ARROW-11630: [Rust] Introduce limit option for sort kernel #9602

sundy-li · 2021-02-28T14:04:49Z

Introduce limit: Option<usize> for sort functions, then we can use partial_sort to achieve better performance in queries with limit & sort. Datafusion can use it later if it can push up the limit to the sort plan (currently use None as default).

github-actions · 2021-02-28T14:05:13Z

https://issues.apache.org/jira/browse/ARROW-11630

codecov-io · 2021-02-28T14:22:42Z

Codecov Report

Merging #9602 (06c503c) into master (5ae63f8) will increase coverage by 0.03%.
The diff coverage is 82.68%.

@@            Coverage Diff             @@
##           master    #9602      +/-   ##
==========================================
+ Coverage   82.32%   82.36%   +0.03%     
==========================================
  Files         245      245              
  Lines       56383    56661     +278     
==========================================
+ Hits        46419    46668     +249     
- Misses       9964     9993      +29

Impacted Files	Coverage Δ
rust/arrow/src/compute/kernels/sort.rs	`93.60% <82.62%> (+0.04%)`	⬆️
rust/datafusion/src/physical_plan/sort.rs	`90.22% <100.00%> (+0.05%)`	⬆️
rust/arrow/src/datatypes/field.rs	`55.47% <0.00%> (-0.66%)`	⬇️
...integration-testing/src/flight_server_scenarios.rs	`0.00% <0.00%> (ø)`
...-testing/src/flight_server_scenarios/middleware.rs	`0.00% <0.00%> (ø)`
...ng/src/flight_server_scenarios/auth_basic_proto.rs	`0.00% <0.00%> (ø)`
...ng/src/flight_server_scenarios/integration_test.rs	`0.00% <0.00%> (ø)`
rust/arrow/src/csv/reader.rs	`93.17% <0.00%> (+0.02%)`	⬆️
rust/arrow/src/compute/kernels/cast.rs	`97.33% <0.00%> (+0.03%)`	⬆️
rust/arrow/src/datatypes/schema.rs	`73.39% <0.00%> (+0.76%)`	⬆️
... and 2 more

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1. Introduce partial_sort 2. Introduce pdqsort

andygrove

I took a quick look through and LGTM. I had a question about introducing the new dependency for sorting. We already have sorting in place so I'm curious why the new dependency is needed and whether we should look at updating other sorting code to use the same dependency?

jorgecarleitao

I also have the same questions as @andygrove . Also, I would be more favourable having a separate function for this: sorting is already quite a complex logic already.

jorgecarleitao · 2021-03-01T17:55:08Z

rust/arrow/Cargo.toml

+partial_sort = "0.1.1"
+pdqsort = "1.0.3"


I am -0 on this without any benchmarks justifying this. Can't we at least feature-gate this?

jorgecarleitao · 2021-03-01T17:56:47Z

rust/arrow/src/compute/kernels/sort.rs

+pub fn sort(
+    values: &ArrayRef,
+    options: Option<SortOptions>,
+    limit: Option<usize>,


I think that this should be done on a separate function instead of adding another parameter to this one. It would also allow to feature-gate said function with the two new dependencies.

Ok, I will introduce partial_sort with limit parameter.

sundy-li · 2021-03-02T03:24:09Z

I removed pdqsort, because the performance didn't show any improvement during the benches in my pc.
Added a separate function partial_sort as @jorgecarleitao suggested.

I did not find any other partial_sort function in Rust like std::partial_sort in c++. So I created one.

And the benche results about partial_sort in arrow are:

sort 2^12                     time:   [753.58 us 755.43 us 758.14 us]
sort nulls 2^12               time:   [633.41 us 635.28 us 637.51 us]

sort 2^12 limit 10            time:   [49.246 us 49.820 us 50.667 us]
sort 2^12 limit 100           time:   [115.11 us 116.26 us 117.76 us]
sort 2^12 limit 1000          time:   [645.91 us 654.36 us 663.78 us]
sort nulls 2^12 limit 10      time:   [66.283 us 66.725 us 67.347 us]
sort nulls 2^12 limit 100     time:   [76.281 us 77.907 us 79.783 us]
sort nulls 2^12 limit 1000    time:   [258.98 us 260.32 us 262.24 us]

paddyhoran · 2021-03-03T11:02:59Z

rust/arrow/src/compute/kernels/sort.rs

+        len = size.min(len);
+    }
+
+    // we are not using partial_sort here, because array is ArrayRef. Something is not working good in that.


