2 Points Introduction. Cluster and Supercomputers. Cluster
Types and Advantages. Our Cluster. Cluster Performance. Cluster
Computer for Basic Problems. General Idea about Sequence Alignment.
BLAST and Parallel BLAST Algorithm. Sequence Alignment and Parallel
Sequence Alignment. Learned Skills.
Slide 3
3 Introduction
Slide 4
4 Points Introduction. Cluster and Supercomputers. Cluster
Types and Advantages. Our Cluster. Cluster Performance. Cluster
Computer for Basic Problems. General Idea about Sequence Alignment.
BLAST and Parallel BLAST Algorithm. Sequence Alignment and Parallel
Sequence Alignment. Learned Skills.
Slide 5
5 Cluster Definition Group of computers and servers ( loosely
connected computers ) that act like a single system. computers Each
system called a Node. Node contain one or more Processor, Ram,Hard
disk and LAN card. Nodes work in Parallel. We can increase
performance by adding more Nodes. A c
Slide 6
07/14/08 These cluster computers are referred to by many names,
from a poor-man's supercomputer to COWs (clusters of workstations),
and NOWs (networks of workstations). cheaper than traditional MPP
systems, and often use the same processors, but are more difficult
to use since the network capabilities are currently much lower.
Cluster computers are also usually much smaller, most often
involving fewer than 100 computers
Slide 7
07/14/08 Figure 1. A Cluster Architecture.
Slide 8
07/14/08 large Linux cluster at the Chemnitz University of
Technology, GermanyLinuxChemnitz University of Technology
Slide 9
9
Slide 10
07/14/08 A simple, home-built Beowulf clusterBeowulf
cluster
Slide 11
11
Slide 12
Motivation for Clusters/Grids Many science and engineering
problems today require large amounts of computational resources and
cannot be executed in a single machine. Large commercial
supercomputers are very expensive A lot of computational power is
underutilized around the world in machines sitting idle.
Slide 13
13 Points Introduction. Cluster and Supercomputers. Cluster
Types and Advantages. Our Cluster. Cluster Performance. Cluster
Computer for Basic Problems. General Idea about Sequence Alignment.
BLAST and Parallel BLAST Algorithm. Sequence Alignment and Parallel
Sequence Alignment. Learned Skills.
07/14/08 A load balancing cluster with two servers and 4 user
stations
Slide 17
07/14/08 Load-balancingLoad-balancing clusters are
configurations in which cluster-nodes share computational workload
to provide better overall performance. For example, a web server
cluster may assign different queries to different nodes, so the
overall response time will be optimized
Slide 18
18 Cluster types:Computing Cluster Task
Slide 19
07/14/08 "Computer clusters" are used for computation-intensive
purposes, rather than handling IO-oriented operations such as web
service or databases.IO-oriented
Slide 20
20 Cluster type:High-availability Clusters
Slide 21
07/14/08 "High-availability clusters improve the availability
of the cluster approach. They operate by having redundant nodes,
which are then used to provide service when system components
failHigh-availability clustersnodes
23 Points Introduction. Cluster and Supercomputers. Cluster
Types and Advantages. Our Cluster. Cluster Performance. Cluster
Computer for Basic Problems. General Idea about Sequence Alignment.
BLAST and Parallel BLAST Algorithm. Sequence Alignment and Parallel
Sequence Alignment. Learned Skills.
26 Operating System OPEN SUSE 10.3
http://software.opensuse.org/ MPICH2
http://www.mcs.anl.gov/research/projects/mpich2/ Cluster
specification (cont)
Slide 27
27 Points Introduction. Cluster and Supercomputers. Cluster
Types and Advantages. Our Cluster. Cluster Performance. Cluster
Computer for Basic Problems. General Idea about Sequence Alignment.
BLAST and Parallel BLAST Algorithm. Sequence Alignment and Parallel
Sequence Alignment. Learned Skills.
Slide 28
28 Performance of the Cluster is affected by 1-Node speed.
2-Running Program.
Slide 29
29 Working Running Program(sequential)
Slide 30
30 Working Running Program(sequential)
Slide 31
31 Working Running Program(sequential)
Slide 32
32 Running Program(sequential)
Slide 33
33 Data sent Running Program(Parallel)
Slide 34
34 Working Running Program(Parallel)
Slide 35
35 Finished Results Get results Running Program(Parallel)
Slide 36
36 Points Introduction. Cluster and Supercomputers. Cluster
Types and Advantages. Our Cluster. Cluster Performance. Cluster
Computer for Basic Problems. General Idea about Sequence Alignment.
