Performance Benchmark of Running Sum Functions

Ross Bennett — written Jan 6, 2013 — source

First, let us consider a running sum function in pure R. To get started, I looked at the source code of the TTR package to see the algorithm used in runSum. The runSum function uses a Fortran routine to compute the running/rolling sum of a vector. The run_sum_R function below is my interpretation of that algorithm implemented in R. Many thanks to the package author, Joshua Ulrich, for pointing out to me that, in many cases, the algorithm is more critical to performance than the language.

run_sum_R <- function(x, n) {

  sz <- length(x)
  
  ov <- vector(mode = "numeric", length = sz)
  
  # sum the values from the beginning of the vector to n
  ov[n] <- sum(x[1:n])
  
  # loop through the rest of the vector
  for(i in (n+1):sz) {
    ov[i] <- ov[i-1] + x[i] - x[i-n]
  }
  
  # pad the first n-1 values with NA
  ov[1:(n-1)] <- NA
  
  return(ov)
}

suppressMessages(library(TTR))
library(rbenchmark)

set.seed(123)
x <- rnorm(10000)

# benchmark run_sum_R for given values of x and n
benchmark( run_sum_R(x, 50), run_sum_R(x, 100),
          run_sum_R(x, 150), run_sum_R(x, 200),
          order = NULL)[,1:4]

               test replications elapsed relative
1  run_sum_R(x, 50)          100   3.364    1.007
2 run_sum_R(x, 100)          100   3.339    1.000
3 run_sum_R(x, 150)          100   3.390    1.015
4 run_sum_R(x, 200)          100   3.590    1.075

For these benchmarks, I will just focus on the performance of the functions for a fixed x and varying the value of n. The results of the benchmark of run_sum_R show that the elapsed time is fairly constant for the given values of n (i.e. O(1)).

Now let us consider a running sum function in C++, call it run_sum_v1. One approach is to loop through each element of the given vector calling std::accumulate to compute the running sum.

#include <Rcpp.h>

using namespace Rcpp;

// [[Rcpp::export]]
NumericVector run_sum_v1(NumericVector x, int n) {
    
    int sz = x.size();

    NumericVector res(sz);
    
    // loop through the vector calling std::accumulate
    for(int i = 0; i < (sz-n+1); i++){
        res[i+n-1] = std::accumulate(x.begin()+i, x.end()-sz+n+i, 0.0);
    }
    
    // pad the first n-1 elements with NA
    std::fill(res.begin(), res.end()-sz+n-1, NA_REAL);
    
	return res;
}

# benchmark run_sum_v1 for given values of x and n
benchmark( run_sum_v1(x, 50), run_sum_v1(x, 100),
          run_sum_v1(x, 150), run_sum_v1(x, 200),
          order = NULL)[,1:4]

                test replications elapsed relative
1  run_sum_v1(x, 50)          100   0.045    1.000
2 run_sum_v1(x, 100)          100   0.088    1.956
3 run_sum_v1(x, 150)          100   0.128    2.844
4 run_sum_v1(x, 200)          100   0.170    3.778

Although the elapsed times of run_sum_v1 are quite fast, note that the time increases approximately linearly as n increases (i.e. O(N)). This will become a problem if we use this function with large values of n.

Now let us write another running sum function in C++ that uses the same algorithm that is used in run_sum_R, call it run_sum_v2.

// [[Rcpp::export]]
NumericVector run_sum_v2(NumericVector x, int n) {
    
    int sz = x.size();
    
    NumericVector res(sz);
    
    // sum the values from the beginning of the vector to n 
    res[n-1] = std::accumulate(x.begin(), x.end()-sz+n, 0.0);
    
    // loop through the rest of the vector
    for(int i = n; i < sz; i++) {
       res[i] = res[i-1] + x[i] - x[i-n];
    }
    
    // pad the first n-1 elements with NA
    std::fill(res.begin(), res.end()-sz+n-1, NA_REAL);
    
    return res;
}

# benchmark run_sum_v2 for given values of x and n
benchmark( run_sum_v2(x, 50), run_sum_v2(x, 100),
          run_sum_v2(x, 150), run_sum_v2(x, 200),
          order = NULL)[,1:4]

                test replications elapsed relative
1  run_sum_v2(x, 50)          100   0.007        1
2 run_sum_v2(x, 100)          100   0.007        1
3 run_sum_v2(x, 150)          100   0.007        1
4 run_sum_v2(x, 200)          100   0.007        1

The benchmark results of run_sum_v2 are quite fast and much more favorable than both run_sum_R and run_sum_v1. The elapsed time is approximately constant across the given values of n (i.e O(N)).

Finally, let us benchmark all three functions as well as runSum from the TTR package for a point of reference using larger values for the size of x and n.

set.seed(42)
y <- rnorm(100000)

# benchmark runSum for given values of x and n
benchmark(    runSum(y, 4500), run_sum_v1(y, 4500),
          run_sum_v2(y, 4500),  run_sum_R(y, 4500),
          order = "relative")[,1:4]

                 test replications elapsed relative
3 run_sum_v2(y, 4500)          100   0.082     1.00
1     runSum(y, 4500)          100   0.889    10.84
4  run_sum_R(y, 4500)          100  33.717   411.18
2 run_sum_v1(y, 4500)          100  37.538   457.78

An interesting result of benchmarking with these larger values is that run_sum_R is faster than run_sum_v1 for the given values. This example demonstrates that it is not always the case that C++ code is faster than R code. The inefficiency of run_sum_v1 is due to having std::accumulate inside the for loop. For a vector of size 100,000 and n = 5000, std::accumulate is called 95,001 times!

This is obviously not an “apples-to-apples” comparison because a different algorithm is used, but the point of the example is to demonstrate the importance of the algorithm regardless of the programming language.

It should be noted that runSum does some extra work in R such as checking for a valid n, non-leading NAs, etc. and should be considered when comparing the benchmark results of run_sum_v2 to runSum.

tags: benchmark

Extending R with C++ and Fortran — Dirk Eddelbuettel and JBrandon Duck-Mayr
Benchmarking Rcpp code with RcppClock — Zach DeBruine
Simulation Smoother using RcppArmadillo — Tomasz Woźniak

Performance Benchmark of Running Sum Functions

Related Articles