High Performance Benchmarks

Joseph Wood

02/04/2023

This document serves as an overview for measuring the performance of RcppAlgos against other tools for generating combinations, permutations, and partitions. This stackoverflow post: How to generate permutations or combinations of object in R? has some benchmarks. You will note that the examples in that post are relatively small. The benchmarks below will focus on larger examples where performance really matters and for this reason we only consider the packages arrangements, partitions, and RcppAlgos.

Setup Information

For the benchmarks below, we used a 2022 Macbook Air Apple M2 24 GB machine.

library(RcppAlgos)
library(partitions)
library(arrangements)
#> 
#> Attaching package: 'arrangements'
#> The following object is masked from 'package:partitions':
#> 
#>     compositions
library(microbenchmark)

options(digits = 4)
options(width = 90)

pertinent_output <- capture.output(sessionInfo())
cat(paste(pertinent_output[1:3], collapse = "\n"))
#> R version 4.2.1 (2022-06-23)
#> Platform: aarch64-apple-darwin20 (64-bit)
#> Running under: macOS Monterey 12.6

pkgs <- c("RcppAlgos", "arrangements", "partitions", "microbenchmark")
sapply(pkgs, packageVersion, simplify = FALSE)
#> $RcppAlgos
#> [1] '2.7.1'
#> 
#> $arrangements
#> [1] '1.1.9'
#> 
#> $partitions
#> [1] '1.10.7'
#> 
#> $microbenchmark
#> [1] '1.4.7'

numThreads <- min(as.integer(RcppAlgos::stdThreadMax() / 2), 6)
numThreads
#> [1] 4

Combinations

Combinations - Distinct

set.seed(13)
v1 <- sort(sample(100, 30))
m <- 21
t1 <- comboGeneral(v1, m, Parallel = T)
t2 <- combinations(v1, m)
stopifnot(identical(t1, t2))
dim(t1)
#> [1] 14307150       21
rm(t1, t2)
invisible(gc())
microbenchmark(cbRcppAlgosPar = comboGeneral(v1, m, nThreads = numThreads),
               cbRcppAlgosSer = comboGeneral(v1, m),
               cbArrangements = combinations(v1, m),
               times = 15, unit = "relative")
#> Warning in microbenchmark(cbRcppAlgosPar = comboGeneral(v1, m, nThreads = numThreads), :
#> less accurate nanosecond times to avoid potential integer overflows
#> Unit: relative
#>            expr   min    lq  mean median    uq   max neval
#>  cbRcppAlgosPar 1.000 1.000 1.000  1.000 1.000 1.000    15
#>  cbRcppAlgosSer 3.438 2.954 2.893  2.866 2.826 2.605    15
#>  cbArrangements 3.471 3.003 2.934  2.912 2.856 2.643    15

Combinations - Repetition

v2 <- v1[1:10]
m <- 20
t1 <- comboGeneral(v2, m, repetition = TRUE, nThreads = numThreads)
t2 <- combinations(v2, m, replace = TRUE)
stopifnot(identical(t1, t2))
dim(t1)
#> [1] 10015005       20
rm(t1, t2)
invisible(gc())
microbenchmark(cbRcppAlgosPar = comboGeneral(v2, m, TRUE, nThreads = numThreads),
               cbRcppAlgosSer = comboGeneral(v2, m, TRUE),
               cbArrangements = combinations(v2, m, replace = TRUE),
               times = 15, unit = "relative")
#> Unit: relative
#>            expr   min    lq  mean median    uq   max neval
#>  cbRcppAlgosPar 1.000 1.000 1.000  1.000 1.000 1.000    15
#>  cbRcppAlgosSer 2.919 2.837 2.732  2.713 2.647 2.494    15
#>  cbArrangements 2.837 2.836 2.717  2.717 2.634 2.453    15

