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From Davey Yan <davey....@gmail.com>
Subject Re: Datanodes shutdown and HBase's regionservers not working
Date Thu, 28 Feb 2013 00:58:41 GMT
Yes, we make sure that inappropriate use of NFS leading to high load
and the lost heartbeat between cluster members.
There was a NFS partition point to one virtual machine for some
purpose, but the virtual machine shutted down frequently.
BTW, the NFS partition was not for the backup of NN metadata, just for
other temporary purpose, and it has been removed now.
The NFS partition(with autofs) for NN metadata backup has no problem.

For more info, google the "NFS high load"...


On Wed, Feb 27, 2013 at 9:58 AM, Jean-Marc Spaggiari
<jean-marc@spaggiari.org> wrote:
> Hi Davey,
>
> So were you able to find the issue?
>
> JM
>
> 2013/2/25 Davey Yan <davey.yan@gmail.com>:
>> Hi Nicolas,
>>
>> I think i found what led to shutdown of all of the datanodes, but i am
>> not completely certain.
>> I will return to this mail list when my cluster returns to be stable.
>>
>> On Mon, Feb 25, 2013 at 8:01 PM, Nicolas Liochon <nkeywal@gmail.com> wrote:
>>> Network error messages are not always friendly, especially if there is a
>>> misconfiguration.
>>> This said,  "connection refused" says that the network connection was made,
>>> but that the remote port was not opened on the remote box. I.e. the process
>>> was dead.
>>> It could be useful to pastebin the whole logs as well...
>>>
>>>
>>> On Mon, Feb 25, 2013 at 12:44 PM, Davey Yan <davey.yan@gmail.com> wrote:
>>>>
>>>> But... there was no log like "network unreachable".
>>>>
>>>>
>>>> On Mon, Feb 25, 2013 at 6:07 PM, Nicolas Liochon <nkeywal@gmail.com>
>>>> wrote:
>>>> > I agree.
>>>> > Then for HDFS, ...
>>>> > The first thing to check is the network I would say.
>>>> >
>>>> >
>>>> >
>>>> >
>>>> > On Mon, Feb 25, 2013 at 10:46 AM, Davey Yan <davey.yan@gmail.com>
wrote:
>>>> >>
>>>> >> Thanks for reply, Nicolas.
>>>> >>
>>>> >> My question: What can lead to shutdown of all of the datanodes?
>>>> >> I believe that the regionservers will be OK if the HDFS is OK.
>>>> >>
>>>> >>
>>>> >> On Mon, Feb 25, 2013 at 5:31 PM, Nicolas Liochon <nkeywal@gmail.com>
>>>> >> wrote:
>>>> >> > Ok, what's your question?
>>>> >> > When you say the datanode went down, was it the datanode processes
or
>>>> >> > the
>>>> >> > machines, with both the datanodes and the regionservers?
>>>> >> >
>>>> >> > The NameNode pings its datanodes every 3 seconds. However it
will
>>>> >> > internally
>>>> >> > mark the datanodes as dead after 10:30 minutes (even if in
the gui
>>>> >> > you
>>>> >> > have
>>>> >> > 'no answer for x minutes').
>>>> >> > HBase monitoring is done by ZooKeeper. By default, a regionserver
is
>>>> >> > considered as dead after 180s with no answer. Before, well,
it's
>>>> >> > considered
>>>> >> > as live.
>>>> >> > When you stop a regionserver, it tries to flush its data to
the disk
>>>> >> > (i.e.
>>>> >> > hdfs, i.e. the datanodes). That's why if you have no datanodes,
or if
>>>> >> > a
>>>> >> > high
>>>> >> > ratio of your datanodes are dead, it can't shutdown. Connection
>>>> >> > refused
>>>> >> > &
>>>> >> > socket timeouts come from the fact that before the 10:30 minutes
hdfs
>>>> >> > does
>>>> >> > not declare the nodes as dead, so hbase tries to use them (and,
>>>> >> > obviously,
>>>> >> > fails). Note that there is now  an intermediate state for hdfs
>>>> >> > datanodes,
>>>> >> > called "stale": an intermediary state where the datanode is
used only
>>>> >> > if
>>>> >> > you
>>>> >> > have to (i.e. it's the only datanode with a block replica you
need).
