Rocks ʻnʼ Rolls# An Introduction to # Programming Clusters # using Rocks# Anoop Rajendra# 2010 UC Regents#

Transcription

1 An Introduction to # Programming Clusters # using Rocks# Rocks ʻnʼ Rolls# Anoop Rajendra#

2 Rules of the Talk# This talk is for YOU!!# Let me know if Iʼm too fast# Donʼt hesitate to stop me and ask questions in the middle.#

3 What is Rocks?# A Linux distribution based on CentOS# Cluster on a DVD ( or set of CDs)# Goals of Rocks# Make Clusters Easy# Reduce dependence on system administrators by reducing system administration# Enable scientists to concentrate on science rather than on computing.#

4 What is Rocks?# Rocks provides a mechanism to install OS on a cluster# Rocks provides a mechanism to install and configure cluster software.# Rocks provides tools to manage/ administer the cluster, after the installation is finished.#

5 How do we get Started?# Get a bunch of x86/x64 machines# Put 2 ethernet cards on one of them - Thisʼll be your front-end/head-node# Wire 'em up.# Download Rocks isos from Burn a bunch of CDs or a DVD# Get started#

6 Topology of a Rocks Cluster# Frontend Node# Public Ethernet# Private# Ethernet# Application# Network (Optional)# Node# Node# Node# Node# Node# Node# Node# Node# Node# Node# Power Distribution# (Net addressable units as option)#

7 Another way to look at it#

8 Installing Rocks# Rocks provides for installation of a cluster with minimum user interaction# Steps involved# Boot from CD or DVD# Answer a few questions# Get favorite beverage# Youʼre on your way to a full fledged cluster in 2 hours or less.#

9 Innards of Automatic Installs# Rocks uses Redhatʼs Kickstart mechanism for automated installs# Kickstart file generated and given to the installer# Installer follows instructions in Kickstart file.# Generation of Kickstart file done automatically by Rocks scripts#

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25 After Frontend Installation#

26 Add compute nodes using insert-ethers#

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30 Cluster Setup# Frontend and Compute nodes - setup with the right software stack# Networking is configured and running# Monitoring and Queuing systems are configured and running.#

31 How does Rocks do all this?# Using a mechanism called Rolls#

32 What are Rolls?# Software components that make up a Rocks system# Mechanism for delivery of packages and configuration# Rolls are how youʼre going to get your software onto a Rocks cluster#

33 What are some of the available rolls?# Sun Grid Engine Roll Deploys queuing system on all nodes and enables job provisioning# Ganglia Roll Deploys monitoring system# Web Server Roll Deploys and configures web server on the frontend.#

34 Some more rolls...# Bio Roll Application Roll for Bioinformatics applications# Xen Roll Roll to deploy virtual machines# Viz Roll Roll that enabled building tile wall displays# PVFS2 Roll Installs and Configures the Parallel Virtual File System on your cluster.#

35 Viz Wall#

36 Another Viz Wall#

37 Roll Infrastructure# Rolls are distributed as ISO images# Add a CD or leave a CD out during installation & you control the configuration and capability of your cluster#

38 Whatʼs inside a Roll?# Binaries - RPM format# Configuration data# Installation Map#

39 Context of a Roll#

40 Normal Redhat Distribution#

41 Distribution based on Rolls#

42 Treasure Hunting# The treasure you seek is a fully installed and configured cluster# What are the things youʼll need#

43 Map#

44 Instruction set#

45 Resources#

46 Translate that to a Roll# Graph file Installation Map Map# Node Files Configuration Data Instruction set# RPM/Binaries Resources#

47 Some Useful Rolls# Required Rolls Kernel, Base, OS# HPC Roll Contains MPI utilities like OpenMPI, MPICH2, some benchmarking utils# SGE Roll Installs and configures a Queuing system on your cluster# Bio Roll Contains a lot of Bio-informatics utilities#

48 Bio Roll#

49 Whatʼs inside the Bio Roll?# Bio-informatics software like# NCBI Blast# MPI Blast# HMMER# GROMACS# EMBOSS# Phylip# TCoffee#

50 Whatʼs inside the Roll?#

51 Whatʼs the graph file?# <graph> <edge from="compute"> <to>bio-base</to> </edge> <edge from="hpc-server"> <to>bio-head</to> </edge> </graph>

52 How does the graph look?#

53 How does a node file look?# <kickstart> <package>hmmer</package> <package>ncbi</package> <package>mpiblast</package> <post> # Shell Scripts to be run after installation <file name=.ncbirc> file contents </file> # Shell Scripts to be run after installation </post> </kickstart>

54 To Re-iterate#

55 Bio-informatics Applications

56 Configuration Information

57 THE ROLL Configuration Information Bio-informatics Application

58 How does it fit in?# Bio Roll

59 How does it fit in?#

60 How does all this help you?# Roll mechanism is the recommended way of deploying software on a Rocks cluster# It fits into the framework of Rocks# Itʼs reproducible# It scales#

61 Other Ways of Software Deployment# More than one way to get your software onto the rocks cluster# Not recommended as it is not reproducible over multiple re-installs.#

62 RPM Based Deployment# Create an RPM using# # rocks create package <directory> <packagename> Create an RPM using the Rocks Makefile infrastructure# Download RPM from trusted repository#

63 RPM Based Deployment# Put your RPM in# /export/rocks/contrib/5.3/arch/rpm# Create the node xml file to reflect new package# # cd /export/rocks/install/site-profiles/5.3/nodes# # cp skeleton.xml extend-compute.xml# Inside extend-compute.xml file, put the line# <package>rpm name</package># Re-create the rocks distribution# # cd /export/rocks/install# # rocks create distro# Re-install your compute nodes#

64 Installing in a Shared directory# /export/apps is shared across the entire cluster as /share/apps# Install your package into # /export/apps/package# On all your compute nodes the package directory will be# /share/apps/package#

65 More Information# More Documentation available at

66 ?#