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new 02f11b9 ARROW-12763: [R] Optimize dplyr queries that use head/tail
after arrange
02f11b9 is described below
commit 02f11b9cf58fc62b3f256c66277576614b1cedde
Author: Neal Richardson <[email protected]>
AuthorDate: Fri Oct 15 14:45:21 2021 -0500
ARROW-12763: [R] Optimize dplyr queries that use head/tail after arrange
* Uses SelectKSinkNode for head/tail on sorted query. tail() is implemented
by reversing the sort orders, taking the top K rows, and then reversing the
resulting row order to match as if we had taken the (ordered) bottom K rows.
* Some subtle differences in expectation: row order appears to be locally
deterministic (within chunks), but SelectK doesn't necessarily follow that when
there are ties. Also, missing value handling by SelectK doesn't match R's
expectations--there may be a sort option that isn't handled the same way in the
SelectK algorithm (I don't see anywhere else to pass in another option but
maybe I missed it)
Closes #11405 from nealrichardson/r-topk
Authored-by: Neal Richardson <[email protected]>
Signed-off-by: Jonathan Keane <[email protected]>
---
r/R/arrow-datum.R | 1 +
r/R/arrowExports.R | 4 ++--
r/R/query-engine.R | 40 ++++++++++++++++++++++------------
r/src/arrowExports.cpp | 11 +++++-----
r/src/compute-exec.cpp | 25 ++++++++++++++++-----
r/tests/testthat/test-dplyr-collapse.R | 1 +
r/tests/testthat/test-dplyr-query.R | 15 ++++++++++++-
r/tests/testthat/test-python.R | 1 +
8 files changed, 70 insertions(+), 28 deletions(-)
diff --git a/r/R/arrow-datum.R b/r/R/arrow-datum.R
index adffe5c..557321f 100644
--- a/r/R/arrow-datum.R
+++ b/r/R/arrow-datum.R
@@ -232,6 +232,7 @@ is.sliceable <- function(i) {
is.numeric(i) &&
length(i) > 0 &&
all(i > 0) &&
+ i[1] <= i[length(i)] &&
identical(as.integer(i), i[1]:i[length(i)])
}
diff --git a/r/R/arrowExports.R b/r/R/arrowExports.R
index 5c1ceee..f5f2dd7 100644
--- a/r/R/arrowExports.R
+++ b/r/R/arrowExports.R
@@ -288,8 +288,8 @@ ExecPlan_create <- function(use_threads) {
.Call(`_arrow_ExecPlan_create`, use_threads)
}
-ExecPlan_run <- function(plan, final_node, sort_options) {
- .Call(`_arrow_ExecPlan_run`, plan, final_node, sort_options)
+ExecPlan_run <- function(plan, final_node, sort_options, head) {
+ .Call(`_arrow_ExecPlan_run`, plan, final_node, sort_options, head)
}
ExecPlan_StopProducing <- function(plan) {
diff --git a/r/R/query-engine.R b/r/R/query-engine.R
index 5aac489..d648321 100644
--- a/r/R/query-engine.R
+++ b/r/R/query-engine.R
@@ -179,7 +179,7 @@ ExecPlan <- R6Class("ExecPlan",
if (length(.data$arrange_vars)) {
node$sort <- list(
names = names(.data$arrange_vars),
- orders = as.integer(.data$arrange_desc),
+ orders = .data$arrange_desc,
temp_columns = names(.data$temp_columns)
)
}
@@ -197,29 +197,41 @@ ExecPlan <- R6Class("ExecPlan",
},
Run = function(node) {
assert_is(node, "ExecNode")
- # TODO (ARROW-12763): pass head/tail to ExecPlan_run so we can maybe TopK
- out <- ExecPlan_run(self, node, node$sort %||% list())
- if (is.null(node$sort)) {
+ # Sorting and head/tail (if sorted) are handled in the SinkNode,
+ # created in ExecPlan_run
+ sorting <- node$sort %||% list()
+ select_k <- node$head %||% -1L
+ has_sorting <- length(sorting) > 0
+ if (has_sorting) {
+ if (!is.null(node$tail)) {
+ # Reverse the sort order and take the top K, then after we'll reverse
+ # the resulting rows so that it is ordered as expected
+ sorting$orders <- !sorting$orders
+ select_k <- node$tail
+ }
+ sorting$orders <- as.integer(sorting$orders)
+ }
+
+ out <- ExecPlan_run(self, node, sorting, select_k)
