COMP3050 Linux Clustering

8/6/2019 COMP3050 Linux Clustering

1/34

Linux clustercomputing

Morris Law, IT Coordinator,

Science Faculty, Hong Kong

Baptist University


2/34

PII 4-node clusters started in

1999


3/34

PIII 16 node

clusterpurchased in

2001.

Plan for grid

For test base


4/34

HKBU - 64-nodes P4-Xeon

cluster at #300 of top500


5/34

16-node P4 Xeon Cluster for

computational research from 2005

16 compute nodes

each with

P4Xeon 3.2GHz x 2

2GB RAM

36GB SCSI harddisk

ROCKS 4.0.0


6/34

The cluster management team


7/34

OUTLINE

What is PC cluster?

Different kinds ofPC cluster

Beowulf cluster SSI cluster

HPCC Cluster and parallel computing

applications


8/34

What is a PC cluster?

An ensemble of networked, stand-alone

common-off-the-shelf computers used

together to solve a given problem.


9/34

Different kinds ofPC cluster

High Performance Computing Cluster

(Beowulf cluster)

Load Balancing High Availability


10/34

High Performance Computing

Cluster (Beowulf)

Start from 1994

Donald Becker of NASA assemble theworlds first cluster with 16 sets of DX4PCsand 10 Mb/s ethernet

Also called Beowulf cluster

Built from commodity off-the-shelf hardware

Applications like data mining, simulations,parallel processing, weather modelling,computer graphical rendering, etc.


11/34

Examples ofBeowulf cluster

Scyld Cluster O.S. originated by Donald Becker

http://www.scyld.com

ROCKS from NPACI

http://www.rocksclusters.org

OSCAR from open cluster group

http://oscar.sourceforge.net

OpenSCE from Thailand

http://www.opensce.org

SCore from PC Cluster Consortium, Japan

http://www.pccluster.org/


12/34

Load Balancing Cluster

PC cluster deliver load balancing

performance

Commonly used with busy ftp and webservers with large client base

Large number of nodes to share load


13/34

High Availability Cluster

Avoid downtime of services

Avoid single point of failure

Always with redundancy Almost all load balancing cluster are with HA

capability


14/34

Examples of Load Balancing

and High Availability Cluster

RedHat Cluster Suite

http://www.redhat.com/cluster_suite/

Turbolinux Cluster Server

http://www.turbolinux.com/products/middleware/tlcs8.html

Linux Virtual ServerProject

http://www.linuxvirtualserver.org/

Single System Image Cluster for Linux

http://www.openssi.org

Shaolin HA cluster http://www.shaolinmicro.com/product/hacluster/


15/34

Snapshots 1

An example of Beowulf Cluster:

ROCKS

(http://www.rocksclusters.org)


16/34

ROCKSSNAPSHOTS

The schematic diagram of a rocks cluster


17/34

ROCKSSNAPSHOTS

Installation of a compute node


18/34

ROCKSSNAPSHOTS

Ganglia Monitoring tools


19/34

HPCC Cluster and parallel

computing applications

Message Passing Interface MPICH (http://www-unix.mcs.anl.gov/mpi/mpich/)

LAM/MPI (http://lam-mpi.org)

Mathematical

fftw (fast fourier transform) pblas (parallel basic linear algebra software)

atlas (a collections of mathematical library)

sprng (scalable parallel random number generator)

MPITB -- MPI toolbox for MATLAB

Quantum Chemistry software gaussian, qchem, amber

Molecular Dynamic solver NAMD, gromacs, gamess

Weather modelling MM5 (http://www.mmm.ucar.edu/mm5/mm5-home.html)


20/34

NAMD2 Software for

Quantum Chemistry


21/34

Single System Image(SSI) Cluster

MOSIX

openMosix


22/34

MOSIX and openMosix

MOSIX: MOSIX is a software package that enhances the Linuxkernel with cluster capabilities. The enhanced kernel supports anysize cluster of X86/Pentium based boxes. MOSIX allows for theautomatic and transparent migration of processes to other nodes

in the cluster, while standard Linux process control utilities, suchas 'ps' will show all processes as if they are running on the nodethe process originated from.

openMosix: openMosix is a spin off of the original Mosix. The firstversion of openMosix is fully compatible with the last version of

Mosix, but is going to go in its own direction.


23/34

OpenMosix installation

Install Linux in each nodes

Download and install

openmosix-kernel-2.4

.26-openmosix

1.i6

86

.rpm openmosix-tools-0.3.6-2.i386.rpm

and related packages like thoses in

www.openmosixview.com

Reboot with openmosix kernel


24/34

Screenshots 2

OpenMosix cluster management


25/34

openMosix cluster

management tools

openMosixView

openMosixmigmon

3dmosmon


26/34

Advantage ofSSI cluster

Not need to parallelize code

Automatic process migration, i.e. load

balancing Add / delete nodes at any time

Well aware of hardware and system

resources


27/34

Reference URLs

Clustering and HA

Beowulf, parallel Linux cluster.

ROCKS from NPACI OPENMOSIX , scalable cluster computing with

process migration

HighP

erformance Cluster Computing CentreSupported by Dell and Intel

Linux Cluster Information Center

The Quantian Scientific Computing Environment


28/34

PC cluster nowadays

Node hardware Multi-core CPUs with L2 and L3 cache

DDR RAM

Large harddisk (over 500GB per disk)

Blade / Rack mount server

Storage

SAN, I/O nodes, parallel file systems


29/34

PC cluster nowadays (cont)

Interconnect

Gigabit Ethernet, Myrinet, Infiniband, Quadrics


30/34

Thank you!

Welcome to visit HPCCC, HKBU

http://www.hkbu.edu.hk/hpccc/

http://www.hkbu.edu.hk/tdgc/


31/34

The Scientific Computing Lab.


32/34

Opening of the High Performance Cluster

Computing Centre Supported by Dell and Intel


33/34

TDG cluster configuration

Master node: DELL PE2650 P4 Xeon

2.8GHz x 2

4GB ECC DDR RAM

36GB x 2 internal HDrunning RAID 1 (mirror)

73GB x 10 HD arrayrunning RAID 5 with hotspare

Compute nodes x 64

each with DELL PE2650 P4 Xeon

2.8GHz x 2

2GB ECC DDR RAM

36GB internal HD


34/34

Interconnect

configuration

ExtremeBlackDiamond

6816 Gigabit

ethernet switch

Documents

COMP3050 Linux Clustering