bench v1.0.1

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High Precision Timing of R Expressions

Tools to accurately benchmark and analyze execution times for R expressions.

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bench

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The goal of bench is to benchmark code, tracking execution time, memory allocations and garbage collections.

Installation

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("r-lib/bench")

Features

bench::mark() is used to benchmark one or a series of expressions, we feel it has a number of advantages over alternatives.

  • Always uses the highest precision APIs available for each operating system (often nanoseconds).
  • Tracks memory allocations for each expression.
  • Tracks the number and type of R garbage collections per expression iteration.
  • Verifies equality of expression results by default, to avoid accidentally benchmarking inequivalent code.
  • Has bench::press(), which allows you to easily perform and combine benchmarks across a large grid of values.
  • Uses adaptive stopping by default, running each expression for a set amount of time rather than for a specific number of iterations.
  • Expressions are run in batches and summary statistics are calculated after filtering out iterations with garbage collections. This allows you to isolate the performance and effects of garbage collection on running time (for more details see Neal 2014).

The times and memory usage are returned as custom objects which have human readable formatting for display (e.g. 104ns) and comparisons (e.g. x$mem_alloc > "10MB").

There is also full support for plotting with ggplot2 including custom scales and formatting.

Usage

bench::mark()

Benchmarks can be run with bench::mark(), which takes one or more expressions to benchmark against each other.

library(bench)
set.seed(42)
dat <- data.frame(x = runif(10000, 1, 1000), y=runif(10000, 1, 1000))

bench::mark() will throw an error if the results are not equivalent, so you don’t accidentally benchmark inequivalent code.

bench::mark(
  dat[dat$x > 500, ],
  dat[which(dat$x > 499), ],
  subset(dat, x > 500))
#> Error: Each result must equal the first result:
#>   `dat[dat$x > 500, ]` does not equal `dat[which(dat$x > 499), ]`

Results are easy to interpret, with human readable units.

bnch <- bench::mark(
  dat[dat$x > 500, ],
  dat[which(dat$x > 500), ],
  subset(dat, x > 500))
bnch
#> # A tibble: 3 x 10
#>   expression                     min     mean   median      max `itr/sec` mem_alloc  n_gc n_itr total_time
#>   <chr>                     <bch:tm> <bch:tm> <bch:tm> <bch:tm>     <dbl> <bch:byt> <dbl> <int>   <bch:tm>
#> 1 dat[dat$x > 500, ]           306µs    361µs    327µs   1.23ms     2770.     416KB    48   989      357ms
#> 2 dat[which(dat$x > 500), ]    231µs    288µs    258µs   1.29ms     3471.     357KB    54  1170      337ms
#> 3 subset(dat, x > 500)         374µs    443µs    405µs   1.59ms     2257.     548KB    55   702      311ms

By default the summary uses absolute measures, however relative results can be obtained by using relative = TRUE in your call to bench::mark() or calling summary(relative = TRUE) on the results.

summary(bnch, relative = TRUE)
#> # A tibble: 3 x 10
#>   expression                  min  mean median   max `itr/sec` mem_alloc  n_gc n_itr total_time
#>   <chr>                     <dbl> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <dbl> <dbl>      <dbl>
#> 1 dat[dat$x > 500, ]         1.32  1.25   1.27  1         1.23      1.16  1     1.41       1.15
#> 2 dat[which(dat$x > 500), ]  1     1      1     1.05      1.54      1     1.12  1.67       1.08
#> 3 subset(dat, x > 500)       1.62  1.54   1.57  1.30      1         1.53  1.15  1          1

bench::press()

bench::press() is used to run benchmarks against a grid of parameters. Provide setup and benchmarking code as a single unnamed argument then define sets of values as named arguments. The full combination of values will be expanded and the benchmarks are then pressed together in the result. This allows you to benchmark a set of expressions across a wide variety of input sizes, perform replications and other useful tasks.