+
+ if (!has_sorting) {
# Since ExecPlans don't scan in deterministic order, head/tail are both
# essentially taking a random slice from somewhere in the dataset.
# And since the head() implementation is way more efficient than
tail(),
# just use it to take the random slice
slice_size <- node$head %||% node$tail
if (!is.null(slice_size)) {
+ # TODO (ARROW-14289): make the head methods return RBR not Table
out <- head(out, slice_size)
}
- # TODO (ARROW-12763): delete these else cases because they'll be
handled
- # with SelectK
- } else if (!is.null(node$head)) {
- # These methods are on RecordBatchReader (but return Table)
- # TODO (ARROW-14289): make the head/tail methods return RBR not Table
- out <- head(out, node$head)
- # We can now tell `self` to StopProducing: we already have
- # everything we need for the head
- self$Stop()
+ # Can we now tell `self$Stop()` to StopProducing? We already have
+ # everything we need for the head (but it seems to segfault:
ARROW-14329)
} else if (!is.null(node$tail)) {
- out <- tail(out, node$tail)
+ # Reverse the row order to get back what we expect
+ # TODO: don't return Table, return RecordBatchReader
+ out <- out$read_table()
+ out <- out[rev(seq_len(nrow(out))), , drop = FALSE]
}
out
diff --git a/r/src/arrowExports.cpp b/r/src/arrowExports.cpp
index b5910a3..c446b77 100644
--- a/r/src/arrowExports.cpp
+++ b/r/src/arrowExports.cpp
@@ -1126,17 +1126,18 @@ extern "C" SEXP _arrow_ExecPlan_create(SEXP
use_threads_sexp){
// compute-exec.cpp
#if defined(ARROW_R_WITH_ARROW)
-std::shared_ptr<arrow::RecordBatchReader> ExecPlan_run(const
std::shared_ptr<compute::ExecPlan>& plan, const
std::shared_ptr<compute::ExecNode>& final_node, cpp11::list sort_options);
-extern "C" SEXP _arrow_ExecPlan_run(SEXP plan_sexp, SEXP final_node_sexp, SEXP
sort_options_sexp){
+std::shared_ptr<arrow::RecordBatchReader> ExecPlan_run(const
std::shared_ptr<compute::ExecPlan>& plan, const
std::shared_ptr<compute::ExecNode>& final_node, cpp11::list sort_options,
int64_t head);
+extern "C" SEXP _arrow_ExecPlan_run(SEXP plan_sexp, SEXP final_node_sexp, SEXP
sort_options_sexp, SEXP head_sexp){
BEGIN_CPP11
arrow::r::Input<const std::shared_ptr<compute::ExecPlan>&>::type
plan(plan_sexp);
arrow::r::Input<const std::shared_ptr<compute::ExecNode>&>::type
final_node(final_node_sexp);
arrow::r::Input<cpp11::list>::type sort_options(sort_options_sexp);
- return cpp11::as_sexp(ExecPlan_run(plan, final_node, sort_options));
+ arrow::r::Input<int64_t>::type head(head_sexp);
+ return cpp11::as_sexp(ExecPlan_run(plan, final_node, sort_options,
head));
END_CPP11
}
#else
-extern "C" SEXP _arrow_ExecPlan_run(SEXP plan_sexp, SEXP final_node_sexp, SEXP
sort_options_sexp){
+extern "C" SEXP _arrow_ExecPlan_run(SEXP plan_sexp, SEXP final_node_sexp, SEXP
sort_options_sexp, SEXP head_sexp){
Rf_error("Cannot call ExecPlan_run(). See
https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow
C++ libraries. ");
}
#endif
@@ -7239,7 +7240,7 @@ static const R_CallMethodDef CallEntries[] = {
{ "_arrow_io___CompressedOutputStream__Make", (DL_FUNC)
&_arrow_io___CompressedOutputStream__Make, 2},
{ "_arrow_io___CompressedInputStream__Make", (DL_FUNC)
&_arrow_io___CompressedInputStream__Make, 2},
{ "_arrow_ExecPlan_create", (DL_FUNC) &_arrow_ExecPlan_create,
1},
- { "_arrow_ExecPlan_run", (DL_FUNC) &_arrow_ExecPlan_run, 3},
+ { "_arrow_ExecPlan_run", (DL_FUNC) &_arrow_ExecPlan_run, 4},
{ "_arrow_ExecPlan_StopProducing", (DL_FUNC)
&_arrow_ExecPlan_StopProducing, 1},
{ "_arrow_ExecNode_output_schema", (DL_FUNC)
&_arrow_ExecNode_output_schema, 1},
{ "_arrow_ExecNode_Scan", (DL_FUNC) &_arrow_ExecNode_Scan, 4},
diff --git a/r/src/compute-exec.cpp b/r/src/compute-exec.cpp
index 0f24ab6..7e0235b 100644
--- a/r/src/compute-exec.cpp
+++ b/r/src/compute-exec.cpp
@@ -58,18 +58,31 @@ std::shared_ptr<compute::ExecNode> MakeExecNodeOrStop(
// [[arrow::export]]
std::shared_ptr<arrow::RecordBatchReader> ExecPlan_run(
const std::shared_ptr<compute::ExecPlan>& plan,
- const std::shared_ptr<compute::ExecNode>& final_node, cpp11::list
sort_options) {
+ const std::shared_ptr<compute::ExecNode>& final_node, cpp11::list
sort_options,
+ int64_t head = -1) {
// For now, don't require R to construct SinkNodes.
