Depends if you have to query .META. first to get the location of the region that hosts the row.
J-D On Tue, Mar 1, 2011 at 10:45 AM, Nanheng Wu <[email protected]> wrote: > Man I appreciate so much all the help you provided so far. I guess > I'll keep digging. Would this meta scan cause Get or Scan on user > tables to be very very slow too? That was actually was the problem I > first noticed: from time to time a client Get or Scan would be > extremely slow on my tables. > > On Tue, Mar 1, 2011 at 10:38 AM, Jean-Daniel Cryans <[email protected]> > wrote: >> The store file looks fairly new, maybe it was just major compacted? >> You could easily figure that out from the region server's log. >> >> Your problem is definitely a .META. region slowness. If scanning 8k >> rows takes 30 minutes, scanning and updating 260 rows at the same time >> probably isn't much faster. >> >> J-D >> >> On Tue, Mar 1, 2011 at 10:34 AM, Nanheng Wu <[email protected]> wrote: >>> J-D, >>> >>> It looks like I don't have that many files: >>> >>> drwxr-xr-x - root supergroup 0 2011-02-28 23:21 >>> /hbase/.META./1028785192 >>> -rw-r--r-- 3 root supergroup 932 2011-02-03 19:23 >>> /hbase/.META./1028785192/.regioninfo >>> drwxr-xr-x - root supergroup 0 2011-03-01 17:13 >>> /hbase/.META./1028785192/info >>> -rw-r--r-- 3 root supergroup 11831330 2011-03-01 17:13 >>> /hbase/.META./1028785192/info/6687606720393313750 >>> drwxr-xr-x - root supergroup 0 2011-03-01 17:13 >>> /hbase/.META./compaction.dir >>> >>> So you think compaction on .META. table on the RS could be the >>> problem? while the log metaScanner is running I saw virtually no logs >>> on that server though, I did see compactions once the meta scan ended >>> and region close started to happen. I wonder what the cluster is doing >>> while the meta scan is going. >>> >>> I would definitely upgrade in the near future, it's just that I am >>> afraid upgrading won't guarantee a fix if I don't understand the >>> nature of the problem more clearly. We also have another test cluster, >>> running the same versions of everything on cheaper hardware and it >>> doesn't have this problem. >>> >>> On Tue, Mar 1, 2011 at 9:52 AM, Jean-Daniel Cryans <[email protected]> >>> wrote: >>>> That long .META. scan might be the culprit, good catch! >>>> >>>> If you run this from the hadoop folder: >>>> >>>> bin/hadoop dfs -lsr /hbase/.META. >>>> >>>> Do you see a ton of files? Let's define "ton" as more than 16 files. >>>> If so, and I see you have a very high number of regions, then you >>>> could be hitting this problem: >>>> https://issues.apache.org/jira/browse/HBASE-3499 >>>> >>>> In short, every few .META. change will result in a flush and it could >>>> be that the region server hosting it isn't able to keep up with the >>>> compactions. It's done so that since append isn't supported in your >>>> hadoop that you won't lose too much data if the node dies, which is >>>> really bad when it happens to .META. >>>> >>>> In your case it might not be so bad to set your .META.'s MEMSTORE_SIZE >>>> back to the default value if you're not writing hence not splitting. >>>> Running the script attached in that jira would do it (don't forget to >>>> restart HBase after running it). >>>> >>>> Lastly, upgrading to HBase 0.90.1 and a hadoop that supports append >>>> should be a priority. >>>> >>>> J-D >>>> >>>> On Tue, Mar 1, 2011 at 9:30 AM, Nanheng Wu <[email protected]> wrote: >>>>> Hi J-D: >>>>> >>>>> I did the scan like you suggested but no splits came up. This kind >>>>> of makes sense to me, since we write Hfiles using a MR job and