Hadoop last reduce job stuck at connection timeout

Question

My hadoop job was stuck at the last reduce tasks. I have seen a lot of connection timeout from 3 different hosts to a single host. However, I am able to ping the troublesome machine from any other machine.

This is a 5 node cluster. It's built very recently. They have the same binary of hadoop and pig. It has 3 new machines and 2 old ones. If I removed the 2 old machines, it's working fine.

Problematic old machine version:

java version "1.6.0_20"
OpenJDK Runtime Environment (IcedTea6 1.9.13) (6b20-1.9.13-0ubuntu1~10.10.1)
OpenJDK 64-Bit Server VM (build 19.0-b09, mixed mode)

New working machine version:

java version "1.6.0_24"
OpenJDK Runtime Environment (IcedTea6 1.11.3) (6b24-1.11.3-1ubuntu0.12.04.1)
OpenJDK 64-Bit Server VM (build 20.0-b12, mixed mode)

Also I have seen insane amount (180) of dup hosts from the logs.

2012-08-28 12:34:53,307 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Need another 4 map output(s) where 1 is already in progress
2012-08-28 12:34:53,307 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Scheduled 0 outputs (0 slow hosts and3 dup hosts)
2012-08-28 12:35:53,308 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Need another 4 map output(s) where 1 is already in progress
2012-08-28 12:35:53,308 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Scheduled 0 outputs (0 slow hosts and3 dup hosts)
2012-08-28 12:36:53,309 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Need another 4 map output(s) where 1 is already in progress
2012-08-28 12:36:53,309 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Scheduled 0 outputs (0 slow hosts and3 dup hosts)
2012-08-28 12:37:18,416 WARN org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 copy failed: attempt_201208231557_0021_m_000002_0 from Han
2012-08-28 12:37:18,417 WARN org.apache.hadoop.mapred.ReduceTask: java.net.SocketTimeoutException: connect timed out
    at java.net.PlainSocketImpl.socketConnect(Native Method)
    at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:327)
    at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:193)
    at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:180)
    at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:384)
    at java.net.Socket.connect(Socket.java:546)
    at sun.net.NetworkClient.doConnect(NetworkClient.java:173)
    at sun.net.www.http.HttpClient.openServer(HttpClient.java:409)
    at sun.net.www.http.HttpClient.openServer(HttpClient.java:530)
    at sun.net.www.http.HttpClient.<init>(HttpClient.java:240)
    at sun.net.www.http.HttpClient.New(HttpClient.java:321)
    at sun.net.www.http.HttpClient.New(HttpClient.java:338)
    at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:935)
    at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:876)
    at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:801)
    at org.apache.hadoop.mapred.ReduceTask$ReduceCopier$MapOutputCopier.getInputStream(ReduceTask.java:1618)
    at org.apache.hadoop.mapred.ReduceTask$ReduceCopier$MapOutputCopier.setupSecureConnection(ReduceTask.java:1575)
    at org.apache.hadoop.mapred.ReduceTask$ReduceCopier$MapOutputCopier.getMapOutput(ReduceTask.java:1483)
    at org.apache.hadoop.mapred.ReduceTask$ReduceCopier$MapOutputCopier.copyOutput(ReduceTask.java:1394)
    at org.apache.hadoop.mapred.ReduceTask$ReduceCopier$MapOutputCopier.run(ReduceTask.java:1326)

2012-08-28 12:37:18,417 INFO org.apache.hadoop.mapred.ReduceTask: Task attempt_201208231557_0021_r_000008_0: Failed fetch #6 from attempt_201208231557_0021_m_000002_0
2012-08-28 12:37:18,417 WARN org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 adding host Han to penalty box, next contact in 48 seconds
2012-08-28 12:37:18,417 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0: Got 1 map-outputs from previous failures
2012-08-28 12:37:53,418 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Need another 4 map output(s) where 0 is already in progress
2012-08-28 12:37:53,418 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Scheduled 0 outputs (1 slow hosts and0 dup hosts)
2012-08-28 12:37:53,418 INFO org.apache.hadoop.mapred.ReduceTask: Penalized(slow) Hosts: 
2012-08-28 12:37:53,418 INFO org.apache.hadoop.mapred.ReduceTask: Han Will be considered after: 13 seconds.
2012-08-28 12:38:08,418 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Scheduled 1 outputs (0 slow hosts and0 dup hosts)
2012-08-28 12:38:53,419 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Need another 4 map output(s) where 1 is already in progress
2012-08-28 12:38:53,419 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Scheduled 0 outputs (0 slow hosts and3 dup hosts)
2012-08-28 12:39:53,420 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Need another 4 map output(s) where 1 is already in progress
2012-08-28 12:39:53,420 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Scheduled 0 outputs (0 slow hosts and3 dup hosts)
2012-08-28 12:40:53,421 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Need another 4 map output(s) where 1 is already in progress
2012-08-28 12:40:53,421 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Scheduled 0 outputs (0 slow hosts and3 dup hosts)
2012-08-28 12:41:08,537 WARN org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 copy failed: attempt_201208231557_0021_m_000002_0 from Han
2012-08-28 12:41:08,538 WARN org.apache.hadoop.mapred.ReduceTask: java.net.SocketTimeoutException: connect timed out
    at java.net.PlainSocketImpl.socketConnect(Native Method)
    at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:327)
    at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:193)
    at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:180)
    at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:384)
    at java.net.Socket.connect(Socket.java:546)
    at sun.net.NetworkClient.doConnect(NetworkClient.java:173)
    at sun.net.www.http.HttpClient.openServer(HttpClient.java:409)
    at sun.net.www.http.HttpClient.openServer(HttpClient.java:530)
    at sun.net.www.http.HttpClient.<init>(HttpClient.java:240)
    at sun.net.www.http.HttpClient.New(HttpClient.java:321)
    at sun.net.www.http.HttpClient.New(HttpClient.java:338)
    at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:935)
    at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:876)
    at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:801)
    at org.apache.hadoop.mapred.ReduceTask$ReduceCopier$MapOutputCopier.getInputStream(ReduceTask.java:1618)
    at org.apache.hadoop.mapred.ReduceTask$ReduceCopier$MapOutputCopier.setupSecureConnection(ReduceTask.java:1575)
    at org.apache.hadoop.mapred.ReduceTask$ReduceCopier$MapOutputCopier.getMapOutput(ReduceTask.java:1483)
    at org.apache.hadoop.mapred.ReduceTask$ReduceCopier$MapOutputCopier.copyOutput(ReduceTask.java:1394)
    at org.apache.hadoop.mapred.ReduceTask$ReduceCopier$MapOutputCopier.run(ReduceTask.java:1326)

