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From Harry Waye <hw...@arachnys.com>
Subject Re: Optimizing bulk load performance
Date Thu, 24 Oct 2013 22:02:10 GMT
Got it!  Re. 50% utilisation, I forgot to mention that 6 cores does not
include hyper-threading.  Foolish I know, but that would explain CPU0 being
at 50%.  The nodes are as stated in
http://www.hetzner.de/en/hosting/produkte_rootserver/ex10 bar the RAID1.


On 24 October 2013 22:50, Jean-Marc Spaggiari <jean-marc@spaggiari.org>wrote:

> Remote calls to a server. Just forget about it ;) Please verify the network
> bandwidth between your nodes.
>
>
> 2013/10/24 Harry Waye <hwaye@arachnys.com>
>
> > Excuse the ignorance, RCP?
> >
> >
> > On 24 October 2013 22:28, Jean-Marc Spaggiari <jean-marc@spaggiari.org
> > >wrote:
> >
> > > Your nodes are almost 50% idle... Might be something else. Sound it's
> not
> > > your disks nor your CPU... Maybe to many RCPs?
> > >
> > > Have you investigate on your network side? netperf might be a good help
> > for
> > > you.
> > >
> > > JM
> > >
> > >
> > > 2013/10/24 Harry Waye <hwaye@arachnys.com>
> > >
> > > > p.s. I guess this is more turning into a general hadoop issue, but
> I'll
> > > > keep the discussion here seeing that I have an audience, unless there
> > are
> > > > objections.
> > > >
> > > >
> > > > On 24 October 2013 22:02, Harry Waye <hwaye@arachnys.com> wrote:
> > > >
> > > > > So just a short update, I'll read into it a little more tomorrow.
> >  This
> > > > is
> > > > > from three of the nodes:
> > > > > https://gist.github.com/hazzadous/1264af7c674e1b3cf867
> > > > >
> > > > > The first is the grey guy.  Just glancing at it, it looks to
> > fluctuate
> > > > > more than the others.  I guess that could suggest that there are
> some
> > > > > issues with reading from the disks.  Interestingly, it's the only
> one
> > > > that
> > > > > doesn't have smartd installed, which alerts us on changes for the
> > other
> > > > > nodes.  I suspect there's probably some mileage in checking its
> smart
> > > > > attributes.  Will do that tomorrow though.
> > > > >
> > > > > Out of curiosity, how do people normally monitor disk issues?  I'm
> > > going
> > > > > to set up collectd to push various things from smartctl tomorrow,
> at
> > > the
> > > > > moment all we do is receive emails, which is mostly noise about
> > problem
> > > > > sector counts increasing +1.
> > > > >
> > > > >
> > > > > On 24 October 2013 19:40, Jean-Marc Spaggiari <
> > jean-marc@spaggiari.org
> > > > >wrote:
> > > > >
> > > > >> Can you try vmstat 2? 2 is the interval in seconds it will display
> > the
> > > > >> disk
> > > > >> usage. On the extract here, nothing is running. only 8% is used.
> (1%
> > > > disk
> > > > >> IO, 6% User, 1% sys)
> > > > >>
> > > > >> Run it on 2 or 3 different nodes while you are putting the load
on
> > the
> > > > >> cluster. And take a look at the 4 last numbers and see what the
> > value
> > > of
> > > > >> the last one?
> > > > >>
> > > > >> On the usercpu0 graph, who is the gray guy showing hight?
> > > > >>
> > > > >> JM
> > > > >>
> > > > >> 2013/10/24 Harry Waye <hwaye@arachnys.com>
> > > > >>
> > > > >> > Ok I'm running a load job atm, I've add some possibly
> > > incomprehensible
> > > > >> > coloured lines to the graph: http://goo.gl/cUGCGG
> > > > >> >
> > > > >> > This is actually with one fewer nodes due to decommissioning
to
> > > > replace
> > > > >> a
> > > > >> > disk, hence I guess the reason for one squiggly line showing
no
> > disk
> > > > >> > activity.  I've included only the cpu stats for CPU0 from
each
> > node.
> > > > >>  The
> > > > >> > last graph should read "Memory Used".  vmstat from one of
the
> > nodes:
> > > > >> >
> > > > >> > procs -----------memory---------- ---swap-- -----io----
> -system--
> > > > >> > ----cpu----
> > > > >> >  r  b   swpd   free   buff  cache   si   so    bi    bo
  in
> cs
> > us
> > > > sy
> > > > >> id
> > > > >> > wa
> > > > >> >  6  0      0 392448 524668 43823900    0    0   501  1044
   0
> >  0
> > >  6
> > > > >>  1
> > > > >> > 91  1
> > > > >> >
> > > > >> > To me the wait doesn't seem that high.  Job stats are
> > > > >> > http://goo.gl/ZYdUKp,  the job setup is
