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fs::path_dir is significantly slower on Windows vs Mac #424

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orgadish opened this issue Jun 12, 2023 · 4 comments
Closed

fs::path_dir is significantly slower on Windows vs Mac #424

orgadish opened this issue Jun 12, 2023 · 4 comments

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@orgadish
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When you use read_csv(..., id="file_path") you end up with a file_path column that has lots of repeats. Manipulations on this kind of column are somewhat slow. I have found that it's much faster to do a left_join(x, distinct(x, file_path) |> mutate(...), by="file_path") than it is to do the mutate directly.

Below I timed using fs::path_dir directly (with no tibble involvement at all) compared to going via a tibble to do the above. Even though the latter is significantly more indirect, it's more than 13X faster:

paths <- fs::path("base", stringr::str_glue("dir{d}", d=1:10), "inner") |> 
  rep(1e3)

bench::mark(
  direct = fs::path_dir(paths),
  indirect = {
    x <- tibble::tibble(a = paths)
    dplyr::left_join(x, dplyr::distinct(x, a) |> dplyr::mutate(b = fs::path_dir(a)), 
                     by = "a") |> 
      dplyr::pull(b)
  },
  iterations = 50
)
#> # A tibble: 2 × 6
#>   expression      min   median `itr/sec` mem_alloc `gc/sec`
#>   <bch:expr> <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
#> 1 direct      54.05ms  55.66ms      17.9  749.02KB    0.746
#> 2 indirect     3.68ms   4.14ms     237.     6.47MB    9.86

Created on 2023-06-12 with reprex v2.0.2

Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.0 (2023-04-21 ucrt)
#>  os       Windows 10 x64 (build 19045)
#>  system   x86_64, mingw32
#>  ui       RTerm
#>  language (EN)
#>  collate  English_United States.utf8
#>  ctype    English_United States.utf8
#>  tz       America/Los_Angeles
#>  date     2023-06-12
#>  pandoc   2.19.2 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  ! package     * version date (UTC) lib source
#>  P bench         1.1.3   2023-05-04 [?] CRAN (R 4.3.0)
#>    cli           3.6.1   2023-03-23 [1] CRAN (R 4.3.0)
#>    digest        0.6.31  2022-12-11 [1] CRAN (R 4.3.0)
#>    dplyr         1.1.2   2023-04-20 [1] CRAN (R 4.3.0)
#>    evaluate      0.21    2023-05-05 [1] CRAN (R 4.3.0)
#>    fansi         1.0.4   2023-01-22 [1] CRAN (R 4.3.0)
#>    fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
#>    fs            1.6.2   2023-04-25 [1] CRAN (R 4.3.0)
#>    generics      0.1.3   2022-07-05 [1] CRAN (R 4.3.0)
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#>    htmltools     0.5.5   2023-03-23 [1] CRAN (R 4.3.0)
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#>    pillar        1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
#>    pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
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#>    R6            2.5.1   2021-08-19 [1] CRAN (R 4.3.0)
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#>    rstudioapi    0.14    2022-08-22 [1] CRAN (R 4.3.0)
#>    sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
#>    stringi       1.7.12  2023-01-11 [1] CRAN (R 4.3.0)
#>    stringr       1.5.0   2022-12-02 [1] CRAN (R 4.3.0)
#>    tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
#>    tidyselect    1.2.0   2022-10-10 [1] CRAN (R 4.3.0)
#>    utf8          1.2.3   2023-01-31 [1] CRAN (R 4.3.0)
#>    vctrs         0.6.2   2023-04-19 [1] CRAN (R 4.3.0)
#>    withr         2.5.0   2022-03-03 [1] CRAN (R 4.3.0)
#>    xfun          0.39    2023-04-20 [1] CRAN (R 4.3.0)
#>    yaml          2.3.7   2023-01-23 [1] CRAN (R 4.3.0)
#> 
#>  [1] C:/Users/LAB/Desktop/2023-05 Sequence Recovery Analysis/renv/library/R-4.3/x86_64-w64-mingw32
#>  [2] C:/Users/LAB/AppData/Local/R/cache/R/renv/sandbox/R-4.3/x86_64-w64-mingw32/830ce55b
#>  [3] C:/Program Files/R/R-4.3.0/library
#> 
#>  P ── Loaded and on-disk path mismatch.
#> 
#> ──────────────────────────────────────────────────────────────────────────────
@orgadish
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orgadish commented Jun 12, 2023

Obviously, even faster without going through a tibble at all. The approach below (using func(unique(x))[match(x, unique(x)]) might be a reasonable approach overall as it doesn't seem to add significant overhead compared to applying directly, even if all paths are already unique.

