In rstudio/sparklyr: R Interface to Apache Spark

knitr::opts_chunk$set(
  eval = TRUE, 
  warning = FALSE,
  collapse = TRUE,
  comment = "#>",
  fig.path = "tools/readme/", 
  dev = "png",
  out.width = "100%"
)

options(width = 60)

library(sparklyr)
library(dplyr)
library(ggplot2)

• Install and connect to Spark using YARN, Mesos, Livy or Kubernetes.
• Use dplyr to filter and aggregate Spark datasets and streams then bring them into R for analysis and visualization.
• Use MLlib, H2O, XGBoost and GraphFrames to train models at scale in Spark.
• Create interoperable machine learning pipelines and productionize them with MLeap.
• Create extensions that call the full Spark API or run distributed R code to support new functionality.

Table of Contents

toc <- function() {
  re <- readLines("README.Rmd")
  has_title <- as.logical(lapply(re, function(x) substr(x, 1, 2) == "##"))
  only_titles <- re[has_title]
  titles <- trimws(gsub("#", "", only_titles))
  links <- trimws(gsub("`", "", titles))
  links <- tolower(links)
  links <- trimws(gsub(" ", "-", links))
  links <- trimws(gsub(",", "", links))
  toc_list <- lapply(
    seq_along(titles),
    function(x) {
      pad <- ifelse(substr(only_titles[x], 1, 3) == "###", "    - ", "  - ")
      paste0(pad, "[", titles[x], "](#",links[x], ")")
    }
  )
  toc_full <- paste(toc_list[2:length(toc_list)], collapse = "\n") 
  cat(toc_full)
}
toc()

• Installation
• Connecting to Spark
• Using dplyr
  • Window Functions
• Using SQL
• Machine Learning
• Reading and Writing Data
• Distributed R
• Extensions
• Table Utilities
• Connection Utilities
• RStudio IDE
• Using H2O
• Connecting through Livy
• Connecting through Databricks Connect

Installation

You can install the sparklyr package from CRAN as follows:

install.packages("sparklyr")

You should also install a local version of Spark for development purposes:

library(sparklyr)
spark_install()

To upgrade to the latest version of sparklyr, run the following command and restart your r session:

install.packages("devtools")
devtools::install_github("sparklyr/sparklyr")

Connecting to Spark

You can connect to both local instances of Spark as well as remote Spark clusters. Here we'll connect to a local instance of Spark via the spark_connect function:

library(sparklyr)
sc <- spark_connect(master = "local")

The returned Spark connection (sc) provides a remote dplyr data source to the Spark cluster.

For more information on connecting to remote Spark clusters see the Deployment section of the sparklyr website.

Using dplyr

We can now use all of the available dplyr verbs against the tables within the cluster.

We'll start by copying some datasets from R into the Spark cluster (note that you may need to install the nycflights13 and Lahman packages in order to execute this code):

install.packages(c("nycflights13", "Lahman"))

library(dplyr)
iris_tbl <- copy_to(sc, iris, overwrite = TRUE)
flights_tbl <- copy_to(sc, nycflights13::flights, "flights", overwrite = TRUE)
batting_tbl <- copy_to(sc, Lahman::Batting, "batting", overwrite = TRUE)
src_tbls(sc)

To start with here's a simple filtering example:

# filter by departure delay and print the first few records
flights_tbl %>% filter(dep_delay == 2)

Introduction to dplyr provides additional dplyr examples you can try. For example, consider the last example from the tutorial which plots data on flight delays:

delay <- flights_tbl %>%
  group_by(tailnum) %>%
  summarise(count = n(), dist = mean(distance), delay = mean(arr_delay)) %>%
  filter(count > 20, dist < 2000, !is.na(delay)) %>%
  collect()

# plot delays
library(ggplot2)
ggplot(delay, aes(dist, delay)) +
  geom_point(aes(size = count), alpha = 1/2) +
  geom_smooth() +
  scale_size_area(max_size = 2)

Window Functions

dplyr window functions are also supported, for example:

batting_tbl %>%
  select(playerID, yearID, teamID, G, AB:H) %>%
  arrange(playerID, yearID, teamID) %>%
  group_by(playerID) %>%
  filter(min_rank(desc(H)) <= 2 & H > 0)

For additional documentation on using dplyr with Spark see the dplyr section of the sparklyr website.

