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[SPARK-18788][SPARKR] Add API for getNumPartitions #16668

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34f9aa5
getNumPartitions
felixcheung Jan 21, 2017
7c057fc
rename getNumPartitions for RDD
felixcheung Jan 21, 2017
ad1bd14
fix generic
felixcheung Jan 21, 2017
bab7466
more broken calls
felixcheung Jan 22, 2017
0353978
improve
felixcheung Jan 26, 2017
c05f786
remove note
felixcheung Jan 26, 2017
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1 change: 1 addition & 0 deletions R/pkg/NAMESPACE
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Expand Up @@ -94,6 +94,7 @@ exportMethods("arrange",
"freqItems",
"gapply",
"gapplyCollect",
"getNumPartitions",
"group_by",
"groupBy",
"head",
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25 changes: 25 additions & 0 deletions R/pkg/R/DataFrame.R
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Expand Up @@ -3406,3 +3406,28 @@ setMethod("randomSplit",
}
sapply(sdfs, dataFrame)
})

#' getNumPartitions
#'
#' Return the number of partitions
#' Note: in order to compute the number of partition the SparkDataFrame has to be converted into a
#' RDD temporarily internally.
#'
#' @param x A SparkDataFrame
#' @family SparkDataFrame functions
#' @aliases getNumPartitions,SparkDataFrame-method
#' @rdname getNumPartitions
#' @name getNumPartitions
#' @export
#' @examples
#'\dontrun{
#' sparkR.session()
#' df <- createDataFrame(cars, numPartitions = 2)
#' getNumPartitions(df)
#' }
#' @note getNumPartitions since 2.1.1
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@HyukjinKwon HyukjinKwon Jan 21, 2017

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@felixcheung, should this be since 2.2.0? Just curious.

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@felixcheung felixcheung Jan 21, 2017

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I debated about this quite a bit - generally it should but we merged createDataFrame(..., numPartitions) to 2.1 and it felt important to have a getNumPartition in the same release too.

setMethod("getNumPartitions",
signature(x = "SparkDataFrame"),
function(x) {
getNumPartitionsRDD(toRDD(x))
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@shivaram shivaram Jan 21, 2017

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As discussed in the JIRA I worry that this will be a very expensive operation for large data frames. Specifically instead of create an RRDD, can we do some operations on the Scala side which might be cheaper ?

cc @yhuai @cloud-fan who know more about DataFrame on the SQL side

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@felixcheung felixcheung Jan 22, 2017

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Right, we agreed.
The conversion, especially into RRDD, is in particular concerning. From what I can see though this df.rdd.getNumPartitions is the recommended practice, which seems to be all over pyspark. (granted, DataFrame to RDD in pyspark is likely slightly more efficient)

An alternative, is we could wrap all of this on the JVM side - at least that should save us the around trip to RRDD.

But agreed, is there a more efficient way this could be exposed in DataFrame/Dataset directly instead?

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@cloud-fan cloud-fan Jan 23, 2017

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shall we add the getNumPartitions to DataFrame/Dataset at scala side?

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@felixcheung felixcheung Jan 23, 2017

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That would be great!

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@cloud-fan cloud-fan Jan 24, 2017

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are you going to do it here? Or do we need to send a new PR for the scala side changes?

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@cloud-fan cloud-fan Jan 24, 2017

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isn't just calling rdd.numPartitions? we need to materialize the RDD inside DataFrame anyway, but it's cheap at scala side.

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@felixcheung felixcheung Jan 24, 2017

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ah, that we could do easily. is that something ok for Spark 2.1.1? If yes, I could go ahead with changes here for Scala, Python and R.

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@cloud-fan cloud-fan Jan 24, 2017

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you said this filled a hole for Spark 2.1, what's this hole? is this Spark R only?

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@felixcheung felixcheung Jan 24, 2017

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sorry, I should clarify. Yes, for R only - since SparkR only has DataFrame APIs and no (publicly supported) RDD APIs, users are left without a way to check number of partitions.

