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Posted to jira@arrow.apache.org by "Miles McBain (Jira)" <ji...@apache.org> on 2021/09/17 01:20:00 UTC
[jira] [Created] (ARROW-14020) [R] Writing datafames with list
columns is slow and scales poorly with nesting level
Miles McBain created ARROW-14020:
------------------------------------
Summary: [R] Writing datafames with list columns is slow and scales poorly with nesting level
Key: ARROW-14020
URL: https://issues.apache.org/jira/browse/ARROW-14020
Project: Apache Arrow
Issue Type: Bug
Components: R
Affects Versions: 5.0.0
Environment: Windows 10 x64
Reporter: Miles McBain
Writing data frames that contain list columns seems much slower than expected:
``` r
library(tidyverse)
#> Warning: package 'tidyverse' was built under R version 4.1.1
#> Warning: package 'tibble' was built under R version 4.1.1
#> Warning: package 'readr' was built under R version 4.1.1
library(arrow)
#> Warning: package 'arrow' was built under R version 4.1.1
#>
#> Attaching package: 'arrow'
#> The following object is masked from 'package:utils':
#>
#> timestamp
dummy <- tibble(
points = rep(list(seq(6)), 2e6),
index = seq(2e6)
)
# very slooooooow
system.time(write_parquet(dummy, "dummy.parquet"))
#> user system elapsed
#> 55.64 0.11 55.98
dummy_txt <- mutate(dummy, points = map_chr(points, deparse))
# orders of magnitude faster
system.time(write_parquet(dummy_txt, "dummytext.parquet"))
#> user system elapsed
#> 0.24 0.02 0.25
```
<sup>Created on 2021-09-17 by the [reprex package]([https://reprex.tidyverse.org|https://reprex.tidyverse.org/]) (v2.0.0)</sup>
<details style="margin-bottom:10px;">
<summary>Session info</summary>
``` r
sessioninfo::session_info()
#> - Session info ---------------------------------------------------------------
#> setting value
#> version R version 4.1.0 (2021-05-18)
#> os Windows 10 x64
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_Australia.1252
#> ctype English_Australia.1252
#> tz Australia/Brisbane
#> date 2021-09-17
#>
#> - Packages -------------------------------------------------------------------
#> package * version date lib source
#> arrow * 5.0.0.2 2021-09-05 [1] CRAN (R 4.1.1)
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0)
#> backports 1.2.1 2020-12-09 [1] CRAN (R 4.1.0)
#> bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.0)
#> bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.0)
#> broom 0.7.7 2021-06-13 [1] CRAN (R 4.1.0)
#> cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.1.0)
#> cli 3.0.1 2021-07-17 [1] CRAN (R 4.1.0)
#> colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.1.0)
#> crayon 1.4.1 2021-02-08 [1] CRAN (R 4.1.0)
#> DBI 1.1.1 2021-01-15 [1] CRAN (R 4.1.0)
#> dbplyr 2.1.1 2021-04-06 [1] CRAN (R 4.1.0)
#> digest 0.6.27 2020-10-24 [1] CRAN (R 4.1.0)
#> dplyr * 1.0.7 2021-06-18 [1] CRAN (R 4.1.0)
#> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0)
#> fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.0)
#> forcats * 0.5.1 2021-01-27 [1] CRAN (R 4.1.0)
#> fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.0)
#> generics 0.1.0 2020-10-31 [1] CRAN (R 4.1.0)
#> ggplot2 * 3.3.5 2021-06-25 [1] CRAN (R 4.1.0)
#> glue 1.4.2 2020-08-27 [1] CRAN (R 4.1.0)
#> gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
#> haven 2.4.1 2021-04-23 [1] CRAN (R 4.1.0)
#> highr 0.9 2021-04-16 [1] CRAN (R 4.1.0)
#> hms 1.1.0 2021-05-17 [1] CRAN (R 4.1.0)
#> htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.1.0)
#> httr 1.4.2 2020-07-20 [1] CRAN (R 4.1.0)
#> jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.1.0)
#> knitr 1.33 2021-04-24 [1] CRAN (R 4.1.0)
#> lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.1.0)
#> lubridate 1.7.10 2021-02-26 [1] CRAN (R 4.1.0)
#> magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0)
#> modelr 0.1.8 2020-05-19 [1] CRAN (R 4.1.0)
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
#> pillar 1.6.2 2021-07-29 [1] CRAN (R 4.1.0)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
#> purrr * 0.3.4 2020-04-17 [1] CRAN (R 4.1.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.1)
#> Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.1.0)
#> readr * 2.0.1 2021-08-10 [1] CRAN (R 4.1.1)
#> readxl 1.3.1 2019-03-13 [1] CRAN (R 4.1.0)
#> reprex 2.0.0 2021-04-02 [1] CRAN (R 4.1.0)
#> rlang 0.4.11 2021-04-30 [1] CRAN (R 4.1.0)
#> rmarkdown 2.9 2021-06-15 [1] CRAN (R 4.1.0)
#> rvest 1.0.1 2021-07-26 [1] CRAN (R 4.1.0)
#> scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.0)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0)
#> stringi 1.7.4 2021-08-25 [1] CRAN (R 4.1.1)
#> stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.1.0)
#> styler 1.4.1 2021-03-30 [1] CRAN (R 4.1.0)
#> tibble * 3.1.4 2021-08-25 [1] CRAN (R 4.1.1)
#> tidyr * 1.1.3 2021-03-03 [1] CRAN (R 4.1.0)
#> tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.0)
#> tidyverse * 1.3.1 2021-04-15 [1] CRAN (R 4.1.1)
#> tzdb 0.1.2 2021-07-20 [1] CRAN (R 4.1.0)
#> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.0)
#> vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.0)
#> withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.0)
#> xfun 0.24 2021-06-15 [1] CRAN (R 4.1.0)
#> xml2 1.3.2 2020-04-23 [1] CRAN (R 4.1.0)
#> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0)
#>
#> [1] C:/Users/msmcbain/libs/R
#> [2] C:/R/R-4.1.0/library
```
</details>
In this case it's actually faster to convert the list columns to text and do the write, than to write with the list columns.
This issue also affects write_arrow:
``` r
library(tidyverse)
#> Warning: package 'tidyverse' was built under R version 4.1.1
#> Warning: package 'tibble' was built under R version 4.1.1
#> Warning: package 'readr' was built under R version 4.1.1
library(arrow)
#> Warning: package 'arrow' was built under R version 4.1.1
#>
#> Attaching package: 'arrow'
#> The following object is masked from 'package:utils':
#>
#> timestamp
dummy <- tibble(
points = rep(list(seq(6)), 2e6),
index = seq(2e6)
)
# very slooooooow
system.time(write_arrow(dummy, "dummy.parquet"))
#> Warning: Use 'write_ipc_stream' or 'write_feather' instead.
#> user system elapsed
#> 56.95 0.08 57.13
dummy_txt <- mutate(dummy, points = map_chr(points, deparse))
# orders of magnitude faster
system.time(write_arrow(dummy_txt, "dummytext.parquet"))
#> Warning: Use 'write_ipc_stream' or 'write_feather' instead.
#> user system elapsed
#> 0.06 0.01 0.10
```
<sup>Created on 2021-09-17 by the [reprex package]([https://reprex.tidyverse.org|https://reprex.tidyverse.org/]) (v2.0.0)</sup>
Interestingly the performance seems to degrade exponentially with the nesting level of the lists:
```r
# add a level of nesting
dummy2 <- tibble(
points = rep(list(list(seq(6))), 2e6),
index = seq(2e6)
)
# order of magnitude slower again, lost patience wating for it ro return
system.time(write_parquet(dummy2, "dummy2.parquet")
```
This has implications for \{sf} dataframes which use list columns to represent spatial data structures. Arrow/parquet are pretty much not viable for moderate to large spatial data in R:
```r
# options(timeout = 1000)
# remotes::install_github("wfmackey/absmapsdata")
library(absmapsdata)
# doesn't return in a resonable amount of time
write_arrow(absmapsdata::sa12016, "sa1.parquet")
# can use the same work around as above by converting geomtry to vector of well known
# text, but it takes time and bloats the files
```
Possibly related to https://issues.apache.org/jira/browse/ARROW-12529 ?
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