External sort
Sorting Algorithm
This is a sorting algorithm. It may be applied to a set of data in order to sort it.
For comparing various sorts, see compare sorts.
For other sorting algorithms, see sorting algorithms, or:
Heap sort | Merge sort | Patience sort | Quick sort
O(n log2n) sorts
Shell Sort
O(n2) sorts
Bubble sort |
Cocktail sort |
Cocktail sort with shifting bounds |
Comb sort |
Cycle sort |
Gnome sort |
Insertion sort |
Selection sort |
Strand sort
other sorts
Bead sort |
Bogo sort |
Common sorted list |
Composite structures sort |
Custom comparator sort |
Counting sort |
Disjoint sublist sort |
External sort |
Jort sort |
Lexicographical sort |
Natural sorting |
Order by pair comparisons |
Order disjoint list items |
Order two numerical lists |
Object identifier (OID) sort |
Pancake sort |
Quickselect |
Permutation sort |
Radix sort |
Ranking methods |
Remove duplicate elements |
Sleep sort |
Stooge sort |
[Sort letters of a string] |
Three variable sort |
Topological sort |
Tree sort
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 (<).
AppleScript
This effort uses an in-place Quicksort, which tends to move things around less than a merge sort and so hopefully means fewer writes to the file and a less long wait for the task to finish. It suits the characteristics of AppleScript's File Read/Write commands and the fact that stable sorting isn't required with integers.
A "half chunk" of integers at a time is read to each of two buffer lists covering different sections of the file range being partitioned. Only those integers needing to be swapped are written back to the file and each list is replaced as it's used up. When the converging sections eventually overlap, a single list is used instead which is updated in parallel with the file to ensure that the partitioning repeat stops in the right place. Partitions less than a "chunk" in length are sorted in memory with a heap sort. (The Foundation framework has a built-in NSMutableArray sort which is faster than a vanilla heap sort — even with the necessary derivation of NSMutableArrays from the lists and lists from the sorted arrays — but I don't know how well this fits the task's "low memory" conceit.)
<lang applescript>(* Quicksort algorithm: S.A.R. (Tony) Hoare, 1960. Optimisations by Robert Sedgewick and others at various times. Heap sort algorithm: J.W.J. Williams, 1964.
- )
use AppleScript version "2.3.1" -- MacOS 10.9 (Mavericks) or later — for these 'use' commands! use internalSorter : script "Heap sort" -- <https://www.rosettacode.org/wiki/Sorting_algorithms/Heapsort#AppleScript>. use scripting additions
-- Configuration. property maxChunkSize : 256000 -- 256 KBytes (64000 AppleScript integers). The larger this figure can be, the less slow the sort. property integerSize : 4 property maxInternalSortSize : maxChunkSize
on externalSort(theFile) -- Param: file, alias, or HFS path.
(* Properties and handlers for the sort. *)
script o
-- Precalculated values.
property twiceIntegerSize : integerSize + integerSize
property maxHalfChunkSize : maxChunkSize div twiceIntegerSize * integerSize
-- Reference number of the system file handle for the open file.
property fRef : missing value
-- Start byte indices of integers in the file.
property i : missing value
property j : missing value
-- Start byte indices of the most recent additions to pivot stores in the file.
property pLeft : missing value
property pRight : missing value
-- Two buffer lists and assocatiated info.
property leftList : missing value
property leftEndByte : missing value -- End byte index of equivalent range in file.
property a : missing value -- Left list index.
property leftListLength : missing value
property rightList : missing value
property rightStartByte : missing value -- Start byte index of equivalent range in file.
property b : missing value -- Right list index.
-- Whether or not down to single-list working.
property singleList : missing value
(* Quicksort handler. Sorts a file of integers in place. *)
on qsrt(l, r) -- Params: start-byte indices in the file of the first and last integers in a range to be partitioned.
repeat -- Tail call elimination repeat.
