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Henrik Bengtsson edited this page Sep 11, 2019 · 3 revisions

matrixStats: Benchmark report

count() benchmarks on subsetted computation

This report benchmark the performance of count() on subsetted computation.

Data type "integer"

Data

> rvector <- function(n, mode = c("logical", "double", "integer"), range = c(-100, +100), na_prob = 0) {
+     mode <- match.arg(mode)
+     if (mode == "logical") {
+         x <- sample(c(FALSE, TRUE), size = n, replace = TRUE)
+     }     else {
+         x <- runif(n, min = range[1], max = range[2])
+     }
+     storage.mode(x) <- mode
+     if (na_prob > 0) 
+         x[sample(n, size = na_prob * n)] <- NA
+     x
+ }
> rvectors <- function(scale = 10, seed = 1, ...) {
+     set.seed(seed)
+     data <- list()
+     data[[1]] <- rvector(n = scale * 100, ...)
+     data[[2]] <- rvector(n = scale * 1000, ...)
+     data[[3]] <- rvector(n = scale * 10000, ...)
+     data[[4]] <- rvector(n = scale * 1e+05, ...)
+     data[[5]] <- rvector(n = scale * 1e+06, ...)
+     names(data) <- sprintf("n = %d", sapply(data, FUN = length))
+     data
+ }
> data <- rvectors(mode = mode)

Results

n = 1000 vector

> x <- data[["n = 1000"]]
> idxs <- sample.int(length(x), size = length(x) * 0.7)
> x_S <- x[idxs]
> gc()
           used  (Mb) gc trigger  (Mb) max used  (Mb)
Ncells  3230079 172.6    5709258 305.0  5709258 305.0
Vcells 12131425  92.6   28649958 218.6 56666022 432.4
> stats <- microbenchmark(count_x_S = count(x_S, value), `count(x, idxs)` = count(x, idxs = idxs, value), 
+     `count(x[idxs])` = count(x[idxs], value), unit = "ms")

Table: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on integer+n = 1000 data. The top panel shows times in milliseconds and the bottom panel shows relative times.

expr min lq mean median uq max
1 count_x_S 0.001619 0.0016630 0.0017513 0.0017065 0.0018110 0.002255
2 count(x, idxs) 0.003229 0.0033065 0.0034167 0.0033545 0.0034935 0.004806
3 count(x[idxs]) 0.003190 0.0033525 0.0049716 0.0034385 0.0035520 0.144710
expr min lq mean median uq max
1 count_x_S 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
2 count(x, idxs) 1.994441 1.988274 1.950957 1.965719 1.929045 2.131264
3 count(x[idxs]) 1.970352 2.015935 2.838766 2.014943 1.961347 64.172949

Figure: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on integer+n = 1000 data. Outliers are displayed as crosses. Times are in milliseconds.

n = 10000 vector

> x <- data[["n = 10000"]]
> idxs <- sample.int(length(x), size = length(x) * 0.7)
> x_S <- x[idxs]
> gc()
           used  (Mb) gc trigger  (Mb) max used  (Mb)
Ncells  3228239 172.5    5709258 305.0  5709258 305.0
Vcells 11802269  90.1   28649958 218.6 56666022 432.4
> stats <- microbenchmark(count_x_S = count(x_S, value), `count(x, idxs)` = count(x, idxs = idxs, value), 
+     `count(x[idxs])` = count(x[idxs], value), unit = "ms")

Table: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on integer+n = 10000 data. The top panel shows times in milliseconds and the bottom panel shows relative times.

expr min lq mean median uq max
1 count_x_S 0.001666 0.0018615 0.0020140 0.0020160 0.0021335 0.003167
3 count(x[idxs]) 0.013703 0.0141310 0.0149449 0.0142755 0.0144655 0.060614
2 count(x, idxs) 0.016783 0.0170145 0.0172585 0.0171785 0.0173070 0.019913
expr min lq mean median uq max
1 count_x_S 1.00000 1.000000 1.000000 1.000000 1.000000 1.000000
3 count(x[idxs]) 8.22509 7.591190 7.420595 7.081101 6.780173 19.139249
2 count(x, idxs) 10.07383 9.140209 8.569340 8.521081 8.112023 6.287654

