History

root f666c25eea Add MPI Edit Distance implementation with three communication strategies - Implemented Needleman-Wunsch algorithm for edit distance calculation - Added three MPI communication strategies: P2P, Scatter-Gather, Gather-based - Included Docker containerization with single and multi-container support - Added multiple input methods: default, command line, interactive - Improved timing precision to show microsecond measurements - Fixed MPI deadlock issues in P2P communication - Complete documentation and usage examples		2025-09-20 13:47:58 +05:00
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.env	Add MPI Edit Distance implementation with three communication strategies	2025-09-20 13:47:58 +05:00
docker-compose.yml	Add MPI Edit Distance implementation with three communication strategies	2025-09-20 13:47:58 +05:00
Dockerfile	Add MPI Edit Distance implementation with three communication strategies	2025-09-20 13:47:58 +05:00
edit_distance_mpi.cpp	Add MPI Edit Distance implementation with three communication strategies	2025-09-20 13:47:58 +05:00
hostfile	Add MPI Edit Distance implementation with three communication strategies	2025-09-20 13:47:58 +05:00
README.md	Add MPI Edit Distance implementation with three communication strategies	2025-09-20 13:47:58 +05:00
req.md	Add MPI Edit Distance implementation with three communication strategies	2025-09-20 13:47:58 +05:00

README.md

MPI Edit Distance Implementation

This project implements the Edit Distance (Needleman-Wunsch) algorithm using MPI with three different communication strategies:

Point-to-Point Communication (MPI_Send/MPI_Recv)
Scatter + Gather Communication (MPI_Scatter/Gather)
Gather-based Multiple Pair Computation (MPI_Gather)

Quick Start

Option 1: Single Container (Recommended - Works Perfectly)

# Build the project
docker compose build

# Method 1: Use default sequences (ACGTAG vs ACTG)
docker run --rm -it pdc-poc-master bash -c "cd /app && mpirun -np 2 --allow-run-as-root ./edit_distance"

# Method 2: Provide custom sequences as command line arguments
docker run --rm -it pdc-poc-master bash -c "cd /app && mpirun -np 2 --allow-run-as-root ./edit_distance HELLO WORLD"

# Method 3: Interactive input (single process only)
docker run --rm -it pdc-poc-master bash -c "cd /app && mpirun -np 1 --allow-run-as-root ./edit_distance -i"

# Run with different process counts
docker run --rm -it pdc-poc-master bash -c "cd /app && mpirun -np 4 --allow-run-as-root ./edit_distance"
docker run --rm -it pdc-poc-master bash -c "cd /app && mpirun -np 8 --allow-run-as-root ./edit_distance"

Option 2: Multi-Container Setup

# Build the project
docker compose build

# Run with 2 processes (1 master + 1 worker)
docker compose up --scale worker1=1 worker2=0 worker3=0 worker4=0

# Run with 4 processes (1 master + 3 workers)
docker compose up --scale worker1=1 worker2=1 worker3=1 worker4=0

# Run with 5 processes (1 master + 4 workers)
docker compose up --scale worker1=1 worker2=1 worker3=1 worker4=1

# View logs to see results
docker compose logs

# Shut down containers
docker compose down

Expected Output

Sequence 1: ACGTAG
Sequence 2: ACTG

Edit Distance (P2P) = 2, Time = 0.000s
Edit Distance (Scatter) = 2, Time = 0.000s
Edit Distance (Gather) = [2, 3, 3], Time = 0.000s

Input Methods

Default Sequences: No arguments - uses "ACGTAG" vs "ACTG"
Command Line: ./edit_distance SEQUENCE1 SEQUENCE2
Interactive: ./edit_distance -i (single process only)

Troubleshooting

SSH errors: Use Option 1 (single container) for reliable execution
Permission errors: Ensure Docker has proper permissions
Build errors: Check that all files are in the correct directory

Files

edit_distance_mpi.cpp - Main MPI implementation
Dockerfile - Container configuration
docker-compose.yml - Multi-container orchestration
hostfile - MPI host configuration
README.md - This file