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 Introduction
 What is cluster computing?
 Classification of Cluster Computing
 Technologies:
 Beowulf cluster
 Construction of Beowulf Cluster
 The use of cluster computing in Bioinformatics & Parallel
Computing
 Folding@Home Project
 High performance clusters (HPC)
a 256-processor Sun cluster.
 Build Your Own Cluster! 2
 Mainly in parallel: Split problem in smaller tasks that are
executed concurrently
 Why?
 Absolute physical limits of hardware components
 Economical reasons – more complex = more expensive
 Performance limits – double frequency <> double performance
 Large applications – demand too much memory & time

 Advantages:
 Increasing speed & optimizing resources utilization
 Disadvantages:
 Complex programming models – difficult development

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  Several applications on parallel processing:

Science Digital Biology Aerospace Resources

Computation Exploration

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 Architectures of Parallel Computer:
 PVP (Parallel Vector Processor)
 SMP (Symmetric Multiprocessor)
 MPP (Massively Parallel Processor)
 COW (Cluster of Workstation)
 DSM (Distributed Shared Memory)
 Towards Inexpensive Supercomputing: Cluster Computing is the
Commodity Supercomputing 58.8%

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 A computer cluster is a group of linked computers, working together closely
so that in many respects they form a single computer. The components of a
cluster are commonly, but not always, connected to each other through fast
local area networks. Clusters are usually deployed to improve performance
and/or availability over that provided by a single computer, while typically
being much more cost-effective than single computers of comparable speed or
availability.

Cluster consists of:

 Nodes(master+computing)
 Network
 OS
 Cluster middleware:
Middleware such as MPI
which permits compute
clustering programs to be …
portable to a wide variety of
clusters
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High Speed Local Network
C C … C
P PCluster P
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 A Beowulf Cluster is a computer design that uses parallel processing
across multiple computers to create cheap and powerful
supercomputers. A Beowulf Cluster in practice is usually a collection
of generic computers, either stock systems or wholesale parts
purchased independently and assembled, connected through an
internal network.
 A cluster has two types of computers, a master computer, and node
computers. When a large problem or set of data is given to a
Beowulf cluster, the master computer first runs a program that breaks
the problem into small discrete pieces; it then sends a piece to each
node to compute. As nodes finish their tasks, the master computer
continually sends more pieces to them until the entire problem has
been computed.

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 ( Ethernet,Myrinet….)
+ (MPI)

 Master: or service node or front node ( used to interact with users and manage the
cluster )
 Nodes : a group of computers (computing node s)( keyboard, mouse, floppy,
video…)
 Communications between nodes on an interconnect network platform ( Ethernet,
Myrinet….)
 In order for the master and node computers to communicate, some sort message 9
passing control structure is required. MPI,(Message Passing Interface) is the most
commonly used such control.
 To construct Beowulf cluster there are four distinct but interrelated areas of
consideration:

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 Brief Technical Parameters:

 OS: CentOS 5 managed by Rochs-cluster

 Service node: 1 (Intel P4 2.4 GHz)
 Computing nodes: 32 (Intel P4 2.4- 2.8 GHz)
 System Memory: 1 GB per node
 Network Platforms: Gigabit Ethernet, 2 cards per node
Myrinet 2 G
 Language: C, C++, Fortran, java
 Compiler: GNU gcc, Intel compiler, sun Java compiler
Parallel Environment: MPICH
 Tools: Ganglia (Monitoring)
Pbs - Torque (Scheduler) 11
OS (Operating System )

 Three of the most commonly used OS are including kernel level support
for parallel programming:
 Windows NT/2000
mainly used to build a High Availability Cluster or a NLB(Network Local
Balance) Cluster, provide services such as Database ,
File/Print,Web,Stream Media .Support 2-4 SMP or 32 processors. Hardly
used to build a Science Computing Cluster
 Redhat Linux
The most used OS for a Beowulf Cluster.
provides High Performance and Scalability / High Reliability / Low Cost
( get freely and uses inexpensive commodity hardware )
 SUN Solaris
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Uses expensive and unpopular hardware
Network Platform
 Some design considerations for the interconnect network are:
• Fast Ethernet (100Mbps): low cost / min latency: 80µs

• Gigabit Ethernet (1Gbps) expensive/ min latency: 300 µs

• Myrinet (high-speed local area networking system) (2Gbps) The best

network platform.
• Some design considerations for the interconnect network are:

• Network structure Bus/Switched

• Maximum bandwidth

• Minimum latency

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Parallel Environment
 Two of the most commonly used Parallel Interface Libraries:
o PVM (Parallel Virtual Machine)
o MPI (Message Passing Interface)
 Parallel Interface Libraries: provide a group of communication interface libraries
that support message passing. Users can call these libraries directly in their
Fortran and C programs.