Figure: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on integer+n = 10000 data. Outliers are displayed as crosses. Times are in milliseconds.

n = 100000 vector

> x <- data[["n = 100000"]]
> idxs <- sample.int(length(x), size = length(x) * 0.7)
> x_S <- x[idxs]
> gc()
           used  (Mb) gc trigger  (Mb) max used  (Mb)
Ncells  3228311 172.5    5709258 305.0  5709258 305.0
Vcells 11865829  90.6   28649958 218.6 56666022 432.4
> stats <- microbenchmark(count_x_S = count(x_S, value), `count(x, idxs)` = count(x, idxs = idxs, value), 
+     `count(x[idxs])` = count(x[idxs], value), unit = "ms")

Table: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on integer+n = 100000 data. The top panel shows times in milliseconds and the bottom panel shows relative times.

expr min lq mean median uq max
1 count_x_S 0.001643 0.0019185 0.0021756 0.0020645 0.0024935 0.002985
3 count(x[idxs]) 0.148818 0.1503995 0.1547928 0.1530510 0.1536240 0.268071
2 count(x, idxs) 0.190942 0.1922220 0.1966419 0.1965080 0.1970690 0.235942
expr min lq mean median uq max
1 count_x_S 1.00000 1.00000 1.00000 1.00000 1.00000 1.00000
3 count(x[idxs]) 90.57699 78.39432 71.14786 74.13466 61.60979 89.80603
2 count(x, idxs) 116.21546 100.19390 90.38305 95.18431 79.03309 79.04255

Figure: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on integer+n = 100000 data. Outliers are displayed as crosses. Times are in milliseconds.

n = 1000000 vector

> x <- data[["n = 1000000"]]
> idxs <- sample.int(length(x), size = length(x) * 0.7)
> x_S <- x[idxs]
> gc()
           used  (Mb) gc trigger  (Mb) max used  (Mb)
Ncells  3228383 172.5    5709258 305.0  5709258 305.0
Vcells 12495878  95.4   28649958 218.6 56666022 432.4
> stats <- microbenchmark(count_x_S = count(x_S, value), `count(x, idxs)` = count(x, idxs = idxs, value), 
+     `count(x[idxs])` = count(x[idxs], value), unit = "ms")

Table: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on integer+n = 1000000 data. The top panel shows times in milliseconds and the bottom panel shows relative times.

expr min lq mean median uq max
1 count_x_S 0.001678 0.0021955 0.0073567 0.0049855 0.0125475 0.044432
2 count(x, idxs) 2.262734 2.3477680 2.5927281 2.4185615 2.7107550 5.827718
3 count(x[idxs]) 2.925195 3.0648270 3.5152259 3.1479515 3.5457175 14.266352
expr min lq mean median uq max
1 count_x_S 1.000 1.000 1.0000 1.0000 1.0000 1.0000
2 count(x, idxs) 1348.471 1069.355 352.4299 485.1191 216.0395 131.1604
3 count(x[idxs]) 1743.263 1395.959 477.8252 631.4214 282.5836 321.0828

Figure: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on integer+n = 1000000 data. Outliers are displayed as crosses. Times are in milliseconds.

n = 10000000 vector

> x <- data[["n = 10000000"]]
> idxs <- sample.int(length(x), size = length(x) * 0.7)
> x_S <- x[idxs]
> gc()
           used  (Mb) gc trigger (Mb) max used  (Mb)
Ncells  3228455 172.5    5709258  305  5709258 305.0
Vcells 18795926 143.5   34459949  263 56666022 432.4
> stats <- microbenchmark(count_x_S = count(x_S, value), `count(x, idxs)` = count(x, idxs = idxs, value), 
+     `count(x[idxs])` = count(x[idxs], value), unit = "ms")

Table: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on integer+n = 10000000 data. The top panel shows times in milliseconds and the bottom panel shows relative times.

expr min lq mean median uq max
1 count_x_S 0.003185 0.006837 0.0213222 0.0111545 0.036879 0.067999
3 count(x[idxs]) 119.062488 132.784881 139.6765763 135.0524170 141.274531 392.878951
2 count(x, idxs) 118.899762 150.948282 151.9656970 152.2712185 154.161277 159.782806
expr min lq mean median uq max
1 count_x_S 1.00 1.00 1.000 1.00 1.000 1.000
3 count(x[idxs]) 37382.26 19421.51 6550.752 12107.44 3830.758 5777.717
2 count(x, idxs) 37331.17 22078.15 7127.105 13651.10 4180.191 2349.782

Figure: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on integer+n = 10000000 data. Outliers are displayed as crosses. Times are in milliseconds.