set.seed(42)

create_df <- function(rows, cols) {
  as.data.frame(setNames(
    replicate(cols, runif(rows, 1, 1000), simplify = FALSE),
    rep_len(c("x", letters), cols)))
}

results <- bench::press(
  rows = c(10000, 100000),
  cols = c(10, 100),
  {
    dat <- create_df(rows, cols)
    bench::mark(
      min_iterations = 100,
      bracket = dat[dat$x > 500, ],
      which = dat[which(dat$x > 500), ],
      subset = subset(dat, x > 500)
    )
  }
)
results
#> # A tibble: 12 x 12
#>    expression   rows  cols      min     mean   median      max `itr/sec` mem_alloc  n_gc n_itr total_time
#>    <chr>       <dbl> <dbl> <bch:tm> <bch:tm> <bch:tm> <bch:tm>     <dbl> <bch:byt> <dbl> <int>   <bch:tm>
#>  1 bracket     10000    10 787.15µs   1.04ms 960.52µs   2.16ms    960.      1.17MB    36   261   271.87ms
#>  2 which       10000    10 438.68µs 567.76µs 520.88µs   1.48ms   1761.    827.04KB    44   497   282.18ms
#>  3 subset      10000    10 883.83µs   1.14ms   1.06ms   2.16ms    874.      1.28MB    38   244   279.11ms
#>  4 bracket    100000    10  13.29ms  15.35ms  15.15ms   18.3ms     65.2    11.54MB    52    48   736.71ms
#>  5 which      100000    10   8.99ms  10.63ms   10.4ms   13.7ms     94.0     7.91MB    34    66   701.81ms
#>  6 subset     100000    10  15.91ms  17.79ms  17.12ms  24.82ms     56.2    12.68MB    74    26   462.46ms
#>  7 bracket     10000   100   6.95ms   8.54ms   8.21ms  11.67ms    117.      9.71MB    34    66   563.77ms
#>  8 which       10000   100   2.83ms   3.62ms   3.69ms   5.17ms    276.      5.91MB    27    88   318.52ms
#>  9 subset      10000   100   6.98ms   8.62ms   8.48ms  11.83ms    116.      9.84MB    44    56   482.46ms
#> 10 bracket    100000   100  94.66ms  99.77ms  99.99ms 104.45ms     10.0    97.47MB    97     4   399.08ms
#> 11 which      100000   100  51.09ms  54.41ms  54.13ms  60.37ms     18.4    59.51MB    57    43      2.34s
#> 12 subset     100000   100  96.94ms 100.78ms 100.61ms 106.91ms      9.92   98.62MB    88    14      1.41s

Plotting

ggplot2::autoplot() can be used to generate an informative default plot. This plot is colored by gc level (0, 1, or 2) and faceted by parameters (if any). By default it generates a beeswarm plot, however you can also specify other plot types (jitter, ridge, boxplot, violin). See ?autoplot.bench_mark for full details.

ggplot2::autoplot(results)

You can also produce fully custom plots by un-nesting the results and working with the data directly.

library(tidyverse)
results %>%
  unnest() %>%
  filter(gc == "none") %>%
  ggplot(aes(x = mem_alloc, y = time, color = expression)) +
    geom_point() +
    scale_color_brewer(type = "qual", palette = 3)

system_time()

bench also includes system_time(), a higher precision alternative to system.time().

bench::system_time({ i <- 1; while(i < 1e7) i <- i + 1 })
#> process    real 
#>   330ms   331ms
bench::system_time(Sys.sleep(.5))
#> process    real 
#>    83µs   501ms

Alternatives

Functions in bench

Name Description
bench_time Human readable times
press Run setup code and benchmarks across a grid of parameters
as_bench_mark Coerce to a bench mark object Bench mark objects
knit_print.bench_mark Custom printing function for bench_mark objects in knitr documents
mark Benchmark a series of functions
summary.bench_mark Summarize bench::mark results.
scale_bench_time Position scales for bench_time data
system_time Return Process CPU and real time that an expression used.
bench_bytes Human readable memory sizes
bench_time_trans Benchmark time transformation
bench-package bench: High Precision Timing of R Expressions
autoplot.bench_mark Autoplot method for bench_mark objects
bench_bytes_trans Benchmark time transformation
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Details

License GPL-3
URL https://github.com/r-lib/bench
BugReports https://github.com/r-lib/bench/issues
Encoding UTF-8
LazyData true
RoxygenNote 6.0.1.9000
NeedsCompilation yes
Packaged 2018-06-05 20:46:23 UTC; jhester
Repository CRAN
Date/Publication 2018-06-06 05:03:17 UTC

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