High Precision Timing of R Expressions

Last updated: 2024-08-29

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File	Version	Author	Date	Message
Rmd	f4c0b1d	Dave Tang	2024-08-29	Benchmarking R expressions

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

You can install the release version from CRAN with:

install.packages("bench")

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

Benchmarks can be run with bench::mark(), which takes one or more expressions to benchmark against each other. Returns a tibble with the additional summary columns; the following summary columns are computed:

expression - bench_expr The deparsed expression that was evaluated (or its name if one was provided).
min - bench_time The minimum execution time.
median - bench_time The sample median of execution time.
itr/sec - double The estimated number of executions performed per second.
mem_alloc - bench_bytes Total amount of memory allocated by R while running the expression. Memory allocated outside the R heap, e.g. by malloc() or new directly is not tracked, take care to avoid misinterpreting the results if running code that may do this.
gc/sec - double The number of garbage collections per second.
n_itr - integer Total number of iterations after filtering garbage collections (if filter_gc == TRUE).
n_gc - double Total number of garbage collections performed over all iterations. This is a psudo-measure of the pressure on the garbage collector, if it varies greatly between to alternatives generally the one with fewer collections will cause fewer allocation in real usage.
total_time - bench_time The total time to perform the benchmarks.
result - list A list column of the object(s) returned by the evaluated expression(s).
memory - list` A list column with results from Rprofmem().
time - list` A list column of bench_time vectors for each evaluated expression.
gc - list A list column with tibbles containing the level of garbage collection (0-2, columns) for each iteration (rows).

library(bench)

bench::mark(
  runif(n = 1000000)
)

# A tibble: 1 × 6
  expression            min   median `itr/sec` mem_alloc `gc/sec`
  <bch:expr>       <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
1 runif(n = 1e+06)   21.4ms   21.5ms      46.3    7.63MB     9.74

`system_time()`

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

system.time(Sys.sleep(.5))

   user  system elapsed 
  0.001   0.000   0.501

bench::system_time(Sys.sleep(.5))

process    real 
  100µs   501ms

sessionInfo()

R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] bench_1.1.3     workflowr_1.7.1

loaded via a namespace (and not attached):
 [1] jsonlite_1.8.8    compiler_4.4.0    promises_1.3.0    Rcpp_1.0.12      
 [5] stringr_1.5.1     git2r_0.33.0      callr_3.7.6       later_1.3.2      
 [9] jquerylib_0.1.4   yaml_2.3.8        fastmap_1.2.0     R6_2.5.1         
[13] knitr_1.47        tibble_3.2.1      rprojroot_2.0.4   bslib_0.7.0      
[17] pillar_1.9.0      rlang_1.1.4       utf8_1.2.4        cachem_1.1.0     
[21] stringi_1.8.4     httpuv_1.6.15     xfun_0.44         getPass_0.2-4    
[25] fs_1.6.4          sass_0.4.9        cli_3.6.3         magrittr_2.0.3   
[29] ps_1.7.6          digest_0.6.37     processx_3.8.4    rstudioapi_0.16.0
[33] lifecycle_1.0.4   vctrs_0.6.5       evaluate_0.24.0   glue_1.7.0       
[37] whisker_0.4.1     profmem_0.6.0     fansi_1.0.6       rmarkdown_2.27   
[41] httr_1.4.7        tools_4.4.0       pkgconfig_2.0.3   htmltools_0.5.8.1