Categories
Offsites

sparklyr 1.5: better dplyr interface, more sdf_* functions, and RDS-based serialization routines

We are thrilled to announce sparklyr 1.5 is now available on

CRAN
!

To install sparklyr 1.5 from CRAN, run

install.packages("sparklyr")

In this blog post, we will highlight the following aspects of
sparklyr 1.5:

Better dplyr interface

A large fraction of pull requests that went into the sparklyr
1.5 release were focused on making Spark dataframes work with
various dplyr verbs in the same way that R dataframes do. The full
list of dplyr-related bugs and feature requests that were resolved
in sparklyr 1.5 can be found in
here
.

In this section, we will showcase three new dplyr
functionalities that were shipped with sparklyr 1.5.

Stratified sampling

Stratified sampling on an R dataframe can be accomplished with a
combination of dplyr::group_by() followed by dplyr::sample_n() or
dplyr::sample_frac(), where the grouping variables specified in the
dplyr::group_by() step are the ones that define each stratum. For
instance, the following query will group mtcars by number of
cylinders and return a weighted random sample of size two from each
group, without replacement, and weighted by the mpg column:

mtcars %>% dplyr::group_by(cyl) %>% dplyr::sample_n(size = 2, weight = mpg, replace = FALSE) %>% print()
## # A tibble: 6 x 11 ## # Groups: cyl [3] ## mpg cyl disp hp drat wt qsec vs am gear carb ## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> ## 1 33.9 4 71.1 65 4.22 1.84 19.9 1 1 4 1 ## 2 22.8 4 108 93 3.85 2.32 18.6 1 1 4 1 ## 3 21.4 6 258 110 3.08 3.22 19.4 1 0 3 1 ## 4 21 6 160 110 3.9 2.62 16.5 0 1 4 4 ## 5 15.5 8 318 150 2.76 3.52 16.9 0 0 3 2 ## 6 19.2 8 400 175 3.08 3.84 17.0 0 0 3 2

Starting from sparklyr 1.5, the same can also be done for Spark
dataframes with Spark 3.0 or above, e.g.,:

library(sparklyr) sc <- spark_connect(master = "local", version = "3.0.0") mtcars_sdf <- copy_to(sc, mtcars, replace = TRUE, repartition = 3) mtcars_sdf %>% dplyr::group_by(cyl) %>% dplyr::sample_n(size = 2, weight = mpg, replace = FALSE) %>% print()
# Source: spark<?> [?? x 11] # Groups: cyl mpg cyl disp hp drat wt qsec vs am gear carb <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> 1 21 6 160 110 3.9 2.62 16.5 0 1 4 4 2 21.4 6 258 110 3.08 3.22 19.4 1 0 3 1 3 27.3 4 79 66 4.08 1.94 18.9 1 1 4 1 4 32.4 4 78.7 66 4.08 2.2 19.5 1 1 4 1 5 16.4 8 276. 180 3.07 4.07 17.4 0 0 3 3 6 18.7 8 360 175 3.15 3.44 17.0 0 0 3 2

or

mtcars_sdf %>% dplyr::group_by(cyl) %>% dplyr::sample_frac(size = 0.2, weight = mpg, replace = FALSE) %>% print()
## # Source: spark<?> [?? x 11] ## # Groups: cyl ## mpg cyl disp hp drat wt qsec vs am gear carb ## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> ## 1 21 6 160 110 3.9 2.62 16.5 0 1 4 4 ## 2 21.4 6 258 110 3.08 3.22 19.4 1 0 3 1 ## 3 22.8 4 141. 95 3.92 3.15 22.9 1 0 4 2 ## 4 33.9 4 71.1 65 4.22 1.84 19.9 1 1 4 1 ## 5 30.4 4 95.1 113 3.77 1.51 16.9 1 1 5 2 ## 6 15.5 8 318 150 2.76 3.52 16.9 0 0 3 2 ## 7 18.7 8 360 175 3.15 3.44 17.0 0 0 3 2 ## 8 16.4 8 276. 180 3.07 4.07 17.4 0 0 3 3

