Posts Tagged: algorithms


31
Oct 11

Distributed locking made easy

There are various situations when one would use a simple mutex to ensure mutual exclusion to a shared resource. This is usually very simple to accomplish using your favorite language library, but that constrains you to a single process mutual exclusion. Even single machine mutual exclusion is rather straight forward, usually just locking a resource (i.e. file) and awaiting for the lock to be released. You can use that for an IPC mutex.

But what if one needs a distributed mutex to allow mutual exclusion amongst distributed clients? At that, the mutex has to offer various guarantees, as is with any shared state. We know shared state is hard to reason about and provokes a lot of bug-prone software, shared distributed state, is much harder, requiring distributed guaranteed consensus all while operating in a non-reliable network environment. There are various distributed consensus algorithms, Paxos being one of the more widely used ones.

But you can deploy your own distributed locking service, without having to implement your own. Apache Zookeeper, offers distributed synchronization and group services. Mutex/locking is just one of the things you can do with Zookeeper. Zookeeper is rather low level, so implementing a distributed lock, although trivial, requires some boilerplate.

Recently we needed a distributed lock service, to ensure only one person in our organization is performing a particular systems activity at any given point and time. We implemented it on top of a homegrown tool written in ruby. The example below is in ruby, though the api calls would translate to any language…

require 'zookeeper'

class Lock
  def initialize(host, root="/my-app")
    @zk = Zookeeper.new(host)
    @root = root
  end
  
  def with_lock(app, timeout, timeout_callback, &block)
    new_lock_res = @zk.create(:path => "#{@root}/#{app}-", :sequence => true, :ephemeral => true)
    unique_lock_path = new_lock_res[:path]
    if get_lock(unique_lock_path, timeout)
      yield
      @zk.delete(:path => unique_lock_path)
    else
      timeout_callback.call
    end
  end

  private
  def get_lock(unique_lock_path, timeout)
    lock_key = unique_lock_path.gsub(/^#{Regexp.quote(@root)}\//, '')

    (0..4).each do
      children = @zk.get_children(:path => @root)[:children].sort
      watcher = Zookeeper::WatcherCallback.new {}
      if (children.first == lock_key)
        return true
      else
        less_than_path_idx = (children.index {|p| p == lock_key}) - 1
        stat_res = @zk.stat(:path => "#{@root}/#{children[less_than_path_idx]}",
                           :watcher => watcher)
        if stat_res[:stat].exists
          success = wait_until(timeout) { watcher.completed? }
          if !success
            return false
          end
        end
      end
    end
    return false
  end

  def wait_until(timeout=10, &block)
    time_to_stop = Time.now + timeout
    until yield do
      if Time.now > time_to_stop
        return false
      end
      sleep 0.1
    end
    return true
  end
end

The usage of this Lock class is such:

    Lock.new("localhost:2181").with_lock(
      "/myapp",
      5, ## Timeout in seconds
      lambda { ## Timeout callback
        abort("Couldn't acquire lock.  Timeout.") },
      lambda { ## Do what ever you want here  }
    )

The details of the algorithm are outlined here.

Of course, before you use it, you must install Zookeeper and create the root path /myapp in order to be able to use it.

Also, please note, I have removed the access control part from the example. In order to use this in production, I strongly encourage you read this.


10
Feb 11

Merge sort in lisp

I’m currently taking (online) MIT’s algorithms course. I needed a good brush-up on algorithms, starting with the basic theory. I’m going to jump in to help a buddy working on a graph database in lisp Vivace Graph, which should be an open source competitor to AllegroGraph. Allegro has probably the best graph db out there right now. There are some competitors in the java world, but they are either expensive or don’t provide enough features, or don’t provide APIs outside of java. Allegro has an extensive list of client libs. I’ll write up more on the graph db in some future, for now, I got back into lisp and implemented the simplest alg (merge sort) in it.

The reason I’m posting is to get some comments. I’d love to hear your thoughts on how a lisp nOOb can improve this :-)

(defun merge-sort (lst)
  (let ((size (length lst)))
    (if (= size 1)
        lst
        (progn
          (let ((seq1 (merge-sort (subseq lst 0 (floor (/ size 2)))))
                (seq2 (merge-sort (subseq lst (floor (/ size 2)) size))))
            (merge-it seq1 seq2))))))


(defun merge-it (l1 l2)
  (let ((new-arr (make-array (+ (length l1)
                                (length l2))
                             :fill-pointer 0)))
    (loop for idx from 0 to (+ (length l1) (length l2)) do
         (let ((x (car l1))
               (y (car l2)))
           (when (and (not (null x)) (not (null y)))
             (if (<= x y)
                 (progn
                   (setf l1 (cdr l1))
                   (vector-push x new-arr))
                 (progn
                   (setf l2 (cdr l2))
                   (vector-push y new-arr))))))
    (mapcar #'(lambda (e) (vector-push e new-arr)) (append l1 l2))
    (coerce new-arr 'list)))


