mse presentation 2 lakshmikanth ganti ganti/mse_pro.htm

MSE Presentation 2

Lakshmikanth Ganti

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

Overview

Updates of First phase artifacts Architecture design Formal Requirements Specification Test plan Formal Technical Inspection Prototype Demo

Updates

Vision Document Software requirements Specification

Critical Requirements Absence of Deadlocks Safety Absence of violation assertions

Updates

Project Plan Implementation Plan

User Documentation Revision of Architecture Design Document Assessment Evaluation Project Evaluation Implementing Individual Classes Integration

Architecture Design Algorithm1. Compute forces.

Clear potential and force accumulatorsV := 0for 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 Find the potential energy contribution

V = V + Vij

2. Integrate equations of motion for i = 1 to Np do

Velinew: = Veli

old + (Fi/mi)DTXi

new: = Xiold + VeliDT

3. Update time counter t: = t + DT

Architecture Design

Architecture Design

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.

Architecture Design Design Modified algorithm Initialize forces and potential energy

for partition1 = 1 to n for partition2 = 1 to n { check if the partitions are neighbors

{ for i = 1 to number of atoms in the partition1 {

initialize force accumulators: sfx = 0, sfy = 0, sfz = 0for j = 1 to number of atoms in the partition2 { check if atom number in partition1 > atom number in partition2 {check if distance between the atoms < cut-off distance {

pot = pot + vlj; fxj = fxj + fx; fyj = fyj + fy; fzj = fzj + fz; sfx = sfx + fjx; sfy = sfy + fjy; sfz = sfz + fjz; } }

} fxi = fxi – sfx; fyi = fyi – sfy; fzi = fzi = fzi – sfz;}

}

Architecture Design

Parallel Program designMap Partition to a threadBounded BufferCommunication

26 neighboring threads

Dimensions [M][M][M][26]

Architecture Design Mapping Buffers Shadows Pseudo code

For time step = 1 to number of iterations{

assign the atoms that belong o this thread depending on their spatial configurationput the atoms in all the shadows.collect the atoms from all the buffers.calculate forces.increment velocities and calculate displacements.calculate energies due to the contribution of this thread’s atoms and

send them to energy writer class.

}

Architecture Design

Class DiagramAtom IO_UtilsLineReaderObjBufEnergyWriterMD_ThreadMD_Par

Architecture Design Use Cases

Read data from input files Assign atoms to threads Transfer atoms to all neighboring threads Get atoms from all the neighboring threads Calculate forces on atoms Increment velocities and displace atoms Calculate Energies Write energies to the file

Formal Requirements Spec.

Java Path Finder : Checks for deadlocks, assertion violations and uncaught exceptions by checking the entire state

space of the parallel program. Model

PC2 PC3

PC1

Buffer 1

Buffer 4

Buffer 3

Buffer 2

put

putput

put

get

get

get

get

Formal Requirements Spec.

ClassesProd-ConsumerBufferVerify

Reference : Java PathFinder User Guide , Klaus Havelund, NASA Ames Research Centre.

Formal Requirements Spec.

AssertionsThe number of objects put into a buffer

by a producer are the same as the number of objects got by a consumer .

The Consumer gets the same objects that are put in the buffer by a producer.

Formal Requirements Spec.

Result

Assertion violations

Deadlocks

Test Plan

Features to be testedRead Data from filesAssignment of atoms to threadsFormatting values for outputPerformance Requirements

Test Plan

DeliverablesTest PlanTest case and results

Formal Technical Inspection

Document to be InspectedArchitecture Design Document

InspectorsTwo Independent MSE Students

Checklist

Demonstration

Questions