R 连接Sprak

  • Connect to Spark from R. The sparklyr package provides a 
    complete dplyr backend.
  • Filter and aggregate Spark datasets then bring them into R for 
    analysis and visualization.
  • Use Spark’s distributed machine learninglibrary from R.
  • Create extensions that call the full Spark API and provide 
    interfaces to Spark packages.

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(version = "1.6.2")

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

devtools::install_github("rstudio/sparklyr")

If you use the RStudio IDE, you should also download the latest preview release of the IDE which includes several enhancements for interacting with Spark (see the RStudio IDE section below for more details).

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 new 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)
flights_tbl <- copy_to(sc, nycflights13::flights, "flights")
batting_tbl <- copy_to(sc, Lahman::Batting, "batting")
src_tbls(sc)
## [1] "batting" "flights" "iris"

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)
## Source:   query [6,233 x 19]
## Database: spark connection master=local[8] app=sparklyr local=TRUE
## 
##     year month   day dep_time sched_dep_time dep_delay arr_time
##    <int> <int> <int>    <int>          <int>     <dbl>    <int>
## 1   2013     1     1      517            515         2      830
## 2   2013     1     1      542            540         2      923
## 3   2013     1     1      702            700         2     1058
## 4   2013     1     1      715            713         2      911
## 5   2013     1     1      752            750         2     1025
## 6   2013     1     1      917            915         2     1206
## 7   2013     1     1      932            930         2     1219
## 8   2013     1     1     1028           1026         2     1350
## 9   2013     1     1     1042           1040         2     1325
## 10  2013     1     1     1231           1229         2     1523
## # ... with 6,223 more rows, and 12 more variables: sched_arr_time <int>,
## #   arr_delay <dbl>, carrier <chr>, flight <int>, tailnum <chr>,
## #   origin <chr>, dest <chr>, air_time <dbl>, distance <dbl>, hour <dbl>,
## #   minute <dbl>, time_hour <dbl>

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)
## `geom_smooth()` using method = 'gam'

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)
## Source:   query [2.562e+04 x 7]
## Database: spark connection master=local[8] app=sparklyr local=TRUE
## Groups: playerID
## 
##     playerID yearID teamID     G    AB     R     H
##        <chr>  <int>  <chr> <int> <int> <int> <int>
## 1  abbotpa01   2000    SEA    35     5     1     2
## 2  abbotpa01   2004    PHI    10    11     1     2
## 3  abnersh01   1992    CHA    97   208    21    58
## 4  abnersh01   1990    SDN    91   184    17    45
## 5  abreujo02   2015    CHA   154   613    88   178
## 6  abreujo02   2014    CHA   145   556    80   176
## 7  acevejo01   2001    CIN    18    34     1     4
## 8  acevejo01   2004    CIN    39    43     0     2
## 9  adamsbe01   1919    PHI    78   232    14    54
## 10 adamsbe01   1918    PHI    84   227    10    40
## # ... with 2.561e+04 more rows

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. Thespark_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
##    Sepal_Length Sepal_Width Petal_Length Petal_Width Species
## 1           5.1         3.5          1.4         0.2  setosa
## 2           4.9         3.0          1.4         0.2  setosa
## 3           4.7         3.2          1.3         0.2  setosa
## 4           4.6         3.1          1.5         0.2  setosa
## 5           5.0         3.6          1.4         0.2  setosa
## 6           5.4         3.9          1.7         0.4  setosa
## 7           4.6         3.4          1.4         0.3  setosa
## 8           5.0         3.4          1.5         0.2  setosa
## 9           4.4         2.9          1.4         0.2  setosa
## 10          4.9         3.1          1.5         0.1  setosa

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-inmtcars 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)

# 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"))
## * No rows dropped by 'na.omit' call
fit
## Call: ml_linear_regression(., response = "mpg", features = c("wt", "cyl"))
## 
## Coefficients:
## (Intercept)          wt         cyl 
##   37.066699   -2.309504   -1.639546

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)
## Call: ml_linear_regression(., response = "mpg", features = c("wt", "cyl"))
## 
## Deviance Residuals::
##     Min      1Q  Median      3Q     Max 
## -2.6881 -1.0507 -0.4420  0.4757  3.3858 
## 
## Coefficients:
##             Estimate Std. Error t value  Pr(>|t|)    
## (Intercept) 37.06670    2.76494 13.4059 2.981e-07 ***
## wt          -2.30950    0.84748 -2.7252   0.02341 *  
## cyl         -1.63955    0.58635 -2.7962   0.02084 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## R-Squared: 0.8665
## Root Mean Squared Error: 1.799

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 lcoal 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)
## [1] "batting"      "flights"      "iris"         "iris_csv"    
## [5] "iris_json"    "iris_parquet" "mtcars"

