduce scan performance
> > >
> > >
> > > The table has hashed keys so rows are evenly distributed amongst the
> > > regionservers, and load on each regionserver is pretty much the same. I
> > > also have per-table balancing turned on. I get mostly data local
> mappers
> > > with only a few rack local (maybe 10 of the 250 mappers).
> > >
> > > Currently the table is a wide table schema, with lists of data
> structures
> > > stored as columns with column prefixes grouping the data structures
> (e.g.
> > > 1_name, 1_address, 1_city, 2_name, 2_address, 2_city). I was thinking
> of
> > > moving those data structures to protobuf which would cut down on the
> > number
> > > of columns. The downside is I can't filter on one value with that, but
> it
> > > is a tradeoff I would make for performance. I was also considering
> > > restructuring the table into a tall table.
> > >
> > > Something interesting is that my old regionserver machines had five 15k
> > > SCSI drives instead of 2 SSDs, and performance was about the same.
> Also,
> > my
> > > old network was 1gbit, now it is 10gbit. So neither network nor disk
> I/O
> > > appear to be the bottleneck. The CPU is rather high for the
> regionserver
> > so
> > > it seems like the best candidate to investigate. I will try profiling
> it
> > > tomorrow and will report back. I may revisit compression on vs off
> since
> > > that is adding load to the CPU.
> > >
> > > I'll also come up with a sample program that generates data similar to
> my
> > > table.
> > >
> > >
> > > On Apr 30, 2013, at 10:01 PM, lars hofhansl <larsh@apache.org> wrote:
> > >
> > > > Your average row is 35k so scanner caching would not make a huge
> > > difference, although I would have expected some improvements by setting
> > it
> > > to 10 or 50 since you have a wide 10ge pipe.
> > > >
> > > > I assume your table is split sufficiently to touch all
> RegionServer...
> > > Do you see the same load/IO on all region servers?
> > > >
> > > > A bunch of scan improvements went into HBase since 0.94.2.
> > > > I blogged about some of these changes here:
> > > http://hadoop-hbase.blogspot.com/2012/12/hbase-profiling.html
> > > >
> > > > In your case - since you have many columns, each of which carry the
> > > rowkey - you might benefit a lot from HBASE-7279.
> > > >
> > > > In the end HBase *is* slower than straight HDFS for full scans. How
> > > could it not be?
> > > > So I would start by looking at HDFS first. Make sure Nagle's is
> > disbaled
> > > in both HBase and HDFS.
> > > >
> > > > And lastly SSDs are somewhat new territory for HBase. Maybe Andy
> > Purtell
> > > is listening, I think he did some tests with HBase on SSDs.
> > > > With rotating media you typically see an improvement with
> compression.
> > > With SSDs the added CPU needed for decompression might outweigh the
> > > benefits.
> > > >
> > > > At the risk of starting a larger discussion here, I would posit that
> > > HBase's LSM based design, which trades random IO with sequential IO,
> > might
> > > be a bit more questionable on SSDs.
> > > >
> > > > If you can, it would be nice to run a profiler against one of the
> > > RegionServers (or maybe do it with the single RS setup) and see where
> it
> > is
> > > bottlenecked.
> > > > (And if you send me a sample program to generate some data - not
> 700g,
> > > though :) - I'll try to do a bit of profiling during the next days as
> my
> > > day job permits, but I do not have any machines with SSDs).
> > > >
> > > > -- Lars
> > > >
> > > >
> > > >
> > > >
> > > > ________________________________
> > > > From: Bryan Keller <bryanck@gmail.com>
> > > > To: user@hbase.apache.org
> > > > Sent: Tuesday, April 30, 2013 9:31 PM
> > > > Subject: Re: Poor HBase map-reduce scan performance
> > > >
> > > >
> > > > Yes, I have tried various settings for setCaching() and I have
> > > setCacheBlocks(false)
> > > >
> > > > On Apr 30, 2013, at 9:17 PM, Ted Yu <yuzhihong@gmail.com> wrote:
> > > >
> > > >> From http://hbase.apache.org/book.html#mapreduce.example :
> > > >>
> > > >> scan.setCaching(500);        // 1 is the default in Scan, which will
> > > >> be bad for MapReduce jobs
> > > >> scan.setCacheBlocks(false);  // don't set to true for MR jobs
> > > >>
> > > >> I guess you have used the above setting.
