f666c25eea
- 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
83 lines
2.5 KiB
Markdown
83 lines
2.5 KiB
Markdown
# MPI Edit Distance Implementation
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This project implements the **Edit Distance (Needleman-Wunsch)** algorithm using MPI with three different communication strategies:
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- **Point-to-Point Communication** (MPI_Send/MPI_Recv)
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- **Scatter + Gather Communication** (MPI_Scatter/Gather)
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- **Gather-based Multiple Pair Computation** (MPI_Gather)
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## Quick Start
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### Option 1: Single Container (Recommended - Works Perfectly)
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```bash
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# Build the project
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docker compose build
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# Method 1: Use default sequences (ACGTAG vs ACTG)
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docker run --rm -it pdc-poc-master bash -c "cd /app && mpirun -np 2 --allow-run-as-root ./edit_distance"
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# Method 2: Provide custom sequences as command line arguments
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docker run --rm -it pdc-poc-master bash -c "cd /app && mpirun -np 2 --allow-run-as-root ./edit_distance HELLO WORLD"
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# Method 3: Interactive input (single process only)
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docker run --rm -it pdc-poc-master bash -c "cd /app && mpirun -np 1 --allow-run-as-root ./edit_distance -i"
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# Run with different process counts
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docker run --rm -it pdc-poc-master bash -c "cd /app && mpirun -np 4 --allow-run-as-root ./edit_distance"
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docker run --rm -it pdc-poc-master bash -c "cd /app && mpirun -np 8 --allow-run-as-root ./edit_distance"
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```
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### Option 2: Multi-Container Setup
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```bash
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# Build the project
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docker compose build
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# Run with 2 processes (1 master + 1 worker)
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docker compose up --scale worker1=1 worker2=0 worker3=0 worker4=0
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# Run with 4 processes (1 master + 3 workers)
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docker compose up --scale worker1=1 worker2=1 worker3=1 worker4=0
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# Run with 5 processes (1 master + 4 workers)
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docker compose up --scale worker1=1 worker2=1 worker3=1 worker4=1
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# View logs to see results
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docker compose logs
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# Shut down containers
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docker compose down
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```
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## Expected Output
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```
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Sequence 1: ACGTAG
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Sequence 2: ACTG
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Edit Distance (P2P) = 2, Time = 0.000s
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Edit Distance (Scatter) = 2, Time = 0.000s
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Edit Distance (Gather) = [2, 3, 3], Time = 0.000s
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```
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## Input Methods
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1. **Default Sequences**: No arguments - uses "ACGTAG" vs "ACTG"
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2. **Command Line**: `./edit_distance SEQUENCE1 SEQUENCE2`
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3. **Interactive**: `./edit_distance -i` (single process only)
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## Troubleshooting
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- **SSH errors**: Use Option 1 (single container) for reliable execution
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- **Permission errors**: Ensure Docker has proper permissions
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- **Build errors**: Check that all files are in the correct directory
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## Files
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- `edit_distance_mpi.cpp` - Main MPI implementation
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- `Dockerfile` - Container configuration
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- `docker-compose.yml` - Multi-container orchestration
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- `hostfile` - MPI host configuration
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- `README.md` - This file
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