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hiphip (array)! simple, performant array manipulation in Clojure
Clojure Java
branch: master

README.md

hiphip (array)! Build Status

hiphip is an array library for Clojure, which provides elegant methods for fast math with primitive arrays.

Leiningen dependency (Clojars): [prismatic/hiphip "0.2.0"]

This is an alpha release. The API and organizational structure are subject to change. Comments and contributions are much appreciated.

Why?

This is what we want, but it's dog slow.

;; 1ms for 10000 doubles
(defn dot-product [^doubles ws ^doubles xs]
  (reduce + (map * ws xs))

This is fast, but not very declarative.

;; 8.5 us
(defn dot-product [^doubles ws ^doubles xs]
  (areduce xs i ret 0.0
    (+ ret (* (aget xs i)
              (aget ws i))))

Why not have both?

;; 8.5 us
(defn dot-product [ws xs] (hiphip.double/asum [x xs w ws] (* x w)))

About

HipHip provides functions and macros that require little or no manual type hinting, with binding semantics similar to those of for. The bindings are explained below, and in hiphip.array.

The library currently provides a suite of operations for fast math on arrays of floats, doubles, ints, and longs, in hiphip.double and so on, as well as simple simple macros for constructing and iterating over arbitrary array types in hiphip.array. Please see DEVELOPERS.md for more information.

Tour de force

Usually numerical code in Clojure is either elegant or fast. Why not both? Suppose you want do calculate the joint probability of an array of probabilities. You write this one-liner:

(dbl/aproduct xs)

But times, they are a-changing. You now wish to weight the probabilities in xs (with weights contained in ys) as well. The result should be normalized, so that the sum of the probabilities equals one. The array is quite large, so you decide to do everything in-place.

(defn normalize! [xs]
  (let [sum (dbl/asum xs)]
    (dbl/afill! [x xs] (/ x sum))))

(defn weight-and-normalize! [xs ys]
  (dbl/afill! [x xs y ys] (* x y))
  (normalize! xs))

Next, your boss tells you to write a function for finding the frequencies of the different probabilities in xs. It's used in some important services, and therefore needs to be fast. Simply use areduce and transients.

(defn afrequencies [xs]
  (persistent!
    (dbl/areduce [x xs] ret (transient {})
      (assoc! ret x (inc (get ret x 0))))))

At the end of the day, there's still a bit of work to do. You realise it'd be darn nice have a function that calculates the standard deviation. You also decide to add some other common utilities.

(defn std-dev [xs]
  (let [mean (dbl/amean xs)
        square-diff-sum (dbl/asum [x xs] (Math/pow (- x mean) 2))]
    (/ square-diff-sum (dbl/alength xs))))

(defn covariance [xs ys]
  (let [ys-mean (dbl/amean ys)
        xs-mean (dbl/amean xs)
        diff-sum (dbl/asum [x xs y ys] (* (- x xs-mean) (- y ys-mean)))]
    (/ diff-sum (dec (dbl/alength xs)))))

(defn correlation [xs ys std-dev1 std-dev2]
  (/ (covariance xs ys) (* std-dev1 std-dev2)))

Why not add quantiles while you're at it?

(defn quantile* 
  "Given a sorted array, returns an element s. t. phi percent of the
  elements are less than this element"
  [xs phi]
  (let [cutoff (int (* (dbl/alength xs) phi))]
    (dbl/aget xs cutoff)))

(defn quantile 
  "Like quantile*, but doesn't require a sorted array."
  [xs phi]
  (let [copy (dbl/aclone xs)]
    (quantile* (dbl/asort! copy) phi)))

A simple and fast data analysis engine. Done.

API overview

HipHip provides typed namespaces (e.g. hiphip.double or hiphip.long) for each supported array type. These namespaces provide:

  • A family of macros for efficiently iterating over array(s) with a common binding syntax, including doarr, afill! (in-place), and our own versions of amap and areduce.

  • Drop-in, pre-hinted versions of most of Clojure's existing utilities for dealing with arrays, e.g. alength and aset. Also new utilities like ainc and amake.

  • Common math operations like amean and dot-product. Also asum and aproduct, which support iterating with bindings as well.