21
Jun 10

Lazy cheap flight calculations with priority queues

There is an interesting problem of utilizing priority queues to figure out the best price combination in a set of flight legs. The problem is as follows:

We need to calculate the cheapest combination of flight legs (connections) for a flight to a particular destination. We’re given a price ordered N set of flight legs and we need to find the winning combination. Each combination would be evaluate for eligibility and would either pass or fail, so the cheapest combination doesn’t necessarily reflect the cheapest possibly combination of prices from the legs. A black box predicate function is consulted to ensure the combination is eligible. This reflects various airline rules, like overlapping times, specials that are only available to certain people, routes, or connections.

Solution: A naive approach for say a two leg flight is to say construct a (n x m) ordered matrix and evaluate each priced ordered combination through the black box predicate routing until one passes. The problem with this approach is that we unendingly construct a full matrix when in many cases one of the first combinations is enough to present the cheapest “valid” price. The key to reducing this is to construct a lazy data structure which will prioritize the cheapest flights and can then be iterated to find one that’s valid. We do so at runtime while constructing matrix combinations. The solutions is generalized, so the same can be used for n leg flights.

The algorithm goes something like this…

Construct the first set of combinations which can reflect the cheapest flight. The first cheapest combinations is always n1 + m1. If that doesn’t pass, the next possible set of cheapest combinations is either n2 + m1 or n1 + m2. We then continue to n1 + ma and na + m1, where a is incremented until the end of the route leg set for either leg.

The worst case running time is quadratic O(n2), but because of the lazy data structure, the algorithm runs in rather constant time, depending on how lucky we are that the first few combinations will yield a “rule valid” price combination.

This problem idea came from reading The Algorithm Design Manual by Steven S. Skiena. I recommend this book for anyone wishing to delve into the world of more advanced algorithm design.

Here is the solution in python. You’ve probably noticed I’ve been using a lot of python. Besides the fact that I like the language, python is an incredibly good language for conveying algorithmic ideas in a concise but very readable way.

The only two functions that matter, are cheapest_price and _pick_combo, the rest are just auxiliary functions used to support an OO structure and running a sample.

  import heapq, random, time

  class Route(object):
      """docstring for TicketFinder"""
      def __init__(self):
          self.heap = []
          self.unique = dict()
          self.legs = []
          self.max_leg_len = 0
          self._counter = 0
          self._loop_counter = 0

      def add_leg(self, leg):
          leg.sort()
          self.legs.append(leg)
          leg_len = len(leg)
          if leg_len > self.max_leg_len:
              self.max_leg_len = leg_len

      def cheapest_price(self, pred_func=lambda x: True):
          for i in range(0, self.max_leg_len):
              combo = self._pick_combo(i, pred_func)
              if combo: return combo

      def print_stats(self):
          print("""Legs: %s
  Combos examined: %s
  Loops: %s
  """ % (len(self.legs), self._counter, self._loop_counter))

      def _pick_combo(self, curr_idx, pred_func):
          num_legs = len(self.legs)
          price_combo = [ leg[curr_idx] for leg in self.legs if not curr_idx >= len(leg) ]
          self._add_combo(price_combo)
          cheapest_price = self._eval_price_combo(pred_func)
          if cheapest_price: return cheapest_price
          for idx in range(1, self.max_leg_len-curr_idx):
              for j in range(0, num_legs):
                  if len(self.legs[j]) &lt= (curr_idx+idx): continue
                  combo = []
                  for k in range(0, num_legs):
                      self._loop_counter += 1
                      if j == k:
                          combo.append(self.legs[k][curr_idx+idx])
                      elif curr_idx &lt len(self.legs[k]):
                          combo.append(self.legs[k][curr_idx])
                  self._add_combo(combo)

              cheapest_price = self._eval_price_combo(pred_func)
              if cheapest_price: return cheapest_price

      def _add_combo(self, combo):
          self._counter += 1
          if len(combo) == len(self.legs) and not self.unique.has_key(str(combo)):
              heapq.heappush(self.heap, combo)
              self.unique[str(combo)] = True

      def _eval_price_combo(self, pred_func):
          for i in range(0, len(self.heap)):
              least_combo = heapq.heappop(self.heap)
              if pred_func(least_combo):
                  print("Winning combo: %s" % [ "%.2f" % l for l in least_combo ])
                  return sum(least_combo)
          return None


  ############### Samples below ##################

  def sample_run(num_legs, pred_func):
      print(("#" * 30) + " Sample Run " + ("#" * 30))
      route = Route()
      for i in range(0, num_legs):
          route.add_leg( [ random.uniform(100, 500) for i in range(0, 100) ] )

      start = time.clock()
      price = route.cheapest_price(pred_func)
      calc_time = time.clock() - start

      if price:
          print("Cheapest price: %.2f" % price)
      else:
          print("No valid route found")
      route.print_stats()
      print(("#" * 72) + "\n")

  if __name__ == '__main__':
      sample_run(2, lambda x: True)
      def pred(x):
          for price in x:
              if price &lt 150: return False
          return True
      sample_run(3, pred)

I haven’t thoroughly tested this for correctness besides numerous runs and some basic validation so let me know if you see anything apparently wrong here.