fast_fs <- function(x, func) {
  ux <- unique(x)
  uy <- func(ux)
  uy[match(x, ux)]
}

repeated_paths <- fs::path("base", stringr::str_glue("dir{d}", d=1:10), "inner") |> 
  rep(1e3)

bench::mark(
  direct = repeated_paths |> fs::path_dir(),
  indirect = repeated_paths |> fast_fs(fs::path_dir),
  iterations = 50
)
#> # A tibble: 2 × 6
#>   expression      min   median `itr/sec` mem_alloc `gc/sec`
#>   <bch:expr> <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
#> 1 direct       54.1ms   56.3ms      17.7     749KB    0.361
#> 2 indirect    283.6µs  395.8µs    2242.      365KB    0

unique_paths <- fs::path("base", stringr::str_glue("dir{d}", d=1:1e4), "inner")

bench::mark(
  direct = unique_paths |> fs::path_dir(),
  indirect = unique_paths |> fast_fs(fs::path_dir),
  iterations = 50
)
#> # A tibble: 2 × 6
#>   expression      min   median `itr/sec` mem_alloc `gc/sec`
#>   <bch:expr> <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
#> 1 direct       56.1ms   57.1ms      17.4  901.88KB    0.726
#> 2 indirect     56.4ms   57.5ms      17.3    1.36MB    0.723

Created on 2023-06-12 with reprex v2.0.2

Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.0 (2023-04-21 ucrt)
#>  os       Windows 10 x64 (build 19045)
#>  system   x86_64, mingw32
#>  ui       RTerm
#>  language (EN)
#>  collate  English_United States.utf8
#>  ctype    English_United States.utf8
#>  tz       America/Los_Angeles
#>  date     2023-06-12
#>  pandoc   2.19.2 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  ! package     * version date (UTC) lib source
#>  P bench         1.1.3   2023-05-04 [?] CRAN (R 4.3.0)
#>    cli           3.6.1   2023-03-23 [1] CRAN (R 4.3.0)
#>    digest        0.6.31  2022-12-11 [1] CRAN (R 4.3.0)
#>    evaluate      0.21    2023-05-05 [1] CRAN (R 4.3.0)
#>    fansi         1.0.4   2023-01-22 [1] CRAN (R 4.3.0)
#>    fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
#>    fs            1.6.2   2023-04-25 [1] CRAN (R 4.3.0)
#>    glue          1.6.2   2022-02-24 [1] CRAN (R 4.3.0)
#>    htmltools     0.5.5   2023-03-23 [1] CRAN (R 4.3.0)
#>    knitr         1.42    2023-01-25 [1] CRAN (R 4.3.0)
#>    lifecycle     1.0.3   2022-10-07 [1] CRAN (R 4.3.0)
#>    magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
#>    pillar        1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
#>    pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.3.0)
#>  P profmem       0.6.0   2020-12-13 [?] CRAN (R 4.3.0)
#>    reprex        2.0.2   2022-08-17 [1] CRAN (R 4.3.0)
#>    rlang         1.1.1   2023-04-28 [1] CRAN (R 4.3.0)
#>    rmarkdown     2.21    2023-03-26 [1] CRAN (R 4.3.0)
#>    rstudioapi    0.14    2022-08-22 [1] CRAN (R 4.3.0)
#>    sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
#>    stringi       1.7.12  2023-01-11 [1] CRAN (R 4.3.0)
#>    stringr       1.5.0   2022-12-02 [1] CRAN (R 4.3.0)
#>    tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
#>    utf8          1.2.3   2023-01-31 [1] CRAN (R 4.3.0)
#>    vctrs         0.6.2   2023-04-19 [1] CRAN (R 4.3.0)
#>    withr         2.5.0   2022-03-03 [1] CRAN (R 4.3.0)
#>    xfun          0.39    2023-04-20 [1] CRAN (R 4.3.0)
#>    yaml          2.3.7   2023-01-23 [1] CRAN (R 4.3.0)
#> 
#>  [1] C:/Users/LAB/Desktop/2023-05 Sequence Recovery Analysis/renv/library/R-4.3/x86_64-w64-mingw32
#>  [2] C:/Users/LAB/AppData/Local/R/cache/R/renv/sandbox/R-4.3/x86_64-w64-mingw32/830ce55b
#>  [3] C:/Program Files/R/R-4.3.0/library
#> 
#>  P ── Loaded and on-disk path mismatch.
#> 
#> ──────────────────────────────────────────────────────────────────────────────

@orgadish
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orgadish commented Jul 7, 2023

Interestingly, path_file and path_dir are 18x slower on Windows than on Mac (see testing in #425). Not sure if that's something that can/should be addressed rather than implementing deduplication to speed up.