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Cluster Computer Architecture

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 HPC platform for scientific applications
 Storage and processing of large data
 Satellites
image processing
 Information Retrieval, Data Mining

 Computing systems in an academic environment

 Geologists also use clusters to emulate and predict
earthquakes and model the interior of the Earth and sea
floor
 clusters are even used to render and manipulate high-
resolution graphics in engineering.

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 What is Bioinformatics:
 Also called “biomedical computing”. The application of computer
science and technology to problems in the biomolecular sciences.
 Cluster Uses:
 The Beowulf cluster computing design is been used by parallel
processing computer systems projects to build a powerful computer
that could assist in Bioinformatics research and data analysis.
 In bioinformatics Clusters are used to run DNA string matching
algorithms or to run protein folding applications. It also use a
computer algorithm known as BLAST,(Basic Local Alignment
Search Tool), to analyze massive sets of DNA sequences for research
into Bioinformatics.

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 For Bioinfomatics MPICH2 is used which is an
implementation of MPI that was specifically designed
for use with cluster computing systems and parallel
processing. It is an open source set of libraries for
various high level programming languages that give
programmers tools to easily control how large problems
are broken apart and distributed to the various computers
in a cluster.

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 Protein folding and how is folding linked to disease?
 Proteins are biology's workhorses -- its "nanomachines." Before proteins can
carry out these important functions, they assemble themselves, or "fold." The
process of protein folding, while critical and fundamental to virtually all of
biology, in many ways remains a mystery.
 when proteins do not fold correctly:
 Alzheimer's, Mad Cow
 How?
 Folding@home is a distributed computing project -- people from throughout
the world download and run software to band together to make one of the
largest supercomputers in the world. In each computer Folding@home uses
novel computational methods coupled to distributed computing, to simulate
problems.
 the results get back to the main server as you computer will automatically
upload the results to the server each time it finishes a work unit, and
download a new job at that time.

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 Brief Architectural information:

 Processor : AMD OPETRON 2218 DUAL CORE DUAL SOCKET

 NO. of Master Nodes : 1
 NO. of Computing Nodes : 64
 CLUSTER Software : ROCKS version 4.3
 Total Peak Performance : 1.3 T. F
 Peak Performance: In network performance management, a set of functions that
evaluate and report the behavior of:
 telecommunications equipment
 Efffectiveness of the network or network element
 Other subfunctions, such as
 gathering statistical information,

 maintaining and examining historical logs,

 determining system performance under natural and artificial conditions

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 altering system modes of operation.
 Calculation procedure for peak performance:
 No of nodes 64
 Memory RAM 4 GB
 Hard Disk Capacity/each node : 250GB
 Storage Cap. 4 TB
 No .of processors and cores: 2 X 2 = 4(dual core + dual
socket)
 CPU speed : 2.6 GHz
 No. of floating point operations per seconds for AMD
processor: 2 (since it is a dual core)
 Total peak performance : No of nodes X No .of processors
and cores X CPU speed X No of floating point operations per
second = 64 X 4 X 2.6GHz X 2 = 1.33 TF 26
 Scheduler used: Sun Grid Engine: Job scheduler
software tool.
 Application software/s and compilers:
 Open MPI Lam MPI
 C, C++, FORTRAN compilers (both GNU AND INTEL)
 Bio roll: for Bio-Chemical applications

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Academically:
 1000 nodes Beowulf Cluster Sy
stem
 Used for genetic algorithm res
earch by John Coza, Stanford
University

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 http://www.pssclabs.com/products_powerwulf.asp

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 Parallel Environments are used in building clusters?
 Two of the most commonly used Parallel Interface Libraries:
 PVM (Parallel Virtual Machine)
 MPI (Message passing Interface)

 Why MPI over PVM?

1. MPI has more than one freely available, quality implementation (LAM, MPICH and
CHIMP).
2. MPI defines a 3rd party profiling mechanism.
3. MPI has full asynchronous communication.
4. MPI groups are solid, efficient, and deterministic.
5. MPI efficiently manages message buffers.
6. MPI synchronization protects 3rd party software.
7. MPI can efficiently program MPP and clusters.
8. MPI is totally portable.
9. MPI is formally specified.
10. MPI is a standard, can be implemented with Linux, NT, on many supercomputers
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 WMU e-books library:
 BeowulfCluster Computing with Windows: Thomas Sterling,
ISBN:9780262692755.
 Construction of a Beowulf Cluster System for Parallel Computing
Kun Feng, Jiaqi Dong, Jinhua Zhang
 http://cs.wmich.edu/

 http://www.wikipedia.org/

 http://folding.stanford.edu/

 http://www.pssclabs.com/

 http://www.genetic-programming.com

 http://www.lam-mpi.org/mpi/mpi_top10.php 31