diff --git a/.rat-excludes b/.rat-excludes index eaefef1b0aa2e..fb6323daf9211 100644 --- a/.rat-excludes +++ b/.rat-excludes @@ -31,6 +31,7 @@ sorttable.js .*data .*log cloudpickle.py +heapq3.py join.py SparkExprTyper.scala SparkILoop.scala diff --git a/python/pyspark/heapq3.py b/python/pyspark/heapq3.py new file mode 100644 index 0000000000000..bc441f138f7fc --- /dev/null +++ b/python/pyspark/heapq3.py @@ -0,0 +1,890 @@ +# -*- encoding: utf-8 -*- +# back ported from CPython 3 +# A. HISTORY OF THE SOFTWARE +# ========================== +# +# Python was created in the early 1990s by Guido van Rossum at Stichting +# Mathematisch Centrum (CWI, see http://www.cwi.nl) in the Netherlands +# as a successor of a language called ABC. Guido remains Python's +# principal author, although it includes many contributions from others. +# +# In 1995, Guido continued his work on Python at the Corporation for +# National Research Initiatives (CNRI, see http://www.cnri.reston.va.us) +# in Reston, Virginia where he released several versions of the +# software. +# +# In May 2000, Guido and the Python core development team moved to +# BeOpen.com to form the BeOpen PythonLabs team. In October of the same +# year, the PythonLabs team moved to Digital Creations (now Zope +# Corporation, see http://www.zope.com). In 2001, the Python Software +# Foundation (PSF, see http://www.python.org/psf/) was formed, a +# non-profit organization created specifically to own Python-related +# Intellectual Property. Zope Corporation is a sponsoring member of +# the PSF. +# +# All Python releases are Open Source (see http://www.opensource.org for +# the Open Source Definition). Historically, most, but not all, Python +# releases have also been GPL-compatible; the table below summarizes +# the various releases. +# +# Release Derived Year Owner GPL- +# from compatible? (1) +# +# 0.9.0 thru 1.2 1991-1995 CWI yes +# 1.3 thru 1.5.2 1.2 1995-1999 CNRI yes +# 1.6 1.5.2 2000 CNRI no +# 2.0 1.6 2000 BeOpen.com no +# 1.6.1 1.6 2001 CNRI yes (2) +# 2.1 2.0+1.6.1 2001 PSF no +# 2.0.1 2.0+1.6.1 2001 PSF yes +# 2.1.1 2.1+2.0.1 2001 PSF yes +# 2.2 2.1.1 2001 PSF yes +# 2.1.2 2.1.1 2002 PSF yes +# 2.1.3 2.1.2 2002 PSF yes +# 2.2.1 2.2 2002 PSF yes +# 2.2.2 2.2.1 2002 PSF yes +# 2.2.3 2.2.2 2003 PSF yes +# 2.3 2.2.2 2002-2003 PSF yes +# 2.3.1 2.3 2002-2003 PSF yes +# 2.3.2 2.3.1 2002-2003 PSF yes +# 2.3.3 2.3.2 2002-2003 PSF yes +# 2.3.4 2.3.3 2004 PSF yes +# 2.3.5 2.3.4 2005 PSF yes +# 2.4 2.3 2004 PSF yes +# 2.4.1 2.4 2005 PSF yes +# 2.4.2 2.4.1 2005 PSF yes +# 2.4.3 2.4.2 2006 PSF yes +# 2.4.4 2.4.3 2006 PSF yes +# 2.5 2.4 2006 PSF yes +# 2.5.1 2.5 2007 PSF yes +# 2.5.2 2.5.1 2008 PSF yes +# 2.5.3 2.5.2 2008 PSF yes +# 2.6 2.5 2008 PSF yes +# 2.6.1 2.6 2008 PSF yes +# 2.6.2 2.6.1 2009 PSF yes +# 2.6.3 2.6.2 2009 PSF yes +# 2.6.4 2.6.3 2009 PSF yes +# 2.6.5 2.6.4 2010 PSF yes +# 2.7 2.6 2010 PSF yes +# +# Footnotes: +# +# (1) GPL-compatible doesn't mean that we're distributing Python under +# the GPL. All Python licenses, unlike the GPL, let you distribute +# a modified version without making your changes open source. The +# GPL-compatible licenses make it possible to combine Python with +# other software that is released under the GPL; the others don't. +# +# (2) According to Richard Stallman, 1.6.1 is not GPL-compatible, +# because its license has a choice of law clause. According to +# CNRI, however, Stallman's lawyer has told CNRI's lawyer that 1.6.1 +# is "not incompatible" with the GPL. +# +# Thanks to the many outside volunteers who have worked under Guido's +# direction to make these releases possible. +# +# +# B. TERMS AND CONDITIONS FOR ACCESSING OR OTHERWISE USING PYTHON +# =============================================================== +# +# PYTHON SOFTWARE FOUNDATION LICENSE VERSION 2 +# -------------------------------------------- +# +# 1. 