@orgadish orgadish changed the title fs::path_dir is significantly slower than expected on vectors with repeats fs::path_dir is significantly slower on Windows vs Mac Jul 27, 2023
@orgadish
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Given that these functions are essentially just wrappers around the equivalent base methods, it's unsurprising that the trend holds for those methods (see reprex below).

As such, I am closing this since this issue is not fs specific. I have submitted the bug by email to the Bugzilla moderators.

Mac Reprex

N <- 10000

generate_vec <- function(l) lapply(1:N, \(dummy) sample(LETTERS, l, replace=T) |> 
                                     paste0(collapse="/")) |>
  unlist()

vec3 <- generate_vec(3)
vec100 <- generate_vec(100)

bench::mark(
  tolower(vec3),
  tolower(vec100),
  check=FALSE,
  iterations=10
)
#> # A tibble: 2 × 6
#>   expression           min   median `itr/sec` mem_alloc `gc/sec`
#>   <bch:expr>      <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
#> 1 tolower(vec3)      2.9ms   3.08ms     319.    78.17KB        0
#> 2 tolower(vec100)   41.6ms  43.84ms      22.1    2.44MB        0

bench::mark(
  basename(vec3),
  basename(vec100),
  check=FALSE,
  iterations=10
)
#> # A tibble: 2 × 6
#>   expression            min   median `itr/sec` mem_alloc `gc/sec`
#>   <bch:expr>       <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
#> 1 basename(vec3)     1.67ms   1.86ms      535.    78.2KB        0
#> 2 basename(vec100)   3.01ms   3.13ms      302.    78.2KB        0

Created on 2023-09-15 with reprex v2.0.2

Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.2.2 (2022-10-31)
#>  os       macOS Big Sur ... 10.16
#>  system   x86_64, darwin17.0
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2023-09-15
#>  pandoc   3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  bench         1.1.2   2021-11-30 [1] CRAN (R 4.2.0)
#>  cli           3.6.1   2023-03-23 [1] CRAN (R 4.2.0)
#>  digest        0.6.31  2022-12-11 [1] CRAN (R 4.2.0)
#>  evaluate      0.19    2022-12-13 [1] CRAN (R 4.2.0)
#>  fansi         1.0.4   2023-01-22 [1] CRAN (R 4.2.0)
#>  fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.2.0)
#>  fs            1.6.2   2023-04-25 [1] CRAN (R 4.2.0)
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#>  stringr       1.5.0   2022-12-02 [1] CRAN (R 4.2.0)
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#>  tibble        3.2.1   2023-03-20 [1] CRAN (R 4.2.0)
#>  utf8          1.2.3   2023-01-31 [1] CRAN (R 4.2.0)
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#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Windows Reprex

N <- 10000

generate_vec <- function(l) lapply(1:N, \(dummy) sample(LETTERS, l, replace=T) |> 
                                     paste0(collapse="/")) |>
  unlist()

vec3 <- generate_vec(3)
vec100 <- generate_vec(100)

bench::mark(
  tolower(vec3),
  tolower(vec100),
  check=FALSE,
  iterations=10
)
#> # A tibble: 2 × 6
#>   expression           min   median `itr/sec` mem_alloc `gc/sec`
#>   <bch:expr>      <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
#> 1 tolower(vec3)     5.54ms   6.06ms     165.    78.17KB        0
#> 2 tolower(vec100)  77.67ms  79.17ms      12.6    2.44MB        0

bench::mark(
  basename(vec3),
  basename(vec100),
  check=FALSE,
  iterations=10
)
#> # A tibble: 2 × 6
#>   expression            min   median `itr/sec` mem_alloc `gc/sec`
#>   <bch:expr>       <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
#> 1 basename(vec3)     52.1ms   53.2ms     18.7    78.17KB     0   
#> 2 basename(vec100)   99.6ms  100.7ms      9.89    4.42MB     1.10