> > > > >> > https://gist.github.com/hazzadous/ac57a384f2ab685f07f6
> > > > >> >
> > > > >> > Does anything jump out at you?
> > > > >> >
> > > > >> > Cheers
> > > > >> > H
> > > > >> >
> > > > >> >
> > > > >> > On 24 October 2013 16:16, Harry Waye <hwaye@arachnys.com>
> wrote:
> > > > >> >
> > > > >> > > Hi JM
> > > > >> > >
> > > > >> > > I took a snapshot on the initial run, before the changes:
> > > > >> > >
> > > > >> >
> > > > >>
> > > >
> > >
> >
> https://www.evernote.com/shard/s95/sh/b8e1516d-7c49-43f0-8b5f-d16bbdd3fe13/00d7c6cd6dd9fba92d6f00f90fb54fc1/res/4f0e20a2-1ecb-4085-8bc8-b3263c23afb5/screenshot.png
> > > > >> > >
> > > > >> > > Good timing, disks appear to be exploding (ATA errors)
atm
> thus
> > > I'm
> > > > >> > > decommissioning and reprovisioning with new disks.
 I'll be
> > > > >> > reprovisioning
> > > > >> > > as without RAID (it's software RAID just to compound
the
> issue)
> > > > >> although
> > > > >> > > not sure how I'll go about migrating all nodes.  I
guess I'd
> > need
> > > to
> > > > >> put
> > > > >> > > more correctly speced nodes in the rack and decommission
the
> > > > existing.
> > > > >> > >  Makes diff. to
> > > > >> > >
> > > > >> > > We're using hetzner at the moment which may not have
been a
> good
> > > > >> choice.
> > > > >> > >  Has anyone had any experience with them wrt. Hadoop?
 They
> > offer
> > > 7
> > > > >> and
> > > > >> > 15
> > > > >> > > disk options, but are low on the cpu front (quad core).
 Our
> > > > workload
> > > > >> > will
> > > > >> > > be I assume on the high side.  There's also a 8 disk
Dell
> > > PowerEdge
> > > > >> what
> > > > >> > is
> > > > >> > > a little more powerful.  What hosting providers would
people
> > > > >> recommended?
> > > > >> > >  (And what would be the strategy for migrating?)
> > > > >> > >
> > > > >> > > Anyhow, when I have things more stable I'll have a
look at
> > > checking
> > > > >> out
> > > > >> > > what's using the cpu.  In the mean time, can anything
be
> gleamed
> > > > from
> > > > >> the
> > > > >> > > above snap?
> > > > >> > >
> > > > >> > > Cheers
> > > > >> > > H
> > > > >> > >
> > > > >> > >
> > > > >> > > On 24 October 2013 15:14, Jean-Marc Spaggiari <
> > > > >> jean-marc@spaggiari.org
> > > > >> > >wrote:
> > > > >> > >
> > > > >> > >> Hi Harry,
> > > > >> > >>
> > > > >> > >> Do you have more details on the exact load? Can
you run
> vmstats
> > > and
> > > > >> see
> > > > >> > >> what kind of load it is? Is it user? cpu? wio?
> > > > >> > >>
> > > > >> > >> I suspect your disks to be the issue. There is
2 things here.
> > > > >> > >>
> > > > >> > >> First, we don't recommend RAID for the HDFS/HBase
disk. The
> > best
> > > is
> > > > >> to
> > > > >> > >> simply mount the disks on 2 mounting points and
give them to
> > > HDFS.
> > > > >> > >> Second, 2 disks per not is very low. On a dev cluster
is not
> > even
> > > > >> > >> recommended. In production, you should go with
12 or more.
> > > > >> > >>
> > > > >> > >> So with only 2 disks in RAID, I suspect your WIO
to be high
> > which
> > > > is
> > > > >> > what
> > > > >> > >> might slow your process.
> > > > >> > >>
> > > > >> > >> Can you take a look on that direction? If it's
not that, we
> > will
> > > > >> > continue
> > > > >> > >> to investigate ;)
> > > > >> > >>
> > > > >> > >> Thanks,
> > > > >> > >>
> > > > >> > >> JM
> > > > >> > >>
> > > > >> > >>
> > > > >> > >> 2013/10/23 Harry Waye <hwaye@arachnys.com>
> > > > >> > >>
> > > > >> > >> > I'm trying to load data into hbase using HFileOutputFormat
> > and
> > > > >> > >> incremental
> > > > >> > >> > bulk load but am getting rather lackluster
performance, 10h
> > for
> > > > >> ~0.5TB
> > > > >> > >> > data, ~50000 blocks.  This is being loaded
into a table
> that
> > > has
> > > > 2
> > > > >> > >> > families, 9 columns, 2500 regions and is ~10TB
in size.
>  Keys
> > > are
> > > > >> md5
> > > > >> > >> > hashes and regions are pretty evenly spread.
 The majority
> of
> > > > time
> > > > >> > >> appears
> > > > >> > >> > to be spend in the reduce phase, with the
map phase
> > completing
> > > > very
> > > > >> > >> > quickly.  The network doesn't appear to be
saturated, but
> the
> > > > load
> > > > >> is
> > > > >> > >> > consistently at 6 which is the number or reduce
