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From Ted Yu <yuzhih...@gmail.com>
Subject Re: Why so many unexpected files like partitions_xxxx are created?
Date Wed, 18 Dec 2013 17:37:10 GMT
>From the stack trace posted I saw:

org.apache.commons.logging.impl.Log4JLogger.error(Log4JLogger.java:257)
    at
org.apache.hadoop.hbase.mapreduce.LoadIncrementalHFiles.tryAtomicRegionLoad(
LoadIncrementalHFiles.java:577)

Assuming 0.94 is used, line 577 at the tip of 0.94 is:
        LOG.warn("Attempt to bulk load region containing "
            + Bytes.toStringBinary(first) + " into table "

But the following should be the corresponding line w.r.t. stack trace:
    } catch (IOException e) {
      LOG.error("Encountered unrecoverable error from region server", e);

Tao:
Can you check the log of LoadIncrementalHFiles to see what was the error
from region server ?

As Jieshan said, checking region server log would reveal something.

Cheers


On Tue, Dec 17, 2013 at 10:40 PM, Bijieshan <bijieshan@huawei.com> wrote:

> It seems LoadIncrementalHFiles is still running.  Can you run "jstack" on
> 1 RegionServer process also?
>
> Which version are you using?
>
> Jieshan.
> -----Original Message-----
> From: Tao Xiao [mailto:xiaotao.cs.nju@gmail.com]
> Sent: Wednesday, December 18, 2013 1:49 PM
> To: user@hbase.apache.org
> Subject: Re: Why so many unexpected files like partitions_xxxx are created?
>
> I did jstack one such process and can see the following output in the
> terminal, and I guess this info told us that the processes started by the
> command "LoadIncrementalHFiles" never exit. Why didn't they exit after
> finished running ?
>
> ... ...
> ... ...
>
> "LoadIncrementalHFiles-0.LruBlockCache.EvictionThread" daemon prio=10
> tid=0x000000004129c000 nid=0x2186 in Object.wait() [0x00007f53f3665000]
>    java.lang.Thread.State: WAITING (on object monitor)
>     at java.lang.Object.wait(Native Method)
>     - waiting on <0x000000075fcf3370> (a
> org.apache.hadoop.hbase.io.hfile.LruBlockCache$EvictionThread)
>     at java.lang.Object.wait(Object.java:485)
>     at
>
> org.apache.hadoop.hbase.io.hfile.LruBlockCache$EvictionThread.run(LruBlockCache.java:631)
>     - locked <0x000000075fcf3370> (a
> org.apache.hadoop.hbase.io.hfile.LruBlockCache$EvictionThread)
>     at java.lang.Thread.run(Thread.java:662)
>
>    Locked ownable synchronizers:
>     - None
>
> "LoadIncrementalHFiles-3" prio=10 tid=0x00007f540ca55800 nid=0x2185
> runnable [0x00007f53f3765000]
>    java.lang.Thread.State: RUNNABLE
>     at java.io.FileOutputStream.writeBytes(Native Method)
>     at java.io.FileOutputStream.write(FileOutputStream.java:282)
>     at java.io.BufferedOutputStream.write(BufferedOutputStream.java:105)
>     - locked <0x0000000763e5af70> (a java.io.BufferedOutputStream)
>     at java.io.PrintStream.write(PrintStream.java:430)
>     - locked <0x0000000763d5b670> (a java.io.PrintStream)
>     at sun.nio.cs.StreamEncoder.writeBytes(StreamEncoder.java:202)
>     at sun.nio.cs.StreamEncoder.implWrite(StreamEncoder.java:263)
>     at sun.nio.cs.StreamEncoder.write(StreamEncoder.java:106)
>     - locked <0x0000000763d6c6d0> (a java.io.OutputStreamWriter)
>     at sun.nio.cs.StreamEncoder.write(StreamEncoder.java:116)
>     at java.io.OutputStreamWriter.write(OutputStreamWriter.java:203)
>     at java.io.Writer.write(Writer.java:140)
>     at org.apache.log4j.helpers.QuietWriter.write(QuietWriter.java:48)
>     at org.apache.log4j.WriterAppender.subAppend(WriterAppender.java:317)
>     at org.apache.log4j.WriterAppender.append(WriterAppender.java:162)
>     at
> org.apache.log4j.AppenderSkeleton.doAppend(AppenderSkeleton.java:251)
>     - locked <0x0000000763d5fb90> (a org.apache.log4j.ConsoleAppender)
