An overengineered solution to `sort | uniq -c` with 25x throughput (hist)

zX41ZdbW

This and similar tasks can be solved efficiently with clickhouse-local [1]. Example:

    ch --input-format LineAsString --query "SELECT line, count() AS c GROUP BY line ORDER BY c DESC" < data.txt

I've tested it and it is faster than both sort and this Rust code:

    time LC_ALL=C sort data.txt | uniq -c | sort -rn > /dev/null
    32 sec.

    time hist data.txt > /dev/null
    14 sec.

    time ch --input-format LineAsString --query "SELECT line, count() AS c GROUP BY line ORDER BY c DESC" < data.txt > /dev/null
    2.7 sec.

It is like a Swiss Army knife for data processing: it can solve various tasks, such as joining data from multiple files and data sources, processing various binary and text formats, converting between them, and accessing external databases.

[1] https://clickhouse.com/docs/operations/utilities/clickhouse-...

nasretdinov

To be more fair you could also add SETTINGS max_threads=1 though?

donatj

I created "unic" a number of years ago because I had need to get the unique lines from a giant file without losing the order they initially appeared. It achieves this using a Cuckoo Filter so it's pretty dang quick about it, faster than sorting a large file in memory for sure.

https://github.com/donatj/unic

noamteyssier

Was sitting around in meetings today and remembered an old shell script I had to count the number of unique lines in a file. Gave it a shot in rust and with a little bit of (over-engineering)™ I managed to get 25x throughput over the naive approach using coreutils as well as improve over some existing tools.

Some notes on the improvements:

1. using csv (serde) for writing leads to some big gains

2. arena allocation of incoming keys + storing references in the hashmap instead of storing owned values heavily reduced the number of allocations and improves cache efficiency (I'm guessing, I did not measure).

There are some regex functionalities and some table filtering built in as well.

happy hacking

theemptiness

Small semantics nit: it is not overengineered, it is engineered. You wanted more throughput, the collection of coreutils tools was not designed for throughput but flexibility.

It is not difficult to construct scenarios where throughput matters but that IMHO that does not determine engineering vs overengineering. What matters is whether there are requirements that need to be met. Debating the requirements is possible but doesn't take away from whether a solution obtained with reasonable effort meets the spec. Overengineering is about unreasonable effort, which could lead to overshoot the requirements, not about unreasonable requirements.

mabster

We had similar thoughts about "premature optimisation" in the games industry. That is it's better to have prematurely optimised things than finding "everything is slow". But I guess in that context there are many many "inner-most loops" to optimise.

chii

> That is it's better to have prematurely optimised things than finding "everything is slow".

or you found that you've optimized a game that is unfun to play and thus doesn't sell, even tho it runs fast...

dbdr

> using csv (serde) for writing leads to some big gains

Could you explain that, if you have the time? Is that for writing the output lines? Is actual CSV functionality used? That crate says "Fast CSV parsing with support for serde", so I'm especially confused how that helps with writing.

nasretdinov

Note that by default sort command has a pretty low memory usage and spills to disk. You can improve the throughput quite a bit by increasing the allowed memory usage: --buffer-size=SIZE

noctune

I built something similarly a few years ago for `sort | uniq -d` using sketches. The downside is you need two passes, but still it's overall faster than sorting: https://github.com/mpdn/sketch-duplicates

Someone

> I am measuring the performance of equivalent cat <file> | sort | uniq -c | sort -n functionality.

It likely won’t matter much here, but invoking cat is unnecessary.

   sort <file> | uniq -c | sort -n

will do the job just fine. GNU’s sort also has a few flags controlling buffer size and parallelism. Those may matter more (see https://www.gnu.org/software/coreutils/manual/html_node/sort...)

flowerthoughts

The win here might be using HashMap to avoid having to sort all entries. Then sorting at the end instead. What's the ratio of duplicates in the benchmark input?

There is no text encoding processing, so this only works for single byte encodings. That probably speeds it up a little bit.

Depending on the size of the benchmark input, sort(1) may have done disk-based sorting. What's the size of the benchmark input?

wodenokoto

To me, the really big win would be _not_ to have to sort at all. Have an option to keep first or last duplicate and remove all others while keeping line order is usually what I need.

mabster

I've written this kind of function so many times it's not funny. I usually want something that is fed from an iterator, removes duplicates, and yields values as soon as possible.

thaumasiotes

That's easy to do if you're keeping the first duplicate. It becomes complex if you're keeping the last duplicate, because every time you find a duplicate you have to go back through your "output" and delete the earlier occurrence.

You could do an annotating pass for learning which of each line is the last one, and then a followup pass for printing (or otherwise echoing) only the lines that are the last of their kind. Technically still faster than sorting.

You could also keep the information on last occurrence of each line in the hash map (that's where it's going to be anyway), and once you're done with the first pass sort the map by earliest last occurrence. That will get you the lines in the right order, but you had to do a sort. If the original input was mostly duplicates, this is probably a better approach.

You could also track last occurrence of each line in a separate self-sorting structure. Now you have slightly more overhead while processing the input, and sorting the output is free.

vlovich123

Why does this test against sort | uniq | sort? It’s kind of weird to sort twice no?

gucci-on-fleek

The first "sort" sorts the input lines lexicographically (which is required for "uniq" to work); the second "sort" sorts the output of "uniq" numerically (so that lines are ordered from most-frequent to least-frequent):

  $ echo c a b c | tr ' ' '\n'
  c
  a
  b
  c
  
  $ echo c a b c | tr ' ' '\n' | sort
  a
  b
  c
  c
  
  $ echo c a b c | tr ' ' '\n' | sort | uniq -c
        1 a
        1 b
        2 c
  
  $ echo c a b c | tr ' ' '\n' | sort | uniq -c | sort -rn
        2 c
        1 b
        1 a

Aaron2222

  sort | uniq -c | sort -n

The second sort is sorting by frequency (the count output by `uniq -c`).

BuildTheRobots

It's something I've done myself in the past. First sort is because it needs to be sorted for uniq -c to count it proper, second sort because uniq doesn't always give the output in the right order.

evertedsphere

more precisely, uniq produces output in the same order as the input to it, just collapsing runs / run-length encoding it

HN

An overengineered solution to `sort | uniq -c` with 25x throughput (hist)

An overengineered solution to `sort | uniq -c` with 25x throughput (hist)