  • Sorting (in-place) and max/min functions (written in Java for pure speed) like amax and apartition!, with additional varities that work on or return arrays of indices.

For general looping needs, the library provides hiphip.array. The API is more limited, but allows you to efficiently loop through arrays of different types, provided they are type-hinted properly. For example:

(defn fill-string-pointwise-product
  [^{:tag "[Ljava.lang.String;"} os ^doubles xs ^longs ys]
  (hiphip.array/afill! String [_ os x xs y ys] (str (* x y))))

Bindings

The looping macros use bindings to efficiently iterate through one or several arrays. They look like this:

(dbl/amap
  [[i x] xs]
  <expression involving i, x>)

This binds i to the current index and x to the ith element of xs. The index-variable is optional, but there must be at least one array binding. You can have as many array bindings as you want. For example:

(dbl/amap
  [x xs
   y ys 
   z zs...]
  <expression involving x, y>)

Iteration is parallel and not nested, unlike for and doseq. Therefore, in

(dbl/amap
  [[i1 x] xs
   [i2 y] ys
   [i3 z] zs ...]
  <expression involving i1, x, i2, y, i3, z>)

the index-variables i1, i2, and i3 will have the same value.

Ranges

You can specify a range for the operations. The default range is from 0 to the length of the first array.

(dbl/afill!
  [[i x] xs
   :range [0 10]]
  i)

Let

The bindings also support let, which works like a regular let in the inner loop. In the typed namespaces, it casts to the array type (for speedy math), e.g.

(dbl/afill!
  [x xs
  :let [alpha 5 delta (- x 9)]]
  (* x alpha delta)) 

Be aware that :let explicitly disallows shadowing the array bindings, e.g. (afill! [myvar xs :let [myvar 5]] myvar) throws an IllegalArgumentException. This is to avoid unhappy accidents. Do also note that destructuring syntax is not supported.

Running the tests

You can run various portions of the test suite using leiningen test selectors.

  • lein test :fast runs just the correctness tests, and should be fast.

  • lein test :gen-test runs generative tests, which are also fast but print a lot.

  • lein test :bench runs the benchmarks, which are very slow, and also a bit flaky currently (due to jitter in timing runs). You can look in test/hiphip/array_test.clj for the generic array tests/benchmarks, and test/hiphip/type_impl_test.clj for the type-specific benchmarks, which include current expected performance numbers vs. Java for a number of common operations (plus ~10% to minimize flakiness). Some things are much slower than we would like currently, but most operations on double arrays are within 0-50% of Java speed.

Known issues

There are still a few performance issues we're working on. For instance, math on index variables and doubles is several times slower than Java:

(hiphip/afill! [[i x] xs] (* x i))

Some operations on non-double primitive arrays are also slower (up to about three times as slow as Java) -- check out the benchmark suite in test/hiphip/type_impl_test.clj for the most up-to-date results. We welcome contributions of performance improvements, or just benchmarks where HipHip is slow, so we can all work together towards making it easy to write maximally performant math in Clojure.

Performance: know your options

Achieving maximal performance for some HipHip operations required a lot of fiddling, and some of the most important things we found involved options to Clojure and the the JVM.

  • Leiningen is a great build tool. To help speed up slow start-up times (a major concern of users), its developers chose to inject options that disable some advanced optimizations into your project's JVM (thanks to Stuart Sierra and others on the Clojure mailing list for pointing this out). If you want your array code to go fast under Leiningen, you probably want to add the following to your project.clj:
;; Clear Leiningen's default jvm-opts.
:jvm-opts ^:replace [] 
  • Clojure provides an *unchecked-math* compiler option to speed up primitive math by omitting overflow checks. We've found mixed results with this option -- it almost always helps, but in some cases (especially with double array operations) it actually hurts performance.

Documentation

Supported Clojure versions

HipHip is currently supported on Clojure 1.5.x and 1.6.x.

Contributors

HipHip is the result of a collaboration between Prismatic, Emil Flakk, and Leon Barrett at Climate Corp.

License

Copyright (C) 2013 Emil Flakk, Leon Barrett, and Prismatic. Distributed under the Eclipse Public License, the same as Clojure.

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