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@cloud-fan cloud-fan Jan 24, 2017

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maybe we can add this slow implementation to Spark 2.1, and improve it in Spark 2.2

})
30 changes: 15 additions & 15 deletions R/pkg/R/RDD.R
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Expand Up @@ -313,7 +313,7 @@ setMethod("checkpoint",
#' @rdname getNumPartitions
#' @aliases getNumPartitions,RDD-method
#' @noRd
setMethod("getNumPartitions",
setMethod("getNumPartitionsRDD",
signature(x = "RDD"),
function(x) {
callJMethod(getJRDD(x), "getNumPartitions")
Expand All @@ -329,7 +329,7 @@ setMethod("numPartitions",
signature(x = "RDD"),
function(x) {
.Deprecated("getNumPartitions")
getNumPartitions(x)
getNumPartitionsRDD(x)
})

#' Collect elements of an RDD
Expand Down Expand Up @@ -460,7 +460,7 @@ setMethod("countByValue",
signature(x = "RDD"),
function(x) {
ones <- lapply(x, function(item) { list(item, 1L) })
collectRDD(reduceByKey(ones, `+`, getNumPartitions(x)))
collectRDD(reduceByKey(ones, `+`, getNumPartitionsRDD(x)))
})

#' Apply a function to all elements
Expand Down Expand Up @@ -780,7 +780,7 @@ setMethod("takeRDD",
resList <- list()
index <- -1
jrdd <- getJRDD(x)
numPartitions <- getNumPartitions(x)
numPartitions <- getNumPartitionsRDD(x)
serializedModeRDD <- getSerializedMode(x)

# TODO(shivaram): Collect more than one partition based on size
Expand Down Expand Up @@ -846,7 +846,7 @@ setMethod("firstRDD",
#' @noRd
setMethod("distinctRDD",
signature(x = "RDD"),
function(x, numPartitions = SparkR:::getNumPartitions(x)) {
function(x, numPartitions = SparkR:::getNumPartitionsRDD(x)) {
identical.mapped <- lapply(x, function(x) { list(x, NULL) })
reduced <- reduceByKey(identical.mapped,
function(x, y) { x },
Expand Down Expand Up @@ -1053,7 +1053,7 @@ setMethod("coalesce",
signature(x = "RDD", numPartitions = "numeric"),
function(x, numPartitions, shuffle = FALSE) {
numPartitions <- numToInt(numPartitions)
if (shuffle || numPartitions > SparkR:::getNumPartitions(x)) {
if (shuffle || numPartitions > SparkR:::getNumPartitionsRDD(x)) {
func <- function(partIndex, part) {
set.seed(partIndex) # partIndex as seed
start <- as.integer(base::sample(numPartitions, 1) - 1)
Expand Down Expand Up @@ -1143,7 +1143,7 @@ setMethod("saveAsTextFile",
#' @noRd
setMethod("sortBy",
signature(x = "RDD", func = "function"),
function(x, func, ascending = TRUE, numPartitions = SparkR:::getNumPartitions(x)) {
function(x, func, ascending = TRUE, numPartitions = SparkR:::getNumPartitionsRDD(x)) {
values(sortByKey(keyBy(x, func), ascending, numPartitions))
})

Expand Down Expand Up @@ -1175,7 +1175,7 @@ takeOrderedElem <- function(x, num, ascending = TRUE) {
resList <- list()
index <- -1
jrdd <- getJRDD(newRdd)
numPartitions <- getNumPartitions(newRdd)
numPartitions <- getNumPartitionsRDD(newRdd)
serializedModeRDD <- getSerializedMode(newRdd)

while (TRUE) {
Expand Down Expand Up @@ -1407,7 +1407,7 @@ setMethod("setName",
setMethod("zipWithUniqueId",
signature(x = "RDD"),
function(x) {
n <- getNumPartitions(x)
n <- getNumPartitionsRDD(x)