What does "not working good" mean here?

Sorry, there is a bug in the previous version. It's fixed in the newest commit

paddyhoran · 2021-03-03T11:05:22Z

rust/arrow/src/compute/kernels/sort.rs

+        Some(limit) => {
+            len = limit.min(len);
+            if !descending {
+                valids.partial_sort(len, |a, b| cmp(a.1, b.1));


Does partial_sort have a fast path when len is the length of the array? The pattern in this block is repeated a few times, if we could just use partial_sort it could be simplified to a simple if let that updates len?

Sorry not "fast path" but would the performance be the same as sort_by?

Sorry not "fast path" but would the performance be the same as sort_by?

I'm afraid not. The sort function in rust is merge sort, it is slightly faster than the heap sort for larger sets to sort all elements.
But it requires twice the memory of the heap sort because of the second array.

sort 2^12 time: [799.70 us 806.41 us 814.15 us] sort 2^12 limit 2^12 time: [1.2848 ms 1.3012 ms 1.3229 ms] sort nulls 2^12 time: [647.20 us 649.27 us 651.61 us] sort nulls 2^12 limit 2^12 time: [780.17 us 788.48 us 798.04 us]

We can make a new function to reduce the repeated patterns or make partial_sort fallback to default sort when limit equals to len.

equals to len size, it will use merge sort by default. 2. update partial_sort version to 0.1.2

alamb

Thank you @sundy-li

I found the idea of implementing "Top K" using a sort with limit option interesting -- thank you for pointing at the clickhouse implementation.

There are other, seemingly more memory efficient (and likely performant) ways, to compute the TopK than buffering the entire input and then doing a partial sort. For example, using a priority queue to keep only the top k values in memory.

That being said I am not opposed to adding a partial_sort to arrow if others would find it useful. One datapoint is that I took a look through the C++ arrow kernels and didn't see a limit (which is fine):
https://github.com/apache/arrow/blob/dfd232313e1538b81a38db1e59cf4a109b61a467/cpp/src/arrow/compute/kernels/vector_sort.cc

If we choose to add this feature, another suggest I have is to inline the partial_sort implementation into the arrow crate so that:

We can evaluate its test coverage / stability (given it has no other users yet I am not sure we can rely on the rest of the rust community to crowdsource this)
Avoid additional crate dependencies (mostly in the future if additional code is added to partial_sort).

I realize you have already gone through the trouble if creating a partial_crate but I think this is worth considering

rust/arrow/src/compute/kernels/sort.rs

alamb · 2021-03-06T12:14:18Z

rust/arrow/src/compute/kernels/sort.rs

+            Some(0),
+            Some(2),
+        ])) as ArrayRef];
+        test_lex_sort_arrays(input, expected, Some(3));


here too I recommend using a limit that is less than the length of the array

Here input size is 4, expected size is 3.

alamb · 2021-03-06T12:20:55Z

rust/datafusion/src/physical_plan/sort.rs

    )?;

    // sort combined record batch
+    // TODO: pushup the limit expression to sort


The way I have seen this done in other systems is a rewrite pass a (Sort) -> (Limit) combination into a new operator TopK

jorgecarleitao

I went through this PR, and also went skimmed through the code of partial_sort, including tests, benchmarks and the CI pipeline.

First of all, @sundy-li , thank you for your interest in this project, for this PR, and for the cool work on partial_sort 💯

With that said, and in summary, I am -0 on this atm.

On the one hand, there is a very good use case here as partial sort is a common operation. I think it is fine that we have different kernels as C++: there is no spec about that. I also think that the API makes sense, the code is simple and easy to understand, and the tests are sufficient.

On the other hand, we are adding a 10-day old crate as a mandatory dependency of the arrow crate. This dependency is also essentially a large unsafe block and has no miri on CI.

This is not to badmouth the implementation, @sundy-li, which I am fine, even though I did not go through all the details. I just feel that the sheer amount of uncommented unsafe on it is an indication that there is some opportunity to revisit and further improve the crate, thereby reducing the risks of undefined behavior (UB).

In summary, I wish to have this, but I sense a large risk wrt to UB.

imo, a first step here would be for partial_sort to mature and stabilize before we take it as a dependency. However, if others feel that the benefits already outweigh the risks, let's go for it.

jorgecarleitao · 2021-03-07T04:31:26Z

rust/arrow/src/compute/kernels/sort.rs

+#[inline]
+fn sort_by<T, F>(array: &mut [T], limit: usize, cmp: F)
+where
+    F: FnMut(&T, &T) -> Ordering,


Why does it need to be FnMut?