-- Prime the properties for this range.
set {i, j, pLeft, pRight, leftEndByte, a, leftListLength, rightStartByte, b, singleList} to ¬
{l, r, l - integerSize, r + integerSize, l - 1, 0, 0, r + integerSize, 0, false}
-- Get the first and last integers in the range, setting up the first two buffer lists in the process.
set leftValue to nextLeftInteger(l, r)
set rightValue to nextRightInteger(l, r)
-- Read a third integer directly from the middle of the range in the file.
set pivot to (read fRef from ((l + r - 2) div twiceIntegerSize * integerSize + 1) for integerSize as integer)
-- Choose one of the three as the pivot (median-of-3 pivot selection).
set leftGreaterThanRight to (leftValue > rightValue)
if (leftValue > pivot) then
if (leftGreaterThanRight) then
if (rightValue > pivot) then set pivot to rightValue
else
set pivot to leftValue
end if
else if (pivot > rightValue) then
if (leftGreaterThanRight) then
set pivot to leftValue
else
set pivot to rightValue
end if
end if
-- Whichever's now the pivot, swap the outermost two if the left's greater than the right.
-- If either of them *is* the pivot, advance the pivot store boundary on the relevant side.
if (leftGreaterThanRight) then
write leftValue to fRef as integer starting at r
write rightValue to fRef as integer starting at l
if (leftValue = pivot) then
set pRight to r
else if (rightValue = pivot) then
set pLeft to l
end if
else
if (leftValue = pivot) then set pLeft to l
if (rightValue = pivot) then set pRight to r
end if
-- Continue partitioning the range.
set i to l + integerSize
set j to r - integerSize
repeat until (i > j) -- Partitioning repeat.
set leftValue to nextLeftInteger(l, r)
repeat while (leftValue < pivot)
set i to i + integerSize
set leftValue to nextLeftInteger(l, r)
end repeat
set rightValue to nextRightInteger(l, r)
repeat while (rightValue > pivot)
set j to j - integerSize
set rightValue to nextRightInteger(l, r)
end repeat
if (j > i) then
-- Three-way partitioning: if either value to be swapped is a pivot instance, extend the pivot store
-- on the destination side and, if the appropriated slot isn't already the pivot destination, swap its
-- current content for (a copy of) the pivot and use the retrieved value instead in the main swap.
if (leftValue = pivot) then
set pRight to pRight - integerSize
if (pRight > j) then
set leftValue to (read fRef from pRight for integerSize as integer)
write pivot as integer to fRef starting at pRight
end if
end if
if (rightValue = pivot) then
set pLeft to pLeft + integerSize
if (pLeft < i) then
set rightValue to (read fRef from pLeft for integerSize as integer)
write pivot as integer to fRef starting at pLeft
end if
end if
-- Write the values to be swapped to the appropriate places in the file.
write rightValue to fRef as integer starting at i
write leftValue to fRef as integer starting at j
-- If down to a single buffer list, update this too so that the repeat will know when to stop.
if (singleList) then
set item a of my leftList to rightValue
set item b of my leftList to leftValue
end if
else if (i > j) then
exit repeat
end if
set i to i + integerSize
set j to j - integerSize
end repeat -- Partitioning.
-- Swap any stored pivot instances into the slots next to the crossed indices
-- and advance the indices to exclude the pivots from the rest of the sort.
repeat with p from l to pLeft by integerSize
if (j > pLeft) then
write (read fRef from j for integerSize as integer) to fRef as integer starting at p
write pivot to fRef as integer starting at j
set j to j - integerSize
else
-- Don't bother swapping where store and target slots overlap.
set j to p - integerSize
exit repeat
end if
end repeat
repeat with p from r to pRight by -integerSize
if (i < pRight) then
write (read fRef from i for integerSize as integer) to fRef as integer starting at p
write pivot to fRef as integer starting at i
set i to i + integerSize
else
set i to p + integerSize
exit repeat
end if
end repeat
-- Where the new partitions are short enough, sort them in memory with a non-recursive sort.
