Clojure Performance For Expensive Algorithms

Question

I have implemented an algorithm to calculate the longest contiguous common subsequence (not to be confused with longest common subsequence, though not important for this questions). I need to squeeze maximum performance from this because I'll be calling it a lot. I have implemented the same algorithm in Clojure and Java in order to compare performance. The Java version runs significantly faster. My question is whether there is anything I can do to the Clojure version to speed it up to the level of Java.

Here's the Java code:

public static int lcs(String[] a1, String[] a2) {
    if (a1 == null || a2 == null) {
        return 0;
    }

    int matchLen = 0;
    int maxLen = 0;

    int a1Len = a1.length;
    int a2Len = a2.length;
    int[] prev = new int[a2Len + 1]; // holds data from previous iteration of inner for loop
    int[] curr = new int[a2Len + 1]; // used for the 'current' iteration of inner for loop

    for (int i = 0; i < a1Len; ++i) {
        for (int j = 0; j < a2Len; ++j) {
            if (a1[i].equals(a2[j])) {
                matchLen = prev[j] + 1; // curr and prev are padded by 1 to allow for this assignment when j=0
            }
            else {
                matchLen = 0;
            }
            curr[j+1] = matchLen;

            if (matchLen > maxLen) {
                maxLen = matchLen;
            }
        }

        int[] swap = prev;
        prev = curr;
        curr = swap;
    }

    return maxLen;
}

Here is the Clojure version of the same:

(defn lcs
  [#^"[Ljava.lang.String;" a1 #^"[Ljava.lang.String;" a2]
  (let [a1-len (alength a1)
        a2-len (alength a2)
        prev (int-array (inc a2-len))
        curr (int-array (inc a2-len))]
    (loop [i 0 max-len 0 prev prev curr curr]
      (if (< i a1-len)
        (recur (inc i)
               (loop [j 0 max-len max-len]
                 (if (< j a2-len)
                   (if (= (aget a1 i) (aget a2 j))
                     (let [match-len (inc (aget prev j))]
                       (do
                         (aset-int curr (inc j) match-len)
                         (recur (inc j) (max max-len match-len))))
                     (do
                       (aset-int curr (inc j) 0)
                       (recur (inc j) max-len)))
                   max-len))
               curr
               prev)
        max-len))))

Now let's test these on my machine:

(def pool "ABC")
(defn get-random-id [n] (apply str (repeatedly n #(rand-nth pool))))
(def a1 (into-array (take 10000 (repeatedly #(get-random-id 5)))))
(def a2 (into-array (take 10000 (repeatedly #(get-random-id 5)))))

Java:

(time (Ratcliff/lcs a1 a2))
"Elapsed time: 1521.455 msecs"

Clojure:

(time (lcs a1 a2))
"Elapsed time: 19863.633 msecs"

Clojure is quick but still an order of magnitude slower than Java. Is there anything I can do to close this gap? Or have I maxed it out and one order of magnitude is the "minimal Clojure overhead."

As you can see I am already using the "low level" construct of loop, I am using native Java arrays and I have type-hinted the parameters to avoid reflection.

There some algorithm optimizations possible, but I don't want to go there right now. I am curious how close to Java performance I can get. If I can't close the gap I'll just go with the Java code. The rest of this project is in Clojure, but perhaps sometimes dropping down to Java for performance is necessary.

Answer 1

EDIT: Added a faster uglier version below the first one.

Here is my take:

(defn my-lcs [^objects a1 ^objects a2]
  (first
    (let [n (inc (alength a1))]
      (areduce a1 i 
        [max-len ^ints prev ^ints curr] [0 (int-array n) (int-array n)]
        [(areduce a2 j max-len (unchecked-long max-len)
           (let [match-len 
                 (if (.equals (aget a1 i) (aget a2 j))
                   (unchecked-inc (aget prev j))
                   0)]
             (aset curr (unchecked-inc j) match-len)
             (if (> match-len max-len)
               match-len
               max-len)))
         curr prev]))))

Main differences with yours: a[gs]et vs a[gs]et-int, use of unchecked- ops (implicitly through areduce), use of a vector as the return value (and "swap" mechanism) and max-len is coerced to primitive before the inner loop (primitive-valued loops are problematic, slightly less since 1.5RC2 but the support isn't perfect yet, however *warn-on-reflection* is not silent).

And I switched to .equals instead of = to avoid the logic in Clojure's equiv.

EDIT: let's get ugly and restore the arrays swap trick:

(deftype F [^:unsynchronized-mutable ^ints curr
            ^:unsynchronized-mutable ^ints prev]
  clojure.lang.IFn
  (invoke [_ a1 a2]
    (let [^objects a1 a1
          ^objects a2 a2]
      (areduce a1 i max-len 0
        (let [m (areduce a2 j max-len (unchecked-long max-len)
                  (let [match-len 
                        (if (.equals (aget a1 i) (aget a2 j))
                          (unchecked-inc (aget prev j))
                          0)]
                    (aset curr (unchecked-inc j) (unchecked-int match-len))
                    (if (> match-len max-len)
                      match-len
                      max-len)))
              bak curr]
          (set! curr prev)
          (set! prev bak)
          m)))))

(defn my-lcs2 [^objects a1 a2]
  (let [n (inc (alength a1))
        f (F. (int-array n) (int-array n))]
    (f a1 a2)))

On my box, it's 30% faster.

Answer 2

Here are a couple improvements:

1. No advantage to fancy type hinting, just use ^objects
2. aset-int is deprecated I believe -- just plain old aget is faster, by about 3x overall it seems

Beyond that (and the long type hint on the recur mentioned above), I don't see any obvious ways to improve further.

(defn lcs
  [^objects a1 ^objects a2]
  (let [a1-len (alength a1)
        a2-len (alength a2)
        prev (int-array (inc a2-len))
        curr (int-array (inc a2-len))]
    (loop [i 0 max-len 0 prev prev curr curr]
      (if (< i a1-len)
        (recur (inc i)
               (long (loop [j 0 max-len max-len]
                 (if (< j a2-len)
                   (if (= (aget a1 i) (aget a2 j))
                     (let [match-len (inc (aget prev j))]
                       (do
                         (aset curr (inc j) match-len)
                         (recur (inc j) (max max-len match-len))))
                     (do
                       (aset curr (inc j) 0)
                       (recur (inc j) max-len)))
                   max-len)))
               curr
               prev)
        max-len))))
#'user/lcs
user> (time (lcs a1 a2))
"Elapsed time: 3862.211 msecs"