External sort

From Rosetta Code
External sort is a draft programming task. It is not yet considered ready to be promoted as a complete task, for reasons that should be found in its talk page.
Sort a huge file too large to fit into memory. The algorithm consists in reading a large file to be sorted in chunks of data small enough to fit in main memory, sort each of the chunks, write them out to a temporary file, and finally combined the smaller subfiles into a single larger file. For more info see: https://en.wikipedia.org/wiki/External_sorting

The sorting algorithm can be any popular sort, like quicksort. For simplicity one can assume that the file consists of fixed length integers and that the sort function is less-than (<).

Go[edit]

This is a translation of the C++ code here which implements external sorting using a merge sort. In the interests of brevity, the extensive comments in the C++ version have been largely omitted.

A small test file consisting of random integers has been generated and sorted to demonstrate that the approach works.

package main
 
import (
"fmt"
"io"
"log"
"math"
"math/rand"
"os"
"time"
)
 
type MinHeapNode struct{ element, index int }
 
type MinHeap struct{ nodes []MinHeapNode }
 
func left(i int) int {
return (2*i + 1)
}
 
func right(i int) int {
return (2*i + 2)
}
 
func newMinHeap(nodes []MinHeapNode) *MinHeap {
mh := new(MinHeap)
mh.nodes = nodes
for i := (len(nodes) - 1) / 2; i >= 0; i-- {
mh.minHeapify(i)
}
return mh
}
 
func (mh *MinHeap) getMin() MinHeapNode {
return mh.nodes[0]
}
 
func (mh *MinHeap) replaceMin(x MinHeapNode) {
mh.nodes[0] = x
mh.minHeapify(0)
}
 
func (mh *MinHeap) minHeapify(i int) {
l, r := left(i), right(i)
smallest := i
heapSize := len(mh.nodes)
if l < heapSize && mh.nodes[l].element < mh.nodes[i].element {
smallest = l
}
if r < heapSize && mh.nodes[r].element < mh.nodes[smallest].element {
smallest = r
}
if smallest != i {
mh.nodes[i], mh.nodes[smallest] = mh.nodes[smallest], mh.nodes[i]
mh.minHeapify(smallest)
}
}
 
func merge(arr []int, l, m, r int) {
n1, n2 := m-l+1, r-m
tl := make([]int, n1)
tr := make([]int, n2)
copy(tl, arr[l:])
copy(tr, arr[m+1:])
i, j, k := 0, 0, l
for i < n1 && j < n2 {
if tl[i] <= tr[j] {
arr[k] = tl[i]
k++
i++
} else {
arr[k] = tr[j]
k++
j++
}
}
for i < n1 {
arr[k] = tl[i]
k++
i++
}
for j < n2 {
arr[k] = tr[j]
k++
j++
}
}
 
func mergeSort(arr []int, l, r int) {
if l < r {
m := l + (r-l)/2
mergeSort(arr, l, m)
mergeSort(arr, m+1, r)
merge(arr, l, m, r)
}
}
 
// Merge k sorted files: es0,es1 etc.
func mergeFiles(outputFile string, n, k int) {
in := make([]*os.File, k)
var err error
for i := 0; i < k; i++ {
fileName := fmt.Sprintf("es%d", i)
in[i], err = os.Open(fileName)
check(err)
}
out, err := os.Create(outputFile)
check(err)
nodes := make([]MinHeapNode, k)
i := 0
for ; i < k; i++ {
_, err = fmt.Fscanf(in[i], "%d", &nodes[i].element)
if err == io.EOF {
break
}
check(err)
nodes[i].index = i
}
hp := newMinHeap(nodes[:i])
count := 0
for count != i {
root := hp.getMin()
fmt.Fprintf(out, "%d ", root.element)
_, err = fmt.Fscanf(in[root.index], "%d", &root.element)
if err == io.EOF {
root.element = math.MaxInt32
count++
} else {
check(err)
}
hp.replaceMin(root)
}
for j := 0; j < k; j++ {
in[j].Close()
}
out.Close()
}
 