Combinations - Multisets

myFreqs <- c(2, 4, 4, 5, 3, 2, 2, 2, 3, 4, 1, 4, 2, 5)
v3 <- as.integer(c(1, 2, 3, 5, 8, 13, 21, 34, 55, 89, 144, 233, 377, 610))
t1 <- comboGeneral(v3, 20, freqs = myFreqs, nThreads = numThreads)
t2 <- combinations(freq = myFreqs, k = 20, x = v3)
stopifnot(identical(t1, t2))
dim(t1)
#> [1] 14594082       20
rm(t1, t2)
invisible(gc())
microbenchmark(cbRcppAlgosPar = comboGeneral(v3, 20, freqs = myFreqs, nThreads = numThreads),
               cbRcppAlgosSer = comboGeneral(v3, 20, freqs = myFreqs),
               cbArrangements = combinations(freq = myFreqs, k = 20, x = v3),
               times = 10, unit = "relative")
#> Unit: relative
#>            expr   min    lq  mean median    uq   max neval
#>  cbRcppAlgosPar 1.000 1.000 1.000  1.000 1.000 1.000    10
#>  cbRcppAlgosSer 3.048 3.014 2.936  2.935 2.906 2.727    10
#>  cbArrangements 5.676 5.722 5.567  5.571 5.520 5.203    10

Permutations

Permutations - Distinct

v4 <- as.integer(c(2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41, 43, 47, 53, 59))
t1 <- permuteGeneral(v4, 6, nThreads = numThreads)
t2 <- permutations(v4, 6)
stopifnot(identical(t1, t2))
dim(t1)
#> [1] 8910720       6
rm(t1, t2)
invisible(gc())
microbenchmark(cbRcppAlgosPar = permuteGeneral(v4, 6, nThreads = numThreads),
               cbRcppAlgosSer = permuteGeneral(v4, 6),
               cbArrangements = permutations(v4, 6),
               times = 15, unit = "relative")
#> Unit: relative
#>            expr   min    lq  mean median    uq   max neval
#>  cbRcppAlgosPar 1.000 1.000 1.000  1.000 1.000 1.000    15
#>  cbRcppAlgosSer 1.462 1.437 1.296  1.418 1.345 1.167    15
#>  cbArrangements 2.508 2.495 2.279  2.441 2.537 1.777    15


## Indexing permutation example with the partitions package
t1 <- permuteGeneral(11, nThreads = 4)
t2 <- permutations(11)
t3 <- perms(11)

dim(t1)
#> [1] 39916800       11

stopifnot(identical(t1, t2), identical(t1, t(as.matrix(t3))))
rm(t1, t2, t3)
invisible(gc())

microbenchmark(cbRcppAlgosPar = permuteGeneral(11, nThreads = 4),
               cbRcppAlgosSer = permuteGeneral(11),
               cbArrangements = permutations(11),
               cbPartitions   = perms(11),
               times = 5, unit = "relative")
#> Unit: relative
#>            expr   min    lq  mean median    uq   max neval
#>  cbRcppAlgosPar 1.000 1.000 1.000  1.000 1.000 1.000     5
#>  cbRcppAlgosSer 2.545 2.843 2.787  2.809 2.799 2.918     5
#>  cbArrangements 4.326 4.229 4.388  4.552 4.490 4.340     5
#>    cbPartitions 7.967 8.048 8.428  8.788 8.733 8.563     5

Permutations - Repetition

v5 <- v3[1:5]
t1 <- permuteGeneral(v5, 10, repetition = TRUE, nThreads = numThreads)
t2 <- permutations(v5, 10, replace = TRUE)
stopifnot(identical(t1, t2))
dim(t1)
#> [1] 9765625      10
rm(t1, t2)
invisible(gc())
microbenchmark(cbRcppAlgosPar = permuteGeneral(v5, 10, TRUE, nThreads = numThreads),
               cbRcppAlgosSer = permuteGeneral(v5, 10, TRUE),
               cbArrangements = permutations(x = v5, k = 10, replace = TRUE),
               times = 10, unit = "relative")
#> Unit: relative
#>            expr   min    lq  mean median    uq    max neval
#>  cbRcppAlgosPar 1.000 1.000 1.000  1.000 1.000 1.0000    10
#>  cbRcppAlgosSer 2.689 2.599 2.055  2.477 2.363 0.8071    10
#>  cbArrangements 3.255 3.156 2.644  2.993 2.821 1.6139    10