>>>> >> > It
>>>> >> > will
>>>> >> > be documented in HBase for the 0.96 release. But if all your
>>>> >> > datanodes
>>>> >> > are
>>>> >> > down it won't change much.
>>>> >> >
>>>> >> > Cheers,
>>>> >> >
>>>> >> > Nicolas
>>>> >> >
>>>> >> >
>>>> >> >
>>>> >> > On Mon, Feb 25, 2013 at 10:10 AM, Davey Yan <davey.yan@gmail.com>
>>>> >> > wrote:
>>>> >> >>
>>>> >> >> Hey guys,
>>>> >> >>
>>>> >> >> We have a cluster with 5 nodes(1 NN and 4 DNs) running
for more than
>>>> >> >> 1
>>>> >> >> year, and it works fine.
>>>> >> >> But the datanodes got shutdown twice in the last month.
>>>> >> >>
>>>> >> >> When the datanodes got shutdown, all of them became "Dead
Nodes" in
>>>> >> >> the NN web admin UI(http://ip:50070/dfshealth.jsp),
>>>> >> >> but regionservers of HBase were still live in the HBase
web
>>>> >> >> admin(http://ip:60010/master-status), of course, they were
zombies.
>>>> >> >> All of the processes of jvm were still running, including
>>>> >> >> hmaster/namenode/regionserver/datanode.
>>>> >> >>
>>>> >> >> When the datanodes got shutdown, the load (using the "top"
command)
>>>> >> >> of
>>>> >> >> slaves became very high, more than 10, higher than normal
running.
>>>> >> >> From the "top" command, we saw that the processes of datanode
and
>>>> >> >> regionserver were comsuming CPU.
>>>> >> >>
>>>> >> >> We could not stop the HBase or Hadoop cluster through normal
>>>> >> >> commands(stop-*.sh/*-daemon.sh stop *).
>>>> >> >> So we stopped datanodes and regionservers by kill -9 PID,
then the
>>>> >> >> load of slaves returned to normal level, and we start the
cluster
>>>> >> >> again.
>>>> >> >>
>>>> >> >>
>>>> >> >> Log of NN at the shutdown point(All of the DNs were removed):
>>>> >> >> 2013-02-22 11:10:02,278 INFO org.apache.hadoop.net.NetworkTopology:
>>>> >> >> Removing a node: /default-rack/192.168.1.152:50010
>>>> >> >> 2013-02-22 11:10:02,278 INFO org.apache.hadoop.hdfs.StateChange:
>>>> >> >> BLOCK* NameSystem.heartbeatCheck: lost heartbeat from
>>>> >> >> 192.168.1.149:50010
>>>> >> >> 2013-02-22 11:10:02,693 INFO org.apache.hadoop.net.NetworkTopology:
>>>> >> >> Removing a node: /default-rack/192.168.1.149:50010
>>>> >> >> 2013-02-22 11:10:02,693 INFO org.apache.hadoop.hdfs.StateChange:
>>>> >> >> BLOCK* NameSystem.heartbeatCheck: lost heartbeat from
>>>> >> >> 192.168.1.150:50010
>>>> >> >> 2013-02-22 11:10:03,004 INFO org.apache.hadoop.net.NetworkTopology:
>>>> >> >> Removing a node: /default-rack/192.168.1.150:50010
>>>> >> >> 2013-02-22 11:10:03,004 INFO org.apache.hadoop.hdfs.StateChange:
>>>> >> >> BLOCK* NameSystem.heartbeatCheck: lost heartbeat from
>>>> >> >> 192.168.1.148:50010
>>>> >> >> 2013-02-22 11:10:03,339 INFO org.apache.hadoop.net.NetworkTopology:
>>>> >> >> Removing a node: /default-rack/192.168.1.148:50010
>>>> >> >>
>>>> >> >>
>>>> >> >> Logs in DNs indicated there were many IOException and
>>>> >> >> SocketTimeoutException:
>>>> >> >> 2013-02-22 11:02:52,354 ERROR
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.DataNode:
>>>> >> >> DatanodeRegistration(192.168.1.148:50010,
>>>> >> >> storageID=DS-970284113-117.25.149.160-50010-1328074119937,
>>>> >> >> infoPort=50075, ipcPort=50020):DataXceiver
>>>> >> >> java.io.IOException: Interrupted receiveBlock
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.BlockReceiver.receiveBlock(BlockReceiver.java:577)