then >>>>> pretty much use HBase for read-only so maybe that's why the regions >>>>> never got split? I think my slow disable problem is related to this >>>>> RegionManager.metaScanner. I greped for that in the Masters log and I >>>>> saw: >>>>> 11/03/01 15:30:37 INFO master.BaseScanner: RegionManager.metaScanner >>>>> scanning meta region {server: 10.146.14.38:60020, regionname: >>>>> .META.,,1, startKey: <>} >>>>> 11/03/01 15:55:40 INFO master.BaseScanner: RegionManager.metaScanner >>>>> scan of 8296 row(s) of meta region {server: 10.146.14.38:60020, >>>>> regionname: .META.,,1, startKey: <>} complete >>>>> 11/03/01 15:55:40 INFO master.BaseScanner: RegionManager.metaScanner >>>>> scanning meta region {server: 10.146.14.38:60020, regionname: >>>>> .META.,,1, startKey: <>} >>>>> Thread 27 (RegionManager.metaScanner): >>>>> 11/03/01 16:21:04 INFO master.BaseScanner: RegionManager.metaScanner >>>>> scan of 8296 row(s) of meta region {server: 10.146.14.38:60020, >>>>> regionname: .META.,,1, startKey: <>} complete >>>>> 11/03/01 16:21:04 INFO master.BaseScanner: RegionManager.metaScanner >>>>> scanning meta region {server: 10.146.14.38:60020, regionname: >>>>> .META.,,1, startKey: <>} >>>>> Thread 27 (RegionManager.metaScanner): >>>>> 11/03/01 16:46:07 INFO master.BaseScanner: RegionManager.metaScanner >>>>> scan of 8298 row(s) of meta region {server: 10.146.14.38:60020, >>>>> regionname: .META.,,1, startKey: <>} complete >>>>> >>>>> It looks like meta scanner is always running, each time taking 20-30 >>>>> minutes. Here's what I did: >>>>> >>>>> 1) disable table -> at 16:28:31, according the log above there's a >>>>> meta scan in progress. >>>>> >>>>> 2 ) the command hangs, no output in .META RS's log >>>>> at 11/03/01 16:46:57 the client got 11/03/01 16:46:58 DEBUG >>>>> zookeeper.ZooKeeperWrapper: Read ZNode /hbase/root-region-server got >>>>> 10.146.14.38:60020 >>>>> 11/03/01 16:46:58 DEBUG client.HConnectionManager$TableServers: Found >>>>> ROOT at 10.146.14.38:60020 >>>>> 11/03/01 16:46:58 DEBUG client.HConnectionManager$TableServers: Cached >>>>> location for .META.,,1 is 10.146.14.38:60020 >>>>> This corresponds exact to when the meta scan completed. .META RS >>>>> started to spew some logs about closing regions. >>>>> >>>>> 3) Another meta scan started and the client hangs again until it >>>>> finishes, and disable command returns.The whole thing took 2688.5930 >>>>> seconds >>>>> >>>>> What kind of problem does it look like to you J-D? What does this >>>>> background task metaScanner do? >>>>> >>>>> Thanks! >>>>> >>>>> >>>>> >>>>> On Mon, Feb 28, 2011 at 5:17 PM, Jean-Daniel Cryans <[email protected]> >>>>> wrote: >>>>>> I didn't get most of the information I was looking for... but I do >>>>>> have something to work with. So I asked whether the metaScanner was >>>>>> making progress or not, and from that log I think I see it does: >>>>>> >>>>>>> 11/03/01 00:47:30 DEBUG client.HConnectionManager$TableServers: >>>>>>> Rowscanned=261, rowsOffline=3 >>>>>>> 11/03/01 00:47:30 DEBUG client.HBaseAdmin: Sleep. Waiting for all >>>>>>> regions to be disabled from myTable >>>>>> >>>>>> Only 3 rows are offline, whereas we expect all the region to be >>>>>> offline. I expect you see those lines a lot? If so, one thing I'd like >>>>>> to see is the result of this command: >>>>>> >>>>>> scan '.META.', {STARTROW => "myTable,,", LIMIT => 261} >>>>>> >>>>>> It's going to be big. Then grep in the result for the string SPLIT, >>>>>> and please post back here the lines that match. >>>>>> >>>>>> J-D >>>>>> >>>>>> On Mon, Feb 28, 2011 at 5:04 