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CNRI SHALL NOT BE LIABLE TO LICENSEE OR ANY OTHER USERS OF PYTHON +# 1.6.1 FOR ANY INCIDENTAL, SPECIAL, OR CONSEQUENTIAL DAMAGES OR LOSS AS +# A RESULT OF MODIFYING, DISTRIBUTING, OR OTHERWISE USING PYTHON 1.6.1, +# OR ANY DERIVATIVE THEREOF, EVEN IF ADVISED OF THE POSSIBILITY THEREOF. +# +# 6. This License Agreement will automatically terminate upon a material +# breach of its terms and conditions. +# +# 7. This License Agreement shall be governed by the federal +# intellectual property law of the United States, including without +# limitation the federal copyright law, and, to the extent such +# U.S. federal law does not apply, by the law of the Commonwealth of +# Virginia, excluding Virginia's conflict of law provisions. +# Notwithstanding the foregoing, with regard to derivative works based +# on Python 1.6.1 that incorporate non-separable material that was +# previously distributed under the GNU General Public License (GPL), the +# law of the Commonwealth of Virginia shall govern this License +# Agreement only as to issues arising under or with respect to +# Paragraphs 4, 5, and 7 of this License Agreement. Nothing in this +# License Agreement shall be deemed to create any relationship of +# agency, partnership, or joint venture between CNRI and Licensee. This +# License Agreement does not grant permission to use CNRI trademarks or +# trade name in a trademark sense to endorse or promote products or +# services of Licensee, or any third party. +# +# 8. By clicking on the "ACCEPT" button where indicated, or by copying, +# installing or otherwise using Python 1.6.1, Licensee agrees to be +# bound by the terms and conditions of this License Agreement. +# +# ACCEPT +# +# +# CWI LICENSE AGREEMENT FOR PYTHON 0.9.0 THROUGH 1.2 +# -------------------------------------------------- +# +# Copyright (c) 1991 - 1995, Stichting Mathematisch Centrum Amsterdam, +# The Netherlands. All rights reserved. +# +# Permission to use, copy, modify, and distribute this software and its +# documentation for any purpose and without fee is hereby granted, +# provided that the above copyright notice appear in all copies and that +# both that copyright notice and this permission notice appear in +# supporting documentation, and that the name of Stichting Mathematisch +# Centrum or CWI not be used in advertising or publicity pertaining to +# distribution of the software without specific, written prior +# permission. +# +# STICHTING MATHEMATISCH CENTRUM DISCLAIMS ALL WARRANTIES WITH REGARD TO +# THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND +# FITNESS, IN NO EVENT SHALL STICHTING MATHEMATISCH CENTRUM BE LIABLE +# FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES +# WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN +# ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT +# OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. +"""Heap queue algorithm (a.k.a. priority queue). + +Heaps are arrays for which a[k] <= a[2*k+1] and a[k] <= a[2*k+2] for +all k, counting elements from 0. For the sake of comparison, +non-existing elements are considered to be infinite. The interesting +property of a heap is that a[0] is always its smallest element. + +Usage: + +heap = [] # creates an empty heap +heappush(heap, item) # pushes a new item on the heap +item = heappop(heap) # pops the smallest item from the heap +item = heap[0] # smallest item on the heap without popping it +heapify(x) # transforms list into a heap, in-place, in linear time +item = heapreplace(heap, item) # pops and returns smallest item, and adds + # new item; the heap size is unchanged + +Our API differs from textbook heap algorithms as follows: + +- We use 0-based indexing. This makes the relationship between the + index for a node and the indexes for its children slightly less + obvious, but is more suitable since Python uses 0-based indexing. + +- Our heappop() method returns the smallest item, not the largest. + +These two make it possible to view the heap as a regular Python list +without surprises: heap[0] is the smallest item, and heap.sort() +maintains the heap invariant! +""" + +# Original code by Kevin O'Connor, augmented by Tim Peters and Raymond Hettinger + +__about__ = """Heap queues + +[explanation by François Pinard] + +Heaps are arrays for which a[k] <= a[2*k+1] and a[k] <= a[2*k+2] for +all k, counting elements from 0. For the sake of comparison, +non-existing elements are considered to be infinite. The interesting +property of a heap is that a[0] is always its smallest element. + +The strange invariant above is meant to be an efficient memory +representation for a tournament. The numbers below are `k', not a[k]: + + 0 + + 1 2 + + 3 4 5 6 + + 7 8 9 10 11 12 13 14 + + 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 + + +In the