>     at
>
> org.apache.log4j.helpers.AppenderAttachableImpl.appendLoopOnAppenders(AppenderAttachableImpl.java:66)
>     at org.apache.log4j.Category.callAppenders(Category.java:206)
>     - locked <0x0000000763d65fe8> (a org.apache.log4j.spi.RootLogger)
>     at org.apache.log4j.Category.forcedLog(Category.java:391)
>     at org.apache.log4j.Category.log(Category.java:856)
>     at
> org.apache.commons.logging.impl.Log4JLogger.error(Log4JLogger.java:257)
>     at
>
> org.apache.hadoop.hbase.mapreduce.LoadIncrementalHFiles.tryAtomicRegionLoad(LoadIncrementalHFiles.java:577)
>     at
>
> org.apache.hadoop.hbase.mapreduce.LoadIncrementalHFiles$1.call(LoadIncrementalHFiles.java:316)
>     at
>
> org.apache.hadoop.hbase.mapreduce.LoadIncrementalHFiles$1.call(LoadIncrementalHFiles.java:314)
>     at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
>     at java.util.concurrent.FutureTask.run(FutureTask.java:138)
>     at
>
> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
>     at
>
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
>     at java.lang.Thread.run(Thread.java:662)
>
>    Locked ownable synchronizers:
>     - <0x000000075fe494c0> (a
> java.util.concurrent.locks.ReentrantLock$NonfairSync)
>
> ... ...
> ... ...
>
> "Reference Handler" daemon prio=10 tid=0x00007f540c138800 nid=0x2172 in
> Object.wait() [0x00007f5401355000]
>    java.lang.Thread.State: WAITING (on object monitor)
>     at java.lang.Object.wait(Native Method)
>     - waiting on <0x0000000763d51078> (a java.lang.ref.Reference$Lock)
>     at java.lang.Object.wait(Object.java:485)
>     at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:116)
>     - locked <0x0000000763d51078> (a java.lang.ref.Reference$Lock)
>
>    Locked ownable synchronizers:
>     - None
>
> "main" prio=10 tid=0x00007f540c00e000 nid=0x216a waiting on condition
> [0x00007f54114ac000]
>    java.lang.Thread.State: WAITING (parking)
>     at sun.misc.Unsafe.park(Native Method)
>     - parking to wait for  <0x000000075ea67310> (a
> java.util.concurrent.FutureTask$Sync)
>     at java.util.concurrent.locks.LockSupport.park(LockSupport.java:156)
>     at
>
> java.util.concurrent.locks.AbstractQueuedSynchronizer.parkAndCheckInterrupt(AbstractQueuedSynchronizer.java:811)
>     at
>
> java.util.concurrent.locks.AbstractQueuedSynchronizer.doAcquireSharedInterruptibly(AbstractQueuedSynchronizer.java:969)
>     at
>
> java.util.concurrent.locks.AbstractQueuedSynchronizer.acquireSharedInterruptibly(AbstractQueuedSynchronizer.java:1281)
>     at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:218)
>     at java.util.concurrent.FutureTask.get(FutureTask.java:83)
>     at
>
> org.apache.hadoop.hbase.mapreduce.LoadIncrementalHFiles.bulkLoadPhase(LoadIncrementalHFiles.java:326)
>     at
>
> org.apache.hadoop.hbase.mapreduce.LoadIncrementalHFiles.doBulkLoad(LoadIncrementalHFiles.java:261)
>     at
>
> org.apache.hadoop.hbase.mapreduce.LoadIncrementalHFiles.run(LoadIncrementalHFiles.java:780)
>     at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:65)
>     at org.apache.hadoop.util.ToolRunner.run(ToolRunner.java:79)
>     at
>
> org.apache.hadoop.hbase.mapreduce.LoadIncrementalHFiles.main(LoadIncrementalHFiles.java:785)
>
>    Locked ownable synchronizers:
>     - None
>
> "VM Thread" prio=10 tid=0x00007f540c132000 nid=0x2170 runnable
>
> "Gang worker#0 (Parallel GC Threads)" prio=10 tid=0x00007f540c01c800
> nid=0x216b runnable
>
> "Gang worker#1 (Parallel GC Threads)" prio=10 tid=0x00007f540c01e800
> nid=0x216c runnable
>
> "Gang worker#2 (Parallel GC Threads)" prio=10 tid=0x00007f540c020000
> nid=0x216d runnable
>
> "Gang worker#3 (Parallel GC Threads)" prio=10 tid=0x00007f540c022000
