Ran your test code (thanks Carlos). Found two things: 1. Store.internalFlushCache(...) should be calling StoreScanner.next(List<KeyValue>, int limit) - currently it does not set a limit.(But this is not the problem).
2. With jstack I found that the code is stuck in a loop in Memstore.MemstoreScanner.getNext(...) Here's the relevant part of the jstack: "IPC Server handler 6 on 60020" daemon prio=10 tid=0x00007f0574625000 nid=0x720c runnable [0x00007f05669e7000] java.lang.Thread.State: RUNNABLE at org.apache.hadoop.hbase.regionserver.MemStore$MemStoreScanner.getNext(MemStore.java:726) at org.apache.hadoop.hbase.regionserver.MemStore$MemStoreScanner.seekInSubLists(MemStore.java:761) - locked <0x00000000c4a8a860> (a org.apache.hadoop.hbase.regionserver.MemStore$MemStoreScanner) at org.apache.hadoop.hbase.regionserver.MemStore$MemStoreScanner.reseek(MemStore.java:800) - locked <0x00000000c4a8a860> (a org.apache.hadoop.hbase.regionserver.MemStore$MemStoreScanner) at org.apache.hadoop.hbase.regionserver.NonLazyKeyValueScanner.doRealSeek(NonLazyKeyValueScanner.java:54) at org.apache.hadoop.hbase.regionserver.KeyValueHeap.generalizedSeek(KeyValueHeap.java:299) at org.apache.hadoop.hbase.regionserver.KeyValueHeap.reseek(KeyValueHeap.java:244) at org.apache.hadoop.hbase.regionserver.StoreScanner.reseek(StoreScanner.java:522) - eliminated <0x00000000ccb54860> (a org.apache.hadoop.hbase.regionserver.StoreScanner) at org.apache.hadoop.hbase.regionserver.StoreScanner.next(StoreScanner.java:403) - locked <0x00000000ccb54860> (a org.apache.hadoop.hbase.regionserver.StoreScanner) at org.apache.hadoop.hbase.regionserver.KeyValueHeap.next(KeyValueHeap.java:127) at org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl.nextInternal(HRegion.java:3459) at org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl.next(HRegion.java:3406) - locked <0x00000000c59ee610> (a org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl) at org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl.next(HRegion.java:3423) - locked <0x00000000c59ee610> (a org.apache.hadoop.hbase.regionserver.HRegion$RegionScannerImpl) at org.apache.hadoop.hbase.regionserver.HRegion.get(HRegion.java:4171) at org.apache.hadoop.hbase.regionserver.HRegion.get(HRegion.java:4144) at org.apache.hadoop.hbase.regionserver.HRegionServer.get(HRegionServer.java:1958) at sun.reflect.GeneratedMethodAccessor12.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:601) at org.apache.hadoop.hbase.ipc.WritableRpcEngine$Server.call(WritableRpcEngine.java:364) at org.apache.hadoop.hbase.ipc.HBaseServer$Handler.run(HBaseServer.java:1389) At the same time I find that flush cannot finish: "regionserver60020.cacheFlusher" daemon prio=10 tid=0x00007f05749ab000 nid=0x71fe waiting for monitor entry [0x00007f05677f6000] java.lang.Thread.State: BLOCKED (on object monitor) at org.apache.hadoop.hbase.regionserver.StoreScanner.updateReaders(StoreScanner.java:443) - waiting to lock <0x00000000ccb54860> (a org.apache.hadoop.hbase.regionserver.StoreScanner) at org.apache.hadoop.hbase.regionserver.Store.notifyChangedReadersObservers(Store.java:904) at org.apache.hadoop.hbase.regionserver.Store.updateStorefiles(Store.java:893) at org.apache.hadoop.hbase.regionserver.Store.access$600(Store.java:107) at org.apache.hadoop.hbase.regionserver.Store$StoreFlusherImpl.commit(Store.java:2291) at org.apache.hadoop.hbase.regionserver.HRegion.internalFlushcache(HRegion.java:1455) at org.apache.hadoop.hbase.regionserver.HRegion.internalFlushcache(HRegion.java:1353) at org.apache.hadoop.hbase.regionserver.HRegion.flushcache(HRegion.java:1294) at org.apache.hadoop.hbase.regionserver.MemStoreFlusher.flushRegion(MemStoreFlusher.java:406) at org.apache.hadoop.hbase.regionserver.MemStoreFlusher.flushRegion(MemStoreFlusher.java:380) at org.apache.hadoop.hbase.regionserver.MemStoreFlusher.run(MemStoreFlusher.java:243) at java.lang.Thread.run(Thread.java:722) Both StoreScanner.updateReaders and StoreScanner.reseek are synchronized. So the problem seems to be that MemStoreScanner loops forever in getNext(...). I took a jstack a bunch of times during execution, this always shows up. Need to dig a bit more, I do not see a good way to deal with this, yet. -- Lars ----- Original Message ----- From: "Espinoza,Carlos" <espino...