-- Otherwise subpartition the shorter one recursively, then the longer iteratively.
set leftDiff to j - l
set rightDiff to r - i
if (leftDiff < rightDiff) then
set {shorterDiff, ls, rs, longerDiff, l} to {leftDiff, l, j, rightDiff, i}
else
set {shorterDiff, ls, rs, longerDiff, r} to {rightDiff, i, r, leftDiff, j}
end if
if (shorterDiff < maxInternalSortSize) then
if (rs > ls) then sortInMemory(ls, rs)
else
qsrt(ls, rs)
end if
if (longerDiff < maxInternalSortSize) then
if (r > l) then sortInMemory(l, r)
exit repeat -- … and return from the handler.
end if
-- Otherwise go round again to handle the longer partition.
end repeat -- Tail call elimination.
end qsrt
(* Return the next integer from the left buffer list, setting up or replacing the list as necessary. *)
on nextLeftInteger(l, r)
set a to a + 1
if (a > leftListLength) then
-- The existing left list has been used up or doesn't yet exist.
set leftEndByte to leftEndByte + maxHalfChunkSize
-- Derive a new left list from the next half-chunk of data — unless any of this is already
-- covered by the other list, in which case replace both lists with a single one.
if (leftEndByte < rightStartByte) then
set leftList to (read fRef from i for maxHalfChunkSize as integer) as list
set a to 1
set leftListLength to (count leftList)
else
goToSingleList(l, r)
set b to b + 1
end if
end if
return item a of my leftList
end nextLeftInteger
(* Return the next integer from the right buffer list, simile. *)
on nextRightInteger(l, r)
set b to b - 1
if (b < 1) then
set rightStartByte to rightStartByte - maxHalfChunkSize
if (rightStartByte > leftEndByte) then
set rightList to (read fRef from rightStartByte for maxHalfChunkSize as integer) as list
set b to (count rightList)
else
goToSingleList(l, r)
end if
end if
return item b of my rightList
end nextRightInteger
(* Set up a single buffer list for use in the closing stage of a partitioning repeat. *)
on goToSingleList(l, r)
-- The range to read from the file is from bytes i to (j + integerSize - 1)
-- PLUS an integer either side, if these are within the range being partitioned,
-- to help ensure that the partitioning repeat stops in the right place.
if (i > l) then
set readStart to i - integerSize
set a to 2
else
set readStart to i
set a to 1
end if
if (j < r) then
set readEnd to j + twiceIntegerSize - 1
else
set readEnd to j + integerSize - 1
end if
-- Ditch the existing right list.
set rightList to missing value
-- Read the integers from the calculated range and set both list properties to the same result instance.
set leftList to (read fRef from readStart to readEnd as integer) as list
set rightList to leftList
-- Set the other relevant properties.
set b to (count rightList)
if (j < r) then set b to b - 1
set leftListLength to b
set singleList to true
end goToSingleList
(* Read integers from a given range in the file, sort them in memory, and write them back to the same range. *)
on sortInMemory(l, r)
set rightList to missing value
set leftList to (read fRef from l to (r + integerSize - 1) as integer) as list
tell internalSorter to sort(leftList, 1, -1)
read fRef from l for 0 -- Set the file handle's position pointer.
repeat with x from 1 to (count leftList)
write (item x of my leftList) as integer to fRef
end repeat
end sortInMemory
end script
(* Main handler code. Sets up and starts the sort. *)
-- Check the input.
try
set theFile to theFile as alias
on error
display dialog "The specified file doesn't exist." buttons {"Stop"} default button 1 cancel button 1 with icon stop
end try
set fileSize to (get eof theFile)
if (fileSize is 0) then
display dialog "The file is empty." buttons {"Stop"} default button 1 cancel button 1 with icon stop
else if (fileSize mod integerSize > 0) then
display dialog ¬
"The file size isn't an exact number of integers." buttons {"Stop"} default button 1 cancel button 1 with icon stop
end if
-- Get the user to specify the destination file. Can be the original.
set oldPath to theFile as text
set astid to AppleScript's text item delimiters
set AppleScript's text item delimiters to ":"
tell oldPath to set {rootPath, oldName} to {text 1 thru text item -2, text item -1}
set AppleScript's text item delimiters to "."
tell oldName to set newName to text 1 thru text item -2 & " (sorted copy)." & text item -1
set AppleScript's text item delimiters to astid
set newFile to ¬
(choose file name with prompt "Save the sorted result as…" default name newName default location (rootPath as alias))
-- If the original wasn't chosen, copy the data to the new location.