> nid=0x216e runnable
>
> "Concurrent Mark-Sweep GC Thread" prio=10 tid=0x00007f540c0b1000
> nid=0x216f runnable "VM Periodic Task Thread" prio=10
> tid=0x00007f540c16b000 nid=0x217a waiting on condition
>
> JNI global references: 1118
>
>
> 2013/12/18 Ted Yu <yuzhihong@gmail.com>
>
> > Tao:
> > Can you jstack one such process next time you see them hanging ?
> >
> > Thanks
> >
> >
> > On Tue, Dec 17, 2013 at 6:31 PM, Tao Xiao <xiaotao.cs.nju@gmail.com>
> > wrote:
> >
> > > BTW, I noticed another problem. I bulk load data into HBase every
> > > five minutes, but I found that whenever the following command was
> executed
> > >     hbase org.apache.hadoop.hbase.mapreduce.LoadIncrementalHFiles
> > > HFiles-Dir  MyTable
> > >
> > > there is a new process called "LoadIncrementalHFiles"
> > >
> > > I can see many processes called "LoadIncrementalHFiles" using the
> > > command "jps" in the terminal´╝î why are these processes still there
> > > even after the command that bulk load HFiles into HBase has finished
> > > executing ? I have
> > to
> > > kill them myself.
> > >
> > >
> > > 2013/12/17 Bijieshan <bijieshan@huawei.com>
> > >
> > > > Yes, it should be cleaned up. But not included in current code in
> > > > my understanding.
> > > >
> > > > Jieshan.
> > > > -----Original Message-----
> > > > From: Ted Yu [mailto:yuzhihong@gmail.com]
> > > > Sent: Tuesday, December 17, 2013 10:55 AM
> > > > To: user@hbase.apache.org
> > > > Subject: Re: Why so many unexpected files like partitions_xxxx are
> > > created?
> > > >
> > > > Should bulk load task clean up partitions_xxxx upon completion ?
> > > >
> > > > Cheers
> > > >
> > > >
> > > > On Mon, Dec 16, 2013 at 6:53 PM, Bijieshan <bijieshan@huawei.com>
> > wrote:
> > > >
> > > > > >  I think I should delete these files immediately after I have
> > > > > > finished
> > > > > bulk loading data into HBase since they are useless at that
> > > > > time,
> > > right ?
> > > > >
> > > > > Ya. I think so. They are useless once bulk load task finished.
> > > > >
> > > > > Jieshan.
> > > > > -----Original Message-----
> > > > > From: Tao Xiao [mailto:xiaotao.cs.nju@gmail.com]
> > > > > Sent: Tuesday, December 17, 2013 9:34 AM
> > > > > To: user@hbase.apache.org
> > > > > Subject: Re: Why so many unexpected files like partitions_xxxx
> > > > > are
> > > > created?
> > > > >
> > > > > Indeed these files are produced by
> org.apache.hadoop.hbase.mapreduce.
> > > > > LoadIncrementalHFiles in the directory specified by what
> > > > > job.getWorkingDirectory()
> > > > > returns, and I think I should delete these files immediately
> > > > > after I have finished bulk loading data into HBase since they
> > > > > are useless at that time, right ?
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > 2013/12/16 Bijieshan <bijieshan@huawei.com>
> > > > >
> > > > > > The reduce partition information is stored in this
> > > > > > partition_XXXX
> > > file.
> > > > > > See the below code:
> > > > > >
> > > > > > HFileOutputFormat#configureIncrementalLoad:
> > > > > >         .....................
> > > > > >     Path partitionsPath = new Path(job.getWorkingDirectory(),
> > > > > >                                    "partitions_" +
> > > UUID.randomUUID());
> > > > > >     LOG.info("Writing partition information to " +
> > > > > > partitionsPath);
> > > > > >
> > > > > >     FileSystem fs = partitionsPath.getFileSystem(conf);
> > > > > >     writePartitions(conf, partitionsPath, startKeys);
> > > > > >         .....................
> > > > > >
> > > > > > Hoping it helps.
> > > > > >
> > > > > > Jieshan
> > > > > > -----Original Message-----
> > > > > > From: Tao Xiao [mailto:xiaotao.cs.nju@gmail.com]