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)
## [1] 336777

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)
## 16/12/19 13:43:42 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 91 (/var/folders/fz/v6wfsg2x1fb1rw4f6r0x4jwm0000gn/T//RtmpcsSFgF/file82259906243.csv MapPartitionsRDD[363] at textFile at NativeMethodAccessorImpl.java:-2)
## 16/12/19 13:43:42 INFO TaskSchedulerImpl: Adding task set 91.0 with 1 tasks
## 16/12/19 13:43:42 INFO TaskSetManager: Starting task 0.0 in stage 91.0 (TID 177, localhost, partition 0,PROCESS_LOCAL, 2429 bytes)
## 16/12/19 13:43:42 INFO Executor: Running task 0.0 in stage 91.0 (TID 177)
## 16/12/19 13:43:42 INFO HadoopRDD: Input split: file:/var/folders/fz/v6wfsg2x1fb1rw4f6r0x4jwm0000gn/T/RtmpcsSFgF/file82259906243.csv:0+33313106
## 16/12/19 13:43:42 INFO Executor: Finished task 0.0 in stage 91.0 (TID 177). 2082 bytes result sent to driver
## 16/12/19 13:43:42 INFO TaskSetManager: Finished task 0.0 in stage 91.0 (TID 177) in 119 ms on localhost (1/1)
## 16/12/19 13:43:42 INFO DAGScheduler: ResultStage 91 (count at NativeMethodAccessorImpl.java:-2) finished in 0.119 s
## 16/12/19 13:43:42 INFO TaskSchedulerImpl: Removed TaskSet 91.0, whose tasks have all completed, from pool 
## 16/12/19 13:43:42 INFO DAGScheduler: Job 61 finished: count at NativeMethodAccessorImpl.java:-2, took 0.121816 s

Finally, we disconnect from Spark:

RStudio IDE

The latest RStudio Preview Release of 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:

The Spark DataFrame preview uses the standard RStudio data viewer:

The RStudio IDE features for sparklyr are available now as part of the RStudio Preview Release.

Connecting through Livy

Livy enables remote connections to Apache Spark clusters. Connecting to Spark clusters through Livy isunder experimental development in sparklyr. Please post any feedback or questions as a GitHub issue as needed.

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:

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")
copy_to(sc, iris)
## Source:   query [150 x 5]
## Database: spark connection master=http://localhost:8998 app= local=FALSE
## 
##    Sepal_Length Sepal_Width Petal_Length Petal_Width Species
##           <dbl>       <dbl>        <dbl>       <dbl>   <chr>
## 1           5.1         3.5          1.4         0.2  setosa
## 2           4.9         3.0          1.4         0.2  setosa
## 3           4.7         3.2          1.3         0.2  setosa
## 4           4.6         3.1          1.5         0.2  setosa
## 5           5.0         3.6          1.4         0.2  setosa
## 6           5.4         3.9          1.7         0.4  setosa
## 7           4.6         3.4          1.4         0.3  setosa
## 8           5.0         3.4          1.5         0.2  setosa
## 9           4.4         2.9          1.4         0.2  setosa
## 10          4.9         3.1          1.5         0.1  setosa
## # ... with 140 more rows

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

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

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

Site built with pkgdown.

### 使用 Spark 的 Python 接口 Apache Spark 是一种分布式计算框架,支持大规模数据处理。为了方便开发者使用 Python 编写 Spark 应用程序,官方提供了 **PySpark** 工具包。通过 PySpark,用户可以利用 Python 脚本操作 Spark 集群。 #### 1. PySpark 基础概念 PySpark 提供了一个名为 `pyspark.SparkContext` 的类来初始化 Spark 上下文环境[^1]。此上下文允许开发人员连接Spark 集群并执行各种任务。此外,PySpark 支持 DataFrame API 和 SQL 查询功能,使得数据分析更加直观高效。 当启用特定配置项(如 `spark.sql.execution.pythonUDF.arrow.enabled=false`),可以通过调整参数优化性能表现。例如设置该选项为 false 可禁用 Arrow 数据传输机制从而兼容旧版本系统需求;而开启此项则能显著提升基于矢量化操作的数据交换速度。 #### 2. 安装与启动 PySpark 要开始使用 PySpark,请先安装必要的依赖库: ```bash pip install pyspark ``` 接着可通过如下方式创建基本的应用实例: ```python from pyspark import SparkConf, SparkContext conf = SparkConf().setAppName("example").setMaster("local[*]") sc = SparkContext(conf=conf) data = sc.parallelize([1, 2, 3, 4]) result = data.map(lambda x: x * 2).collect() print(result) ``` 上述代码展示了如何定义一个简单的 RDD 并对其进行转换和行动操作。 #### 3. 结合 Pandas 进行分析 除了原生的支持外,还可以借助第三方工具增强功能集。比如,在某些场景下可能希望对结果进一步统计汇总时,可引入 pandas 来完成更复杂的运算逻辑[^2]: ```python import pandas as pd df_spark = ... # some spark dataframe operations here pdf = df_spark.toPandas() average_metrics = pdf['metric_column'].mean() std_deviation = pdf['another_col'].std() total_sum = pdf.sum(axis=0)['yet_another'] ``` 以上片段说明了怎样把 Spark DataFrames 转换成 Pandas DataFrames 后再调用其内置的方法实现平均数、标准差以及求和等功能。 #### 4. 执行计划解析 深入理解内部工作机制有助于编写高效的查询语句。以 executePlan 方法为例,它是整个流程的核心部分之一,负责构建完整的 QueryExecution 对象以便后续阶段能够按照预定策略运行作业[^3]: ```scala def executePlan(plan: LogicalPlan): QueryExecution = { createQueryExecution(plan) } ``` 这段 Scala 实现揭示了传入 logical plan 如何被转化为实际可行的任务结构体形式。 ---
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