tree above, each cell `k' is topping `2*k+1' and `2*k+2'. In +an usual binary tournament we see in sports, each cell is the winner +over the two cells it tops, and we can trace the winner down the tree +to see all opponents s/he had. However, in many computer applications +of such tournaments, we do not need to trace the history of a winner. +To be more memory efficient, when a winner is promoted, we try to +replace it by something else at a lower level, and the rule becomes +that a cell and the two cells it tops contain three different items, +but the top cell "wins" over the two topped cells. + +If this heap invariant is protected at all time, index 0 is clearly +the overall winner. The simplest algorithmic way to remove it and +find the "next" winner is to move some loser (let's say cell 30 in the +diagram above) into the 0 position, and then percolate this new 0 down +the tree, exchanging values, until the invariant is re-established. +This is clearly logarithmic on the total number of items in the tree. +By iterating over all items, you get an O(n ln n) sort. + +A nice feature of this sort is that you can efficiently insert new +items while the sort is going on, provided that the inserted items are +not "better" than the last 0'th element you extracted. This is +especially useful in simulation contexts, where the tree holds all +incoming events, and the "win" condition means the smallest scheduled +time. When an event schedule other events for execution, they are +scheduled into the future, so they can easily go into the heap. So, a +heap is a good structure for implementing schedulers (this is what I +used for my MIDI sequencer :-). + +Various structures for implementing schedulers have been extensively +studied, and heaps are good for this, as they are reasonably speedy, +the speed is almost constant, and the worst case is not much different +than the average case. However, there are other representations which +are more efficient overall, yet the worst cases might be terrible. + +Heaps are also very useful in big disk sorts. You most probably all +know that a big sort implies producing "runs" (which are pre-sorted +sequences, which size is usually related to the amount of CPU memory), +followed by a merging passes for these runs, which merging is often +very cleverly organised[1]. It is very important that the initial +sort produces the longest runs possible. Tournaments are a good way +to that. If, using all the memory available to hold a tournament, you +replace and percolate items that happen to fit the current run, you'll +produce runs which are twice the size of the memory for random input, +and much better for input fuzzily ordered. + +Moreover, if you output the 0'th item on disk and get an input which +may not fit in the current tournament (because the value "wins" over +the last output value), it cannot fit in the heap, so the size of the +heap decreases. The freed memory could be cleverly reused immediately +for progressively building a second heap, which grows at exactly the +same rate the first heap is melting. When the first heap completely +vanishes, you switch heaps and start a new run. Clever and quite +effective! + +In a word, heaps are useful memory structures to know. I use them in +a few applications, and I think it is good to keep a `heap' module +around. :-) + +-------------------- +[1] The disk balancing algorithms which are current, nowadays, are +more annoying than clever, and this is a consequence of the seeking +capabilities of the disks. On devices which cannot seek, like big +tape drives, the story was quite different, and one had to be very +clever to ensure (far in advance) that each tape movement will be the +most effective possible (that is, will best participate at +"progressing" the merge). Some tapes were even able to read +backwards, and this was also used to avoid the rewinding time. +Believe me, real good tape sorts were quite spectacular to watch! +From all times, sorting has always been a Great Art! :-) +""" + +__all__ = ['heappush', 'heappop', 'heapify', 'heapreplace', 'merge', + 'nlargest', 'nsmallest', 'heappushpop'] + +def heappush(heap, item): + """Push item onto heap, maintaining the heap invariant.""" + heap.append(item) + _siftdown(heap, 0, len(heap)-1) + +def heappop(heap): + """Pop the smallest item off the heap, maintaining