@oclc.org> To: u...@hbase.apache.org Cc: Sent: Friday, August 10, 2012 3:12 PM Subject: RE: Extremely long flush times We were able to replicate this behavior in a pseudo-distributed hbase (hbase-0.94.1) environment. We wrote a test program that creates a test table "MyTestTable" and populates it with random rows, then it creates a row with 60,000 columns and repeatedly updates it. Each column has a 18 byte qualifier and a 50 byte value. In our tests, when we ran the program, we usually never got beyond 15 updates before it would flush for a really long time. The rows that are being updated are about 4MB each (minues any hbase metadata). It doesn't seem like it's caused by GC. I turned on gc logging, and didn't see any long pauses. This is the gc log during the flush. http://pastebin.com/vJKKXDx5 This is the regionserver log with debug on during the same flush http://pastebin.com/Fh5213mg This is the test program we wrote. http://pastebin.com/aZ0k5tx2 You should be able to just compile it, and run it against a running HBase cluster. $ java TestTable Carlos -----Original Message----- From: jdcry...@gmail.com [mailto:jdcry...@gmail.com] On Behalf Of Jean-Daniel Cryans Sent: Monday, August 06, 2012 8:04 PM To: u...@hbase.apache.org Subject: Re: Extremely long flush times Hi Ron, I think this is caused by GC, for example there's 7 minutes between the last blocking message and the end of the flush: 2012-08-06 11:44:36,348 INFO org.apache.hadoop.hbase.regionserver.HRegion: Blocking updates for 'IPC Server handler 42 on 9009' on region Works,73658752:eng,1337915462169.1cfc92481a74ec278337871563d189d6.: memstore size 271.9m is >= than blocking 256.0m size 2012-08-06 11:51:28,139 INFO org.apache.hadoop.hbase.regionserver.HRegion: Finished memstore flush of ~155.4m/162905016, currentsize=116.5m/122172880 for region Works,73658752:eng,1337915462169.1cfc92481a74ec278337871563d189d6. in 501337ms, sequenceid=1792264092, compaction requested=true During that time I would expect that clients got socket timeouts, tried to write again, and data would just pile up in the RPC queue. Do you have the gc log handy? Also did you set the zookeeper session timeout higher than the default of 3 minutes? Thx, J-D On Mon, Aug 6, 2012 at 2:37 PM, Buckley,Ron <buckl...@oclc.org> wrote: > We ran into this situation today on our production instance, I'm > wondering if anyone has seen or knows a way around it. > > > > We were repeatedly updating the same 60,000 column wide row. With > each update, we were updating nearly every column of the row. Each > update generated nearly 9 MB in the WAL. > > This worked OK most of the time. We saw frequent messages like this in > the region server log, indicating a 2.6 second flush time: > > 2012-08-06 11:42:52,316 INFO > org.apache.hadoop.hbase.regionserver.HRegion: Finished memstore flush > of ~155.4m/162931400, currentsize=2.7k/2760 for region > Works,73658752:eng,1337915462169.1cfc92481a74ec278337871563d189d6. in > 2610ms, sequenceid=1792263953, compaction requested=false > > > > However, sometimes we would see a flush times around 8 - 10 Minutes. > > 2012-08-06 11:51:28,139 INFO > org.apache.hadoop.hbase.regionserver.HRegion: Finished memstore flush > of ~155.4m/162905016, currentsize=116.5m/122172880 for region > Works,73658752:eng,1337915462169.1cfc92481a74ec278337871563d189d6. in > 501337ms, sequenceid=1792264092, compaction requested=true > > > > During these long flushes, we would end up taking all the ipc handler > slots into that region server that we had configured (50). It looked > to our application like the region server was unavailable. > > > > After the long delay, the region server would continue running fine, > but then do it again a few minutes later. > > > > I thought it was most likely something with Garbage Collection, so I > got a stack trace during one of the events. The trace doesn't look > like GC was running. > > > > > > http://pastebin.com/ANBiUzX4 - Stack Trace when the region server was > unreachable > > http://pastebin.com/naTYQxZR - Region Server Log during the same > interval > > > > > > Versions: > > HBase 0.92.1, r1298924 > > Hadoop 0.20.2-cdh3u3 > > > > > > ---------------------------------------------------------------------- > > Ron Buckley > > x6365 > > >