Using SQL

It's also possible to execute SQL queries directly against tables within a Spark cluster. The spark_connection object implements a DBI interface for Spark, so you can use dbGetQuery() to execute SQL and return the result as an R data frame:

library(DBI)
iris_preview <- dbGetQuery(sc, "SELECT * FROM iris LIMIT 10")
iris_preview

Machine Learning

You can orchestrate machine learning algorithms in a Spark cluster via the machine learning functions within sparklyr. These functions connect to a set of high-level APIs built on top of DataFrames that help you create and tune machine learning workflows.

Here's an example where we use ml_linear_regression to fit a linear regression model. We'll use the built-in mtcars dataset, and see if we can predict a car's fuel consumption (mpg) based on its weight (wt), and the number of cylinders the engine contains (cyl). We'll assume in each case that the relationship between mpg and each of our features is linear.

# copy mtcars into spark
mtcars_tbl <- copy_to(sc, mtcars, overwrite = TRUE)

# transform our data set, and then partition into 'training', 'test'
partitions <- mtcars_tbl %>%
  filter(hp >= 100) %>%
  mutate(cyl8 = cyl == 8) %>%
  sdf_partition(training = 0.5, test = 0.5, seed = 1099)

# fit a linear model to the training dataset
fit <- partitions$training %>%
  ml_linear_regression(response = "mpg", features = c("wt", "cyl"))
fit

For linear regression models produced by Spark, we can use summary() to learn a bit more about the quality of our fit, and the statistical significance of each of our predictors.

summary(fit)

Spark machine learning supports a wide array of algorithms and feature transformations and as illustrated above it's easy to chain these functions together with dplyr pipelines. To learn more see the machine learning section.

Reading and Writing Data

You can read and write data in CSV, JSON, and Parquet formats. Data can be stored in HDFS, S3, or on the local filesystem of cluster nodes.

temp_csv <- tempfile(fileext = ".csv")
temp_parquet <- tempfile(fileext = ".parquet")
temp_json <- tempfile(fileext = ".json")

spark_write_csv(iris_tbl, temp_csv)
iris_csv_tbl <- spark_read_csv(sc, "iris_csv", temp_csv)

spark_write_parquet(iris_tbl, temp_parquet)
iris_parquet_tbl <- spark_read_parquet(sc, "iris_parquet", temp_parquet)

spark_write_json(iris_tbl, temp_json)
iris_json_tbl <- spark_read_json(sc, "iris_json", temp_json)

src_tbls(sc)

Distributed R

You can execute arbitrary r code across your cluster using spark_apply(). For example, we can apply rgamma over iris as follows:

spark_apply(iris_tbl, function(data) {
  data[1:4] + rgamma(1,2)
})

You can also group by columns to perform an operation over each group of rows and make use of any package within the closure:

spark_apply(
  iris_tbl,
  function(e) broom::tidy(lm(Petal_Width ~ Petal_Length, e)),
  columns = c("term", "estimate", "std.error", "statistic", "p.value"),
  group_by = "Species"
)

Extensions

The facilities used internally by sparklyr for its dplyr and machine learning interfaces are available to extension packages. Since Spark is a general purpose cluster computing system there are many potential applications for extensions (e.g. interfaces to custom machine learning pipelines, interfaces to 3rd party Spark packages, etc.).

Here's a simple example that wraps a Spark text file line counting function with an R function:

# write a CSV
tempfile <- tempfile(fileext = ".csv")
write.csv(nycflights13::flights, tempfile, row.names = FALSE, na = "")

# define an R interface to Spark line counting
count_lines <- function(sc, path) {
  spark_context(sc) %>%
    invoke("textFile", path, 1L) %>%
      invoke("count")
}

# call spark to count the lines of the CSV
count_lines(sc, tempfile)

To learn more about creating extensions see the Extensions section of the sparklyr website.