Row sums

The rowSums() functionality offered by dplyr is handy when one
needs to sum up a large number of columns within an R dataframe
that are impractical to be enumerated individually. For example,
here we have a six-column dataframe of random real numbers, where
the partial_sum column in the result contains the sum of columns b
through d within each row:

ncols <- 6 nums <- seq(ncols) %>% lapply(function(x) runif(5)) names(nums) <- letters[1:ncols] tbl <- tibble::as_tibble(nums) tbl %>% dplyr::mutate(partial_sum = rowSums(.[2:5])) %>% print()
## # A tibble: 5 x 7 ## a b c d e f partial_sum ## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> ## 1 0.781 0.801 0.157 0.0293 0.169 0.0978 1.16 ## 2 0.696 0.412 0.221 0.941 0.697 0.675 2.27 ## 3 0.802 0.410 0.516 0.923 0.190 0.904 2.04 ## 4 0.200 0.590 0.755 0.494 0.273 0.807 2.11 ## 5 0.00149 0.711 0.286 0.297 0.107 0.425 1.40

Beginning with sparklyr 1.5, the same operation can be performed
with Spark dataframes:

library(sparklyr) sc <- spark_connect(master = "local") sdf <- copy_to(sc, tbl, overwrite = TRUE) sdf %>% dplyr::mutate(partial_sum = rowSums(.[2:5])) %>% print()
## # Source: spark<?> [?? x 7] ## a b c d e f partial_sum ## <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> ## 1 0.781 0.801 0.157 0.0293 0.169 0.0978 1.16 ## 2 0.696 0.412 0.221 0.941 0.697 0.675 2.27 ## 3 0.802 0.410 0.516 0.923 0.190 0.904 2.04 ## 4 0.200 0.590 0.755 0.494 0.273 0.807 2.11 ## 5 0.00149 0.711 0.286 0.297 0.107 0.425 1.40

As a bonus from implementing the rowSums feature for Spark
dataframes, sparklyr 1.5 now also offers limited support for the
column-subsetting operator on Spark dataframes. For example, all
code snippets below will return some subset of columns from the
dataframe named sdf:

# select columns `b` through `e` sdf[2:5]
# select columns `b` and `c` sdf[c("b", "c")]
# drop the first and third columns and return the rest sdf[c(-1, -3)]

Weighted-mean summarizer

Similar to the two dplyr functions mentioned above, the
weighted.mean() summarizer is another useful function that has
become part of the dplyr interface for Spark dataframes in sparklyr
1.5. One can see it in action by, for example, comparing the output
from the following

library(sparklyr) sc <- spark_connect(master = "local") mtcars_sdf <- copy_to(sc, mtcars, replace = TRUE) mtcars_sdf %>% dplyr::group_by(cyl) %>% dplyr::summarize(mpg_wm = weighted.mean(mpg, wt)) %>% print()

with output from the equivalent operation on mtcars in R:

mtcars %>% dplyr::group_by(cyl) %>% dplyr::summarize(mpg_wm = weighted.mean(mpg, wt)) %>% print()

both of them should evaluate to the following:

## cyl mpg_wm ## <dbl> <dbl> ## 1 4 25.9 ## 2 6 19.6 ## 3 8 14.8

New additions to the sdf_* family of functions

sparklyr provides a large number of convenience functions for
working with Spark dataframes, and all of them have names starting
with the sdf_ prefix.

In this section we will briefly mention four new additions and
show some example scenarios in which those functions are
useful.

sdf_expand_grid()

As the name suggests, sdf_expand_grid() is simply the Spark
equivalent of expand.grid(). Rather than running expand.grid() in R
and importing the resulting R dataframe to Spark, one can now run
sdf_expand_grid(), which accepts both R vectors and Spark
dataframes and supports hints for broadcast hash joins. The example
below shows sdf_expand_grid() creating a 100-by-100-by-10-by-10
grid in Spark over 1000 Spark partitions, with broadcast hash join
hints on variables with small cardinalities:

library(sparklyr) sc <- spark_connect(master = "local") grid_sdf <- sdf_expand_grid( sc, var1 = seq(100), var2 = seq(100), var3 = seq(10), var4 = seq(10), broadcast_vars = c(var3, var4), repartition = 1000 ) grid_sdf %>% sdf_nrow() %>% print()
## [1] 1e+06

sdf_partition_sizes()

