MSE Presentation 2

1
MSE Presentation 2

• Lakshmikanth Ganti
• www.cis.ksu.edu/ganti/mse_pro.htm

2
Overview

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

3
Updates

• Vision Document
• Software requirements Specification
• Critical Requirements
• Absence of Deadlocks
• Safety
• Absence of violation assertions

4
Updates

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

5
Architecture Design

• Algorithm
• 1. Compute forces.
• Clear potential and force accumulators
• V 0
• 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
• Find the potential energy contribution
• V V Vij
• 2. Integrate equations of motion
• for i 1 to Np do
• Velinew Veliold (Fi/mi)DT
• Xinew Xiold VeliDT
• 3. Update time counter

6
Architecture Design
7
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.

8
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 0 for 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

9
Architecture Design

• Parallel Program design
• Map Partition to a thread
• Bounded Buffer
• Communication
• 26 neighboring threads
• Dimensions
• MMM26

10
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
  configuration put 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
  threads atoms and send them to energy writer
  class.

11
Architecture Design

• Class Diagram
• Atom
• IO_Utils
• LineReader
• ObjBuf
• EnergyWriter
• MD_Thread
• MD_Par

12
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

13
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

Buffer 3
put
get
PC3
PC2
get
Buffer 4
put
put
get
Buffer 1
Buffer 2
put
get
PC1
14
Formal Requirements Spec.

• Classes
• Prod-Consumer
• Buffer
• Verify
• Reference Java PathFinder User Guide , Klaus
  Havelund, NASA Ames Research Centre.

15
Formal Requirements Spec.

• Assertions
• The 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.

16
Formal Requirements Spec.

• Result
• Assertion violations
• Deadlocks

17
Test Plan

• Features to be tested
• Read Data from files
• Assignment of atoms to threads
• Formatting values for output
• Performance Requirements

18
Test Plan

• Deliverables
• Test Plan
• Test case and results

19
Formal Technical Inspection

• Document to be Inspected
• Architecture Design Document
• Inspectors
• Two Independent MSE Students
• Checklist

20
Demonstration
21
Questions