// Instead, just pass the node we should collect as an argument.
arrow::AsyncGenerator<arrow::util::optional<compute::ExecBatch>> sink_gen;
// Sorting uses a different sink node; there is no general sort yet
if (sort_options.size() > 0) {
- MakeExecNodeOrStop("order_by_sink", plan.get(), {final_node.get()},
- compute::OrderBySinkNodeOptions{
- *std::dynamic_pointer_cast<compute::SortOptions>(
- make_compute_options("sort_indices",
sort_options)),
- &sink_gen});
+ if (head >= 0) {
+ // Use the SelectK node to take only what we need
+ MakeExecNodeOrStop(
+ "select_k_sink", plan.get(), {final_node.get()},
+ compute::SelectKSinkNodeOptions{
+ arrow::compute::SelectKOptions(
+ head, std::dynamic_pointer_cast<compute::SortOptions>(
+ make_compute_options("sort_indices", sort_options))
+ ->sort_keys),
+ &sink_gen});
+ } else {
+ MakeExecNodeOrStop("order_by_sink", plan.get(), {final_node.get()},
+ compute::OrderBySinkNodeOptions{
+ *std::dynamic_pointer_cast<compute::SortOptions>(
+ make_compute_options("sort_indices",
sort_options)),
+ &sink_gen});
+ }
} else {
MakeExecNodeOrStop("sink", plan.get(), {final_node.get()},
compute::SinkNodeOptions{&sink_gen});
diff --git a/r/tests/testthat/test-dplyr-collapse.R
b/r/tests/testthat/test-dplyr-collapse.R
index f87d963..13d870f 100644
--- a/r/tests/testthat/test-dplyr-collapse.R
+++ b/r/tests/testthat/test-dplyr-collapse.R
@@ -197,6 +197,7 @@ See $.data for the source Arrow object",
q %>% head(1) %>% collect(),
tibble::tibble(lgl = FALSE, total = 8L, extra = 40)
)
+ skip("TODO (ARROW-1XXXX): implement sorting option about where NAs go")
expect_equal(
q %>% tail(1) %>% collect(),
tibble::tibble(lgl = NA, total = 25L, extra = 125)
diff --git a/r/tests/testthat/test-dplyr-query.R
b/r/tests/testthat/test-dplyr-query.R
index cd0cdb0..07cdf08 100644
--- a/r/tests/testthat/test-dplyr-query.R
+++ b/r/tests/testthat/test-dplyr-query.R
@@ -226,7 +226,8 @@ test_that("head", {
test_that("arrange then head returns the right data (ARROW-14162)", {
expect_dplyr_equal(
input %>%
- arrange(mpg) %>%
+ # mpg has ties so we need to sort by two things to get deterministic
order
+ arrange(mpg, disp) %>%
head(4) %>%
collect(),
mtcars,
@@ -234,6 +235,18 @@ test_that("arrange then head returns the right data
(ARROW-14162)", {
)
})
+test_that("arrange then tail returns the right data", {
+ expect_dplyr_equal(
+ input %>%
+ # mpg has ties so we need to sort by two things to get deterministic
order
+ arrange(mpg, disp) %>%
+ tail(4) %>%
+ collect(),
+ mtcars,
+ ignore_attr = "row.names"
+ )
+})
+
test_that("tail", {
batch <- record_batch(tbl)
diff --git a/r/tests/testthat/test-python.R b/r/tests/testthat/test-python.R
index 82b3bfc..5ad7513 100644
--- a/r/tests/testthat/test-python.R
+++ b/r/tests/testthat/test-python.R
@@ -17,6 +17,7 @@
test_that("install_pyarrow", {
skip_on_cran()
+ skip_if_offline()
skip_if_not_dev_mode()
# Windows CI machine doesn't pick up the right python or something
skip_on_os("windows")