PM, Nanheng Wu <[email protected]> wrote: >>>>>>> I issued two more disable commands and looked at the .META RS. The >>>>>>> last log entry looks like: >>>>>>> >>>>>>> 11/03/01 00:29:14 INFO regionserver.HLog: Roll >>>>>>> /hbase/.logs/<RS_HOSTNAME>,60020,1298935751670/hlog >>>>>>> .dat.1298935752660, entries=13527, calcsize=3839046, filesize=2560143. >>>>>>> New hlog >>>>>>> /hbase/.logs/<RS_HOSTNAME>,60020,1298935751670/hlog.dat.1298939354072 >>>>>>> >>>>>>> I issued the command at: 00:34:59, the client debug message has >>>>>>> nothing but "11/03/01 00:34:59 DEBUG zookeeper.ClientCnxn: Got ping >>>>>>> response for sessionid:0x12e6e938e9c000b after 90ms" until 00:47:19. >>>>>>> Then all of a sudden it outputs the following: >>>>>>> >>>>>>> 0:47:28 DEBUG client.HConnectionManager$TableServers: Cache hit for >>>>>>> row <> in tableName .META.: location server 10.146.14.38:60020, >>>>>>> location region name .META.,,1 >>>>>>> 11/03/01 00:47:28 DEBUG zookeeper.ZooKeeperWrapper: Read ZNode >>>>>>> /hbase/root-region-server got 10.146.14.38:60020 >>>>>>> 11/03/01 00:47:28 DEBUG client.HConnectionManager$TableServers: Found >>>>>>> ROOT at 10.146.14.38:60020 >>>>>>> 11/03/01 00:47:28 DEBUG client.HConnectionManager$TableServers: Cached >>>>>>> location for .META.,,1 is 10.146.14.38:60020 >>>>>>> 11/03/01 00:47:30 DEBUG client.HConnectionManager$TableServers: >>>>>>> Rowscanned=261, rowsOffline=3 >>>>>>> 11/03/01 00:47:30 DEBUG client.HBaseAdmin: Sleep. Waiting for all >>>>>>> regions to be disabled from myTable >>>>>>> 11/03/01 00:47:31 DEBUG client.HBaseAdmin: Wake. Waiting for all >>>>>>> regions to be disabled from myTable >>>>>>> >>>>>>> Here's the full thread dump of the .META RS from 00:34:59 to 00:47:31 >>>>>>> http://pastebin.com/Ywwx8afQ >>>>>>> >>>>>>> I hope I compiled some useful information here. I am pretty lost at >>>>>>> this point, I would really appreciate your help! >>>>>>> >>>>>>> Thanks! >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Mon, Feb 28, 2011 at 2:58 PM, Jean-Daniel Cryans >>>>>>> <[email protected]> wrote: >>>>>>>> Ok so no debug from the disable command? BTW you should output your GC >>>>>>>> somewhere else like the .out file or a completely separate file. >>>>>>>> >>>>>>>> J-D >>>>>>>> >>>>>>>> On Mon, Feb 28, 2011 at 2:54 PM, Nanheng Wu <[email protected]> >>>>>>>> wrote: >>>>>>>>> I see, so I should jstack the .META region. I'll do that. >>>>>>>>> >>>>>>>>> The master log pretty much looks like this: should I grep for >>>>>>>>> something specific? >>>>>>>>> >>>>>>>>> 11/02/28 22:52:56 INFO master.BaseScanner: RegionManager.rootScanner >>>>>>>>> scan of 1 row(s) of meta region complete >>>>>>>>> 2011-02-28T22:52:57.138+0000: 263241.014: [GC 263241.014: [ParNew: >>>>>>>>> 19136K->2112K(19136K), 0.0033350 secs] 378606K->36159 >>>>>>>>> 6K(641944K) icms_dc=0 , 0.0034330 secs] [Times: user=0.02 sys=0.00, >>>>>>>>> real=0.00 secs] >>>>>>>>> 2011-02-28T22:53:04.956+0000: 263248.832: [GC 263248.832: [ParNew: >>>>>>>>> 19068K->2112K(19136K), 0.0029690 secs] 378552K->36163 >>>>>>>>> 0K(641944K) icms_dc=0 , 0.0030460 secs] [Times: user=0.02 sys=0.00, >>>>>>>>> real=0.00 secs] >>>>>>>>> 2011-02-28T22:53:12.664+0000: 263256.540: [GC 263256.541: [ParNew: >>>>>>>>> 19136K->2112K(19136K), 0.0037690 secs] 378654K->36164 >>>>>>>>> 7K(641944K) icms_dc=0 , 0.0038660 secs] [Times: user=0.01 sys=0.00, >>>>>>>>> real=0.01 secs] >>>>>>>>> 2011-02-28T22:53:20.608+0000: 263264.484: [GC 263264.484: [ParNew: >>>>>>>>> 19136K->1810K(19136K), 0.0032600 secs] 378671K->36134 >>>>>>>>> 6K(641944K) icms_dc=0 , 0.0033470 