Permutations - Multisets

v6 <- sort(runif(12))
t1 <- permuteGeneral(v6, 7, freqs = rep(1:3, 4), nThreads = numThreads)
t2 <- permutations(freq = rep(1:3, 4), k = 7, x = v6)
stopifnot(identical(t1, t2))
dim(t1)
#> [1] 19520760        7
rm(t1, t2)
invisible(gc())
microbenchmark(cbRcppAlgosPar = permuteGeneral(v6, 7, freqs = rep(1:3, 4), nThreads = numThreads),
               cbRcppAlgosSer = permuteGeneral(v6, 7, freqs = rep(1:3, 4)),
               cbArrangements = permutations(freq = rep(1:3, 4), k = 7, x = v6),
               times = 10, unit = "relative")
#> Unit: relative
#>            expr   min    lq  mean median   uq   max neval
#>  cbRcppAlgosPar 1.000 1.000 1.000  1.000 1.00 1.000    10
#>  cbRcppAlgosSer 3.549 3.555 3.156  3.520 2.41 2.622    10
#>  cbArrangements 3.916 3.925 3.559  3.912 2.97 2.860    10

Partitions

Partitions - Distinct

All Distinct Partitions

t1 <- comboGeneral(0:140, freqs=c(140, rep(1, 140)),
                   constraintFun = "sum", comparisonFun = "==",
                   limitConstraints = 140)
t2 <- partitions(140, distinct = TRUE)
t3 <- diffparts(140)

# Each package has different output formats... we only examine dimensions
# and that each result is a partition of 140
stopifnot(identical(dim(t1), dim(t2)), identical(dim(t1), dim(t(t3))),
                    all(rowSums(t1) == 140), all(rowSums(t2) == 140),
                    all(colSums(t3) == 140))
dim(t1)
#> [1] 9617150      16
rm(t1, t2, t3)
invisible(gc())
microbenchmark(cbRcppAlgosPar = partitionsGeneral(0:140, freqs=c(140, rep(1, 140)), nThreads = numThreads),
               cbRcppAlgosSer = partitionsGeneral(0:140, freqs=c(140, rep(1, 140))),
               cbArrangements = partitions(140, distinct = TRUE),
               cbPartitions   = diffparts(140),
               times = 10, unit = "relative")
#> Unit: relative
#>            expr    min     lq   mean median     uq    max neval
#>  cbRcppAlgosPar  1.000  1.000  1.000  1.000  1.000  1.000    10
#>  cbRcppAlgosSer  3.247  3.225  2.711  2.621  2.564  2.138    10
#>  cbArrangements  2.578  2.562  2.146  2.016  2.127  1.680    10
#>    cbPartitions 18.349 18.331 14.919 14.522 13.754 11.296    10

Restricted Distinct Partitions

t1 <- comboGeneral(160, 10,
                   constraintFun = "sum", comparisonFun = "==",
                   limitConstraints = 160)
t2 <- partitions(160, 10, distinct = TRUE)
stopifnot(identical(t1, t2))
dim(t1)
#> [1] 8942920      10
rm(t1, t2)
invisible(gc())
microbenchmark(cbRcppAlgosPar = partitionsGeneral(160, 10, nThreads = numThreads),
               cbRcppAlgosSer = partitionsGeneral(160, 10),
               cbArrangements = partitions(160, 10, distinct = TRUE),
               times = 10, unit = "relative")
#> Unit: relative
#>            expr   min    lq  mean median    uq   max neval
#>  cbRcppAlgosPar 1.000 1.000 1.000  1.000 1.000 1.000    10
#>  cbRcppAlgosSer 3.360 3.343 3.317  3.118 3.519 3.441    10
#>  cbArrangements 4.405 4.344 4.223  4.060 4.029 4.284    10