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.DataXceiver.writeBlock(DataXceiver.java:398)
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.DataXceiver.run(DataXceiver.java:107)
>>>> >> >>         at java.lang.Thread.run(Thread.java:662)
>>>> >> >> 2013-02-22 11:03:44,823 WARN
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.DataNode:
>>>> >> >> DatanodeRegistration(192.168.1.148:50010,
>>>> >> >> storageID=DS-970284113-117.25.149.160-50010-1328074119937,
>>>> >> >> infoPort=50075, ipcPort=50020):Got exception while serving
>>>> >> >> blk_-1985405101514576650_247001 to /192.168.1.148:
>>>> >> >> java.net.SocketTimeoutException: 480000 millis timeout
while waiting
>>>> >> >> for channel to be ready for write. ch :
>>>> >> >> java.nio.channels.SocketChannel[connected local=/192.168.1.148:50010
>>>> >> >> remote=/192.168.1.148:48654]
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.net.SocketIOWithTimeout.waitForIO(SocketIOWithTimeout.java:246)
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.net.SocketOutputStream.waitForWritable(SocketOutputStream.java:159)
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.net.SocketOutputStream.transferToFully(SocketOutputStream.java:198)
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.BlockSender.sendChunks(BlockSender.java:350)
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.BlockSender.sendBlock(BlockSender.java:436)
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.DataXceiver.readBlock(DataXceiver.java:197)
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.DataXceiver.run(DataXceiver.java:99)
>>>> >> >>         at java.lang.Thread.run(Thread.java:662)
>>>> >> >> 2013-02-22 11:09:42,294 ERROR
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.DataNode:
>>>> >> >> DatanodeRegistration(192.168.1.148:50010,
>>>> >> >> storageID=DS-970284113-117.25.149.160-50010-1328074119937,
>>>> >> >> infoPort=50075, ipcPort=50020):DataXceiver
>>>> >> >> java.net.SocketTimeoutException: 480000 millis timeout
while waiting
>>>> >> >> for channel to be ready for write. ch :
>>>> >> >> java.nio.channels.SocketChannel[connected local=/192.168.1.148:50010
>>>> >> >> remote=/192.168.1.148:37188]
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.net.SocketIOWithTimeout.waitForIO(SocketIOWithTimeout.java:246)
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.net.SocketOutputStream.waitForWritable(SocketOutputStream.java:159)
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.net.SocketOutputStream.transferToFully(SocketOutputStream.java:198)
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.BlockSender.sendChunks(BlockSender.java:350)
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.BlockSender.sendBlock(BlockSender.java:436)
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.DataXceiver.readBlock(DataXceiver.java:197)
>>>> >> >>         at
>>>> >> >>
>>>> >> >>
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.DataXceiver.run(DataXceiver.java:99)
>>>> >> >>         at java.lang.Thread.run(Thread.java:662)
>>>> >> >> 2013-02-22 11:12:41,892 INFO
>>>> >> >> org.apache.hadoop.hdfs.server.datanode.DataBlockScanner:
>>>> >> >> Verification
>>>> >> >> succeeded for blk_-2674357249542194287_43419
>>>> >> >>
>>>> >> >>
>>>> >> >> Here is our env:
>>>> >> >> hadoop 1.0.3
>>>> >> >> hbase 0.94.1(snappy enabled)
>>>> >> >>
>>>> >> >> java version "1.6.0_31"
>>>> >> >> Java(TM) SE Runtime Environment (build 1.6.0_31-b04)
>>>> >> >> Java HotSpot(TM) 64-Bit Server VM (build 20.6-b01, mixed
mode)
>>>> >> >>
>>>> >> >> # ulimit -a
>>>> >> >> core file size          (blocks, -c) 0
>>>> >> >> data seg size           (kbytes, -d) unlimited
>>>> >> >> scheduling priority             (-e) 20
>>>> >> >> file size               (blocks, -f) unlimited
>>>> >> >> pending signals                 (-i) 16382
>>>> >> >> max locked memory       (kbytes, -l) 64
>>>> >> >> max memory size         (kbytes, -m) unlimited
>>>> >> >> open files                      (-n) 32768
>>>> >> >> pipe size            (512 bytes, -p) 8
>>>> >> >> POSIX message queues     (bytes, -q) 819200
>>>> >> >> real-time priority              (-r) 0
>>>> >> >> stack size              (kbytes, -s) 8192
>>>> >> >> cpu time               (seconds, -t) unlimited
>>>> >> >> max user processes              (-u) 32768
>>>> >> >> virtual memory          (kbytes, -v) unlimited
>>>> >> >> file locks                      (-x) unlimited
>>>> >> >>
>>>> >> >> # uname -a
>>>> >> >> Linux ubuntu6401 2.6.32-33-server #70-Ubuntu SMP Thu Jul
7 22:28:30
>>>> >> >> UTC 2011 x86_64 GNU/Linux
>>>> >> >>
>>>> >> >>
>>>> >> >> # free(master)
>>>> >> >>              total       used       free     shared   
buffers
>>>> >> >> cached
>>>> >> >> Mem:      24732936    8383708   16349228          0   
 490584
>>>> >> >> 2580356
>>>> >> >> -/+ buffers/cache:    5312768   19420168
>>>> >> >> Swap:     72458232          0   72458232
>>>> >> >>
>>>> >> >>
>>>> >> >> # free(slaves)
>>>> >> >>              total       used       free     shared   
buffers
>>>> >> >> cached
>>>> >> >> Mem:      24733000   22824276    1908724          0   
 862556
>>>> >> >> 15303304
>>>> >> >> -/+ buffers/cache:    6658416   18074584
>>>> >> >> Swap:     72458232        264   72457968
>>>> >> >>
>>>> >> >>
>>>> >> >> Some important conf:
>>>> >> >> core-site.xml
>>>> >> >>         <property>
>>>> >> >>                 <name>io.file.buffer.size</name>
>>>> >> >>                 <value>65536</value>
>>>> >> >>         </property>
>>>> >> >>
>>>> >> >> hdfs-site.xml
>>>> >> >>         <property>
>>>> >> >>                 <name>dfs.block.size</name>
>>>> >> >>                 <value>134217728</value>
>>>> >> >>         </property>
>>>> >> >>         <property>
>>>> >> >>                 <name>dfs.datanode.max.xcievers</name>
>>>> >> >>                 <value>4096</value>
>>>> >> >>         </property>
>>>> >> >>         <property>
>>>> >> >>                 <name>dfs.support.append</name>
>>>> >> >>                 <value>true</value>
>>>> >> >>         </property>
>>>> >> >>         <property>
>>>> >> >>                 <name>dfs.replication</name>
>>>> >> >>                 <value>2</value>
>>>> >> >>         </property>
>>>> >> >>
>>>> >> >>
>>>> >> >> Hope you can help us.
>>>> >> >> Thanks in advance.
>>>> >> >>
>>>> >> >>
>>>> >> >>
>>>> >> >> --
>>>> >> >> Davey Yan
>>>> >> >
>>>> >> >
>>>> >>
>>>> >>
>>>> >>
>>>> >> --
>>>> >> Davey Yan
>>>> >
>>>> >
>>>>
>>>>
>>>>
>>>> --
>>>> Davey Yan
>>>
>>>
>>
>>
>>
>> --
>> Davey Yan



-- 
Davey Yan

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