1. MSE Presentation 1 Lakshmikanth Ganti www.cis.ksu.edu/~ganti/mse_pro.htm

2. Introduction Vision Document  Project Overview  Project Requirements Specification Project Plan  Work Breakdown Schedule  Cost Estimation  Architecture Elaboration Plan Software Quality Assurance Plan Demonstration

3. Overview Objective: To develop software in Java that uses MD simulation technique to simulate the interaction between atoms in a group of water molecules. Use: The results of the current simulation of water molecules are used in protein folding studies. Direction:  Inputs Parameter Data file (.dat) Initial Coordinates file (.pdb) Velocities Data file (.dat)  Calculations  Outputs Data File (.dat) Final Coordinates file (.pdb)

4. Overview (Contd.) Features  Multi-threaded programming  Paradigms for process interaction Manager/Workers (Distributed bag of tasks) Heartbeat Algorithm  Synchronization techniques Hand threaded Structured approach Risks  Safety  Liveness  Deadlock  Achieve Max Speed up and efficiency

5. Project Requirements General Requirements  Neat Interface  Statistical Data  API Documentation  User Manual  Design Specification  SQA Plan  Test Plan  Project Plan  Object Model and Interaction Diagrams

6. Project Requirements Performance Requirements  Scalability  Speed up and efficiency  Different Synchronization Mechanisms  Read Data in a specified format  Stability constraints on data  Minimize memory usage Hardware/Software Requirements  J2SDK V 1.2 or above  Processor speed 400 MHz or above

7. Work Breakdown Schedule Inception Phase  Prototype Demo  Vision Document  Project Plan  SQA Plan Elaboration Phase  Architectural Baseline  Critical Use Cases  Second Executable Prototype Production Phase  Coding

8. Work Breakdown Schedule Testing Phase  Unit testing  Integration Testing Documentation Phase  Artifacts developed during earlier phases  User Manual  Test Report  Evaluation Report

9. Project Plan Phase 1 – Requirements Deliverables : Overview, Requirement Specification, Cost Estimation, Software Quality Assurance Plan (SQAP) and a Project Plan  First Presentation – January 9 th 2004 Phase 2 – Design Deliverables : Overall Design, Formal Specifications, Test Plan and a Formal Technical Inspection  Second Presentation - February 9 th 2004 (Tentative) Phase 3 – Final Deliverables: Source Code, Tests, User Manual  Final Presentation – April 22 nd 2004 (Tentative) A Project Time Log will be maintained at all times.

10. Cost Estimation The cost and size of developing the application are estimated using Functional Point Analysis Constructive Cost Model (COCOMO)

11. Cost Estimation Functional Point Analysis  Sequential Program Process Complexity Adjustments =.65 + 0.01 * (sum of influence ratings) =.93 FPadjusted = FPunadjusted * (.65 + 0.01 * (sum of ratings)) = 71 * (.65 +.01 * (28)) = 66.03 Source lines of code (SLOC) = FP * Language Factor (for Java) = 66.03 * 40 = 2641.2  Parallel Program Process Complexity Adjustments =.65 + 0.01 * (sum of influence ratings) =.98 FPadjusted = FPunadjusted * (.65 + 0.01 * (sum of ratings)) = 71 * (.65 +.01 * (33)) = 76.44 Source lines of code (SLOC) = FP * Language Factor (for Java) = 76.44 * 40 = 3057.6

12. Cost Estimation COCOMO TDEVProgrammer Productivity Development Time (Month) Application Programs PM = 2.4 * (KDSI) 1.05 PM = 2.5 * (PM) 0.38 Utility ProgramsPM = 3.0 * (KDSI) 1.12 PM = 2.5 * (PM) 0.35 System ProgramsPM = 3.6 * (KDSI) 1.20 PM = 2.5 * (PM) 0.32

13. Cost Estimation COCOMO  Sequential Program Person Month: PM = 2.4 * (KLOC) 1.05 = 2.4 * 2.6 1.05 = 6.5 Development Time (Months): TDEV = 2.5 * (PM) 0.38 = 2.5 * 6.5 0.38 = 5.1 Average Staffing Levels: ASL = PM / TDEV = 6.5/5.1 = 1.27  Parallel Program Person Month: PM = 2.4 * (KLOC) 1.05 = 2.4 * 3.05 1.05 = 7.75 Development Time (Months): TDEV = 2.5 * (PM) 0.38 = 2.5 * 7.750.38 = 7.36 Average Staffing Levels: ASL = PM / TDEV = 7.75/7.36 = 1.05

14. Architecture Elaboration Plan Action Items Updated Vision document Updated Project Plan Formal Requirement Specification Architecture Design Test Plan Formal Technical Inspection Executable Architecture Prototype

15. SQA Plan Management  Organization  Roles  Tasks & Responsibilities Documentation  Software Requirements Specification  Software Design Description  Software Test Plan  Software User Manual

16. SQA Plan SQA Program Requirements  Standards  Metrics  Software Documentation Audit  Requirements Traceability  Software Development Process  Project Reviews  Testing and Quality Check Training

17. Demonstration

18. Particle-Particle (PP) Method Timestep loop of PP method 1. Compute forces. Clear force accumulators for i = 1 to Np do Fi: = 0 Accumulate forces for i = 1 to Np – 1 do for j = i + 1 to Np do Find force Fij of particle j on particle I Fi: = Fi + Fij Fj: = Fj + Fij 2. Integrate equations of motion for i = 1 to Np do Vinew: = Viold + (Fi/mi)DT Xinew: = Xiold + ViDT 3. Update time counter t: = t + DT

19. Lennard-Jones Force

20.  and  are the specific Lennard--Jones parameters, different for different interacting particles. r is the distance between the interacting particles. For water, the values of these parameters are:  = 0.316555 nanometers and  = 0.6501696 KJ/mole.

21. Questions