Transcript of 07/14/08. 2 Points Introduction. Cluster and Supercomputers. Cluster Types and Advantages. Our...
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- 07/14/08
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- 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.
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- 3 Introduction
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- 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.
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- 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
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- 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
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- 07/14/08 Figure 1. A Cluster Architecture.
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- 07/14/08 large Linux cluster at the Chemnitz University of
Technology, GermanyLinuxChemnitz University of Technology
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- 07/14/08 A simple, home-built Beowulf clusterBeowulf
cluster
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- 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.
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- 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.
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- 14 Cluster types Load Balancing Cluster (Parallel BLAST).
Computing Cluster(Parallel sequence alignment). High-availability
(HA) clusters.
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- 15 Cluster types:Load Balancing Cluster Task
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- 07/14/08 A load balancing cluster with two servers and 4 user
stations
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- 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
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- 18 Cluster types:Computing Cluster Task
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- 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
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- 20 Cluster type:High-availability Clusters
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- 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
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- 22 Cluster advantages Performance. Scalability. Maintenance.
Cost.
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- 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.
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- 24 Node 1 switch Node 4 Node 2 Node 3 Internet Cluster
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- 25 Communication : Switch 5-Port 10/100Mbps. Processor and Ram:
-Master Node Duo core Processor 1.86 GHZ. Ram 1GB. -Node 1 Pentium
4 Ram 1GB. -Node 2 Pentium 4 Ram 1GB -Node 3 Pentium 4 Ram 512 MB
Cluster specification
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- 26 Operating System OPEN SUSE 10.3
http://software.opensuse.org/ MPICH2
http://www.mcs.anl.gov/research/projects/mpich2/ Cluster
specification (cont)
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- 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.
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- 28 Performance of the Cluster is affected by 1-Node speed.
2-Running Program.
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- 29 Working Running Program(sequential)
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- 30 Working Running Program(sequential)
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- 31 Working Running Program(sequential)
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- 32 Running Program(sequential)
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- 33 Data sent Running Program(Parallel)
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- 34 Working Running Program(Parallel)
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- 35 Finished Results Get results Running Program(Parallel)
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- 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.
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- 37 Sequence Alignment
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- 38 Sequence Alignment Used to : 1-Compare between sequences.
2-Search databases.
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- 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
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- 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.
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- 41 BLAST (Basic Local Alignment Search Tool) Searching
DataBases
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- 42 BLAST Algorithm (High scoring pairs)
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- 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.
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- 44 Why We need BLAST to be parallelized ?
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- 45 Our Program:Parallel BLAST
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- 46 Parallel BLAST(cont) Formatdb.c Nucleotide sequence database
formatdb -i DATABASE -p F . Protein sequence database formatdb -i
DATABASE -p T .
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- 47 Linux_Cluster_BLASTALL.c blastall -p BLAST Search Type -d
DATABASE -i QUERY FILE -o out. Txt Parallel BLAST(cont)
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- 48 Results Average of running 1000 Query, 1000 times.
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- 49 Results(cont) Average of running 1000 Query, 1000
times.
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- 50 Results(cont) Average of running 1000 Query, 1000
times.
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- 51 Conclusion about Parallel BLAST. Performane: Batter by using
CLUSTER. Scalability:More Nodes time decrease.
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- 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.
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- 53 Sequence Alignment Compare between sequences
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- 54 Sequence Alignment Introduction. Sequence Alignment
Benefits. Sequence Alignment Types.
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- 55 Needleman-Wunsch Algorithm
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- 56 Why We need Sequence Alignment to be parallelized ?
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- 57 Parallel Sequence Alignment algorithm
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- 58 Our Sequence Alignment Program Pairwise Alignment. Built
Using Needleman-Wunsch algorithm.
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- 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.
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- 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
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- 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.
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- 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
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- 63 Thank you