the heap invariant.""" + lastelt = heap.pop() # raises appropriate IndexError if heap is empty + if heap: + returnitem = heap[0] + heap[0] = lastelt + _siftup(heap, 0) + return returnitem + return lastelt + +def heapreplace(heap, item): + """Pop and return the current smallest value, and add the new item. + + This is more efficient than heappop() followed by heappush(), and can be + more appropriate when using a fixed-size heap. Note that the value + returned may be larger than item! That constrains reasonable uses of + this routine unless written as part of a conditional replacement: + + if item > heap[0]: + item = heapreplace(heap, item) + """ + returnitem = heap[0] # raises appropriate IndexError if heap is empty + heap[0] = item + _siftup(heap, 0) + return returnitem + +def heappushpop(heap, item): + """Fast version of a heappush followed by a heappop.""" + if heap and heap[0] < item: + item, heap[0] = heap[0], item + _siftup(heap, 0) + return item + +def heapify(x): + """Transform list into a heap, in-place, in O(len(x)) time.""" + n = len(x) + # Transform bottom-up. The largest index there's any point to looking at + # is the largest with a child index in-range, so must have 2*i + 1 < n, + # or i < (n-1)/2. If n is even = 2*j, this is (2*j-1)/2 = j-1/2 so + # j-1 is the largest, which is n//2 - 1. If n is odd = 2*j+1, this is + # (2*j+1-1)/2 = j so j-1 is the largest, and that's again n//2-1. + for i in reversed(range(n//2)): + _siftup(x, i) + +def _heappop_max(heap): + """Maxheap version of a heappop.""" + lastelt = heap.pop() # raises appropriate IndexError if heap is empty + if heap: + returnitem = heap[0] + heap[0] = lastelt + _siftup_max(heap, 0) + return returnitem + return lastelt + +def _heapreplace_max(heap, item): + """Maxheap version of a heappop followed by a heappush.""" + returnitem = heap[0] # raises appropriate IndexError if heap is empty + heap[0] = item + _siftup_max(heap, 0) + return returnitem + +def _heapify_max(x): + """Transform list into a maxheap, in-place, in O(len(x)) time.""" + n = len(x) + for i in reversed(range(n//2)): + _siftup_max(x, i) + +# 'heap' is a heap at all indices >= startpos, except possibly for pos. pos +# is the index of a leaf with a possibly out-of-order value. Restore the +# heap invariant. +def _siftdown(heap, startpos, pos): + newitem = heap[pos] + # Follow the path to the root, moving parents down until finding a place + # newitem fits. + while pos > startpos: + parentpos = (pos - 1) >> 1 + parent = heap[parentpos] + if newitem < parent: + heap[pos] = parent + pos = parentpos + continue + break + heap[pos] = newitem + +# The child indices of heap index pos are already heaps, and we want to make +# a heap at index pos too. We do this by bubbling the smaller child of +# pos up (and so on with that child's children, etc) until hitting a leaf, +# then using _siftdown to move the oddball originally at index pos into place. +# +# We *could* break out of the loop as soon as we find a pos where newitem <= +# both its children, but turns out that's not a good idea, and despite that +# many books write the algorithm that way. During a heap pop, the last array +# element is sifted in, and that tends to be large, so that comparing it +# against values starting from the root usually doesn't pay (= usually doesn't +# get us out of the loop early). See Knuth, Volume 3, where this is +# explained and quantified in an exercise. +# +# Cutting the # of comparisons is important, since these routines have no +# way to extract "the priority" from an array element, so that intelligence +# is likely to be hiding in custom comparison methods, or in array elements +# storing (priority, record) tuples. Comparisons are thus potentially +# expensive. +# +# On random arrays of length 1000, making this change cut the number of +# comparisons made by heapify() a little, and those made by exhaustive +# heappop() a lot, in accord with theory. Here are typical results from 3 +# runs (3 just to demonstrate how small the variance is): +# +# Compares needed by heapify Compares needed by 1000 heappops +# -------------------------- -------------------------------- +# 1837 cut to 1663 14996 cut to 8680 +# 1855 cut to 1659 14966 cut to 8678 +# 1847 cut to 1660 15024 cut to 8703 +# +# Building the heap by using heappush() 1000 times instead required +# 2198, 