Partitions - Repetition

All Partitions

t1 <- comboGeneral(0:65, repetition = TRUE, constraintFun = "sum",
                   comparisonFun = "==", limitConstraints = 65)
t2 <- partitions(65)
t3 <- parts(65)

# Each package has different output formats... we only examine dimensions
# and that each result is a partition of 65
stopifnot(identical(dim(t1), dim(t2)), identical(dim(t1), dim(t(t3))),
          all(rowSums(t1) == 65), all(rowSums(t2) == 65),
          all(colSums(t3) == 65))
dim(t1)
#> [1] 2012558      65
rm(t1, t2, t3)
invisible(gc())
microbenchmark(cbRcppAlgosPar = partitionsGeneral(0:65, repetition = TRUE,
                                                  nThreads = numThreads),
               cbRcppAlgosSer = partitionsGeneral(0:65, repetition = TRUE),
               cbArrangements = partitions(65),
               cbPartitions   = parts(65),
               times = 20, unit = "relative")
#> Unit: relative
#>            expr   min    lq  mean median    uq   max neval
#>  cbRcppAlgosPar 1.000 1.000 1.000  1.000 1.000 1.000    20
#>  cbRcppAlgosSer 2.888 2.742 2.210  2.371 2.090 1.636    20
#>  cbArrangements 2.157 2.049 1.653  1.814 1.638 1.046    20
#>    cbPartitions 9.243 8.946 6.833  7.935 6.458 4.037    20

Restricted Partitions

t1 <- comboGeneral(100, 15, TRUE, constraintFun = "sum",
                   comparisonFun = "==", limitConstraints = 100)
t2 <- partitions(100, 15)
stopifnot(identical(t1, t2))
dim(t1)
#> [1] 9921212      15
rm(t1, t2)

# This takes a really long time... not because of restrictedparts,
# but because apply is not that fast. This transformation is
# needed for proper comparisons. As a result, we will compare
# a smaller example
# t3 <- t(apply(as.matrix(restrictedparts(100, 15, include.zero = F)), 2, sort))
t3 <- t(apply(as.matrix(restrictedparts(50, 15, include.zero = F)), 2, sort))
stopifnot(identical(partitions(50, 15), t3))
rm(t3)
invisible(gc())
microbenchmark(cbRcppAlgosPar = partitionsGeneral(100, 15, TRUE,
                                                  nThreads = numThreads),
               cbRcppAlgosSer = partitionsGeneral(100, 15, TRUE),
               cbArrangements = partitions(100, 15),
               cbPartitions   = restrictedparts(100, 15,
                                                include.zero = FALSE),
               times = 10, unit = "relative")
#> Unit: relative
#>            expr    min     lq   mean median     uq    max neval
#>  cbRcppAlgosPar  1.000  1.000  1.000  1.000  1.000  1.000    10
#>  cbRcppAlgosSer  3.420  3.341  2.948  3.131  2.682  2.479    10
#>  cbArrangements  4.296  4.227  3.772  4.200  3.352  3.087    10
#>    cbPartitions 15.608 15.547 13.366 14.594 11.587 10.851    10

Partitions - Multisets

Currenlty, RcppAlgos is the only package capable of efficiently generating partitions of multisets. Therefore, we will only time RcppAlgos and use this as a reference for future improvements.

