Three Algorithm Optimizations Outside [Place], [Other place]

Recently, I came across an ad for a job that had a precondition for application: it required you to first solve a ✨programming challenge✨:

Given a list of words, two “strings” are classified as “matching” if there exists a one-to-one mapping between them. Thus, the strings FOOFOOFOO and BAABAABAA are considered matching, because F and B, and O and A map to each other, producing the same “pattern”.
Given a newline-delimited file of 500k strings, how many of them are “matching”?

Setting aside for a moment the infinitely more interesting questions “What even is a string?” and “Programming challenge?” I spent a slow afternoon pondering the problem:

  • The strings in the file are uppercase ASCII
  • We can keep a “stack” of characters we’ve seen, and the order in which they’ve been seen
  • If the first character in each string is somehow mapped to 0, and mappings for subsequent new characters that are “seen” increase by 1, patterns can trivially be compared to see whether they match.

I write a lot of Rust these days, and I was curious to see how fast it would be, but more importantly, how much more code I’d have to write compared to my usual go-to for this kind of thing: Python. By now, all thoughts of applying for the job had long been forgotten. I typed the dread words cargo new --bin patterns into my terminal.


Speeding Up Your Program, 101

Before you write any Rust code, ask yourself: “Is it possible that any of the operations in my program could be carried out in a way which is embarassingly parallel” If the answer is yes, Rayon is probably the best, most robust solution. What do we mean by “embarrassingly parallel”? We mean tasks or operations that
“[…] can easily be divided into components that can be executed concurrently.” (Herlihy and Shavit, 2012, p.14)

This is obviously the case here: when transforming strings into integer lists each transformation is independent, and there’s no need to keep track of any other state, or carry out any other operations that have side-effects. In practice, this meant that I’d be able to replace sequential iteration with parallel iteration in several hot loops.

“the means of labour passes through different metamorphoses, whose culmination is the machine”

The next question I asked myself was “Have I turned on LTO"? The drawback of LTO is that it can severely increase compilation times, but one can cope with that by compiling in release mode as rarely as possible. To use LTO for release and benchmark builds, edit Cargo.toml, adding two sections:

[profile.release]
lto = true
[profile.bench]
lto = true

The last thing I needed to do was specify how many codegen units I wanted. Recently, Rust has been improving its compile times by generating multiple codegen units, allowing LLVM to process them in parallel. The performance impact is the opposite of LTO: keeping it switched on can make your program a little slower. But just like LTO, you can mitigate this at the expense of compilation time: add codegen-units = 1 to the release and bench profiles.


Opening a File and Getting Strings

This is how you should (probably) do it: BufRead is fast and easy to use.

fn file_to_lines<P>(filename: P) -> Vec<String>
where
P: AsRef<Path>,
{
let file = File::open(filename).expect("Couldn't open file");
let buf = BufReader::new(file);
buf.lines()
.map(|line| line.expect("Could not parse line"))
.collect()
}

I won’t spend too much time on this, but if you’re wondering what that AsRef<Path> thing is, this is a good explanation: it’s a convenient way of being able to pass any of several types to the function, any of which can be used to open the file they point to. The error-handling is intentionally unsophisticated, because it can be; if we can’t open the file or map its contents into Strings, we may as well give up.


Generating Patterns

The First Attempt

fn generate_pattern(hs: &str) -> Vec<u8> {
let mut stack = String::with_capacity(hs.len()).to_owned();
let mut pattern = Vec::with_capacity(hs.len());
for character in hs.chars() {
if let Some(needle) = stack.find(character) {
pattern.push(needle as u8)
} else {
stack.push_str(&character.to_string());
pattern.push((stack.len() - 1) as u8)
}
}
pattern
}

The function accepts a string slice, and I used a mutable String to keep track of characters I’d “seen”, storing the pattern in a Vec. I pre-allocated their lengths to ensure that they wouldn’t have to re-allocate, because that’s slow. Next, I looped through the input, Using find to check the stack for the character. find returns an Option containing the index (remember “if we could somehow map the first character to 0”), if it was found, or None. In that case, I pushed the new character onto the stack, and pushed its length-1 (i.e. the new character’s index position) onto the pattern. Pretty simple. Alas, the benchmark was the harbinger of bad news: 
1,288 ns/iter (+/- 990)
Assuming the measurement noise on my ancient laptop is constant, that’s almost 0.0013 ms for the string GRUNDRISSE. Give me strength.

The Second Attempt

Because the input was uppercase ASCII, I realised that I could use bytes, which can be translated into base-10 integers very quickly:

fn generate_pattern(haystack: &str) -> Vec<usize> {
let mut stack: Vec<&u8> = Vec::with_capacity(haystack.len());
let mut pattern = Vec::with_capacity(haystack.len());
for b in haystack.as_bytes() {
if let Some(n) = stack.iter().position(|&elem| elem == b) {
pattern.push(n)
} else {
stack.push(byte);
pattern.push(stack.len() - 1);
}
}
pattern
}

I was now using a Vec as my stack, and using the position method on an iterator over it to check whether I’d “seen” a byte, allowing me to avoid all the String overhead. What about the benchmark? 
130 ns/iter (+/- 52)
An order of magnitude speedup in what is probably the hottest code in the program. This was better. But the usize types continued to bother me. This is all ASCII, so I should be able to use u8 everywhere.