secs] [Times: user=0.02 sys=0.00, >>>>>>>>> real=0.01 secs] >>>>>>>>> 2011-02-28T22:53:28.278+0000: 263272.154: [GC 263272.154: [ParNew: >>>>>>>>> 18834K->2112K(19136K), 0.0029870 secs] 378370K->36166 >>>>>>>>> 1K(641944K) icms_dc=0 , 0.0030670 secs] [Times: user=0.01 sys=0.00, >>>>>>>>> real=0.01 secs] >>>>>>>>> 2011-02-28T22:53:35.919+0000: 263279.795: [GC 263279.795: [ParNew: >>>>>>>>> 19136K->1747K(19136K), 0.0037090 secs] 378685K->36129 >>>>>>>>> 8K(641944K) icms_dc=0 , 0.0037920 secs] [Times: user=0.02 sys=0.00, >>>>>>>>> real=0.01 secs] >>>>>>>>> 11/02/28 22:53:36 INFO master.ServerManager: 9 region servers, 0 dead, >>>>>>>>> average load 760.2222222222222 >>>>>>>>> >>>>>>>>> >>>>>>>>> On Mon, Feb 28, 2011 at 2:49 PM, Jean-Daniel Cryans >>>>>>>>> <[email protected]> wrote: >>>>>>>>>> Are you able to tell if that call in metaScanner is hanging or it's >>>>>>>>>> making multiple calls to the .META. region? >>>>>>>>>> >>>>>>>>>> If former, then jstack the region server that hosts .META. and see >>>>>>>>>> where it's blocked. >>>>>>>>>> >>>>>>>>>> if latter, then it means your .META. region is slow? Again, what's >>>>>>>>>> going on on the RS that hosts .META.? >>>>>>>>>> >>>>>>>>>> Finally, what's the master's log like during that time? >>>>>>>>>> >>>>>>>>>> J-D >>>>>>>>>> >>>>>>>>>> On Mon, Feb 28, 2011 at 2:41 PM, Nanheng Wu <[email protected]> >>>>>>>>>> wrote: >>>>>>>>>>> J-D, >>>>>>>>>>> >>>>>>>>>>> Thanks so much for your help so far! I sent disable commands on 4 >>>>>>>>>>> rather small tables and they got stuck for a long time again, so I >>>>>>>>>>> took jstack of the master. From what I can tell, all disableTable >>>>>>>>>>> calls are blocked by a meta scanner thread (sample log below). At >>>>>>>>>>> the >>>>>>>>>>> moment there were no other requests to the server at all. How >>>>>>>>>>> should I >>>>>>>>>>> investigate this further? If it helps, here's some background: I >>>>>>>>>>> have >>>>>>>>>>> several datasets, each of them is in a separate table; Our data >>>>>>>>>>> pipeline produces a new version of each dataset everyday and only >>>>>>>>>>> the >>>>>>>>>>> lastest version should be used. This is how the data is loaded: for >>>>>>>>>>> each dataset 1) run a MR job and outputs HFiles 2) call loadTable.rb >>>>>>>>>>> to create a new table 3) disable and drop the previous version. As a >>>>>>>>>>> result some calls to load table and drop table would overlap. Please >>>>>>>>>>> let me know if something stands out to you as a potential culprit. >>>>>>>>>>> Thanks! >>>>>>>>>>> >>>>>>>>>>> BTW, I am running Hadoop 0.20.2 with HBase 0.20.6 >>>>>>>>>>> >>>>>>>>>>> Thread 47 (IPC Server handler 13 on 60000): >>>>>>>>>>> State: BLOCKED >>>>>>>>>>> Blocked count: 3801 >>>>>>>>>>> Waited count: 72719 >>>>>>>>>>> Blocked on java.lang.Object@75ac522c >>>>>>>>>>> Blocked by 27 (RegionManager.metaScanner) >>>>>>>>>>> Stack: >>>>>>>>>>> >>>>>>>>>>> org.apache.hadoop.hbase.master.TableOperation.process(TableOperation.java:154) >>>>>>>>>>> >>>>>>>>>>> org.apache.hadoop.hbase.master.HMaster.disableTable(HMaster.java:842) >>>>>>>>>>> sun.reflect.GeneratedMethodAccessor9.invoke(Unknown Source) >>>>>>>>>>> >>>>>>>>>>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) >>>>>>>>>>> java.lang.reflect.Method.invoke(Method.java:597) >>>>>>>>>>> >>>>>>>>>>> org.apache.hadoop.hbase.ipc.HBaseRPC$Server.call(HBaseRPC.java:657) >>>>>>>>>>> >>>>>>>>>>> org.apache.hadoop.hbase.ipc.HBaseServer$Handler.run(HBaseServer.java:915) >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Thread 27 (RegionManager.metaScanner): >>>>>>>>>>> State: WAITING >>>>>>>>>>> Blocked count: 1526058 >>>>>>>>>>> Waited count: 1488998 >>>>>>>>>>> Waiting on org.apache.hadoop.hbase.ipc.HBaseClient$Call@4dd44ab0 >>>>>>>>>>> Stack: >>>>>>>>>>> java.lang.Object.wait(Native Method) >>>>>>>>>>> java.lang.Object.wait(Object.java:485) >>>>>>>>>>> >>>>>>>>>>> org.apache.hadoop.hbase.ipc.HBaseClient.call(HBaseClient.java:722) >>>>>>>>>>> >>>>>>>>>>> org.apache.hadoop.hbase.ipc.HBaseRPC$Invoker.invoke(HBaseRPC.java:333) >>>>>>>>>>> $Proxy1.get(Unknown Source) >>>>>>>>>>> >>>>>>>>>>> org.apache.hadoop.hbase.master.BaseScanner.checkAssigned(BaseScanner.java:543) >>>>>>>>>>> >>>>>>>>>>> org.apache.hadoop.hbase.master.BaseScanner.scanRegion(BaseScanner.java:192) >>>>>>>>>>> >>>>>>>>>>> org.apache.hadoop.hbase.master.MetaScanner.scanOneMetaRegion(MetaScanner.java:73) >>>>>>>>>>> >>>>>>>>>>> org.apache.hadoop.hbase.master.MetaScanner.maintenanceScan(MetaScanner.java:129) >>>>>>>>>>> >>>>>>>>>>> org.apache.hadoop.hbase.master.BaseScanner.chore(BaseScanner.java:153) >>>>>>>>>>> org.apache.hadoop.hbase.Chore.run(Chore.java:68) >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Fri, Feb 25, 2011 at 10:23 AM, Jean-Daniel Cryans >>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>> An hour to disable? That doesn't sound right at all :) >>>>>>>>>>>> >>>>>>>>>>>> I would approach this problem like I generally do with HBase issue, >>>>>>>>>>>> first check the master log for any weirdness regarding my problem >>>>>>>>>>>> (in >>>>>>>>>>>> this case, grep for the table name). >>>>>>>>>>>> >>>>>>>>>>>> Then I would look the region server log(s) of the nodes that were >>>>>>>>>>>> hosting regions from that table. You should see the steps taken to >>>>>>>>>>>> disable the regions (starting to close, flush, region completely >>>>>>>>>>>> closed). >>>>>>>>>>>> >>>>>>>>>>>> If you are able to do it while it's taking a very long time to >>>>>>>>>>>> disable, try to jstack the process the seems to be hanging. >>>>>>>>>>>> >>>>>>>>>>>> Finally, like I said in another thread, there's a bug in 0.20.6 >>>>>>>>>>>> that >>>>>>>>>>>> almost prevent disabling a table (or re-enabling) if any region >>>>>>>>>>>> recently split and the parent wasn't cleaned yet from .META. and >>>>>>>>>>>> that >>>>>>>>>>>> is fixed in 0.90.1 >>>>>>>>>>>> >>>>>>>>>>>> J-D >>>>>>>>>>>> >>>>>>>>>>>> On Thu, Feb 24, 2011 at 11:37 PM, Nanheng Wu <[email protected]> >>>>>>>>>>>> wrote: >>>>>>>>>>>>> I think you are right, maybe in the long run I need to >>>>>>>>>>>>> re-architect my >>>>>>>>>>>>> system so that it doesn't need to create new and delete old >>>>>>>>>>>>> tables all >>>>>>>>>>>>> the time. In the short term I am having a really hard time with >>>>>>>>>>>>> the >>>>>>>>>>>>> disabling function, I ran a disable command on a very small table >>>>>>>>>>>>> (probably dozen of MBs in size) and are no client using the >>>>>>>>>>>>> cluster at >>>>>>>>>>>>> all, and that took about 1 hour to complete! The weird thing is >>>>>>>>>>>>> on the >>>>>>>>>>>>> web UI only the region server carrying the META table has non-zero >>>>>>>>>>>>> requests, all other RS have 0 requests the entire time. I would >>>>>>>>>>>>> think >>>>>>>>>>>>> they should get some request to flush the memstore at least. I >>>>>>>>>>>>> *am* >>>>>>>>>>>>> using the same RS nodes for some map reduce job at the time and >>>>>>>>>>>>> top >>>>>>>>>>>>> shows the memory usage is almost full on the META region. Would >>>>>>>>>>>>> you >>>>>>>>>>>>> have some idea of what I should investigate? >>>>>>>>>>>>> Thanks so much. >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