> > > >>
> > > >> 0.94.x releases are compatible. Have you considered upgrading to,
> say
> > > >> 0.94.7 which was recently released ?
> > > >>
> > > >> Cheers
> > > >>
> > > >> On Tue, Apr 30, 2013 at 9:01 PM, Bryan Keller <bryanck@gmail.com>
> > > wrote:
> > > >>
> > > >>> I have been attempting to speed up my HBase map-reduce scans for a
> > > while
> > > >>> now. I have tried just about everything without much luck. I'm
> > running
> > > out
> > > >>> of ideas and was hoping for some suggestions. This is HBase 0.94.2
> > and
> > > >>> Hadoop 2.0.0 (CDH4.2.1).
> > > >>>
> > > >>> The table I'm scanning:
> > > >>> 20 mil rows
> > > >>> Hundreds of columns/row
> > > >>> Column keys can be 30-40 bytes
> > > >>> Column values are generally not large, 1k would be on the large
> side
> > > >>> 250 regions
> > > >>> Snappy compression
> > > >>> 8gb region size
> > > >>> 512mb memstore flush
> > > >>> 128k block size
> > > >>> 700gb of data on HDFS
> > > >>>
> > > >>> My cluster has 8 datanodes which are also regionservers. Each has 8
> > > cores
> > > >>> (16 HT), 64gb RAM, and 2 SSDs. The network is 10gbit. I have a
> > separate
> > > >>> machine acting as namenode, HMaster, and zookeeper (single
> > instance). I
> > > >>> have disk local reads turned on.
> > > >>>
> > > >>> I'm seeing around 5 gbit/sec on average network IO. Each disk is
> > > getting
> > > >>> 400mb/sec read IO. Theoretically I could get 400mb/sec * 16 =
> > > 6.4gb/sec.
> > > >>>
> > > >>> Using Hadoop's TestDFSIO tool, I'm seeing around 1.4gb/sec read
> > speed.
> > > Not
> > > >>> really that great compared to the theoretical I/O. However this is
> > far
> > > >>> better than I am seeing with HBase map-reduce scans of my table.
> > > >>>
> > > >>> I have a simple no-op map-only job (using TableInputFormat) that
> > scans
> > > the
> > > >>> table and does nothing with data. This takes 45 minutes. That's
> about
> > > >>> 260mb/sec read speed. This is over 5x slower than straight HDFS.
> > > >>> Basically, with HBase I'm seeing read performance of my 16 SSD
> > cluster
> > > >>> performing nearly 35% slower than a single SSD.
> > > >>>
> > > >>> Here are some things I have changed to no avail:
> > > >>> Scan caching values
> > > >>> HDFS block sizes
> > > >>> HBase block sizes
> > > >>> Region file sizes
> > > >>> Memory settings
> > > >>> GC settings
> > > >>> Number of mappers/node
> > > >>> Compressed vs not compressed
> > > >>>
> > > >>> One thing I notice is that the regionserver is using quite a bit of
> > CPU
> > > >>> during the map reduce job. When dumping the jstack of the process,
> it
> > > seems
> > > >>> like it is usually in some type of memory allocation or
> decompression
> > > >>> routine which didn't seem abnormal.
> > > >>>
> > > >>> I can't seem to pinpoint the bottleneck. CPU use by the
> regionserver
> > is
> > > >>> high but not maxed out. Disk I/O and network I/O are low, IO wait
> is
> > > low.
> > > >>> I'm on the verge of just writing the dataset out to sequence files
> > > once a
> > > >>> day for scan purposes. Is that what others are doing?
> > >
> >
>

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