2148, and 2219 compares: heapify() is more efficient, when +# you can use it. +# +# The total compares needed by list.sort() on the same lists were 8627, +# 8627, and 8632 (this should be compared to the sum of heapify() and +# heappop() compares): list.sort() is (unsurprisingly!) more efficient +# for sorting. + +def _siftup(heap, pos): + endpos = len(heap) + startpos = pos + newitem = heap[pos] + # Bubble up the smaller child until hitting a leaf. + childpos = 2*pos + 1 # leftmost child position + while childpos < endpos: + # Set childpos to index of smaller child. + rightpos = childpos + 1 + if rightpos < endpos and not heap[childpos] < heap[rightpos]: + childpos = rightpos + # Move the smaller child up. + heap[pos] = heap[childpos] + pos = childpos + childpos = 2*pos + 1 + # The leaf at pos is empty now. Put newitem there, and bubble it up + # to its final resting place (by sifting its parents down). + heap[pos] = newitem + _siftdown(heap, startpos, pos) + +def _siftdown_max(heap, startpos, pos): + 'Maxheap variant of _siftdown' + newitem = heap[pos] + # Follow the path to the root, moving parents down until finding a place + # newitem fits. + while pos > startpos: + parentpos = (pos - 1) >> 1 + parent = heap[parentpos] + if parent < newitem: + heap[pos] = parent + pos = parentpos + continue + break + heap[pos] = newitem + +def _siftup_max(heap, pos): + 'Maxheap variant of _siftup' + endpos = len(heap) + startpos = pos + newitem = heap[pos] + # Bubble up the larger child until hitting a leaf. + childpos = 2*pos + 1 # leftmost child position + while childpos < endpos: + # Set childpos to index of larger child. + rightpos = childpos + 1 + if rightpos < endpos and not heap[rightpos] < heap[childpos]: + childpos = rightpos + # Move the larger child up. + heap[pos] = heap[childpos] + pos = childpos + childpos = 2*pos + 1 + # The leaf at pos is empty now. Put newitem there, and bubble it up + # to its final resting place (by sifting its parents down). + heap[pos] = newitem + _siftdown_max(heap, startpos, pos) + +def merge(iterables, key=None, reverse=False): + '''Merge multiple sorted inputs into a single sorted output. + + Similar to sorted(itertools.chain(*iterables)) but returns a generator, + does not pull the data into memory all at once, and assumes that each of + the input streams is already sorted (smallest to largest). + + >>> list(merge([1,3,5,7], [0,2,4,8], [5,10,15,20], [], [25])) + [0, 1, 2, 3, 4, 5, 5, 7, 8, 10, 15, 20, 25] + + If *key* is not None, applies a key function to each element to determine + its sort order. + + >>> list(merge(['dog', 'horse'], ['cat', 'fish', 'kangaroo'], key=len)) + ['dog', 'cat', 'fish', 'horse', 'kangaroo'] + + ''' + + h = [] + h_append = h.append + + if reverse: + _heapify = _heapify_max + _heappop = _heappop_max + _heapreplace = _heapreplace_max + direction = -1 + else: + _heapify = heapify + _heappop = heappop + _heapreplace = heapreplace + direction = 1 + + if key is None: + for order, it in enumerate(map(iter, iterables)): + try: + next = it.next + h_append([next(), order * direction, next]) + except StopIteration: + pass + _heapify(h) + while len(h) > 1: + try: + while True: + value, order, next = s = h[0] + yield value + s[0] = next() # raises StopIteration when exhausted + _heapreplace(h, s) # restore heap condition + except StopIteration: + _heappop(h) # remove empty iterator + if h: + # fast case when only a single iterator remains + value, order, next = h[0] + yield value + for value in next.__self__: + yield value + return + + for order, it in enumerate(map(iter, iterables)): + try: + next = it.next + value = next() + h_append([key(value), order * direction, value, next]) + except StopIteration: + pass + _heapify(h) + while len(h) > 1: + try: + while True: + key_value, order, value, next = s = h[0] + yield value + value = next() + s[0] = key(value) + s[2] = value + _heapreplace(h, s) + except StopIteration: + _heappop(h) + if h: + key_value, order, value, next = h[0] + yield value + for value in next.