Author: Stavros Stavroglou, Athanasios Pantelous, Hui Wang

# Parallel Computing in Pattern Causality Analysis

#### Stavros Stavroglou, Athanasios Pantelous, Hui Wang

Pattern causality analysis involves computationally intensive tasks, especially when dealing with complex systems and large datasets. This vignette demonstrates how to leverage parallel computing capabilities in the `patterncausality` package to significantly reduce computation time and improve efficiency.

## Key Benefits of Parallel Computing

The parallel computing features in this package are particularly effective for:

1. Bootstrap Analysis:
   - Distributing bootstrap iterations across multiple cores
   - Ideal for uncertainty quantification
   - Significant speed improvements for large numbers of iterations
2. Matrix Computations:
   - Processing large causality matrices efficiently
   - Handling multiple time series simultaneously
   - Reducing computation time for system-wide analyses
3. Cross-validation Studies:
   - Parallel processing of different sample sizes
   - Efficient handling of repeated computations
   - Improved performance for robustness analysis

## Performance Comparison: Sequential vs Parallel Computing

Let’s explore how parallel computing can enhance the performance of different pattern causality analyses:

    library(patterncausality)
    data(climate_indices)

## Create test data

    X <- climate_indices$PNA
    Y <- climate_indices$NAO

## Function to measure execution time

    run_cv_test <- function(n_cores) {
        start_time <- Sys.time()
        result <- pcCrossValidation(
            X = X,
            Y = Y,
            numberset = c(100, 200, 300, 400, 500),
            E = 3,
            tau = 2,
            metric = "euclidean",
            h = 1,
            weighted = FALSE,
            random = TRUE,
            bootstrap = 100,
            n_cores = n_cores,
            verbose = TRUE
        )
        end_time <- Sys.time()
        return(difftime(end_time, start_time, units = "secs"))
    }

# Compare sequential vs parallel

    time_seq <- run_cv_test(1)
    time_par <- run_cv_test(parallel::detectCores() - 1)

    cat("Sequential computation time:", time_seq, "seconds\n")
    cat("Parallel computation time:", time_par, "seconds\n")
    cat("Speed-up factor:", as.numeric(time_seq) / as.numeric(time_par), "x\n")

## Matrix Analysis with Multiple Time Series

When analyzing causality between multiple time series, parallel computing can significantly reduce computation time:

    # Create larger test dataset
    n_series <- 20
    n_points <- 1000
    test_data <- matrix(rnorm(n_series * n_points), ncol = n_series)
    colnames(test_data) <- paste0("Series_", 1:n_series)

    # Function to measure execution time
    run_matrix_test <- function(n_cores) {
      start_time <- Sys.time()

      result <- pcMatrix(
        dataset = test_data,
        E = 3,
        tau = 2,
        metric = "euclidean",
        h = 1,
        weighted = FALSE,
        n_cores = n_cores,
        verbose = TRUE
      )

      end_time <- Sys.time()
      return(difftime(end_time, start_time, units = "secs"))
    }

    # Compare sequential vs parallel
    time_seq <- run_matrix_test(1)
    time_par <- run_matrix_test(parallel::detectCores() - 1)

    cat("Sequential computation time:", time_seq, "seconds\n")
    cat("Parallel computation time:", time_par, "seconds\n")
    cat("Speed-up factor:", as.numeric(time_seq) / as.numeric(time_par), "x\n")

## Understanding Parallel Performance

### Key Factors Affecting Speed-up

1. Data Characteristics
   - Size of time series
   - Number of series
   - Sample sizes in cross-validation
   - Number of bootstrap iterations
2. Hardware Considerations
   - Number of CPU cores
   - Available memory
   - System architecture (Windows/Linux/Mac)
3. Analysis Type
   - Bootstrap analysis: Excellent parallelization potential
   - Matrix computation: Good for large matrices
   - Cross-validation: Depends on sample sizes

### Best Practices for Optimal Performance

    # Get available cores
    n_cores <- parallel::detectCores()
    # Use n_cores - 1 for computation
    recommended_cores <- max(1, n_cores - 1)
    cat("Recommended number of cores:", recommended_cores, "\n")

    # Example of memory-efficient parallel computation
    result <- pcCrossValidation(
      X = X,
      Y = Y,
      numberset = c(100, 200, 300),
      E = 3,
      tau = 2,
      bootstrap = 50,
      n_cores = 2,  # Use modest number of cores for memory efficiency
      verbose = TRUE
    )

## System-Specific Considerations

### Windows Systems

- Uses PSOCK clusters
- Slightly higher overhead
- Consider using fewer cores

### Linux/Mac Systems

- Uses FORK clusters
- Better parallel performance
- Can utilize more cores effectively

### Memory Usage Guidelines

- Monitor system memory during computation
- Reduce core count if memory pressure is high
- Consider batch processing for very large datasets

## Conclusion

Parallel computing in pattern causality analysis can provide significant performance improvements, especially for: - Large-scale bootstrap analysis - Multi-series causality matrices - Extensive cross-validation studies

Choose parallel computing parameters based on: - Your system capabilities - Dataset characteristics - Analysis requirements - Available computational resources

For optimal results, always monitor system performance and adjust parameters accordingly.