Hadoop on Palmetto HPC

Pengfei Xuan

Jan 8, 2015

School of ComputingClemson University

Outline

• Introduction

• Hadoop over Palmetto HPC Cluster

• Hands-on Practice

HPC Cluster vs. Hadoop Cluster

Networking

ComputeNode

Data Node

…

HDD

SSD

RAM

Data Node

Data Node

ComputeNode

ComputeNode

ComputeNode Hadoop

HPC

HPC Clusters

Forge (NVIDIA GPU Cluster)• 44 GPU Nodes• 6 or 8 NVIDIA Fermi M2070 GPUs per Node• 6GB Graphics Memory per GPU • 600 TB GPFS File System• 40GB/sec InfiniBand QDR per Node

(Point-to-point unidirectional speed)

The National Center for Supercomputing Application

+ +

InfiniBand Switch 40GB InfiniBand Adapter 8 NVIDIA Fermi M2070 GPUs

Hadoop Clusters

History of Hadoop

1998 Google Funded2003 GFS Paper2004 MapReduce Paper Nutch DFS Impl.2005 Nutch MR Impl.2006 BigTable Paper Hadoop Project2008 World’s Largest Hadoop2010 Facebook 21 PB Data 2011 Microsoft, IBM, Oracle, Twitter, AmazonNow Everywhere, Our Class!

Jeffrey Dean Doug Cutting

Google vs. Hadoop Infrastructures

Dremel

Evenflow Evenflow Dremel

MySQLGateway

SawzallBigtable

MapReduce / GFS

Chubby

Azkaban Azkaban

SqoopKafka

PigVoldemort

Hadoop

Zookeeper

HiPal

Databee Databee Hive

ScribeHive

HBaseHadoop

Zookeeper

Oozie Oozie Hive

Data Highway

Hive / PigHBase

Hadoop

Zookeeper

Hue Crunch

Oozie Oozie Hive

SqoopFlume

Hive / PigHBase

Hadoop

Zookeeper

I. Data Coordination Layer

II. Data Storage and Computing Layer

III. Data Flow Layer

IV. Data Analysis Layer

MapReduce Word Count Example

cat * | grep | sort | uniq -c | cat > file

Run Hadoop over Palmetto Cluster

1. Setup Hadoop configuration files

2. Start Hadoop services

3. Copy input files to HDFS (stage-in)

4. Run Hadoop job (MapReduce WordCount)

5. Copy output files from HDFS to your home directory (stage-out)

6. Stop Hadoop services

7. Clear up

Commands

1. Create job directory: $> mkdir myHadoopJob1$> cd myHadoopJob1

2. Get Hadoop PBS Script:$> cp /tmp/runHadoop.pbs .Or,$> wget https://raw.githubusercontent.com/pfxuan/myhadoop/master/examples/runHadoop.pbs

3. Submit job to Palmetto cluster:$> qsub runHadoop.pbs

4. Check status of your job:$> qstat -anu your_cu_username

5. Verify the correctness of your result:$> grep Hadoop wordcount-output/* | grep 51