t1 <- comboGeneral(120, 10, freqs=rep(1:8, 15),
                   constraintFun = "sum", comparisonFun = "==",
                   limitConstraints = 120)
dim(t1)
#> [1] 7340225      10
stopifnot(all(rowSums(t1) == 120))
microbenchmark(cbRcppAlgos = partitionsGeneral(120, 10, freqs=rep(1:8, 15)),
               times = 10)
#> Unit: milliseconds
#>         expr   min    lq  mean median    uq   max neval
#>  cbRcppAlgos 281.6 283.3 289.5  285.3 288.5 318.8    10

Compositions

Compositions - Repetition

All Compositions (Small case)

t1 <- compositionsGeneral(0:15, repetition = TRUE)
t2 <- arrangements::compositions(15)
t3 <- partitions::compositions(15)

# Each package has different output formats... we only examine dimensions
# and that each result is a partition of 15
stopifnot(identical(dim(t1), dim(t2)), identical(dim(t1), dim(t(t3))),
          all(rowSums(t1) == 15), all(rowSums(t2) == 15),
          all(colSums(t3) == 15))
dim(t1)
#> [1] 16384    15
rm(t1, t2, t3)
invisible(gc())
microbenchmark(cbRcppAlgosSer = compositionsGeneral(0:15, repetition = TRUE),
               cbArrangements = arrangements::compositions(15),
               cbPartitions   = partitions::compositions(15),
               times = 20, unit = "relative")
#> Unit: relative
#>            expr     min      lq    mean median      uq     max neval
#>  cbRcppAlgosSer   1.000   1.000   1.000   1.00   1.000   1.000    20
#>  cbArrangements   1.173   1.233   1.232   1.23   1.229   1.184    20
#>    cbPartitions 131.727 138.033 187.548 184.94 222.031 232.619    20

For the next two examples, we will exclude the partitions package for efficiency reasons.

All Compositions (Larger case)

t1 <- compositionsGeneral(0:23, repetition = TRUE)
t2 <- arrangements::compositions(23)

# Each package has different output formats... we only examine dimensions
# and that each result is a partition of 23
stopifnot(identical(dim(t1), dim(t2)), all(rowSums(t1) == 23),
          all(rowSums(t2) == 23))
dim(t1)
#> [1] 4194304      23
rm(t1, t2)
invisible(gc())
microbenchmark(cbRcppAlgosPar = compositionsGeneral(0:23, repetition = TRUE,
                                                    nThreads = numThreads),
               cbRcppAlgosSer = compositionsGeneral(0:23, repetition = TRUE),
               cbArrangements = arrangements::compositions(23),
               times = 20, unit = "relative")
#> Unit: relative
#>            expr   min    lq  mean median    uq   max neval
#>  cbRcppAlgosPar 1.000 1.000 1.000  1.000 1.000 1.000    20
#>  cbRcppAlgosSer 3.431 3.381 3.365  3.377 3.348 3.314    20
#>  cbArrangements 3.836 3.777 3.758  3.772 3.743 3.680    20

Restricted Compositions

t1 <- compositionsGeneral(30, 10, repetition = TRUE)
t2 <- arrangements::compositions(30, 10)

stopifnot(identical(t1, t2), all(rowSums(t1) == 30))
dim(t1)
#> [1] 10015005       10
rm(t1, t2)
invisible(gc())
microbenchmark(cbRcppAlgosPar = compositionsGeneral(30, 10, repetition = TRUE,
                                                    nThreads = numThreads),
               cbRcppAlgosSer = compositionsGeneral(30, 10, repetition = TRUE),
               cbArrangements = arrangements::compositions(30, 10),
               times = 20, unit = "relative")
#> Unit: relative
#>            expr   min    lq  mean median    uq   max neval
#>  cbRcppAlgosPar 1.000 1.000 1.000  1.000 1.000 1.000    20
#>  cbRcppAlgosSer 3.050 3.082 3.040  3.048 2.956 3.305    20
#>  cbArrangements 3.149 3.117 3.039  3.074 2.971 2.803    20

Iterators

We will show one example from each category to demonstrate the efficiency of the iterators in RcppAlgos. The results are similar for the rest of the cases not shown.

