8. Twister with FutureGrid HPC

Author: Tak-Lon Stephen Wu Version: 0.1 Date: 2011-10-30

Twister is widely used by domain scientists for running their scientific applications in parallel fashion. Here, we provide a detail instruction to use Hadoop on FutureGrid test-bed with FutureGrid India Cluster.

8.1. Requirement

  1. FutureGrid HPC account, please apply via FutureGrid portal and request a HPC account.
  2. Linux command experience.

8.2. Get HPC compute nodes

First, you will need to login to IU-india using the command:

Login command: ssh –i [ssh private key] [username]@india.futuregrid.org
ssh –i key.pem johnny@india.futuregrid.org
Enter passphrase for key 'ssh_id_rsa':
[johnny@i136 ~]$

Here, “i136” is the headnode (first login node) of IU-india cluster. You will obtain several HPC compute nodes from this node. Noted that, DO NOT run any of your program on the “i136” headnode. Then, on the command prompt, type the following command to get a set of compute nodes:

Obtain compute nodes command: qsub -I -l nodes=[numOfComputeNodes]:ppn=[CpuPerNode],walltime=[hh]:[mm]:[ss]

[johnny@i136 ~]$ module load torque
[johnny@i136 ~]$ qsub -I -l nodes=2:ppn=8,walltime=12:00:00
qsub: waiting for job 44418.i136 to start
qsub: job 44420.i136 ready
[johnny@i55 ~]$ cat $PBS_NODEFILE

As shown above, “i55” and “i56” are the assigned compute nodes where these nodes information are stored to environment parameter $PBS_NODEFILE.

8.3. Twister Configuration

We provide a detail instruction to startup twister 0.9. In this example, we use i55 as Driver/Master node, i56 as Worker/Slave node.

8.3.1. Download Twister 0.9

[johnny@i55 ~]$ wget http://salsahpc.indiana.edu/tutorial/apps/Twister-0.9.tar.gz
[johnny@i55 ~]$ tar -zxvf Twister-0.9.tar.gz

8.3.2. Set $TWISTER_HOME, $JAVA_HOME and Worker nodes

Before running Twister configuration script, we need to setup several environment parameters:

[johnny@i55 ~]$ echo export TWISTER_HOME=/N/u/johnny/twister-0.9 >> ~/.bashrc
[johnny@i55 ~]$ echo export JAVA_HOME=/N/soft/jdk1.6.0_20-x86_64 >> ~/.bashrc
[johnny@i55 ~]$ source ~/.bashrc
[johnny@i55 ~]$ vi $TWISTER_HOME/bin/nodes

8.3.3. Run TwisterPowerMakeUp.sh

Within twister 0.9 package, there is a TwisterPowerMakeUp.sh script to automatically configure Twister. Generally, it randomly picks one of the working nodes as ActiveMQ messaging broker, sets working daemon per node, and worker (mapper/reducer) per daemon. Also, it creates Twister required directories such as app_dir and data_dir.

[johnny@i55 bin]$ cd $TWISTER_HOME/bin
[johnny@i55 bin]$ ./TwisterPowerMakeUp.sh
use normal MultiNode Setup
no special processing to nodes
ActiveMQ uri=failover:(tcp://i56:61616)
i55:/N/u/johnny/twister-0.9/data created.
i56:/N/u/johnny/twister-0.9/data created.
Change max memory to 16054 MB
copied to i55:/N/u/johnny/twister-0.9
copied to i56:/N/u/johnny/twister-0.9
Auto configuration is done.

As shown in the message above “ActiveMQ uri=failover:(tcp://i56:61616)”, i56 is the selected node where ActiveMQ messaging broker will be started.

8.3.4. Download and start ActiveMQ on specific nodes

Now ssh to the selected node, i56, then download and unzip the ActiveMQ package. Finally start it up and return the previous master node, i56.