partitionFunc <- function(partIndex, part) {
mapply(
Expand Down Expand Up @@ -1450,7 +1450,7 @@ setMethod("zipWithUniqueId",
setMethod("zipWithIndex",
signature(x = "RDD"),
function(x) {
n <- getNumPartitions(x)
n <- getNumPartitionsRDD(x)
if (n > 1) {
nums <- collectRDD(lapplyPartition(x,
function(part) {
Expand Down Expand Up @@ -1566,8 +1566,8 @@ setMethod("unionRDD",
setMethod("zipRDD",
signature(x = "RDD", other = "RDD"),
function(x, other) {
n1 <- getNumPartitions(x)
n2 <- getNumPartitions(other)
n1 <- getNumPartitionsRDD(x)
n2 <- getNumPartitionsRDD(other)
if (n1 != n2) {
stop("Can only zip RDDs which have the same number of partitions.")
}
Expand Down Expand Up @@ -1637,7 +1637,7 @@ setMethod("cartesian",
#' @noRd
setMethod("subtract",
signature(x = "RDD", other = "RDD"),
function(x, other, numPartitions = SparkR:::getNumPartitions(x)) {
function(x, other, numPartitions = SparkR:::getNumPartitionsRDD(x)) {
mapFunction <- function(e) { list(e, NA) }
rdd1 <- map(x, mapFunction)
rdd2 <- map(other, mapFunction)
Expand Down Expand Up @@ -1671,7 +1671,7 @@ setMethod("subtract",
#' @noRd
setMethod("intersection",
signature(x = "RDD", other = "RDD"),
function(x, other, numPartitions = SparkR:::getNumPartitions(x)) {
function(x, other, numPartitions = SparkR:::getNumPartitionsRDD(x)) {
rdd1 <- map(x, function(v) { list(v, NA) })
rdd2 <- map(other, function(v) { list(v, NA) })

Expand Down Expand Up @@ -1714,7 +1714,7 @@ setMethod("zipPartitions",
if (length(rrdds) == 1) {
return(rrdds[[1]])
}
nPart <- sapply(rrdds, getNumPartitions)
nPart <- sapply(rrdds, getNumPartitionsRDD)
if (length(unique(nPart)) != 1) {
stop("Can only zipPartitions RDDs which have the same number of partitions.")
}
Expand Down
8 changes: 6 additions & 2 deletions R/pkg/R/generics.R
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Expand Up @@ -138,9 +138,9 @@ setGeneric("sumRDD", function(x) { standardGeneric("sumRDD") })
# @export
setGeneric("name", function(x) { standardGeneric("name") })

# @rdname getNumPartitions
# @rdname getNumPartitionsRDD
# @export
setGeneric("getNumPartitions", function(x) { standardGeneric("getNumPartitions") })
setGeneric("getNumPartitionsRDD", function(x) { standardGeneric("getNumPartitionsRDD") })

# @rdname getNumPartitions
# @export
Expand Down Expand Up @@ -492,6 +492,10 @@ setGeneric("gapply", function(x, ...) { standardGeneric("gapply") })
#' @export
setGeneric("gapplyCollect", function(x, ...) { standardGeneric("gapplyCollect") })

# @rdname getNumPartitions
# @export
setGeneric("getNumPartitions", function(x) { standardGeneric("getNumPartitions") })

#' @rdname summary
#' @export
setGeneric("describe", function(x, col, ...) { standardGeneric("describe") })
Expand Down
4 changes: 2 additions & 2 deletions R/pkg/R/pairRDD.R
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Expand Up @@ -780,7 +780,7 @@ setMethod("cogroup",
#' @noRd
setMethod("sortByKey",
signature(x = "RDD"),
function(x, ascending = TRUE, numPartitions = SparkR:::getNumPartitions(x)) {
function(x, ascending = TRUE, numPartitions = SparkR:::getNumPartitionsRDD(x)) {
rangeBounds <- list()

if (numPartitions > 1) {
Expand Down Expand Up @@ -850,7 +850,7 @@ setMethod("sortByKey",
#' @noRd
setMethod("subtractByKey",
signature(x = "RDD", other = "RDD"),
function(x, other, numPartitions = SparkR:::getNumPartitions(x)) {
function(x, other, numPartitions = SparkR:::getNumPartitionsRDD(x)) {
filterFunction <- function(elem) {
iters <- elem[[2]]
(length(iters[[1]]) > 0) && (length(iters[[2]]) == 0)
Expand Down
10 changes: 5 additions & 5 deletions R/pkg/inst/tests/testthat/test_rdd.R
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Expand Up @@ -29,8 +29,8 @@ intPairs <- list(list(1L, -1), list(2L, 100), list(2L, 1), list(1L, 200))
intRdd <- parallelize(sc, intPairs, 2L)