Just to be compatible with std::sort_by.

jorgecarleitao · 2021-03-07T04:31:57Z

rust/arrow/src/compute/kernels/sort.rs

 }

 /// Sort elements from `ArrayRef` into an unsigned integer (`UInt32Array`) of indices.
 /// For floating point arrays any NaN values are considered to be greater than any other non-null value


The doc could be updated :)

sundy-li · 2021-03-07T05:16:28Z

For example, using a priority queue to keep only the top k values in memory.

Yes, but lots of codes may duplicate with sort kernel. partial_sort used priority queue inside. It maybe good to do sorting in pipeline OLAP systems

In ClickHouse, PartialSortingTransform(Each block in each thread) --> MergeSortingTransform(Blocks to one block in each thread) --> MergingSortedTransform(N Block in N Thread to one block) .

┌─explain────────────────────────────────┐
│ (Expression)                           │
│ ExpressionTransform                    │
│   (Limit)                              │
│   Limit                                │
│     (MergingSorted)                    │
│     MergingSortedTransform 16 → 1      │
│       (MergeSorting)                   │
│       MergeSortingTransform × 16       │
│         (PartialSorting)               │
│         LimitsCheckingTransform × 16   │
│           PartialSortingTransform × 16 │
│             (Expression)               │
│             ExpressionTransform × 16   │
│               (SettingQuotaAndLimits)  │
│                 (ReadFromStorage)      │
│                 NumbersMt × 16 0 → 1   │
└────────────────────────────────────────┘

I just feel that the sheer amount of uncommented unsafe on it is an indication that there is some opportunity to revisit and further improve the crate, thereby reducing the risks of undefined behavior (UB).

@alamb @jorgecarleitao Thanks for all your reviews. I also have the consideration about unsafe codes in partial_sort may break arrow, because it was just created, without any used in production(BTW I am new to rust).

We can keep this MR open currently until you think it's safe enough or must have it.

Dandandan · 2021-03-07T11:37:07Z

I think there are some very nice use-cases of this optimization (top-k kind of queries), I think it would be very cool to have more advanced features like this in Arrow/DataFusion/...

The partial_sort crate seems also quite small (about 60 lines without tests/imports). What about having the code in Arrow for now, and (try to) limit the amount of unsafety @sundy-li and we can have a next review iteration?

alamb · 2021-03-07T11:53:51Z

In ClickHouse, PartialSortingTransform(Each block in each thread)

This is a very cool idea (effectively to compute top-k for each block in parallel and then merge them together). Thank you for the explanation @sundy-li

jorgecarleitao · 2021-03-07T13:03:39Z

Thanks @sundy-li for the explanation.

The partial_sort crate seems also quite small (about 60 lines without tests/imports). What about having the code in Arrow for now, and (try to) limit the amount of unsafety @sundy-li and we can have a next review iteration?

I do not follow the argument. Isn't the whole purpose of crates and dependencies to separate concerns and allow code reuse across the ecosystem without dragging dependencies?

From what I've seen, the crate:

addresses one problem and one alone (unlike our repo or our workspace)
has CI and CD in place
it is easy to publish in crates.io (via a github action) which makes CD also easy
it is duo license, as it is the standard in Rust
it uses SemVer

If I were @sundy-li, I would keep the setup exactly like it is: it enables the implementation to be used by more projects without having to drag arrow and its dependencies with it, while at the same time maintains the generality that the algorithm itself has. I would be behaving exactly how @sundy-li is behaving: engage with potential "customers" like Arrow to identify value, how it can be adopted, and what are the points to improve.

From our side, I am not sure I agree with copy-pasting code from a crate to our own crate. IMO we should instead actively engage with our "providers" by contributing upstream. In this particular case, one step is to have MIRI run on CI. The other is to either limit or document the usage of unsafe. This way, the Rust community as a whole benefits from these, instead of the benefit be limited to users of the Arrow crate. I created a PR upstream to address one of the steps: sundy-li/partial_sort#1 .

Side note: @alamb , what just happened (on which I could trivially PR upstream without any complications, issues, etc.) is a concrete example of what I have been trying to express on the mailing list wrt to the UX that IMO our repo lacks: I can't do that on this repo.

Dandandan · 2021-03-07T14:18:23Z

@jorgecarleitao

I'm perfectly fine with that approach too.

