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
60 lines
1.9 KiB
Markdown
60 lines
1.9 KiB
Markdown
# Problem Statement: MPI Edit Distance Implementation
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## Objective
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Implement the Edit Distance (Needleman-Wunsch global alignment) algorithm using MPI with three different communication strategies and compare their performance.
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## Requirements
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### 1. Algorithm Implementation
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- Implement the Needleman-Wunsch algorithm for global sequence alignment
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- Calculate edit distance between two DNA/protein sequences
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- Use dynamic programming approach
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### 2. MPI Communication Strategies
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#### Strategy 1: Point-to-Point Communication
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- Use `MPI_Send` and `MPI_Recv` for data distribution
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- Distribute computation across multiple processes
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- Collect results using point-to-point communication
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#### Strategy 2: Scatter + Gather Communication
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- Use `MPI_Scatter` to distribute data
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- Use `MPI_Gather` to collect results
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- Implement collective communication patterns
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#### Strategy 3: Gather-based Multiple Pair Computation
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- Process multiple sequence pairs in parallel
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- Use `MPI_Gather` to collect results from all processes
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- Implement load balancing across processes
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### 3. Input/Output Format
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**Input:**
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```
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Sequence 1: ACGTAG
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Sequence 2: ACTG
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```
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**Output:**
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```
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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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### 4. Performance Requirements
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- Measure execution time for each strategy
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- Support different numbers of MPI processes (2, 4, 8)
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- Compare performance across communication strategies
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### 5. Docker Environment
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- Containerize the application
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- Support both single-container and multi-container execution
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- Provide easy setup and execution instructions
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## Expected Results
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- Correct edit distance calculations for all strategies
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- Performance comparison showing time differences
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- Scalable implementation that works with different process counts
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- Clean, readable output matching the specified format
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