Table Utilities

You can cache a table into memory with:

tbl_cache(sc, "batting")

and unload from memory using:

tbl_uncache(sc, "batting")

Connection Utilities

You can view the Spark web console using the spark_web() function:

spark_web(sc)

You can show the log using the spark_log() function:

spark_log(sc, n = 10)

Finally, we disconnect from Spark:

  spark_disconnect(sc)

RStudio IDE

The RStudio IDE includes integrated support for Spark and the sparklyr package, including tools for:

• Creating and managing Spark connections
• Browsing the tables and columns of Spark DataFrames
• Previewing the first 1,000 rows of Spark DataFrames

Once you've installed the sparklyr package, you should find a new Spark pane within the IDE. This pane includes a New Connection dialog which can be used to make connections to local or remote Spark instances:

Once you've connected to Spark you'll be able to browse the tables contained within the Spark cluster and preview Spark DataFrames using the standard RStudio data viewer:

You can also connect to Spark through Livy through a new connection dialog:

Using H2O

rsparkling is a CRAN package from H2O that extends sparklyr to provide an interface into Sparkling Water. For instance, the following example installs, configures and runs h2o.glm:

library(rsparkling)
library(sparklyr)
library(dplyr)
library(h2o)

sc <- spark_connect(master = "local", version = "2.3.2")
mtcars_tbl <- copy_to(sc, mtcars, "mtcars", overwrite = TRUE)

mtcars_h2o <- as_h2o_frame(sc, mtcars_tbl, strict_version_check = FALSE)

mtcars_glm <- h2o.glm(x = c("wt", "cyl"),
                      y = "mpg",
                      training_frame = mtcars_h2o,
                      lambda_search = TRUE)

mtcars_glm

#> Model Details:
#> ==============
#>
#> H2ORegressionModel: glm
#> Model ID:  GLM_model_R_1527265202599_1
#> GLM Model: summary
#>     family     link                              regularization
#> 1 gaussian identity Elastic Net (alpha = 0.5, lambda = 0.1013 )
#>                                                                lambda_search
#> 1 nlambda = 100, lambda.max = 10.132, lambda.min = 0.1013, lambda.1se = -1.0
#>   number_of_predictors_total number_of_active_predictors
#> 1                          2                           2
#>   number_of_iterations                                training_frame
#> 1                  100 frame_rdd_31_ad5c4e88ec97eb8ccedae9475ad34e02
#>
#> Coefficients: glm coefficients
#>       names coefficients standardized_coefficients
#> 1 Intercept    38.941654                 20.090625
#> 2       cyl    -1.468783                 -2.623132
#> 3        wt    -3.034558                 -2.969186
#>
#> H2ORegressionMetrics: glm
#> ** Reported on training data. **
#>
#> MSE:  6.017684
#> RMSE:  2.453097
#> MAE:  1.940985
#> RMSLE:  0.1114801
#> Mean Residual Deviance :  6.017684
#> R^2 :  0.8289895
#> Null Deviance :1126.047
#> Null D.o.F. :31
#> Residual Deviance :192.5659
#> Residual D.o.F. :29
#> AIC :156.2425

spark_disconnect(sc)

Connecting through Livy

Livy enables remote connections to Apache Spark clusters. However, please notice that connecting to Spark clusters through Livy is much slower than any other connection method.

Before connecting to Livy, you will need the connection information to an existing service running Livy. Otherwise, to test livy in your local environment, you can install it and run it locally as follows:

livy_install()

livy_service_start()

To connect, use the Livy service address as master and method = "livy" in spark_connect(). Once connection completes, use sparklyr as usual, for instance:

sc <- spark_connect(master = "http://localhost:8998", method = "livy", version = "3.0.0")
copy_to(sc, iris, overwrite = TRUE)

spark_disconnect(sc)

Once you are done using livy locally, you should stop this service with:

livy_service_stop()

To connect to remote livy clusters that support basic authentication connect as:

config <- livy_config(username="<username>", password="<password>")
sc <- spark_connect(master = "<address>", method = "livy", config = config)
spark_disconnect(sc)

Connecting through Databricks Connect v2

sparklyr is able to interact with Databricks Connect v2 via a new extension called pysparklyr. To learn how to use, and the latest updates on this integration see the article in sparklyr's official website.

rstudio/sparklyr documentation built on April 30, 2024, 4:01 p.m.