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From Harry Waye <hw...@arachnys.com>
Subject Re: Optimizing bulk load performance
Date Thu, 24 Oct 2013 21:34:17 GMT
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.

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