test_that("get number of partitions in RDD", {
expect_equal(getNumPartitions(rdd), 2)
expect_equal(getNumPartitions(intRdd), 2)
expect_equal(getNumPartitionsRDD(rdd), 2)
expect_equal(getNumPartitionsRDD(intRdd), 2)
})

test_that("first on RDD", {
Expand Down Expand Up @@ -305,18 +305,18 @@ test_that("repartition/coalesce on RDDs", {

# repartition
r1 <- repartitionRDD(rdd, 2)
expect_equal(getNumPartitions(r1), 2L)
expect_equal(getNumPartitionsRDD(r1), 2L)
count <- length(collectPartition(r1, 0L))
expect_true(count >= 8 && count <= 12)

r2 <- repartitionRDD(rdd, 6)
expect_equal(getNumPartitions(r2), 6L)
expect_equal(getNumPartitionsRDD(r2), 6L)
count <- length(collectPartition(r2, 0L))
expect_true(count >= 0 && count <= 4)

# coalesce
r3 <- coalesce(rdd, 1)
expect_equal(getNumPartitions(r3), 1L)
expect_equal(getNumPartitionsRDD(r3), 1L)
count <- length(collectPartition(r3, 0L))
expect_equal(count, 20)
})
Expand Down
14 changes: 7 additions & 7 deletions R/pkg/inst/tests/testthat/test_sparkSQL.R
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Expand Up @@ -196,26 +196,26 @@ test_that("create DataFrame from RDD", {
expect_equal(dtypes(df), list(c("name", "string"), c("age", "int"), c("height", "float")))
expect_equal(as.list(collect(where(df, df$name == "John"))),
list(name = "John", age = 19L, height = 176.5))
expect_equal(getNumPartitions(toRDD(df)), 1)
expect_equal(getNumPartitions(df), 1)

df <- as.DataFrame(cars, numPartitions = 2)
expect_equal(getNumPartitions(toRDD(df)), 2)
expect_equal(getNumPartitions(df), 2)
df <- createDataFrame(cars, numPartitions = 3)
expect_equal(getNumPartitions(toRDD(df)), 3)
expect_equal(getNumPartitions(df), 3)
# validate limit by num of rows
df <- createDataFrame(cars, numPartitions = 60)
expect_equal(getNumPartitions(toRDD(df)), 50)
expect_equal(getNumPartitions(df), 50)
# validate when 1 < (length(coll) / numSlices) << length(coll)
df <- createDataFrame(cars, numPartitions = 20)
expect_equal(getNumPartitions(toRDD(df)), 20)
expect_equal(getNumPartitions(df), 20)

df <- as.DataFrame(data.frame(0))
expect_is(df, "SparkDataFrame")
df <- createDataFrame(list(list(1)))
expect_is(df, "SparkDataFrame")
df <- as.DataFrame(data.frame(0), numPartitions = 2)
# no data to partition, goes to 1
expect_equal(getNumPartitions(toRDD(df)), 1)
expect_equal(getNumPartitions(df), 1)

setHiveContext(sc)
sql("CREATE TABLE people (name string, age double, height float)")
Expand All @@ -234,7 +234,7 @@ test_that("createDataFrame uses files for large objects", {
conf <- callJMethod(sparkSession, "conf")
callJMethod(conf, "set", "spark.r.maxAllocationLimit", "100")
df <- suppressWarnings(createDataFrame(iris, numPartitions = 3))
expect_equal(getNumPartitions(toRDD(df)), 3)
expect_equal(getNumPartitions(df), 3)

# Resetting the conf back to default value
callJMethod(conf, "set", "spark.r.maxAllocationLimit", toString(.Machine$integer.max / 10))
Expand Down