MSE Presentation 2 Lakshmikanth Ganti

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 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 + V ij 2. Integrate equations of motion for i = 1 to Np do Vel i new : = Vel i old + (Fi/mi)DT X i new : = X i old + Vel i DT 3. Update time counter t: = t + DT

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:  = nanometers and  = 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 = 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; } }

Architecture Design Parallel Program design  Map Partition to a thread  Bounded Buffer  Communication 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 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 thread’s atoms and send them to energy writer class. }

Architecture Design Class Diagram  Atom  IO_Utils  LineReader  ObjBuf  EnergyWriter  MD_Thread  MD_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 get

Formal Requirements Spec. Classes  Prod-Consumer  Buffer  Verify Reference : Java PathFinder User Guide, Klaus Havelund, NASA Ames Research Centre.

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.

Formal Requirements Spec. Result Assertion violations Deadlocks

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

Test Plan Deliverables  Test Plan  Test case and results

Formal Technical Inspection Document to be Inspected  Architecture Design Document Inspectors  Two Independent MSE Students Checklist

Demonstration

Questions