As sparklyr user @sbottelli suggested here, one
thing that would be great to have in sparklyr is an efficient way
to query partition sizes of a Spark dataframe. In sparklyr 1.5,
sdf_partition_sizes() does exactly that:

library(sparklyr) sc <- spark_connect(master = "local") sdf_len(sc, 1000, repartition = 5) %>% sdf_partition_sizes() %>% print(row.names = FALSE)
## partition_index partition_size ## 0 200 ## 1 200 ## 2 200 ## 3 200 ## 4 200

sdf_unnest_longer() and sdf_unnest_wider()

sdf_unnest_longer() and sdf_unnest_wider() are the equivalents
of tidyr::unnest_longer() and tidyr::unnest_wider() for Spark
dataframes. sdf_unnest_longer() expands all elements in a struct
column into multiple rows, and sdf_unnest_wider() expands them into
multiple columns. As illustrated with an example dataframe
below,

library(sparklyr) sc <- spark_connect(master = "local") sdf <- copy_to( sc, tibble::tibble( id = seq(3), attribute = list( list(name = "Alice", grade = "A"), list(name = "Bob", grade = "B"), list(name = "Carol", grade = "C") ) ) )
sdf %>% sdf_unnest_longer(col = record, indices_to = "key", values_to = "value") %>% print()

evaluates to

## # Source: spark<?> [?? x 3] ## id value key ## <int> <chr> <chr> ## 1 1 A grade ## 2 1 Alice name ## 3 2 B grade ## 4 2 Bob name ## 5 3 C grade ## 6 3 Carol name

whereas

sdf %>% sdf_unnest_wider(col = record) %>% print()

evaluates to

## # Source: spark<?> [?? x 3] ## id grade name ## <int> <chr> <chr> ## 1 1 A Alice ## 2 2 B Bob ## 3 3 C Carol

RDS-based serialization routines

Some readers must be wondering why a brand new serialization
format would need to be implemented in sparklyr at all. Long story
short, the reason is that RDS serialization is a strictly better
replacement for its CSV predecessor. It possesses all desirable
attributes the CSV format has, while avoiding a number of
disadvantages that are common among text-based data formats.

In this section, we will briefly outline why sparklyr should
support at least one serialization format other than arrow,
deep-dive into issues with CSV-based serialization, and then show
how the new RDS-based serialization is free from those issues.

Why arrow is not for everyone?

To transfer data between Spark and R correctly and efficiently,
sparklyr must rely on some data serialization format that is
well-supported by both Spark and R. Unfortunately, not many
serialization formats satisfy this requirement, and among the ones
that do are text-based formats such as CSV and JSON, and binary
formats such as Apache Arrow, Protobuf, and as of recent, a small
subset of RDS version 2. Further complicating the matter is the
additional consideration that sparklyr should support at least one
serialization format whose implementation can be fully
self-contained within the sparklyr code base, i.e., such
serialization should not depend on any external R package or system
library, so that it can accommodate users who want to use sparklyr
but who do not necessarily have the required C++ compiler tool
chain and other system dependencies for setting up R packages such
as arrow
or protolite.
Prior to sparklyr 1.5, CSV-based serialization was the default
alternative to fallback to when users do not have the arrow package
installed or when the type of data being transported from R to
Spark is unsupported by the version of arrow available.

Why is the CSV format not ideal?

There are at least three reasons to believe CSV format is not
the best choice when it comes to exporting data from R to
Spark.

One reason is efficiency. For example, a double-precision
floating point number such as .Machine$double.eps needs to be
expressed as “2.22044604925031e-16” in CSV format in order to not
incur any loss of precision, thus taking up 20 bytes rather than 8
bytes.