Created on 2023-09-15 with reprex v2.0.2

Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.0 (2023-04-21 ucrt)
#>  os       Windows 10 x64 (build 19045)
#>  system   x86_64, mingw32
#>  ui       RTerm
#>  language (EN)
#>  collate  English_United States.utf8
#>  ctype    English_United States.utf8
#>  tz       America/Los_Angeles
#>  date     2023-09-15
#>  pandoc   2.19.2 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  ! package     * version date (UTC) lib source
#>  P bench         1.1.3   2023-05-04 [?] CRAN (R 4.3.0)
#>    cli           3.6.1   2023-03-23 [1] CRAN (R 4.3.0)
#>    digest        0.6.31  2022-12-11 [1] CRAN (R 4.3.0)
#>    evaluate      0.21    2023-05-05 [1] CRAN (R 4.3.0)
#>    fansi         1.0.4   2023-01-22 [1] CRAN (R 4.3.0)
#>    fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.3.0)
#>    fs            1.6.2   2023-04-25 [1] CRAN (R 4.3.0)
#>    glue          1.6.2   2022-02-24 [1] CRAN (R 4.3.0)
#>    htmltools     0.5.5   2023-03-23 [1] CRAN (R 4.3.0)
#>    knitr         1.42    2023-01-25 [1] CRAN (R 4.3.0)
#>    lifecycle     1.0.3   2022-10-07 [1] CRAN (R 4.3.0)
#>    magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.3.0)
#>    pillar        1.9.0   2023-03-22 [1] CRAN (R 4.3.0)
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#>  P profmem       0.6.0   2020-12-13 [?] CRAN (R 4.3.0)
#>    purrr         1.0.1   2023-01-10 [1] CRAN (R 4.3.0)
#>    R.cache       0.16.0  2022-07-21 [1] CRAN (R 4.3.1)
#>    R.methodsS3   1.8.2   2022-06-13 [1] CRAN (R 4.3.0)
#>    R.oo          1.25.0  2022-06-12 [1] CRAN (R 4.3.0)
#>    R.utils       2.12.2  2022-11-11 [1] CRAN (R 4.3.1)
#>    reprex        2.0.2   2022-08-17 [1] CRAN (R 4.3.0)
#>    rlang         1.1.1   2023-04-28 [1] CRAN (R 4.3.0)
#>    rmarkdown     2.21    2023-03-26 [1] CRAN (R 4.3.0)
#>    rstudioapi    0.14    2022-08-22 [1] CRAN (R 4.3.0)
#>    sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.3.0)
#>    styler        1.10.2  2023-08-29 [1] CRAN (R 4.3.1)
#>    tibble        3.2.1   2023-03-20 [1] CRAN (R 4.3.0)
#>    utf8          1.2.3   2023-01-31 [1] CRAN (R 4.3.0)
#>    vctrs         0.6.2   2023-04-19 [1] CRAN (R 4.3.0)
#>    withr         2.5.0   2022-03-03 [1] CRAN (R 4.3.0)
#>    xfun          0.39    2023-04-20 [1] CRAN (R 4.3.0)
#>    yaml          2.3.7   2023-01-23 [1] CRAN (R 4.3.0)
#> 
#>  [1] C:/Users/LAB/Desktop/2023-05 Sequence Recovery Analysis/renv/library/R-4.3/x86_64-w64-mingw32
#>  [2] C:/Users/LAB/AppData/Local/R/cache/R/renv/sandbox/R-4.3/x86_64-w64-mingw32/830ce55b
#>  [3] C:/Program Files/R/R-4.3.0/library
#> 
#>  P ── Loaded and on-disk path mismatch.
#> 
#> ──────────────────────────────────────────────────────────────────────────────

@orgadish orgadish closed this as not planned Won't fix, can't repro, duplicate, stale Sep 16, 2023
@orgadish
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To anyone that comes across this and is looking for a solution, I've written a package to do the general case of fast_fs shown above:

# if(!requireNamespace("deduped")) install.packages("deduped")

library(deduped)

N_TOTAL <- 1e4
repeated_paths <- fs::path("base", stringr::str_glue("dir{d}", d=1:10), "inner") |> 
  rep(N_TOTAL/10) |> 
  sample()

bench::mark(
  direct = repeated_paths |> fs::path_dir(),
  indirect = repeated_paths |> deduped(fs::path_dir)(),
  iterations = 10
)
#> # A tibble: 2 × 6
#>   expression      min   median `itr/sec` mem_alloc `gc/sec`
#>   <bch:expr> <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
#> 1 direct       51.8ms   52.5ms      18.9  749.02KB     2.10
#> 2 indirect    206.3µs  213.5µs    4574.     6.13MB     0

all_unique_paths <- fs::path("base", stringr::str_glue("dir{d}", d=1:N_TOTAL), "inner")

bench::mark(
  direct = all_unique_paths |> fs::path_dir(),
  indirect = all_unique_paths |> deduped(fs::path_dir)(),
  iterations = 10
)
#> # A tibble: 2 × 6
#>   expression      min   median `itr/sec` mem_alloc `gc/sec`
#>   <bch:expr> <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
#> 1 direct       53.6ms   54.6ms      18.3  901.88KB     0   
#> 2 indirect     53.6ms   54.9ms      18.2    1.03MB     2.02

Created on 2023-10-26 with reprex v2.0.2

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