func check(err error) {
if err != nil {
log.Fatal(err)
}
}
 
// Create initial runs, divide them evenly amongst the output files
// and then merge-sort them.
func createInitialRuns(inputFile string, runSize, numWays int) {
in, err := os.Open(inputFile)
out := make([]*os.File, numWays)
for i := 0; i < numWays; i++ {
fileName := fmt.Sprintf("es%d", i) // es0, es1 etc.
out[i], err = os.Create(fileName)
check(err)
}
arr := make([]int, runSize)
moreInput := true
nextOutputFile := 0
var i int
for moreInput {
for i = 0; i < runSize; i++ {
_, err := fmt.Fscanf(in, "%d", &arr[i])
if err == io.EOF {
moreInput = false
break
}
check(err)
}
mergeSort(arr, 0, i-1)
for j := 0; j < i; j++ {
fmt.Fprintf(out[nextOutputFile], "%d ", arr[j])
}
nextOutputFile++
}
for j := 0; j < numWays; j++ {
out[j].Close()
}
in.Close()
}
 
func externalSort(inputFile, outputFile string, numWays, runSize int) {
createInitialRuns(inputFile, runSize, numWays)
mergeFiles(outputFile, runSize, numWays)
}
 
func main() {
// Create a small test file of 40 random ints and split it into 4 files
// of 10 integers each.
numWays := 4
runSize := 10
inputFile := "input.txt"
outputFile := "output.txt"
in, err := os.Create(inputFile)
check(err)
rand.Seed(time.Now().UnixNano())
for i := 0; i < numWays*runSize; i++ {
fmt.Fprintf(in, "%d ", rand.Intn(math.MaxInt32))
}
in.Close()
externalSort(inputFile, outputFile, numWays, runSize)
// remove temporary files
for i := 0; i < numWays; i++ {
fileName := fmt.Sprintf("es%d", i)
err = os.Remove(fileName)
check(err)
}
}
Output:

Contents of input.txt:

921996447 760852351 223421434 1245608832 745990119 1414811249 1947335121 762344474 588429291 993452626 2592794 491133923 1275871423 1152039534 649892156 278215570 595760601 1878223040 1267371451 2097209826 1409628494 1147072290 309824251 108477605 1705270413 1821354697 1703557665 473708588 110138202 1292465428 946557804 148800949 1471244316 1508853596 1306802817 1016358698 1661284048 527644251 546155704 337874167

Contents of output.txt:

2592794 108477605 110138202 148800949 223421434 278215570 309824251 337874167 473708588 491133923 527644251 546155704 588429291 595760601 649892156 745990119 760852351 762344474 921996447 946557804 993452626 1016358698 1147072290 1152039534 1245608832 1267371451 1275871423 1292465428 1306802817 1409628494 1414811249 1471244316 1508853596 1661284048 1703557665 1705270413 1821354697 1878223040 1947335121 2097209826

j[edit]

Untested on a memory mapped file.

 
NB. Apply an in-place sorting algorithm to a memory mapped file
NB. in-place sort is translation of in-place python quicksort.
 
require 'jmf'
JCHAR map_jmf_ 'DATA'; 'file.huge'
NB. The noun DATA now refers to the memory mapped file.
NB. Use: quicksort DATA
 
 
NB. use: quicksort DATA
quicksort=: 3 :'qsinternal 0 , <:@:# ARRAY=: y' NB. ARRAY is global
 
qsinternal=: 3 :0
'start stop'=. y
if. 0 < stop - start do.
'left right pivot'=. start, stop, start{ARRAY NB. pivot, left, right = array[start], start, stop
while. left <: right do. NB. while left <= right:
while. pivot > left { ARRAY do. NB. while array[left] < pivot:
left=. >: left
end.
while. pivot < right { ARRAY do. NB. while array[right] > pivot:
right=. <: right NB. right -= 1
end.
if. left <: right do. NB. if left <= right:
 