-- There are simpler ways to copy a file, but this still practically instantaneous
-- and definitely only involves maxChunkSize bytes at a time.
if (newFile as text is not oldPath) then
set readRef to (open for access theFile)
set writeRef to (open for access newFile with write permission)
try
set eof writeRef to 0
repeat with i from 1 to fileSize by maxChunkSize
set d to (read readRef for maxChunkSize as data)
write d as data to writeRef
end repeat
close access writeRef
close access readRef
on error errMsg
close access writeRef
close access readRef
display dialog errMsg buttons {"Stop"} default button 1 cancel button 1 with icon stop
end try
set theFile to newFile
end if
-- Open the target file with write permission and perform the sort.
set o's fRef to (open for access theFile with write permission)
try
-- Handler parameters: first-byte indices of the first and last integers in the file.
if (fileSize > maxChunkSize) then
tell o to qsrt(1, fileSize + 1 - integerSize)
else
tell o to sortInMemory(1, fileSize + 1 - integerSize)
end if
close access o's fRef
on error errMsg
close access o's fRef
display dialog errMsg buttons {"Stop"} default button 1 cancel button 1 with icon stop
end try
-- Return the specifier for the sorted file.
return theFile
end externalSort
set theFile to (path to desktop as text) & "Test.dat" set sortedFile to externalSort(theFile)</lang>
C++
Sort a file of integers using external merge sort.
The input file is read into a single 32 byte buffer (8 ints) and the 8 ints are sorted and then written to a temp file on disk as strings.
This continues until all the numbers from the input file are read and distributed into files of 8 integer strings.
The last file may be less than 8 integers.
All the temp files are opened as ifstreams in a dynamic pointer array.
A minheap reads ints from each file stream in turn, and outputs its contents to the output file.
(The heap generally only fills to 6 items before it writes its contents to the output file.)
All sorted streams are merged in this way out to an external output file merged.txt.
<lang cpp> /* ExternalSort.cpp */
- include <iostream>
- include <fstream>
- include <queue>
- include <string>
- include <algorithm>
- include <cstdio>
/* function signatures */
int main(int argc, char* argv[]); void write_vals(int* const, const size_t, const size_t); std::string mergeFiles(size_t);
/* Comparison object
compares first item of 2 std::pairs of ints true if first item is larger or the same.
MinHeap sorts with this. It gets called a lot, so the simpler the better.
STL api stipulates boolean predicate
A "functor" object defines a function call operator () that returns a value.
- /
struct Compare {
// compare 2 pairs by first element
bool operator() ( std::pair<int, int>& p1, std::pair<int, int>& p2 )
{
return p1.first >= p2.first; // Ascending order
}
};
/* aliases */
using ipair = std::pair<int,int>;
using pairvector = std::vector<ipair>;
using MinHeap = std::priority_queue< ipair, pairvector, Compare >;
/* constants */
const size_t memsize = 32; // 32 bytes
const size_t chunksize = memsize / sizeof(int); // 8 int
const std::string tmp_prefix{"tmp_out_"}; // tmpfile prefix
const std::string tmp_suffix{".txt"}; // tmpfile suffix
const std::string merged_file{"merged.txt"}; // output file
/* functions */
// write int array to file void write_vals( int* const values, const size_t size, const size_t chunk ) {
// tmp_out_1.txt, tmp_out_2.txt ... std::string output_file = (tmp_prefix + std::to_string(chunk) + tmp_suffix); std::ofstream ofs(output_file.c_str()); //output file
for (int i=0; i<size; i++) ofs << values[i] << '\t'; ofs << '\n';
ofs.close();
}
/* merge all external sorted files into one
output file (same size as original input file) */
std::string mergeFiles(size_t chunks, const std::string& merge_file ) {
std::ofstream ofs( merge_file.c_str() ); MinHeap minHeap;
// array of ifstreams
std::ifstream* ifs_tempfiles = new std::ifstream[chunks];
for (size_t i = 1; i<=chunks; i++)
{
int topval = 0;
// generate a unique name for temp file (temp_out_1.txt , temp_out_2.txt ..)