> > > > > > Sent: Monday, December 16, 2013 6:48 PM
> > > > > > To: user@hbase.apache.org
> > > > > > Subject: Why so many unexpected files like partitions_xxxx are
> > > created?
> > > > > >
> > > > > > I imported data into HBase in the fashion of bulk load,  but
> > > > > > after that I found many unexpected file were created in the
> > > > > > HDFS
> > directory
> > > > > > of /user/root/, and they like these:
> > > > > >
> > > > > > /user/root/partitions_fd74866b-6588-468d-8463-474e202db070
> > > > > > /user/root/partitions_fd867cd2-d9c9-48f5-9eec-185b2e57788d
> > > > > > /user/root/partitions_fda37b8a-a882-4787-babc-8310a969f85c
> > > > > > /user/root/partitions_fdaca2f4-2792-41f6-b7e8-61a8a5677dea
> > > > > > /user/root/partitions_fdd55baa-3a12-493e-8844-a23ae83209c5
> > > > > > /user/root/partitions_fdd85a3c-9abe-45d4-a0c6-76d2bed88ea5
> > > > > > /user/root/partitions_fe133460-5f3f-4c6a-9fff-ff6c62410cc1
> > > > > > /user/root/partitions_fe29a2b0-b281-465f-8d4a-6044822d960a
> > > > > > /user/root/partitions_fe2fa6fa-9066-484c-bc91-ec412e48d008
> > > > > > /user/root/partitions_fe31667b-2d5a-452e-baf7-a81982fe954a
> > > > > > /user/root/partitions_fe3a5542-bc4d-4137-9d5e-1a0c59f72ac3
> > > > > > /user/root/partitions_fe6a9407-c27b-4a67-bb50-e6b9fd172bc9
> > > > > > /user/root/partitions_fe6f9294-f970-473c-8659-c08292c27ddd
> > > > > > ... ...
> > > > > > ... ...
> > > > > >
> > > > > >
> > > > > > It seems that they are HFiles, but I don't know why the were
> > created
> > > > > here?
> > > > > >
> > > > > > I bulk load data into HBase in the following way:
> > > > > >
> > > > > > Firstly,   I wrote a MapReduce program which only has map tasks.
> > The
> > > > map
> > > > > > tasks read some text data and emit them in the form of  RowKey
> > > > > > and KeyValue.The following is my program:
> > > > > >
> > > > > >         @Override
> > > > > >         protected void map(NullWritable NULL,
> > > > > > GtpcV1SignalWritable signal, Context ctx) throws
> InterruptedException, IOException {
> > > > > >             String strRowkey = xxx;
> > > > > >             byte[] rowkeyBytes = Bytes.toBytes(strRowkey);
> > > > > >
> > > > > >             rowkey.set(rowkeyBytes);
> > > > > >
> > > > > >             part1.init(signal);
> > > > > >             part2.init(signal);
> > > > > >
> > > > > >             KeyValue kv = new KeyValue(rowkeyBytes, Family_A,
> > > > > > Qualifier_Q, part1.serialize());
> > > > > >             ctx.write(rowkey, kv);
> > > > > >
> > > > > >             kv = new KeyValue(rowkeyBytes, Family_B,
> > > > > > Qualifier_Q, part2.serialize());
> > > > > >             ctx.write(rowkey, kv);
> > > > > >         }
> > > > > >
> > > > > >
> > > > > > after the MR programs finished, there were several HFiles
> > > > > > generated in the output directory I specified.
> > > > > >
> > > > > > Then I bean to load these HFiles into HBase using the
> > > > > > following
> > > > command:
> > > > > >        hbase
> > org.apache.hadoop.hbase.mapreduce.LoadIncrementalHFiles
> > > > > > HFiles-Dir  MyTable
> > > > > >
> > > > > > Finally , I could see that the data were indeed loaded into
> > > > > > the table in HBase.
> > > > > >
> > > > > >
> > > > > > But, I could also see that there were many unexpected files
> > > > > > generated in the HDFS directory of  /user/root/,  just as I
> > > > > > have mentioned at the begining of this mail,  and I did not
> > > > > > specify any files to be produced in this directory.
> > > > > >
> > > > > > What happened ? Who can tell me what there files are and who
> > > > > > produced
> > > > > them?
> > > > > >
> > > > > > Thanks
> > > > > >
> > > > >
> > > >
> > >
> >
>

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