Cluster Computer For Bioinformatics Applications Nile University, Bioinformatics Group. Hisham Adel 2008.

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Presentation transcript:

Cluster Computer For Bioinformatics Applications Nile University, Bioinformatics Group. Hisham Adel 2008

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.

7

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.

11 Cluster types:Load Balancing Cluster Task

12 Cluster types:Computing Cluster Task

13 Cluster type:High-availability Clusters

14 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.

16 Node 1 switch Node 4 Node 2 Node 3 Internet Our Cluster

17 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

18  Operating System OPEN SUSE  MPICH2 Our Cluster specification (cont’)‏

19 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.

20 Performance of the Cluster is affected by 1-Node speed. 2-Running Program.

21 Working… Running Program(sequential)‏

22 Working… Running Program(sequential)‏

23 Working… Running Program(sequential)‏

24 Running Program(sequential)‏

25 Data sent Running Program(Parallel)‏

26 Working… Running Program(Parallel)‏

27 Finished… Results Get results… Running Program(Parallel)‏

28 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.

29 Sequence Alignment

30 Sequence Alignment Used to : 1-Compare between sequences. 2-Search databases.

31 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

32 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.

33 BLAST (Basic Local Alignment Search Tool)‏ Searching DataBases

34 BLAST Algorithm (High scoring pairs)‏

35 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.

36 Why We need BLAST to be parallelized ?

37 Our Program:Parallel BLAST

38 Parallel BLAST(cont’)‏ Formatdb.c Nucleotide sequence database “formatdb -i DATABASE -p F “. Protein sequence database “formatdb -i DATABASE -p T “.

39 Linux_Cluster_BLASTALL.c “blastall -p BLAST Search Type -d DATABASE -i QUERY FILE -o out. Txt” Parallel BLAST(cont’)‏

40 Results Average of running 1000 Query, 1000 times.

41 Results(cont’)‏ Average of running 1000 Query, 1000 times.

42 Results(cont’)‏ Average of running 1000 Query, 1000 times.

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 Alignment Compare between sequences

46 Sequence Alignment Introduction. Sequence Alignment Benefits. Sequence Alignment Types.

47 Needleman-Wunsch Algorithm

48 Why We need Sequence Alignment to be parallelized ?

49 Parallel Sequence Alignment algorithm

50 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