2012-08-28 12:41:08,538 INFO org.apache.hadoop.mapred.ReduceTask: Task attempt_201208231557_0021_r_000008_0: Failed fetch #7 from attempt_201208231557_0021_m_000002_0
2012-08-28 12:41:08,538 WARN org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 adding host Han to penalty box, next contact in 62 seconds
2012-08-28 12:41:08,538 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0: Got 1 map-outputs from previous failures
2012-08-28 12:41:53,539 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Need another 4 map output(s) where 0 is already in progress
2012-08-28 12:41:53,539 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Scheduled 0 outputs (1 slow hosts and0 dup hosts)
2012-08-28 12:41:53,539 INFO org.apache.hadoop.mapred.ReduceTask: Penalized(slow) Hosts: 
2012-08-28 12:41:53,539 INFO org.apache.hadoop.mapred.ReduceTask: Han Will be considered after: 17 seconds.
2012-08-28 12:42:13,540 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Scheduled 1 outputs (0 slow hosts and0 dup hosts)
2012-08-28 12:42:53,540 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Need another 4 map output(s) where 1 is already in progress
2012-08-28 12:42:53,540 INFO org.apache.hadoop.mapred.ReduceTask: attempt_201208231557_0021_r_000008_0 Scheduled 0 outputs (0 slow hosts and3 dup hosts)

More logs:

2012-09-06 11:01:47,719 INFO org.apache.hadoop.mapred.TaskTracker: attempt_201209041720_0010_r_000014_0 1.0% reduce > reduce
2012-09-06 11:01:47,720 INFO org.apache.hadoop.mapred.TaskTracker: Task attempt_201209041720_0010_r_000014_0 is done.
2012-09-06 11:01:47,720 INFO org.apache.hadoop.mapred.TaskTracker: reported output size for attempt_201209041720_0010_r_000014_0  was -1
2012-09-06 11:01:47,720 INFO org.apache.hadoop.mapred.TaskTracker: addFreeSlot : current free slots : 6
2012-09-06 11:01:47,769 INFO org.apache.hadoop.mapred.JvmManager: JVM : jvm_201209041720_0010_r_1617080101 exited with exit code 0. Number of tasks it ran: 1
2012-09-06 11:01:47,913 INFO org.apache.hadoop.mapred.JvmManager: JVM : jvm_201209041720_0010_r_-434797671 exited with exit code 0. Number of tasks it ran: 1
2012-09-06 11:01:50,428 INFO org.apache.hadoop.mapred.TaskTracker: Received KillTaskAction for task: attempt_201209041720_0010_r_000014_0
2012-09-06 11:01:50,428 INFO org.apache.hadoop.mapred.TaskTracker: About to purge task: attempt_201209041720_0010_r_000014_0
2012-09-06 11:01:50,429 INFO org.apache.hadoop.mapred.TaskTracker: Received KillTaskAction for task: attempt_201209041720_0010_r_000020_0
2012-09-06 11:01:50,429 INFO org.apache.hadoop.mapred.TaskTracker: About to purge task: attempt_201209041720_0010_r_000020_0

Answer 1

Task trackers need to shuffle inter media among data nodes when HADOOP job is in reduce phase. It occur connection timeout error if you setup data nodes host name in slaves configuration file, while cannot resolve host names. Add host name and IP address to /etc/hosts is a quick solution.

Answer 2

Not sure why this might be happening, but I had the same issue... My datanode was trying to access a namenode on localhost, instead of my actual 'master' namenode...

I solved this by going to my hosts file:

etc/hosts

and removing the localhost line from there. I'm pretty sure there should be a cleaner way to fix this, but this solution worked for me.

If anybody has a cleaner way to prevent the datanode from trying to access the namenode on localhost, please let me know!!!

Answer 3

It might be due to the slow hard drives. On new machines (Samsung 830 SSD) I am seeing transfer rate of 3MB/s and slow machines (spinning hard drives) 0.12 MB/s. It probably just got a large reducer job and too slow.

Answer 4

Are you using the default speculative execution settings? (4 tries) - here's an article that may help.