I do think that depending on crates that are useful instead of building our own or even duplicating code is what we should do in general, and indeed will benefit others in the Rust community.

My reasoning behind my suggestion above was

The crate has no currently no users and (I think) only 1 maintainer.
The code size is small
The PR author is the same as the maintainer of the crate (and I guess it was created for this use case for now?)
It would be easier to review the code / run Miri checks, etc. when it was included in the PR

Of course, there might be some other parties that would be interested in partial_sort or maybe it will at some point make it to the standard library.

Also dependencies have some costs, some of them being:

Has some risk that the crated will become unmaintained at some point, but causes a bug / security problem, etc. in Arrow. Or we would like to improve it, but a crate maintainer might be unresponsive. A recent example of this I saw in the memmap crate which now has a fork memmap2 which is quite hard to find as the docs / repo of memmap are still online.
Non-semver breaking changes can not be caught in PRs
Build times become larger compared to having the same code in the project (as the crate will be downloaded / compiled separately). Of course one extra small dependency won't matter that much, but it accumulates with lots of dependencies.

jorgecarleitao · 2021-03-07T16:17:13Z

Thanks for that, @Dandandan, all great points 👍, to which I generally agree with.

It would be easier to review the code / run Miri checks, etc. when it was included in the PR

I agree. My concern atm is that our own crate does not pass miri checks (our miri checks are cargo miri test || true), thus, any potential soundness issues new code may have cannot be identified by our own CI. I only recently was able to have a version of a arrow crate to pass miri checks, and I am still deactivating some checks and investigating. My hypothesis is that it is very difficult to write safe code in this crate's design and thus my state of mind is that our best bet is to push the soundness checks about specific parts of the code to places where those can be done in a more contained environment (i.e. without all the transmutes and the like that we do here). We should still of course try to fix our own miri checks. xD

Build times become larger compared to having the same code in the project (as the crate will be downloaded / compiled separately). Of course one extra small dependency won't matter that much, but it accumulates with lots of dependencies.

I agree. And I think that this is already a problem for DataFusion and parquet. I do get the feeling that the culprits there are crossbeam, tokio, tower and the like. These small crates seem to be downloaded and compiled in parallel and thus have a small impact when compared to the big beasts that block compilation (i.e. we have unbalanced-sized tasks). In arrows' case, the largest is flatbuffer I think, which we could feature-gate under e.g. io_ipc in case people do not need that. We can't get away with these during testing, but I think it is by design; if we want, IMO we need a new compilation unit (e.g. a crate).

Has some risk that the crated will become unmaintained at some point, but causes a bug / security problem, etc. in Arrow. Or we would like to improve it, but a crate maintainer might be unresponsive. A recent example of this I saw in the memmap crate which now has a fork memmap2 which is quite hard to find as the docs / repo of memmap are still online.

I agree. That IMO should be sufficient for us to bring the crate to arrow.

alamb · 2021-03-07T18:01:12Z

From our side, I am not sure I agree with copy-pasting code from a crate to our own crate. IMO we should instead actively engage with our "providers" by contributing upstream.

@jorgecarleitao as you and @Dandandan have elucidated, I think there are tradeoffs to the two approaches. I am happy with either approach in general -- I suggested the "include it in arrow approach" in this case as I felt it had less overhead for @sundy-li who has already worked on this PR a great deal, but that may not be the best approach either short or long term.

sundy-li · 2021-03-12T07:28:18Z

Hi, all. From other user's advice, partial_sort could be

pub fn partial_sort<T, F>(v: &mut [T], limit: usize, mut is_less: F)
where
    F: FnMut(&T, &T) -> Ordering,
{
    let (before, _mid, _after) = v.select_nth_unstable_by(limit, &mut is_less);
    before.sort_unstable_by(is_less);
}

So I abandon to use of custom partial_sort. This could fix the issue and risk we are arguing about.

alamb

I think this PR is looking good now. Given the lengthy discussion I would like at least one other person (e.g @jorgecarleitao @paddyhoran @andygrove ) to give their signoff on this PR as well

Thank you for sticking with it @sundy-li and I really like how this PR has shaped up.

Dandandan · 2021-03-14T11:28:59Z

rust/arrow/src/compute/kernels/sort.rs

+    F: FnMut(&T, &T) -> Ordering,
+{
+    let (before, _mid, _after) = v.select_nth_unstable_by(limit, &mut is_less);
+    before.sort_unstable_by(is_less);


I am wondering, why can we use unstable sort here, while we use stable sort for the normal sort kernel?
Shouldn't that be an option of the kernel?