The Third Attempt

In despair, I turned to IRC. A couple of people had some interesting suggestions, and we eventually settled on:

fn generate_pattern(haystack: &str) -> Vec<u8> {
let mut total = 0u8;
let mut stack = [0u8; 128];
let mut pattern = Vec::with_capacity(haystack.len());
for &byte in haystack.as_bytes() {
if byte as usize > 127 {
println!("Got a non-uppercase ASCII character!");
exit(1)
}
let mut needle = stack[byte as usize];
if needle == 0 {
total += 1;
stack[byte as usize] = total;
needle = total;
}
pattern.push(needle - 1)
}
pattern
}

We started off with an array representing ASCII characters, all initialised to 0. If we saw a “new” byte, we bumped total by 1, and set that byte’s entry to total’s current value, before pushing it onto the pattern. Otherwise, it was an existing entry, and we simply pushed its value onto the pattern. But was it faster? 
54 ns/iter (+/- 47)

Good enough. If you really want to go down the rabbit-hole, this StackOverflow thread is probably a good place to start — a cursory glance looks like 54 ns is good performance for the string above.

A final note: by checking for byte values greater than 127, gracefully exiting if we encounter one, the function performs some rudimentary error-handling. A more sophisticated approach might use get_mut() instead of indexing into the array, as it would return None (meaning a byte outside the ASCII uppercase range was encountered), and since Option can trivially be mapped to Result you could be even more flexible about handling unexpected input.


Frequency Counting

Things became slightly more complicated at this point (but not that complicated, don’t worry):

pub fn count_frequency(patterns: &[Vec<u8>]) -> u32 {
let mut freq: HashMap<&[u8], u32> =
HashMap::with_capacity(patterns.len());
patterns
.iter()
.for_each(|pattern| *freq.entry(pattern).or_insert(0) += 1);
freq
.par_iter()
.filter(|&(_, &value)| value > 1)
.fold(|| 0, |accum, entry| accum + entry.1)
.sum()
}

The function accepts a slice of the patterns, in case I wanted to use them for something afterwards, and then instantiates a new HashMap which has the same capacity as the slice, to avoid re-allocating. Next, I iterated over the slice, adding each pattern to the HashMap using its Entry API. This is a fast, compact way of updating values: if a pattern (key) exists, bump its value by 1. Otherwise, insert it as a new key.

This is also one part of the program that couldn’t be trivially parallelised: because the iterator needed mutable access to every key (I didn’t know which one, if any, I’d need to update), it had to iterate sequentially — even if I hadn’t realised this, the compiler would have helped me out by refusing to mutably borrow freq in more than one place.

Once I’d built the HashMap (which is in fact a frequency table), I needed to filter, then aggregate the results:

  • filter its values, retaining only counts greater than 1
  • use a fold to accumulate the remaining values
  • sum the result of the fold, giving me the final count.

In theory, the final step shouldn’t have been necessary, because fold should accumulate the values into a single result, but Rayon’s fold is slightly different: it returns a Struct containing intermediate sums of the input sequence, which have been calculated in parallel. The number of these summed items and their sequence is non-deterministic, requiring us to specify a final sum(), in order to produce the count.

The benchmark showed ~15 ms. I had no idea whether that was slow, but I did know that Rust’s default SipHash algorithm isn’t the fastest, because it’s also intended to be robust against DoS attacks. In this case, that wasn’t a concern, so I swapped in the HashMap from the Fnv crate. The Fowler-Noll-Vo algorithm yields better hashing performance for small integer keys. And the benchmark?

10,001 ns/iter (+/- 500)

I was now ready to actually run the program.


Results

On my desktop 3.4 GHz Core i7, with a warm cache, it runs in 200 ms. Is that fast? I…don’t really know. It certainly feels fast. That’s actually all I’m interested in.


Complexity

I was reasonably sure that the program as a whole ran in linear time: building the initial String Vec, followed by one pass over each String, a handful of hopefully constant-time Vec-insertion and HashMap operations, and a final linear-time pass to aggregate the result. Still, why not verify? Oh, but I have no intention of embarrassing myself and you by attempting a big-O proof of my program — that would be ridiculous. Instead, I sliced up the input into files increasing by 5k strings each time, then ran the program on each one, timing it using Hyperfine. Finally, I opened a Jupyter notebook, pulled the results into a Pandas DataFrame, fitted a line using Statsmodels, and graphed the results using Matplotlib:

This image is huge

While I was using Python, I took the opportunity to write my comparison program:

#!/usr/bin/env python
# coding: utf-8
from sys import exit
from collections import Counter

def generate_patterns(haystack):
""" Generate tuples of integers from ASCII uppercase strings """
total = 0
# we begin having seen no bytes
stack = [0] * 128
pattern = []
for char in haystack:
byte = ord(char)
if byte > 127:
print("Found a non-uppercase ASCII character!")
exit(1)
else:
needle = stack[byte]
if needle == 0:
total += 1
stack[byte] = total
needle = total
pattern.append(needle - 1)
# we need tuples because lists aren't hashable
return tuple(pattern)
if __name__ == "__main__":
with open("words.txt", 'r') as f:
cts = Counter((generate_patterns(line) for line in f))
friendly = sum(
{ptn: ct for ptn, ct in cts.items() if ct > 1}.values()
)
print("Number of friendly strings: %s" % friendly)

Python has several features that make the program trivial to write:

  • A context manager closes the file when we finish reading from it
  • We can iterate over one line at a time, generating its pattern
  • Generators mean we don’t have to worry about intermediate allocations
  • The built-in Collections library makes frequency-counting easy
  • Dict comprehensions make filtering on values easy.

I ended up with 26 LoC, and a wall-clock time of around 7 seconds to process 500k strings. Quite compact (Rust is around 59 LoC), but nowhere near as fast (Rust is around 33x faster). Of course, there’s lots of low-hanging fruit here, and I didn’t even look at NumPy, so the speed comparison isn’t intended to be meaningful, but I was pleasantly surprised by the length and conciseness of my Rust program.