tasks per
> > node.
> > > > >> > >> >
> > > > >> > >> > 12 hosts (6 cores, 2 disk as RAID0, 1GB eth,
no one else on
> > the
> > > > >> rack).
> > > > >> > >> >
> > > > >> > >> > MR conf: 6 mappers, 6 reducers per node.
> > > > >> > >> >
> > > > >> > >> > I spoke to someone on IRC and they recommended
reducing job
> > > > output
> > > > >> > >> > replication to 1, and reducing the number
of mappers which
> I
> > > > >> reduced
> > > > >> > to
> > > > >> > >> 2.
> > > > >> > >> >  Reducing replication appeared not to make
any difference,
> > > > reducing
> > > > >> > >> > reducers appeared just to slow the job down.
 I'm going to
> > > have a
> > > > >> look
> > > > >> > >> at
> > > > >> > >> > running the benchmarks mentioned on Michael
Noll's blog and
> > see
> > > > >> what
> > > > >> > >> that
> > > > >> > >> > turns up.  I guess some questions I have are:
> > > > >> > >> >
> > > > >> > >> > How does the global number/size of blocks
affect perf.?  (I
> > > have
> > > > a
> > > > >> lot
> > > > >> > >> of
> > > > >> > >> > 10mb files, which are the input files)
> > > > >> > >> >
> > > > >> > >> > How does the job local number/size of input
blocks affect
> > > perf.?
> > > > >> > >> >
> > > > >> > >> > What is actually happening in the reduce phase
that
> requires
> > so
> > > > >> much
> > > > >> > >> CPU?
> > > > >> > >> >  I assume the actual construction of HFiles
isn't
> intensive.
> > > > >> > >> >
> > > > >> > >> > Ultimately, how can I improve performance?
> > > > >> > >> > Thanks
> > > > >> > >> >
> > > > >> > >>
> > > > >> > >
> > > > >> > >
> > > > >> > >
> > > > >> > > --
> > > > >> > > Harry Waye, Co-founder/CTO
> > > > >> > > harry@arachnys.com
> > > > >> > > +44 7890 734289
> > > > >> > >
> > > > >> > > Follow us on Twitter: @arachnys <
> > https://twitter.com/#!/arachnys>
> > > > >> > >
> > > > >> > > ---
> > > > >> > > Arachnys Information Services Limited is a company
registered
> in
> > > > >> England
> > > > >> > &
> > > > >> > > Wales. Company number: 7269723. Registered office:
40
> Clarendon
> > > St,
> > > > >> > > Cambridge, CB1 1JX.
> > > > >> > >
> > > > >> >
> > > > >> >
> > > > >> >
> > > > >> > --
> > > > >> > Harry Waye, Co-founder/CTO
> > > > >> > harry@arachnys.com
> > > > >> > +44 7890 734289
> > > > >> >
> > > > >> > Follow us on Twitter: @arachnys <
> https://twitter.com/#!/arachnys>
> > > > >> >
> > > > >> > ---
> > > > >> > Arachnys Information Services Limited is a company registered
in
> > > > >> England &
> > > > >> > Wales. Company number: 7269723. Registered office: 40 Clarendon
> > St,
> > > > >> > Cambridge, CB1 1JX.
> > > > >> >
> > > > >>
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Harry Waye, Co-founder/CTO
> > > > > harry@arachnys.com
> > > > > +44 7890 734289
> > > > >
> > > > > Follow us on Twitter: @arachnys <https://twitter.com/#!/arachnys>
> > > > >
> > > > > ---
> > > > > Arachnys Information Services Limited is a company registered in
> > > England
> > > > &
> > > > > Wales. Company number: 7269723. Registered office: 40 Clarendon St,
> > > > > Cambridge, CB1 1JX.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Harry Waye, Co-founder/CTO
> > > > harry@arachnys.com
> > > > +44 7890 734289
> > > >
> > > > Follow us on Twitter: @arachnys <https://twitter.com/#!/arachnys>
> > > >
> > > > ---
> > > > Arachnys Information Services Limited is a company registered in
> > England
> > > &
> > > > Wales. Company number: 7269723. Registered office: 40 Clarendon St,
> > > > Cambridge, CB1 1JX.
> > > >
> > >
> >
> >
> >
> > --
> > Harry Waye, Co-founder/CTO
> > harry@arachnys.com
> > +44 7890 734289
> >
> > Follow us on Twitter: @arachnys <https://twitter.com/#!/arachnys>
> >
> > ---
> > Arachnys Information Services Limited is a company registered in England
> &
> > Wales. Company number: 7269723. Registered office: 40 Clarendon St,
> > Cambridge, CB1 1JX.
> >
>



-- 
Harry Waye, Co-founder/CTO
harry@arachnys.com
+44 7890 734289

Follow us on Twitter: @arachnys <https://twitter.com/#!/arachnys>

---
Arachnys Information Services Limited is a company registered in England &
Wales. Company number: 7269723. Registered office: 40 Clarendon St,
Cambridge, CB1 1JX.

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