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
   


Julia[edit]

intfile = open("/tmp/mmap.bin", "r+")
 
arr = Mmap.mmap(intfile, Vector{Int64}, (div(stat(intfile).size, 8))) # Int64 is 8 bytes
 
sort!(arr)
 

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

Phix[edit]

Slight variation on Stream_Merge

include builtins/pqueue.e
include builtins/pfile.e -- write_lines() - not [yet] documented
 
procedure add(integer fn, pq)
object line = gets(fn)
if line=-1 then
close(fn)
else
pq_add({fn,line}, pq)
end if
end procedure
 
procedure sort_files(sequence filenames)
for i=1 to length(filenames) do
sequence lines = get_text(filenames[i],GT_LF_STRIPPED),
sorted = sort(lines)
printf(1,"%s:%v => %v\n",{filenames[i],lines,sorted})
if write_lines(filenames[i],sorted)!=1 then ?9/0 end if
end for
end procedure
 
procedure merge_files(integer outfn, sequence filenames)
integer pq = pq_new()
for i=1 to length(filenames) do
add(open(filenames[i], "r"),pq)
end for
while not pq_empty(pq) do
{integer fn, string line} = pq_pop(pq)
puts(outfn,line)
add(fn, pq)
end while
pq_destroy(pq)
end procedure
 
procedure test()
integer nf = rand(5), -- number of files
lp = 3 -- lines per file
sequence filenames = {},
lines = shuffle(tagset(nf*lp))
for i=1 to nf do
string filename = sprintf("file%d.txt",i)
filenames = append(filenames,filename)
integer fn = open(filename,"w")
for l=1 to lp do
printf(fn,"Line %02d\n",lines[l])
end for
lines = lines[lp+1..$]
close(fn)
end for
printf(1,"sorting %d lines split over %d files\n",{nf*lp,nf})
sort_files(filenames)
integer outfn = 1 -- or open("results.txt","w")
merge_files(outfn,filenames)
-- close(outfn)
for i=1 to nf do
{} = delete_file(filenames[i])
end for
end procedure
test()
Output:
sorting 9 lines split over 3 files
file1.txt:{"Line 04","Line 01","Line 09"} => {"Line 01","Line 04","Line 09"}
file2.txt:{"Line 06","Line 07","Line 02"} => {"Line 02","Line 06","Line 07"}
file3.txt:{"Line 08","Line 03","Line 05"} => {"Line 03","Line 05","Line 08"}
Line 01
Line 02
Line 03
Line 04
Line 05
Line 06
Line 07
Line 08
Line 09

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()
 

REXX[edit]

Programming note:   the method used to generate the input file is to generate   N   records,
breaking up the records into sort work files of no more than   10   records   (limit).
The sort work files are then sorted with an external sort, and then merged into one big file.

This particular example uses the DOS   SORT   and   DEL   commands.

/*REXX pgm reads a file, splits into smaller files, sorts 'em, combines into sorted file*/
parse arg FID n lim seed . /*obtain optional arguments from the CL*/
if FID=='' | FID=="," then FID= 'SORT_EXT.OUT' /*name of the output (sorted) file. */
if n=='' | n=="," then n= 500 /*number of records (rand #s) to gen. */
if lim=='' | lim=="," then lim= 10 /*number of records per SORTWORK file. */
if datatype(seed, 'W') then call random ,,seed /*Numeric? Then use it as a rand seed.*/
sWork = 'SORTWORK.' /*the filename of the SORTWORK files.*/
call gen n,lim /*generate SORTWORK.nnn files. */
call srt # /*sort records in all SORTWORK files.*/
call mrg /*merge records in the SORTWORK files.*/
exit /*stick a fork in it, we're all done. */
/*──────────────────────────────────────────────────────────────────────────────────────*/
mrg: procedure expose FID sWork; parse arg # /*#: the number of SORTWORK files. */
@.= copies('ff'x, 1e5) /*no value should be larger than this. */
call lineout FID, , 1 /*position the output file at rec # 1. */
do j=1 until @.[email protected].; call rdr j /*read any number of SORTWORK files, */
end /*j*/ /*but initially just 1 record per file.*/
j=j-1 /*adj. J; read from a non─existent file*/
do forever; [email protected].; z=0 /*find the lowest value for N values.*/
do k=1 for j /*traipse through the stemmed @ array.*/
if @.[email protected]. then call rdr k /*Not defined? Then read a file record*/
if @.k<<y then do; [email protected].k; z=k; end /*Lowest so far? Then mark this as min.*/
end /*k*/ /* [↑] note use of << exact comparison*/
if z==0 then leave /*Any more records? No, close file. */
call lineout FID, @.z /*write the value to the output file. */
call rdr z /*re-populate a value from the # file. */
end /*forever*/ /*keep reading/merging until exhausted.*/
call lineout FID /*close the output file (just in case).*/
'DEL' sWORK"*" /*delete all the SORTWORK files. */
return
/*──────────────────────────────────────────────────────────────────────────────────────*/
gen: procedure expose #; parse arg m,siz; d= digits() /*for justify. */
# = 0 /*number of SORTWORK.nnn files so far*/
do j=1 for m; #= 1 + j % siz /*create workfile#*/
call lineout 'SORTWORK.'#, right(random(, 1e5), d) /*write rand #. */
end /*j*/
do k=1 for #; call lineout 'SORTWORK.'#; end /*close a workfile*/
return
/*──────────────────────────────────────────────────────────────────────────────────────*/
rdr: parse arg a; @.[email protected].; f=sWork||a; if lines(f)\==0 then @.a= linein(f); return
/*──────────────────────────────────────────────────────────────────────────────────────*/
srt: procedure expose sWork; parse arg #
do j=1 for #; fn= sWORK || j; 'SORT' fn "/O" fn; end /*j*/; return