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mpich-yarn

#Introduction

MPICH-yarn is an application running on Hadoop YARN that enables MPI programs running on Hadoop YARN clusters.

##Prerequisite

As a prerequisite, you need to

  1. The cluster has been deployed Hadoop YARN and HDFS.
  2. Each node in the cluster has installed mpich-3.1.2 and its ./bin folder has been added to PATH.

This version of mpich-yarn uses MPICH-3.1.2 as implementation of MPI and uses ssh as communication daemon.

##Recommended Configuation

  1. Ubuntu 12.04 LTS
  2. hadoop 2.4.1
  3. gcc 4.6.3
  4. jdk 1.7.0_25
  5. Apache Maven 3.2.3

#Compile

To compile MPICH-yarn, first you need to have maven installed. Then type command at source folder:

mvn clean package -Dmaven.test.skip=true

You need to ensure Internet connected as maven needs to download plugins on the maven repository, this may take minutes.

After this command, you will get mpich2-yarn-1.0-SNAPSHOT.jar at ./target folder. This is the application running at YARN to execute MPI programs.

#Configuation

There are many tutorials on the Internet about configuring Hadoop. However, there are many troubles in configuring YARN to make it work well with mpich2- yarn. To save your time, here is a sample configuration that has successfully run in our cluster for your reference.

yarn-site.xml

<configuration>
<property>
    <name>yarn.resourcemanager.resource-tracker.address</name>
    <value>${YOUR_HOST_IP_OR_NAME}:8031</value>
  </property>
  <property>
    <name>yarn.resourcemanager.address</name>
    <value>${YOUR_HOST_IP_OR_NAME}:8032</value>
  </property>
  <property>
    <name>yarn.resourcemanager.hostname</name>
    <value>${YOUR_HOST_IP_OR_NAME}</value>
  </property>
  <property>
    <name>yarn.resourcemanager.scheduler.address</name>
    <value>${YOUR_HOST_IP_OR_NAME}:8030</value>
  </property>
  <property>
    <name>yarn.resourcemanager.admin.address</name>
    <value>${YOUR_HOST_IP_OR_NAME}:8033</value>
  </property>
  <property>
    <name>yarn.resourcemanager.webapp.address</name>
    <value>${YOUR_HOST_IP_OR_NAME}:8088</value>
  </property>
<property>
	<name>yarn.nodemanager.aux-services</name>
	<value>mapreduce_shuffle</value>
</property>
<property>
	<name>yarn.nodemanager.resource.cpu-vcore</name>
	<value>16</value>
</property>
<property>
	<name>yarn.nodemanager.aux-services.mapreduce.shuffle.class</name>
	<value>org.apache.hadoop.mapred.ShuffleHandler</value>
</property>
<property>
	<name>yarn.application.classpath</name>
	<value>
		/home/hadoop/hadoop-2.4.1/etc/hadoop,
		/home/hadoop/hadoop-2.4.1/share/hadoop/common/*,
		/home/hadoop/hadoop-2.4.1/share/hadoop/hdfs/*,
		/home/hadoop/hadoop-2.4.1/share/hadoop/yarn/*,
		/home/hadoop/hadoop-2.4.1/share/hadoop/common/lib/*,
		/home/hadoop/hadoop-2.4.1/share/hadoop/hdfs/lib/*,
		/home/hadoop/hadoop-2.4.1/share/hadoop/yarn/lib/*
	</value>
</property>
</configuration>

mpi-site.conf

<configuration>
	<property>
		<name>yarn.mpi.scratch.dir</name>
		<value></value>
		<description>
			The HDFS address that stores temporary file like:
			hdfs://sandking04:9000/home/hadoop/mpi-tmp
		</description>
	</property>
	<property>
		<name>yarn.mpi.ssh.authorizedkeys.path</name>
		<value>/home/hadoop/.ssh/authorized_keys</value>
		<description>
			MPICH-YARN will create a temporary RSA key pair for
			password-less login and automatically configure it. 
			All of your hosts should enable public_key login.
		</description>
	</property>
</configuration>

#Submit Jobs

CPI

On the client nodes:

mpicc -o cpi cpi.c
hadoop jar mpich2-yarn-1.0-SNAPSHOT.jar -a cpi -M 1024 -m 1024 -n 2

Hello world

hadoop jar mpich2-yarn-1.0-SNAPSHOT.jar -a hellow -M 1024 -m 1024 -n 2

PLDA

svn checkout http://plda.googlecode.com/svn/trunk/ plda  # Prepare source code
cd plda
make  # call mpicc to compile
cd ..

Put the input data to the hdfs (P.S. there is a testdata in the PLDA source code dir):

hadoop fs -mkdir /group/dc/zhuoluo.yzl/plda\_input
hadoop fs -put plda/testdata/test\_data.txt /group/dc/zhuoluo.yzl/plda\_input/
hadoop jar mpich2-yarn-1.0-SNAPSHOT.jar -a plda/mpi\_lda -M 1024 -m 1024 -n 2\
 -o "--num_topics 2 --alpha 0.1 --beta 0.01 --training_data_file MPIFILE1 --model_file MPIOUTFILE1 --total_iterations 150"\
 -DMPIFILE1=/group/dc/zhuoluo.yzl/plda_input -SMPIFILE1=true -OMPIOUTFILE1=/group/dc/zhuoluo.yzl/lda_model_output.txt -ppc 2