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Cluster Computer For Bioinformatics
Applications
Nile University,
Bioinformatics Group.
Hisham Adel2008
2
Done By:1. Hisham Adel Hassan.
Supervised by:
Dr. Mohamed Aboualhouda
3
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.
4
Introduction
5
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.
6
Cluster Definition
•Group of computers and servers (connected together) that act like a single system.
•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.
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8
9
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.
10
Cluster types
•Load Balancing Cluster (Parallel BLAST).
•Computing Cluster(Parallel sequence alignment).
•High-availability (HA) clusters.
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Cluster types:Load Balancing Cluster
Task
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Cluster types:Computing Cluster
Task
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Cluster type:High-availability Clusters
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Cluster advantages
•Performance.
•Scalability.
•Maintenance.
•Cost.
15
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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Node 1
switch
Node 4
Node 2
Node 3
Internet
Internet
Internet
Internet
Our Cluster
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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
Our Cluster specification
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Operating System OPEN SUSE 10.3
http://software.opensuse.org/
MPICH2
http://www.mcs.anl.gov/research/projects/mpich2/
Our Cluster specification (cont’)
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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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Performance of the Cluster is affected by
1-Node speed.
2-Running Program.
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Working…
Running Program(sequential)
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Working…
Running Program(sequential)
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Working…
Running Program(sequential)
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Running Program(sequential)
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Data sent
Data sent
Data sent
Running Program(Parallel)
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Working…
Working…
Working…
Working…
Running Program(Parallel)
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Finished…
Finished…
Finished…
Results
Results
Results
Get results…
Running Program(Parallel)
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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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Sequence Alignment
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Sequence Alignment
Used to :
1-Compare between sequences.
2-Search databases.
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How to Align two Sequences.
if we have two sequences A A A C G A A A T G ALet 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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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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BLAST(Basic Local Alignment Search Tool)
Searching DataBases
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BLAST Algorithm
(High scoring pairs)
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Blast search types.
BLASTN - Compares a nucleotide query sequence against a nucleotide sequencedatabase.
BLASTP- Compares an amino acid query sequence against a protein sequencedatabase.
TBLASTN- Compares a protein query sequence against a nucleotide sequenceDatabase.
BLASTX- Compares nucleotide query sequence against a protein sequence database.
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Why We need BLAST to be parallelized ?
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Our Program:Parallel BLAST
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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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Linux_Cluster_BLASTALL.c
“blastall -p BLAST Search Type -d DATABASE -i QUERY FILE -o out . Txt”
Parallel BLAST(cont’)
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Results Average of running 1000 Query, 1000 times.
month.htgs (573 MB)drosoph.nt (118,6 MB))
igseqnt (67.5 MB)Yeastnt (3.2 MB)
mito.nt (3.2 MB)Pdbnt (1.7 MB)
0.0000000
0.2000000
0.4000000
0.6000000
0.8000000
1.0000000
1.2000000
1.4000000
1.6000000
1.8000000Nucleotide-Nucleotide
1 Node3 Nodes-Query time3-Nodes-Query and communication time
Database(Size)
Tim
e(S)
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Results(cont’) Average of running 1000 Query, 1000 times.
env_nr(1.6GB) nr(573MB) SwissProt(160MB) Pdbaa(20MB) Yeast.aa(3.2MB)0.000000
10.000000
20.000000
30.000000
40.000000
50.000000
60.000000
70.000000
80.000000
90.000000
Amino acid_Amino acid
1 Node-Query Time 3 Nodes-Query time3 Nodes-Query and communication time
Database(size)
Tim
e(S)
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Results(cont’) Average of running 1000 Query, 1000 times.
env_nr(1.6GB) Swissprot(160MB) nr(84.7MB) Pdbaa(20.4MB) yeast.aa(3.2MB)0.0000000
10.0000000
20.0000000
30.0000000
40.0000000
50.0000000
60.0000000
70.0000000
80.0000000
90.0000000
Amino acid_Nucltide
1 Node Query time3 Nodes Query time only3 Nodes Query and Communication time
Database(Size)
Tim
e(S
)
43
Conclusion about Parallel BLAST.
•Performane: Batter by using CLUSTER.
•Scalability:More Nodes time decrease.
44
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.
45
Sequence AlignmentCompare between sequences
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Sequence Alignment
•Introduction.
•Sequence Alignment Benefits.
•Sequence Alignment Types.
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Needleman-Wunsch Algorithm
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Why We need Sequence Alignment to be parallelized ?
49
Parallel Sequence Alignment algorithm
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Our Sequence Alignment Program
•Pairwise Alignment.
•Built Using Needleman-Wunsch algorithm.
51
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.
52
Thank you for your time.
Hisham Adel