__self__: + yield value + + +# Algorithm notes for nlargest() and nsmallest() +# ============================================== +# +# Make a single pass over the data while keeping the k most extreme values +# in a heap. Memory consumption is limited to keeping k values in a list. +# +# Measured performance for random inputs: +# +# number of comparisons +# n inputs k-extreme values (average of 5 trials) % more than min() +# ------------- ---------------- --------------------- ----------------- +# 1,000 100 3,317 231.7% +# 10,000 100 14,046 40.5% +# 100,000 100 105,749 5.7% +# 1,000,000 100 1,007,751 0.8% +# 10,000,000 100 10,009,401 0.1% +# +# Theoretical number of comparisons for k smallest of n random inputs: +# +# Step Comparisons Action +# ---- -------------------------- --------------------------- +# 1 1.66 * k heapify the first k-inputs +# 2 n - k compare remaining elements to top of heap +# 3 k * (1 + lg2(k)) * ln(n/k) replace the topmost value on the heap +# 4 k * lg2(k) - (k/2) final sort of the k most extreme values +# +# Combining and simplifying for a rough estimate gives: +# +# comparisons = n + k * (log(k, 2) * log(n/k) + log(k, 2) + log(n/k)) +# +# Computing the number of comparisons for step 3: +# ----------------------------------------------- +# * For the i-th new value from the iterable, the probability of being in the +# k most extreme values is k/i. For example, the probability of the 101st +# value seen being in the 100 most extreme values is 100/101. +# * If the value is a new extreme value, the cost of inserting it into the +# heap is 1 + log(k, 2). +# * The probabilty times the cost gives: +# (k/i) * (1 + log(k, 2)) +# * Summing across the remaining n-k elements gives: +# sum((k/i) * (1 + log(k, 2)) for i in range(k+1, n+1)) +# * This reduces to: +# (H(n) - H(k)) * k * (1 + log(k, 2)) +# * Where H(n) is the n-th harmonic number estimated by: +# gamma = 0.5772156649 +# H(n) = log(n, e) + gamma + 1 / (2 * n) +# http://en.wikipedia.org/wiki/Harmonic_series_(mathematics)#Rate_of_divergence +# * Substituting the H(n) formula: +# comparisons = k * (1 + log(k, 2)) * (log(n/k, e) + (1/n - 1/k) / 2) +# +# Worst-case for step 3: +# ---------------------- +# In the worst case, the input data is reversed sorted so that every new element +# must be inserted in the heap: +# +# comparisons = 1.66 * k + log(k, 2) * (n - k) +# +# Alternative Algorithms +# ---------------------- +# Other algorithms were not used because they: +# 1) Took much more auxiliary memory, +# 2) Made multiple passes over the data. +# 3) Made more comparisons in common cases (small k, large n, semi-random input). +# See the more detailed comparison of approach at: +# http://code.activestate.com/recipes/577573-compare-algorithms-for-heapqsmallest + +def nsmallest(n, iterable, key=None): + """Find the n smallest elements in a dataset. + + Equivalent to: sorted(iterable, key=key)[:n] + """ + + # Short-cut for n==1 is to use min() + if n == 1: + it = iter(iterable) + sentinel = object() + if key is None: + result = min(it, default=sentinel) + else: + result = min(it, default=sentinel, key=key) + return [] if result is sentinel else [result] + + # When n>=size, it's faster to use sorted() + try: + size = len(iterable) + except (TypeError, AttributeError): + pass + else: + if n >= size: + return sorted(iterable, key=key)[:n] + + # When key is none, use simpler decoration + if key is None: + it = iter(iterable) + # put the range(n) first so that zip() doesn't + # consume one too many elements from the iterator + result = [(elem, i) for i, elem in zip(range(n), it)] + if not result: + return result + _heapify_max(result) + top = result[0][0] + order = n + _heapreplace = _heapreplace_max + for elem in it: + if elem < top: + _heapreplace(result, (elem, order)) + top = result[0][0] + order += 1 + result.sort() + return [r[0] for r in result] + + # General case, slowest method + it = iter(iterable) + result = [(key(elem), i, elem) for i, elem in zip(range(n), it)] + if not result: + return result + _heapify_max(result) + top = result[0][0] + order = n + _heapreplace = _heapreplace_max + for elem in it: + k = key(elem) + if k < top: + _heapreplace(result, (k, order, elem)) + top = result[0][0] + order += 1 + result.sort() + return [r[2] for r in result] + +def nlargest(n, iterable, key=None): + """Find the n largest elements in a dataset. + + Equivalent to: sorted(iterable, key=key, reverse=True)[:n] + """ + + # Short-cut for n==1 is to use max() + if n == 1: + it = iter(iterable) + sentinel = object() + if key is None: + result = max(it, default=sentinel) + else: + result = max(it, default=sentinel, key=key) + return [] if result is