Data type "double"

Data

> rvector <- function(n, mode = c("logical", "double", "integer"), range = c(-100, +100), na_prob = 0) {
+     mode <- match.arg(mode)
+     if (mode == "logical") {
+         x <- sample(c(FALSE, TRUE), size = n, replace = TRUE)
+     }     else {
+         x <- runif(n, min = range[1], max = range[2])
+     }
+     storage.mode(x) <- mode
+     if (na_prob > 0) 
+         x[sample(n, size = na_prob * n)] <- NA
+     x
+ }
> rvectors <- function(scale = 10, seed = 1, ...) {
+     set.seed(seed)
+     data <- list()
+     data[[1]] <- rvector(n = scale * 100, ...)
+     data[[2]] <- rvector(n = scale * 1000, ...)
+     data[[3]] <- rvector(n = scale * 10000, ...)
+     data[[4]] <- rvector(n = scale * 1e+05, ...)
+     data[[5]] <- rvector(n = scale * 1e+06, ...)
+     names(data) <- sprintf("n = %d", sapply(data, FUN = length))
+     data
+ }
> data <- rvectors(mode = mode)

Results

n = 1000 vector

> x <- data[["n = 1000"]]
> idxs <- sample.int(length(x), size = length(x) * 0.7)
> x_S <- x[idxs]
> gc()
           used  (Mb) gc trigger (Mb) max used  (Mb)
Ncells  3228533 172.5    5709258  305  5709258 305.0
Vcells 17353131 132.4   34459949  263 56666022 432.4
> stats <- microbenchmark(count_x_S = count(x_S, value), `count(x, idxs)` = count(x, idxs = idxs, value), 
+     `count(x[idxs])` = count(x[idxs], value), unit = "ms")

Table: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on double+n = 1000 data. The top panel shows times in milliseconds and the bottom panel shows relative times.

expr min lq mean median uq max
1 count_x_S 0.001658 0.0017330 0.0018447 0.001779 0.0019170 0.002773
2 count(x, idxs) 0.003308 0.0033625 0.0035267 0.003414 0.0035550 0.006260
3 count(x[idxs]) 0.003438 0.0036185 0.0042375 0.003720 0.0038325 0.048690
expr min lq mean median uq max
1 count_x_S 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
2 count(x, idxs) 1.995175 1.940277 1.911854 1.919056 1.854460 2.257483
3 count(x[idxs]) 2.073583 2.087998 2.297137 2.091062 1.999218 17.558601

Figure: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on double+n = 1000 data. Outliers are displayed as crosses. Times are in milliseconds.

n = 10000 vector

> x <- data[["n = 10000"]]
> idxs <- sample.int(length(x), size = length(x) * 0.7)
> x_S <- x[idxs]
> gc()
           used  (Mb) gc trigger (Mb) max used  (Mb)
Ncells  3228599 172.5    5709258  305  5709258 305.0
Vcells 17362618 132.5   34459949  263 56666022 432.4
> stats <- microbenchmark(count_x_S = count(x_S, value), `count(x, idxs)` = count(x, idxs = idxs, value), 
+     `count(x[idxs])` = count(x[idxs], value), unit = "ms")

Table: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on double+n = 10000 data. The top panel shows times in milliseconds and the bottom panel shows relative times.