Running the above yields

    ############################## Sample Run ##############################
    Winning combo: ['103.62', '106.40']
    Cheapest price: 210.03
    Legs: 2
    Combos examined: 1
    Loops: 0

    ########################################################################

    ############################## Sample Run ##############################
    Winning combo: ['150.74', '150.25', '173.95']
    Cheapest price: 474.95
    Legs: 3
    Combos examined: 2852
    Loops: 8523

    ########################################################################

For the first sample run, we use a predicate function which yields True, so we never examine anything other than the first combo n1 + m1. For the second sample, I add a predicate function which only accepts any price combination where all legs are above $150. (Of course this is not anything resembling airline rules, just good enough to simulate some sample cases, where the first n combinations are rejected). In the second sample run, we utilized 3 legs and examined 2852 combinations before coming up with the winning leg combination for the route. Each price within the combination is the smallest possible price above $150 for each leg.


27
May 10

Random points in polygon generation algorithm

I needed to generate a set of random points within a polygon, including convex and concave. The need arouse in a geospatial domain where polygons are rather small (on a geo-scale) and wouldn’t span more than say 10 miles, though the benefit of employing more complex algorithms to deal with spheroid properties are negligible. Plane geometry provided enough to meet this requirement. Point-in-Polygon tests are rather simple and are used to test whether a point exists in a polygon. The test is performed using a Ray casting algorithm which test the intersections of a ray across the x-axis starting from the point in question.

Another concept is the Minimum Bounding Rectangle (Bounding Box), which is the minimal rectangle needed to enclose a geographical object (i.e. polygon).

So, one can generate random points within a polygon by…

  1. Generating a bounding box
  2. Generating a point within the bounding box. This is a simple algorithm.
  3. Using Point-in-Polygon to test whether this point exists within the polygon.

Because of the random sampling nature and false positives from step 2, which must be tested in step 3, the above must be performed in a loop until the Point-in-Polygon test passes.

This works quite well for generating test data, as there are no tight bounds on the performance characteristics of random generation. One could also use the above algorithm in production as long as the ration of polygon to bounding box is rather large, which is usually the case for convex polygons. The ratio might be too small convex polygons, though causing a more than acceptable number of false positives in step #2.

I’ve implemented this in the geo-utils python package and made available on github. Feel free to use and provide any feedback.

To utilize the geo-utils to generate random points within a polygon, you would do the following:

  from vtown import geo
  from vtown.geo.polygon import Polygon


  polygon = Polygon(  geo.LatLon(42.39321,-82.92114),
                      geo.LatLon(42.39194,-82.91669),
                      geo.LatLon(42.39147,-82.91796),
                      geo.LatLon(42.39090,-82.91974),
                      geo.LatLon(42.39321,-82.92114))

  point = polygon.random_point()

The above polygon is generated using lat/lon coordinates, but you can generate them using simple x/y coordinates with geo.Point(x,y)

Here are some code snippets from the implementation. I only pasted the relevant parts. For boilerplate and relevant data structures, see the geo-utils package.

class BoundingBox(object):

    def __init__(self, *points):
        """docstring for __init__"""
        xmin = ymin = float('inf')
        xmax = ymax = float('-inf')
        for p in points:
            if p.x &lt; xmin: xmin = p.x
            if p.y &lt; ymin: ymin = p.y
            if p.x > xmax: xmax = p.x
            if p.y > ymax: ymax = p.y
        self.interval_x = Interval(xmin, xmax)
        self.interval_y = Interval(ymin, ymax)

    def random_point(self):
        x = self.interval_x.random_point()
        y = self.interval_y.random_point()
        return Point(x, y)

class Polygon:
  ## __init__ omitted here...