sentinel else [result] + + # When n>=size, it's faster to use sorted() + try: + size = len(iterable) + except (TypeError, AttributeError): + pass + else: + if n >= size: + return sorted(iterable, key=key, reverse=True)[:n] + + # When key is none, use simpler decoration + if key is None: + it = iter(iterable) + result = [(elem, i) for i, elem in zip(range(0, -n, -1), it)] + if not result: + return result + heapify(result) + top = result[0][0] + order = -n + _heapreplace = heapreplace + for elem in it: + if top < elem: + _heapreplace(result, (elem, order)) + top = result[0][0] + order -= 1 + result.sort(reverse=True) + return [r[0] for r in result] + + # General case, slowest method + it = iter(iterable) + result = [(key(elem), i, elem) for i, elem in zip(range(0, -n, -1), it)] + if not result: + return result + heapify(result) + top = result[0][0] + order = -n + _heapreplace = heapreplace + for elem in it: + k = key(elem) + if top < k: + _heapreplace(result, (k, order, elem)) + top = result[0][0] + order -= 1 + result.sort(reverse=True) + return [r[2] for r in result] + +# If available, use C implementation +try: + from _heapq import * +except ImportError: + pass +try: + from _heapq import _heapreplace_max +except ImportError: + pass +try: + from _heapq import _heapify_max +except ImportError: + pass +try: + from _heapq import _heappop_max +except ImportError: + pass + + +if __name__ == "__main__": + + import doctest + print(doctest.testmod()) diff --git a/python/pyspark/rdd.py b/python/pyspark/rdd.py index 3934bdda0a466..b820ab4c55988 100644 --- a/python/pyspark/rdd.py +++ b/python/pyspark/rdd.py @@ -44,7 +44,7 @@ from pyspark.storagelevel import StorageLevel from pyspark.resultiterable import ResultIterable from pyspark.shuffle import Aggregator, InMemoryMerger, ExternalMerger, \ - get_used_memory + get_used_memory, ExternalSorter from py4j.java_collections import ListConverter, MapConverter @@ -587,14 +587,19 @@ def sortByKey(self, ascending=True, numPartitions=None, keyfunc=lambda x: x): if numPartitions is None: numPartitions = self._defaultReducePartitions() + spill = (self.ctx._conf.get("spark.shuffle.spill", 'True').lower() == 'true') + memory = _parse_memory(self.ctx._conf.get("spark.python.worker.memory", "512m")) + serializer = self._jrdd_deserializer + + def sortPartition(iterator): + if spill: + sorted = ExternalSorter(memory * 0.9, serializer).sorted + return sorted(iterator, key=lambda (k, v): keyfunc(k), reverse=(not ascending)) + if numPartitions == 1: if self.getNumPartitions() > 1: self = self.coalesce(1) - - def sort(iterator): - return sorted(iterator, reverse=(not ascending), key=lambda (k, v): keyfunc(k)) - - return self.mapPartitions(sort) + return self.mapPartitions(sortPartition) # first compute the boundary of each part via sampling: we want to partition # the key-space into bins such that the bins have roughly the same @@ -617,10 +622,8 @@ def rangePartitionFunc(k): else: return numPartitions - 1 - p - def mapFunc(iterator): - return sorted(iterator, reverse=(not ascending), key=lambda (k, v): keyfunc(k)) - - return self.partitionBy(numPartitions, rangePartitionFunc).mapPartitions(mapFunc, True) + return (self.partitionBy(numPartitions, rangePartitionFunc) + .mapPartitions(sortPartition, True)) def sortBy(self, keyfunc, ascending=True, numPartitions=None): """ diff --git a/python/pyspark/shuffle.py b/python/pyspark/shuffle.py index 2c68cd4921deb..63bf71ee39c7a 100644 --- a/python/pyspark/shuffle.py +++ b/python/pyspark/shuffle.py @@ -21,7 +21,10 @@ import shutil import warnings import gc +import itertools +import operator +import pyspark.heapq3 as heapq from pyspark.serializers import BatchedSerializer, PickleSerializer try: @@ -54,6 +57,13 @@ def get_used_memory(): return 0 +def _get_local_dirs(sub): + """ Get all the directories """ + path = os.environ.get("SPARK_LOCAL_DIR", "/tmp") + dirs = path.split(",") + return [os.path.join(d, "python", str(os.getpid()), sub) for d in dirs] + + class Aggregator(object): """ @@ -196,7 +206,7 @@ def __init__(self, aggregator, memory_limit=512, serializer=None, # default serializer is only used for tests self.serializer = serializer or \ BatchedSerializer(PickleSerializer(), 1024) - self.localdirs = localdirs or self._get_dirs() + self.localdirs = localdirs or _get_local_dirs(str(id(self))) # number of partitions