expr min lq mean median uq max
1 count_x_S 0.001675 0.0019025 0.0020680 0.0020680 0.0022010 0.003167
3 count(x[idxs]) 0.016112 0.0167550 0.0178118 0.0170035 0.0173945 0.072023
2 count(x, idxs) 0.017637 0.0178775 0.0180867 0.0180085 0.0181525 0.022179
expr min lq mean median uq max
1 count_x_S 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000
3 count(x[idxs]) 9.619105 8.806833 8.613154 8.222195 7.902999 22.741711
2 count(x, idxs) 10.529552 9.396846 8.746090 8.708172 8.247388 7.003158

Figure: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on double+n = 10000 data. Outliers are displayed as crosses. Times are in milliseconds.

n = 100000 vector

> x <- data[["n = 100000"]]
> idxs <- sample.int(length(x), size = length(x) * 0.7)
> x_S <- x[idxs]
> gc()
           used  (Mb) gc trigger (Mb) max used  (Mb)
Ncells  3228671 172.5    5709258  305  5709258 305.0
Vcells 17457495 133.2   34459949  263 56666022 432.4
> stats <- microbenchmark(count_x_S = count(x_S, value), `count(x, idxs)` = count(x, idxs = idxs, value), 
+     `count(x[idxs])` = count(x[idxs], value), unit = "ms")

Table: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on double+n = 100000 data. The top panel shows times in milliseconds and the bottom panel shows relative times.

expr min lq mean median uq max
1 count_x_S 0.001662 0.0019560 0.0022419 0.002221 0.0025330 0.002890
3 count(x[idxs]) 0.187506 0.1892825 0.2515486 0.196456 0.3197070 0.392828
2 count(x, idxs) 0.217537 0.2179915 0.2202523 0.218266 0.2186345 0.267948
expr min lq mean median uq max
1 count_x_S 1.0000 1.00000 1.00000 1.00000 1.00000 1.00000
3 count(x[idxs]) 112.8195 96.77019 112.20481 88.45385 126.21674 135.92664
2 count(x, idxs) 130.8887 111.44760 98.24492 98.27375 86.31445 92.71557

Figure: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on double+n = 100000 data. Outliers are displayed as crosses. Times are in milliseconds.

n = 1000000 vector

> x <- data[["n = 1000000"]]
> idxs <- sample.int(length(x), size = length(x) * 0.7)
> x_S <- x[idxs]
> gc()
           used  (Mb) gc trigger (Mb) max used  (Mb)
Ncells  3228743 172.5    5709258  305  5709258 305.0
Vcells 18402936 140.5   34459949  263 56666022 432.4
> stats <- microbenchmark(count_x_S = count(x_S, value), `count(x, idxs)` = count(x, idxs = idxs, value), 
+     `count(x[idxs])` = count(x[idxs], value), unit = "ms")

Table: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on double+n = 1000000 data. The top panel shows times in milliseconds and the bottom panel shows relative times.

expr min lq mean median uq max
1 count_x_S 0.003542 0.0043465 0.013231 0.008344 0.0220045 0.035122
2 count(x, idxs) 7.223669 9.0095400 10.220966 9.615808 9.9312620 23.321479
3 count(x[idxs]) 5.099413 9.4980355 10.540235 10.415299 10.7106510 23.115483
expr min lq mean median uq max
1 count_x_S 1.000 1.000 1.0000 1.000 1.0000 1.0000
2 count(x, idxs) 2039.432 2072.826 772.5020 1152.422 451.3287 664.0134
3 count(x[idxs]) 1439.699 2185.215 796.6324 1248.238 486.7482 658.1483

Figure: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on double+n = 1000000 data. Outliers are displayed as crosses. Times are in milliseconds.

n = 10000000 vector

> x <- data[["n = 10000000"]]
> idxs <- sample.int(length(x), size = length(x) * 0.7)
> x_S <- x[idxs]
> gc()
           used  (Mb) gc trigger  (Mb) max used  (Mb)
Ncells  3228812 172.5    5709258 305.0  5709258 305.0
Vcells 27852979 212.6   41431938 316.2 56666022 432.4
> stats <- microbenchmark(count_x_S = count(x_S, value), `count(x, idxs)` = count(x, idxs = idxs, value), 
+     `count(x[idxs])` = count(x[idxs], value), unit = "ms")

