JUNOHUB-test/question1/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

1. Default Sequences: No arguments - uses "ACGTAG" vs "ACTG"
2. Command Line: ./edit_distance SEQUENCE1 SEQUENCE2
3. 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