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 <[email protected]> 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 <[email protected]>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 <[email protected]> >> >> > 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 <[email protected]> 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 < >> [email protected] >> > >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 <[email protected]> >> > >> >> > >> > 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 >> > > [email protected] >> > > +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 >> > [email protected] >> > +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 > [email protected] > +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 [email protected] +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.