Table: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on double+n = 10000000 data. The top panel shows times in milliseconds and the bottom panel shows relative times.

expr min lq mean median uq max
1 count_x_S 0.004525 0.0070435 0.0224937 0.011471 0.041713 0.053685
3 count(x[idxs]) 147.007862 164.1726900 177.7612231 169.873675 178.636941 456.497123
2 count(x, idxs) 149.775005 167.5224960 174.0146670 170.718605 179.378404 201.964168
expr min lq mean median uq max
1 count_x_S 1.00 1.00 1.000 1.00 1.000 1.000
3 count(x[idxs]) 32487.93 23308.40 7902.726 14808.97 4282.524 8503.253
2 count(x, idxs) 33099.45 23783.98 7736.165 14882.63 4300.300 3762.022

Figure: Benchmarking of count_x_S(), count(x, idxs)() and count(x[idxs])() on double+n = 10000000 data. Outliers are displayed as crosses. Times are in milliseconds.

Appendix

Session information

R version 3.6.1 Patched (2019-08-27 r77078)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /home/hb/software/R-devel/R-3-6-branch/lib/R/lib/libRblas.so
LAPACK: /home/hb/software/R-devel/R-3-6-branch/lib/R/lib/libRlapack.so

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       

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

other attached packages:
[1] microbenchmark_1.4-6    matrixStats_0.55.0-9000 ggplot2_3.2.1          
[4] knitr_1.24              R.devices_2.16.0        R.utils_2.9.0          
[7] R.oo_1.22.0             R.methodsS3_1.7.1       history_0.0.0-9002     

loaded via a namespace (and not attached):
 [1] Biobase_2.45.0       bit64_0.9-7          splines_3.6.1       
 [4] network_1.15         assertthat_0.2.1     highr_0.8           
 [7] stats4_3.6.1         blob_1.2.0           robustbase_0.93-5   
[10] pillar_1.4.2         RSQLite_2.1.2        backports_1.1.4     
[13] lattice_0.20-38      glue_1.3.1           digest_0.6.20       
[16] colorspace_1.4-1     sandwich_2.5-1       Matrix_1.2-17       
[19] XML_3.98-1.20        lpSolve_5.6.13.3     pkgconfig_2.0.2     
[22] genefilter_1.66.0    purrr_0.3.2          ergm_3.10.4         
[25] xtable_1.8-4         mvtnorm_1.0-11       scales_1.0.0        
[28] tibble_2.1.3         annotate_1.62.0      IRanges_2.18.2      
[31] TH.data_1.0-10       withr_2.1.2          BiocGenerics_0.30.0 
[34] lazyeval_0.2.2       mime_0.7             survival_2.44-1.1   
[37] magrittr_1.5         crayon_1.3.4         statnet.common_4.3.0
[40] memoise_1.1.0        laeken_0.5.0         R.cache_0.13.0      
[43] MASS_7.3-51.4        R.rsp_0.43.1         tools_3.6.1         
[46] multcomp_1.4-10      S4Vectors_0.22.1     trust_0.1-7         
[49] munsell_0.5.0        AnnotationDbi_1.46.1 compiler_3.6.1      
[52] rlang_0.4.0          grid_3.6.1           RCurl_1.95-4.12     
[55] cwhmisc_6.6          rappdirs_0.3.1       labeling_0.3        
[58] bitops_1.0-6         base64enc_0.1-3      boot_1.3-23         
[61] gtable_0.3.0         codetools_0.2-16     DBI_1.0.0           
[64] markdown_1.1         R6_2.4.0             zoo_1.8-6           
[67] dplyr_0.8.3          bit_1.1-14           zeallot_0.1.0       
[70] parallel_3.6.1       Rcpp_1.0.2           vctrs_0.2.0         
[73] DEoptimR_1.0-8       tidyselect_0.2.5     xfun_0.9            
[76] coda_0.19-3

Total processing time was 1.34 mins.

Reproducibility

To reproduce this report, do:

html <- matrixStats:::benchmark('count_subset')

Copyright Dongcan Jiang. Last updated on 2019-09-10 20:57:36 (-0700 UTC). Powered by RSP.

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