But more important than efficiency are correctness concerns. In
a R dataframe, one can store both NA_real_ and NaN in a column of
floating point numbers. NA_real_ should ideally translate to null
within a Spark dataframe, whereas NaN should continue to be NaN
when transported from R to Spark. Unfortunately, NA_real_ in R
becomes indistinguishable from NaN once serialized in CSV format,
as evident from a quick demo shown below:

original_df <- data.frame(x = c(NA_real_, NaN)) original_df %>% dplyr::mutate(is_nan = is.nan(x)) %>% print()
## x is_nan ## 1 NA FALSE ## 2 NaN TRUE
csv_file <- "/tmp/data.csv" write.csv(original_df, file = csv_file, row.names = FALSE) deserialized_df <- read.csv(csv_file) deserialized_df %>% dplyr::mutate(is_nan = is.nan(x)) %>% print()
## x is_nan ## 1 NA FALSE ## 2 NA FALSE

Another correctness issue very much similar to the one above was
the fact that “NA” and NA within a string column of an R dataframe
become indistinguishable once serialized in CSV format, as
correctly pointed out in this Github
issue
by @caewok and
others.

RDS to the rescue!

RDS format is one of the most widely used binary formats for
serializing R objects. It is described in some detail in chapter 1,
section 8 of this
document
. Among advantages of the RDS format are efficiency and
accuracy: it has a reasonably efficient implementation in base R,
and supports all R data types.

Also worth noticing is the fact that when an R dataframe
containing only data types with sensible equivalents in Apache
Spark (e.g., RAWSXP, LGLSXP, CHARSXP, REALSXP, etc) is saved using
RDS version 2, (e.g., serialize(mtcars, connection = NULL, version
= 2L, xdr = TRUE)), only a tiny subset of the RDS format will be
involved in the serialization process, and implementing
deserialization routines in Scala capable of decoding such a
restricted subset of RDS constructs is in fact a reasonably simple
and straightforward task (as shown in
here
).

Last but not least, because RDS is a binary format, it allows
NA_character_, “NA”, NA_real_, and NaN to all be encoded in an
unambiguous manner, hence allowing sparklyr 1.5 to avoid all
correctness issues detailed above in non-arrow serialization use
cases.

Other benefits of RDS serialization

In addition to correctness guarantees, RDS format also offers
quite a few other advantages.

One advantage is of course performance: for example, importing a
non-trivially-sized dataset such as nycflights13::flights from R to
Spark using the RDS format in sparklyr 1.5 is roughly 40%-50%
faster compared to CSV-based serialization in sparklyr 1.4. The
current RDS-based implementation is still nowhere as fast as
arrow-based serialization though (arrow is about 3-4x faster), so
for performance-sensitive tasks involving heavy serialization,
arrow should still be the top choice.

Another advantage is that with RDS serialization, sparklyr can
import R dataframes containing raw columns directly into binary
columns in Spark. Thus, use cases such as the one below will work
in sparklyr 1.5

library(sparklyr) sc <- spark_connect(master = "local") tbl <- tibble::tibble( x = list(serialize("sparklyr", NULL), serialize(c(123456, 789), NULL)) ) sdf <- copy_to(sc, tbl)

While most sparklyr users probably won’t find this capability
of importing binary columns to Spark immediately useful in their
typical sparklyr::copy_to() or sparklyr::collect() usages, it does
play a crucial role in reducing serialization overheads in the
Spark-based foreach
parallel backend that was first introduced in sparklyr 1.2. This is
because Spark workers can directly fetch the serialized R closures
to be computed from a binary Spark column instead of extracting
those serialized bytes from intermediate representations such as
base64-encoded strings. Similarly, the R results from executing
worker closures will be directly available in RDS format which can
be efficiently deserialized in R, rather than being delivered in
other less efficient formats.

Acknowledgement

In chronological order, we would like to thank the following
contributors for making their pull requests part of sparklyr
1.5:

We would also like to express our gratitude towards numerous bug
reports and feature requests for sparklyr from a fantastic
open-source community.

Finally, the author of this blog post is indebted to @javierluraschi, @batpigandme, and @skeydan for their valuable
editorial inputs.

If you wish to learn more about sparklyr, check out sparklyr.ai, spark.rstudio.com, and some of the
previous release posts such as
sparklyr 1.4
and sparklyr
1.3
.

Thanks for reading!

Leave a Reply

Your email address will not be published.