when spill data into disks self.partitions = partitions # check the memory after # of items merged @@ -212,13 +222,6 @@ def __init__(self, aggregator, memory_limit=512, serializer=None, # randomize the hash of key, id(o) is the address of o (aligned by 8) self._seed = id(self) + 7 - def _get_dirs(self): - """ Get all the directories """ - path = os.environ.get("SPARK_LOCAL_DIR", "/tmp") - dirs = path.split(",") - return [os.path.join(d, "python", str(os.getpid()), str(id(self))) - for d in dirs] - def _get_spill_dir(self, n): """ Choose one directory for spill by number n """ return os.path.join(self.localdirs[n % len(self.localdirs)], str(n)) @@ -434,6 +437,63 @@ def _recursive_merged_items(self, start): os.remove(os.path.join(path, str(i))) +class ExternalSorter(object): + """ + ExtenalSorter will divide the elements into chunks, sort them in + memory and dump them into disks, finally merge them back. + + The spilling will only happen when the used memory goes above + the limit. + """ + def __init__(self, memory_limit, serializer=None): + self.memory_limit = memory_limit + self.local_dirs = _get_local_dirs("sort") + self.serializer = serializer or BatchedSerializer(PickleSerializer(), 1024) + + def _get_path(self, n): + """ Choose one directory for spill by number n """ + d = self.local_dirs[n % len(self.local_dirs)] + if not os.path.exists(d): + os.makedirs(d) + return os.path.join(d, str(n)) + + def sorted(self, iterator, key=None, reverse=False): + """ + Sort the elements in iterator, do external sort when the memory + goes above the limit. + """ + batch = 10 + chunks, current_chunk = [], [] + iterator = iter(iterator) + while True: + # pick elements in batch + chunk = list(itertools.islice(iterator, batch)) + current_chunk.extend(chunk) + if len(chunk) < batch: + break + + if get_used_memory() > self.memory_limit: + # sort them inplace will save memory + current_chunk.sort(key=key, reverse=reverse) + path = self._get_path(len(chunks)) + with open(path, 'w') as f: + self.serializer.dump_stream(current_chunk, f) + chunks.append(self.serializer.load_stream(open(path))) + current_chunk = [] + + elif not chunks: + batch = min(batch * 2, 10000) + + current_chunk.sort(key=key, reverse=reverse) + if not chunks: + return current_chunk + + if current_chunk: + chunks.append(iter(current_chunk)) + + return heapq.merge(chunks, key=key, reverse=reverse) + + if __name__ == "__main__": import doctest doctest.testmod() diff --git a/python/pyspark/tests.py b/python/pyspark/tests.py index 22b51110ed671..aaad62ce419da 100644 --- a/python/pyspark/tests.py +++ b/python/pyspark/tests.py @@ -30,6 +30,7 @@ import tempfile import time import zipfile +import random if sys.version_info[:2] <= (2, 6): import unittest2 as unittest @@ -40,7 +41,7 @@ from pyspark.context import SparkContext from pyspark.files import SparkFiles from pyspark.serializers import read_int -from pyspark.shuffle import Aggregator, InMemoryMerger, ExternalMerger +from pyspark.shuffle import Aggregator, InMemoryMerger, ExternalMerger, ExternalSorter _have_scipy = False _have_numpy = False @@ -117,6 +118,28 @@ def test_huge_dataset(self): m._cleanup() +class TestSorter(unittest.TestCase): + def test_in_memory_sort(self): + l = range(1024) + random.shuffle(l) + sorter = ExternalSorter(1024) + self.assertEquals(sorted(l), sorter.sorted(l)) + self.assertEquals(sorted(l, reverse=True), sorter.sorted(l, reverse=True)) + self.assertEquals(sorted(l, key=lambda x: -x), sorter.sorted(l, key=lambda x: -x)) + self.assertEquals(sorted(l, key=lambda x: -x, reverse=True), + sorter.sorted(l, key=lambda x: -x, reverse=True)) + + def test_external_sort(self): + l = range(100) + random.shuffle(l) + sorter = ExternalSorter(1) + self.assertEquals(sorted(l), list(sorter.sorted(l))) + self.assertEquals(sorted(l, reverse=True), list(sorter.sorted(l, reverse=True))) + self.assertEquals(sorted(l, key=lambda x: -x), list(sorter.sorted(l, key=lambda x: -x))) + self.assertEquals(sorted(l, key=lambda x: -x, reverse=True), + list(sorter.sorted(l, key=lambda x: -x, reverse=True))) + + class SerializationTestCase(unittest.TestCase): def test_namedtuple(self): diff --git a/tox.ini b/tox.ini index a1fefdd0e176f..b568029a204cc 100644 --- a/tox.ini +++ b/tox.ini @@ -15,4 +15,4 @@ [pep8] max-line-length=100 -exclude=cloudpickle.py +exclude=cloudpickle.py,heapq3.py