Rust function as slow as its python counterpart

Question

I am trying to speed up Python programs using Rust, a language in which I am a total beginner. I wrote a function that counts the occurrences of each possible string of length n within a larger string. For instance, if the main string is "AAAAT" and n=3, the outcome would be a hashmap {"AAA":2,"AAT":1}. I use pyo3 to call the Rust function from Python. The code of the Rust function is:

fn count_nmers(seq: &str, n: usize) -> PyResult<HashMap<&str,u64>> {
    let mut current_pos: usize = 0;
    let mut counts: HashMap<&str,u64> = HashMap::new();
    while current_pos+n <= seq.len() {
        //print!("{}n", &seq[current_pos..current_pos+n]);
        match counts.get(&seq[current_pos..current_pos+n]) {
            Some(repeats) => counts.insert(&seq[current_pos..current_pos+n],repeats+1),
            None => counts.insert(&seq[current_pos..current_pos+n],1)
        };
        current_pos +=1;
    }
    //print!("{:?}",counts)
    Ok(counts)
}

When I use small values for n (n<10), Rust is about an order of magnitude faster than Python, but as the length of n increases, the gap tends to zero with both functions having the same speed by n=200. (see graph)
Times to count for different n-mer lengths (Python black, rust red)

I must be doing something wrong with the strings, but I can’t find the mistake.

The python code is:

def nmer_freq_table(sequence,nmer_length=6):
    nmer_dict=dict()
    for nmer in seq_win(sequence,window_size=nmer_length):
        if str(nmer) in nmer_dict.keys():
            nmer_dict[str(nmer)]=nmer_dict[str(nmer)]+1
        else:
            nmer_dict[str(nmer)]=1
    return nmer_dict

def seq_win(seq,window_size=2):
    length=len(seq)
    i=0
    while i+window_size <= length:
        yield seq[i:i+window_size]
        i+=1

Asked By: Alberto Marin Sanguino

||

Source

Answer 1

You are computing hash function multiple times, this may matter for large n values. Try using entry function instead of manual inserts:

while current_pos+n <= seq.len() {
    let en = counts.entry(&seq[current_pos..current_pos+n]).or_default();
    *en += 1;
    current_pos +=1;
}

Complete code here

Next, make sure you are running --release compiled code like cargo run --release.

And one more thing to take in mind is discussed here, Rust may use non-optimal hash function for your case which you can change.

And finally, on large data, most of time is spent in HashMap/dict internals which are not a python, but compiled code. So don’t expect it to scale well.

Answered By: Evgeniy

Answer 2

Could it be because as n gets larger the number of iterations through the loop gets smaller?

Fewer iterations through the loop would reduce the performance gain seen by using Rust. I’m sure there is a small per function call performance cost for transition/marshaling to Rust from Python. This would explain how eventually the performance from pure Python and Python/Rust becomes the same.

Answered By: SargeATM

Rust function as slow as its python counterpart

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