BLAST and Parallel BLAST Algorithm. Sequence Alignment and Parallel
Sequence Alignment. Learned Skills.
Slide 37
37 Sequence Alignment
Slide 38
38 Sequence Alignment Used to : 1-Compare between sequences.
2-Search databases.
Slide 39
39 How to Align two Sequences. if we have two sequences A A A C
G A A A T G A Let match=1, gap=-1, miss-match=0. they can be
aligned as: 1- A A A C G A | | | | | | Score=3 A A T _ G A 2- A A A
C _ G A | | | | | | | Score=1 A A _ _ T G A
Slide 40
40 Points Introduction. Cluster and Supercomputers. Cluster
Types and Advantages. Our Cluster. Cluster Performance Cluster
Computer for Basic Problems.. General Idea about Sequence
Alignment. BLAST and Parallel BLAST Algorithm. Sequence Alignment
and Parallel Sequence Alignment. Learned Skills.
Slide 41
41 BLAST (Basic Local Alignment Search Tool) Searching
DataBases
Slide 42
42 BLAST Algorithm (High scoring pairs)
Slide 43
43 Blast search types. BLASTN - Compares a nucleotide query
sequence against a nucleotide sequence database. BLASTP- Compares
an amino acid query sequence against a protein sequence database.
TBLASTN- Compares a protein query sequence against a nucleotide
sequence Database. BLASTX- Compares nucleotide query sequence
against a protein sequence database.
Slide 44
44 Why We need BLAST to be parallelized ?
Slide 45
45 Our Program:Parallel BLAST
Slide 46
46 Parallel BLAST(cont) Formatdb.c Nucleotide sequence database
formatdb -i DATABASE -p F . Protein sequence database formatdb -i
DATABASE -p T .
48 Results Average of running 1000 Query, 1000 times.
Slide 49
49 Results(cont) Average of running 1000 Query, 1000
times.
Slide 50
50 Results(cont) Average of running 1000 Query, 1000
times.
Slide 51
51 Conclusion about Parallel BLAST. Performane: Batter by using
CLUSTER. Scalability:More Nodes time decrease.
Slide 52
52 Points Introduction. Cluster and Supercomputers. Cluster
Types and Advantages. Our Cluster. Cluster Performance. Cluster
Computer for Basic Problems. General Idea about Sequence Alignment.
BLAST and Parallel BLAST Algorithm. Sequence Alignment and Parallel
Sequence Alignment. Learned Skills.
56 Why We need Sequence Alignment to be parallelized ?
Slide 57
57 Parallel Sequence Alignment algorithm
Slide 58
58 Our Sequence Alignment Program Pairwise Alignment. Built
Using Needleman-Wunsch algorithm.
Slide 59
59 Learned Skills. Using Linux (Suse 10.3) operating system.
Programming using C language. Cluster computers and how to build
one. MPICH2 for message passing interfaces between nodes. Latex.
Team working, and helping each other. Presentation skills.
Slide 60
07/14/08 Message passing and communication Two widely used
approaches for communication between cluster nodes are PVM,
Parallel Virtual Machine :(1989)PVM provides a run- time
environment for message-passing, task and resource management, and
fault notification. PVM can be used by user programs written in C,
C++, or Fortran, etcParallel Virtual Machine MPI, Message Passing
Interface (1990)MPI implementations typically use TCP/IP and socket
connections. [ MPI is now a widely available communications model
that enables parallel programs to be written in languages such as
C, Fortran, Python, etcMessage Passing InterfaceTCP/IP
[CFortranPython
Slide 61
07/14/08 Cluster management: Task scheduling When a large
multi-user cluster needs to access very large amounts of data, task
scheduling becomes a challenge.task scheduling Node failure
management When a node in a cluster fails, strategies such as
"fencing" may be employed to keep the rest of the system
operational.fencing Fencing is the process of isolating a node or
protecting shared resources when a node appears to be
malfunctioning.
Slide 62
Cluster Computing - challenges Software to create a single
system image Fault tolerance Debugging tools Job scheduling All
these have been/are being addressed since then and are leading
towards a successful era for cluster computing