NB. mapped files work by reference, assignment not required, but for testing.
ARRAY=: (left, right) {`(|[email protected]:[)`]} ARRAY NB. array[left], array[right] = array[right], array[left]
 
left=. >: left NB. left += 1
right=. <: right NB. right -= 1
end.
end.
qsinternal start , right NB. _quicksort(array, start, right)
qsinternal left , stop NB. _quicksort(array, left, stop)
end.
i. 0 0 NB. verbs return the final noun
)
 

Demonstration the sorting works:

   quicksort ?~10
   ARRAY
0 1 2 3 4 5 6 7 8 9
   

Perl[edit]

Simulate task by reading from 'DATA' handle and using tiny record limit. As written, works for any numeric input, but could define any kind of customized sorting.

use strict;
use warnings;
 
my $max = 4; # records per merge file
my(@chunk,@tempf);
 
sub mysort ($$) { return $_[0] <=> $_[1] }
 
sub store {
my($a) = @_;
my $f = IO::File->new_tmpfile; # self-deleting after program exit
print $f sort mysort @$a;
seek $f, 0, 0 or warn "Oops: $!";
push(@tempf, { fh => $f, queued => scalar <$f> } );
}
 
# read input and create sorted temporary files
while (<DATA>) {
push @chunk, $_;
store(\@chunk), @chunk = () if @chunk == $max;
}
store(\@chunk) if @chunk;
 
# merge everything
while (1) {
my($lowest) = (sort { mysort($a->{queued}, $b->{queued}); } grep(defined $_->{queued}, @tempf) )[0];
last unless $lowest->{queued};
print $lowest->{queued};
$lowest->{queued} = $lowest->{fh}->getline();
}
 
__DATA__
432
345
321
543
987
456
678
123
765
567
876
654
789
234
Output:
123
234
321
345
432
456
543
567
654
678
765
789
876
987

Python[edit]

A technique demonstrated with a short string character data.

 
#! /usr/bin/python3
 
'''
$ # example session in bash
$ python3 external_sort.py
expect 123456789
memory size 1 passed
memory size 2 passed
memory size 3 passed
memory size 4 passed
memory size 5 passed
memory size 6 passed
memory size 7 passed
memory size 8 passed
memory size 9 passed
memory size 10 passed
memory size 11 passed
'''

 
import io
 
def sort_large_file(n: int, source: open, sink: open, file_opener = open)->None:
 
'''
approach:
break the source into files of size n
sort each of these files
merge these onto the sink
'''

 
# store sorted chunks into files of size n
mergers = []
while True:
text = list(source.read(n))
if not len(text):
break;
text.sort()
merge_me = file_opener()
merge_me.write(''.join(text))
mergers.append(merge_me)
merge_me.seek(0)
 
# merge onto sink
stack_tops = [f.read(1) for f in mergers]
while stack_tops:
c = min(stack_tops)
sink.write(c)
i = stack_tops.index(c)
t = mergers[i].read(1)
if t:
stack_tops[i] = t
else:
del stack_tops[i]
mergers[i].close()
del mergers[i] # __del__ method of file_opener should delete the file
 
def main():
'''
test case
sort 6,7,8,9,2,5,3,4,1 with several memory sizes
'''

 
# load test case into a file like object
input_file_too_large_for_memory = io.StringIO('678925341')
 
# generate the expected output
t = list(input_file_too_large_for_memory.read())
t.sort()
expect = ''.join(t)
print('expect', expect)
 
# attempt to sort with several memory sizes
for memory_size in range(1,12):
input_file_too_large_for_memory.seek(0)
output_file_too_large_for_memory = io.StringIO()
sort_large_file(memory_size, input_file_too_large_for_memory, output_file_too_large_for_memory, io.StringIO)
output_file_too_large_for_memory.seek(0)
assert(output_file_too_large_for_memory.read() == expect)
print('memory size {} passed'.format(memory_size))
 
if __name__ == '__main__':
example = main
example()