[johnny@i55 bin]$ ssh i56
[johnny@i56 ~]$ wget http://www.iterativemapreduce.org/apache-activemq-5.4.2-bin.tar.gz
[johnny@i56 ~]$ cd apache-activemq-5.4.2
[johnny@i56 apache-activemq-5.4.2]$ cd bin
[johnny@i56 bin]$ ./activemq console &
[1] 4009
[johnny@i56 bin]$ INFO: Using default configuration
(you can configure options in one of these file: /etc/default/activemq /N/u/johnny/.activemqrc)
INFO: Invoke the following command to create a configuration file
./activemq setup [ /etc/default/activemq /N/u/johnny/.activemqrc ]
INFO: Using java '/N/soft/jdk1.6.0_20-x86_64/bin/java'
INFO: Starting in foreground, this is just for debugging purposes (stop process by pressing CTRL+C)
Java Runtime: Sun Microsystems Inc. 1.6.0_20 /N/soft/jdk1.6.0_20-x86_64/jre
  Heap sizes: current=251264k  free=247327k  max=251264k
    JVM args: -Xms256M -Xmx256M -Dorg.apache.activemq.UseDedicatedTaskRunner=true -Djava.util.logging.config.file=logging.properties -Dcom.sun.management.jmxremote -Dactivemq.classpath=/N/u/johnny/apache-activemq-5.4.2/conf; -Dactivemq.home=/N/u/johnny/apache-activemq-5.4.2 -Dactivemq.base=/N/u/johnny/apache-activemq-5.4.2
ACTIVEMQ_HOME: /N/u/johnny/apache-activemq-5.4.2
ACTIVEMQ_BASE: /N/u/johnny/apache-activemq-5.4.2
Loading message broker from: xbean:activemq.xml
 INFO Refreshing org.apache.activemq.xbean.XBeanBrokerFactory$1@245e13ad: startup date [Sun Oct 30 23:33:22 EDT 2011]; root of context hierarchy
 WARN destroyApplicationContextOnStop parameter is deprecated, please use shutdown hooks instead
 INFO PListStore:/N/u/johnny/apache-activemq-5.4.2/data/localhost/tmp_storage started
 INFO Using Persistence Adapter: KahaDBPersistenceAdapter[/N/u/johnny/apache-activemq-5.4.2/data/kahadb]
 INFO KahaDB is version 3
 INFO Recovering from the journal ...
 INFO Recovery replayed 1 operations from the journal in 0.0080 seconds.
 INFO ActiveMQ 5.4.2 JMS Message Broker (localhost) is starting
 INFO For help or more information please see: http://activemq.apache.org/
 INFO Listening for connections at: tcp://i56:61616
 INFO Connector openwire Started
 INFO ActiveMQ JMS Message Broker (localhost, ID:i56-56404-1320032003342-0:1) started
 INFO jetty-7.1.6.v20100715
 INFO ActiveMQ WebConsole initialized.
 INFO Initializing Spring FrameworkServlet 'dispatcher'
 INFO ActiveMQ Console at
 INFO Initializing Spring root WebApplicationContext
 INFO camel-osgi.jar/camel-spring-osgi.jar not detected in classpath
 INFO Apache Camel 2.4.0 (CamelContext: camel) is starting
 INFO JMX enabled. Using ManagedManagementStrategy.
 INFO Found 4 packages with 15 @Converter classes to load
 INFO Loaded 146 type converters in 0.337 seconds
 INFO Connector vm://localhost Started
 INFO Route: route1 started and consuming from: Endpoint[activemq://example.A]
 INFO Started 1 routes
 INFO Apache Camel 2.4.0 (CamelContext: camel) started in 0.783 seconds
 INFO Camel Console at
 INFO ActiveMQ Web Demos at
 INFO RESTful file access application at
 INFO Started SelectChannelConnector@
[johnny@i56 bin]$ exit
[johnny@i55 bin]$

8.3.5. Start Twister

After you go back to the master node (i55), simply type command ./start_twister.sh & under $TWISTER_HOME/bin.

[johnny@i55 bin]$ ./start_twister.sh &
[1] 7844
[johnny@i55 bin]$ i55
Oct 30, 2011 11:34:38 PM org.apache.activemq.transport.failover.FailoverTransport doReconnect
INFO: Successfully connected to tcp://i56:61616
1    [main] INFO  cgl.imr.worker.DaemonWorker  - Daemon no: 0 started with 8 workers.
Oct 30, 2011 11:34:39 PM org.apache.activemq.transport.failover.FailoverTransport doReconnect
INFO: Successfully connected to tcp://i56:61616
0    [main] INFO  cgl.imr.worker.DaemonWorker  - Daemon no: 1 started with 8 workers.

[1]+  Done                    ./start_twister.sh

If you can see similar message above, twister has started successfully.

8.4. Verify Twister Status

Also you can use command “jps” on each node to make sure Twister (TwisterDaemon) is running.

On master node:

# on master node
[johnny@i55 bin]$ jps
7878 TwisterDaemon
7909 Jps

On slave and ActiveMQ node:

# on slave and ActiveMQ node
[johnny@i56 bin]$ jps
4265 Jps
4025 run.jar
4185 TwisterDaemon

Next step, try out the Twister Applications section to run Twister Kmeans or Twister Blast.