Combinations

pkg_arrangements <- function(n, total) {
    a <- icombinations(n, as.integer(n / 2))
    for (i in 1:total) a$getnext()
}

pkg_RcppAlgos <- function(n, total) {
    a <- comboIter(n, as.integer(n / 2))
    for (i in 1:total) a@nextIter()
}

total <- comboCount(18, 9)
total
#> [1] 48620

microbenchmark(cbRcppAlgos    = pkg_RcppAlgos(18, total),
               cbArrangements = pkg_arrangements(18, total),
               times = 15, unit = "relative")
#> Unit: relative
#>            expr   min    lq  mean median    uq   max neval
#>     cbRcppAlgos  1.00  1.00  1.00   1.00  1.00  1.00    15
#>  cbArrangements 19.78 19.54 18.99  19.07 18.56 17.43    15

Permutations

pkg_arrangements <- function(n, total) {
    a <- ipermutations(n)
    for (i in 1:total) a$getnext()
}

pkg_RcppAlgos <- function(n, total) {
    a <- permuteIter(n)
    for (i in 1:total) a@nextIter()
}

total <- permuteCount(8)
total
#> [1] 40320

microbenchmark(cbRcppAlgos    = pkg_RcppAlgos(8, total),
               cbArrangements = pkg_arrangements(8, total),
               times = 15, unit = "relative")
#> Unit: relative
#>            expr   min    lq  mean median    uq  max neval
#>     cbRcppAlgos  1.00  1.00  1.00   1.00  1.00  1.0    15
#>  cbArrangements 19.64 19.27 18.91  18.79 18.43 18.8    15

Partitions

pkg_partitions <- function(n, total) {
    a <- firstpart(n)
    for (i in 1:(total - 1)) a <- nextpart(a)
}

pkg_arrangements <- function(n, total) {
    a <- ipartitions(n)
    for (i in 1:total) a$getnext()
}

pkg_RcppAlgos <- function(n, total) {
    a <- partitionsIter(0:n, repetition = TRUE)
    for (i in 1:total) a@nextIter()
}

total <- partitionsCount(0:40, repetition = TRUE)
total
#> [1] 37338

microbenchmark(cbRcppAlgos    = pkg_RcppAlgos(40, total),
               cbArrangements = pkg_arrangements(40, total),
               cbPartitions   = pkg_partitions(40, total),
               times = 15, unit = "relative")
#> Unit: relative
#>            expr   min    lq  mean median    uq   max neval
#>     cbRcppAlgos  1.00  1.00  1.00   1.00  1.00  1.00    15
#>  cbArrangements 16.07 15.87 15.08  15.73 14.21 13.51    15
#>    cbPartitions 25.90 25.58 24.56  25.33 22.91 22.94    15

Compositions

pkg_partitions <- function(n, total) {
    a <- firstcomposition(n)
    for (i in 1:(total - 1)) a <- nextcomposition(a, FALSE)
}

pkg_arrangements <- function(n, total) {
    a <- icompositions(n)
    for (i in 1:total) a$getnext()
}

pkg_RcppAlgos <- function(n, total) {
    a <- compositionsIter(0:n, repetition = TRUE)
    for (i in 1:total) a@nextIter()
}

total <- compositionsCount(0:15, repetition = TRUE)
total
#> [1] 16384

microbenchmark(cbRcppAlgos    = pkg_RcppAlgos(15, total),
               cbArrangements = pkg_arrangements(15, total),
               cbPartitions   = pkg_partitions(15, total),
               times = 15, unit = "relative")
#> Unit: relative
#>            expr   min    lq  mean median    uq   max neval
#>     cbRcppAlgos  1.00  1.00  1.00   1.00  1.00  1.00    15
#>  cbArrangements 14.26 14.06 13.52  13.97 13.63 11.71    15
#>    cbPartitions 46.44 46.50 44.77  46.16 44.63 40.38    15