  def contains(self, point):
        seg_counter = private.SegmentCounter(point)
        for i in range(1, len(self.points)):
            line = Line(*self.points[i-1:i+1])
            if seg_counter.process_segment(line):
                return True
        return seg_counter.crossings % 2 == 1

  def random_point(self):
        bb = BoundingBox(*self.points)
        while True:
            print("GENERATING RANDOM POINT...")
            p = bb.random_point()
            if self.contains(p):
                return p

class SegmentCounter(object):

    def __init__(self, point):
        self.point = point
        self.crossings = 0

    def process_segment(self, line):
        p, p1, p2 = self.point, line.point1, line.point2
        if p1.x &lt; p.x and p2.x &lt; p.x:
            return False

        if (p.x == p2.x and p.y == p2.y):
            return True

        if p1.y == p.y and p2.y == p.y:
            minx = p1.x
            maxx = p2.x
            if minx > maxx:
                minx = p2.x
                maxx = p1.x
            if p.x >= minx and p.x &lt;= maxx:
                return True
            return False


        if ((p1.y > p.y) and (p2.y &lt;= p.y)) \
                or ((p2.y > p.y) and (p1.y &lt;= p.y)):
            x1 = p1.x - p.x
            y1 = p1.y - p.y
            x2 = p2.x - p.x
            y2 = p2.y - p.y

            det = numpy.linalg.det([[x1, y1], [x2, y2]])
            if det == 0.0:
                return True
            if y2 &lt; y1:
                det = -det

            if det > 0.0:
                self.crossings += 1

17
May 10

Divide and conquer for exponentiation

Here is an awesome way to demonstrate divide and conquer algorithm performing exponentiation. Naive exponentiation algorithms xn would perform n-1 multiplications as n x n … x n-1. This has an algorithmic complexity of O(n) which of course scales poorly for any significantly large number. This is not even including the overhead of performing integer multiplication beyond CPUs capacity is slower than staying within the CPU integer range. Now, do that n times and you have a problem.

Logarithmic performance O(log n) is one of the best common algorithmic complexities there is (outside of constant complexity of course, which is rare). One can achieve calculating power by utilizing the power of logarithms, which are clearly apparent in divide and conquer problem solutions.

Logarithms grow very slow compared to number of inputs, though for a calculating a power of say n1000000, with the naive algorithm, you’d have to perform 999,999 multiplications. With a logarithmic complexity algorithm this drops to log21000000 = ceil(19.93) = 20 steps. 20 steps with a few extra operations for step compared to 1million multiplications.

Here is an example of both exponentiation algorithms, the logarithmic complexity and linear complexity (called naive), as well as built in python pow() function. Both our logarithmic power function and python’s built in one perform the same, where the naive linear function starts to truly deteriorate once any reasonable number is used as the exponent.

_Note: this function is recursive though you can run out of stack space for very large exponents (you can also easily reimplement it as recursion). On a system with a 1024 stack limit, this would mean your exponent would have to be above 21024 or

17976931348623159077293051907890247336179769789423065727343008 11577326758055009631327084773224075360211201138798713933576587 89768814416622492847430639474124377767893424865485276302219601 24609411945308295208500576883815068234246288147391311054082723 7163350510684586298239947245938479716304835356329624224137216

before you run out of stack space._

Here is a benchmarked python implementation. The relevant algorithm part is highlighted.

#!/usr/bin/env python
import math
import time
import sys

def power(b, e):
    """logarithmic divide/conquer algorithm"""
    if e == 0: return 1
    x = power(b, math.floor(e/2))
    if e % 2 == 0: return pow(x, 2)
    else: return b * pow(x, 2)

def naive_power(b, e):
    """linear power algorithm"""
    x = b;
    for i in range(1, e):
        x *= b
    return x

def perform(name, base, exp, pfunc):
    print("%s: %d^%d: %d" % (name, base, exp, pfunc(base, exp)))

if __name__ == '__main__':
    if len(sys.argv) != 3:
        sys.exit("You must provide a base and an exponent.  (Usage: exp.py base exp)")
    base = int(sys.argv[1])
    exp = int(sys.argv[2])
    for func in (power, naive_power, pow):
        print("Benchmarking %s..." % func.__name__)
        bench = []
        for i in range(0,5):
            start = time.time()
            ans = func(base, exp)
            end = time.time()
            bench.append(end-start)
        print("\tCalculated in: %s" % min(bench))
]]>

Running above to calculate 2200000

$ python exp.py 2 200000
Benchmarking power…
    Calculated in: 0.0042099952697753906
Benchmarking naive_power…
    Calculated in: 6.078423023223877
Benchmarking pow…
    Calculated in: 0.0041148662567138672

Hmmm, both pow() (python’s built in power) and power() (logarithmic complexity) calculated the power in 4 millis (above is in seconds) and our naive_power() function calculates the same result in 6 seconds.

I tried running the script to calculate 21000000, which calculated using logarithmic functions in 25 milliseconds and I killed the naive_power() calculation after a few minutes of impatiently waiting for it to complete.

Power to the logarithms!!! :-)