MSE Presentation 1

Lakshmikanth Ganti

www.cis.ksu.edu/~ganti/mse_pro.htm

Introduction

Vision Document Project Overview Project Requirements Specification

Project Plan Work Breakdown Schedule Cost Estimation Architecture Elaboration Plan

Software Quality Assurance Plan Demonstration

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)

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

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

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

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

Work Breakdown Schedule

Testing Phase Unit testing Integration Testing

Documentation Phase Artifacts developed during earlier phases User Manual Test Report Evaluation Report

Project Plan

Phase 1 – RequirementsDeliverables : Overview, Requirement Specification, Cost Estimation, Software Quality Assurance Plan (SQAP) and a Project Plan

First Presentation – January 9th 2004 Phase 2 – Design

Deliverables : Overall Design, Formal Specifications, Test Plan and a Formal Technical Inspection

Second Presentation - February 9th 2004 (Tentative) Phase 3 – Final

Deliverables: Source Code, Tests, User Manual Final Presentation – April 22nd 2004 (Tentative)

A Project Time Log will be maintained at all times.

Cost Estimation

The cost and size of developing the application are estimated

using Functional Point Analysis Constructive Cost Model (COCOMO)

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

Cost Estimation

COCOMO

TDEV Programmer Productivity

Development Time

(Month)

Application Programs

PM = 2.4 * (KDSI) 1.05

PM = 2.5 * (PM) 0.38

Utility Programs PM = 3.0 * (KDSI) 1.12

PM = 2.5 * (PM) 0.35

System Programs PM = 3.6 * (KDSI) 1.20

PM = 2.5 * (PM) 0.32

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

Architecture Elaboration Plan

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

SQA Plan

Management Organization Roles Tasks & Responsibilities

Documentation Software Requirements Specification Software Design Description Software Test Plan Software User Manual

SQA Plan

SQA Program Requirements Standards Metrics Software Documentation Audit Requirements Traceability Software Development Process Project Reviews Testing and Quality Check

Training

Demonstration

Particle-Particle (PP) Method

Timestep loop of PP method1. Compute forces.

Clear force accumulatorsfor i = 1 to Np do

Fi: = 0Accumulate forcesfor i = 1 to Np – 1 dofor 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)DTXinew: = Xiold + ViDT

3. Update time counter t: = t + DT

Lennard-Jones Force

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.

Questions