There are some reasons for using unstable_sort.

select_nth_unstable_by is unstable, so using before.sort_stable_by don't ensure it's stable. Currently we do not have select_nth_stable_by

sort_unstable is faster than sort_stable, refer to doc

Clear, thanks @sundy-li.

Maybe some docs can be added about this?

I think it probably is not really a problem, but might be surprising by someone using the kernel. And we might want to see whether we could use a (faster) unstable version of the normal sort kernel as well (that could be used by DataFusion as well I think).

What do you think @alamb

alamb · 2021-03-15T13:18:25Z

Any last thoughts prior to merge? I'll plan to merge this later today unless I hear otherwise

alamb · 2021-03-16T10:24:21Z

Merged. Thanks again @sundy-li for getting this done. It is a cool piece of functionality

alamb · 2021-03-16T11:16:23Z

BTW when I was writing some doc examples for this functionality, it occured to me that there is another potential way to expose this functionality -- #9722

@sundy-li

# Rationale Examples in the docs serve as both tests and makes the library easier to use I figured this would be helpful the wake of the very helpful #9602 by @sundy-li I think I am in a documenting kind of mood this week Closes #9721 from alamb/alamb/sort_doc_examples Authored-by: Andrew Lamb <[email protected]> Signed-off-by: Andrew Lamb <[email protected]>

@sundy-li

# Rationale Examples in the docs serve as both tests and makes the library easier to use I figured this would be helpful the wake of the very helpful apache/arrow#9602 by @sundy-li I think I am in a documenting kind of mood this week Closes #9721 from alamb/alamb/sort_doc_examples Authored-by: Andrew Lamb <[email protected]> Signed-off-by: Andrew Lamb <[email protected]>

github-actions bot added Component: Rust - DataFusion Component: Rust labels Feb 28, 2021

sundy-li added 2 commits March 1, 2021 10:20

[Rust] Introduce limit option for sort kernel

abfb7c9

1. Introduce partial_sort 2. Introduce pdqsort

Add tests and benchmarks

06c503c

sundy-li force-pushed the limit-sort branch from 85439c1 to 06c503c Compare March 1, 2021 07:25

sundy-li added 2 commits March 1, 2021 17:50

update comment

c7df0d6

update styles

4f4dc62

andygrove changed the title ~~ARROW-11630: [Rust] Introduce limit option for sort kenerl~~ ARROW-11630: [Rust] Introduce limit option for sort kernel Mar 1, 2021

andygrove reviewed Mar 1, 2021

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jorgecarleitao reviewed Mar 1, 2021

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Remove pdqsort && add a separate function partial_sort

dc3167e

sundy-li force-pushed the limit-sort branch from f19fc16 to dc3167e Compare March 2, 2021 03:30

paddyhoran reviewed Mar 3, 2021

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1. Introduce a wrap function for sort and partial_sort, if limit size

b98b0b3

equals to len size, it will use merge sort by default. 2. update partial_sort version to 0.1.2

alamb reviewed Mar 6, 2021

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Update tests

bb6a77e

jorgecarleitao reviewed Mar 7, 2021

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jorgecarleitao mentioned this pull request Mar 7, 2021

Added Miri checks to CI sundy-li/partial_sort#1

Merged

jorgecarleitao mentioned this pull request Mar 7, 2021

Re-activated test with random values sundy-li/partial_sort#2

Merged

Include partial_sort to arrow

0461668

sundy-li closed this Mar 8, 2021

sundy-li reopened this Mar 8, 2021

sundy-li added 2 commits March 8, 2021 23:23

Make clippy test happy

86672cc

partial_sort from select_nth_unstable_by + sort

2dd16a7

alamb approved these changes Mar 14, 2021

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Dandandan reviewed Mar 14, 2021

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Add docs about unstable_sort

fd6a234

alamb closed this in 2a30cd0 Mar 16, 2021

This was referenced Mar 16, 2021

ARROW-11977: [Rust] Add documentation examples for sort kernel #9721

Closed

ARROW-11979: Combine limit into SortOptions - REQUEST FOR COMMENT #9722

Closed

asfimport mentioned this pull request Mar 16, 2021

[Rust] Introduce partial_sort and limit option for sort kernel #27493

Closed

ARROW-11630: [Rust] Introduce limit option for sort kernel #9602

ARROW-11630: [Rust] Introduce limit option for sort kernel #9602

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