std::string sorted_file = (tmp_prefix + std::to_string(i) + tmp_suffix);
// open an input file stream object for each name
ifs_tempfiles[i-1].open( sorted_file.c_str() ); // bind to tmp_out_{i}.txt
// get val from temp file
if (ifs_tempfiles[i-1].is_open())
{ ifs_tempfiles[i-1] >> topval; // first value in the file (min)
ipair top(topval, (i-1)); // 2nd value is tempfile number
minHeap.push( top ); // minHeap autosorts }
}
while (minHeap.size() > 0)
{
int next_val = 0;
ipair min_pair = minHeap.top(); // get min
minHeap.pop();
ofs << min_pair.first << ' '; // write value to file
std::flush(ofs);
if ( ifs_tempfiles[min_pair.second] >> next_val)
{
ipair np( next_val, min_pair.second );
minHeap.push( np ); }
}
// close open files
for (int i = 1; i <= chunks; i++)
{
ifs_tempfiles[i-1].close();
}
ofs << '\n'; ofs.close(); delete[] ifs_tempfiles; // free memory return merged_file; // string
}
int main(int argc, char* argv[] )
{
if (argc < 2)
{
std::cerr << "usage: ExternalSort <filename> \n";
return 1;
}
// open input file for reading
std::ifstream ifs( argv[1] );
if ( ifs.fail() )
{
std::cerr << "error opening " << argv[1] << "\n";
return 2;
}
// temp array for input (small) (32 bytes -- 8 ints) int* inputValues = new int[chunksize]; int chunk = 1; // counter (which chunk)
int val = 0; // int for reading
int count = 0; // count reads
bool done = false;
std::cout << "internal buffer is " << memsize << " bytes" << "\n";
// read chunksize values from input file
while (ifs >> val)
{
done = false;
inputValues[count] = val;
count++;
if (count == chunksize)
{
std::sort(inputValues, inputValues + count);
write_vals(inputValues, count, chunk); // output vals to
chunk ++;
count = 0;
done = true; }
} // while
if (! done) // one more file
{
std::sort(inputValues, inputValues + count);
write_vals(inputValues, count, chunk); // output vals to
}
else
{
chunk --; // fix overshoot
}
ifs.close(); // done with original input file
delete[] inputValues; // free dynamically allocated memory
// perform external mergesort on sorted temp files, if any.
if ( chunk == 0 )
std::cout << "no data found\n";
else
std::cout << "Sorted output is in file: " << mergeFiles(chunk, merged_file ) << "\n";
return EXIT_SUCCESS;
}
/* compile: clang++ -std=c++11 -Wall -pedantic -o ExternalSort ExternalSort.cpp */
/* inputfile integers -- one per line for simplicity */ </lang>
- Output:
input:
2 65 76 88 55 22 35 11 76 99 7 111 4 55 34 63 22 13 45 9 0 112 123 345 456 8 654 678 999 888 10 3 555 534 236 143 860 648 1 627 711 223 332 5 443 445
tmp_out_1.txt
2 11 22 35 55 65 76 88
tmp_out_2.txt
4 7 34 55 63 76 99 111
tmp_out_3.txt
0 9 13 22 45 112 123 345
tmp_out_4.txt
3 8 10 456 654 678 888 999
tmp_out_5.txt
1 143 236 534 555 627 648 860
tmp_out_6.txt
5 223 332 443 445 711
merged.txt:
0 1 2 3 4 5 7 8 9 10 11 13 22 22 34 35 45 55 55 63 65 76 76 88 99 111 112 123 143 223 236 332 345 443 445 456 534 555 627 648 654 678 711 860 888 999
Go
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. <lang go>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)
}
}</lang>
- 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
Untested on a memory mapped file. <lang J> 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) {`(|.@:[)`]} 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
) </lang>
Demonstration the sorting works:
quicksort ?~10 ARRAY 0 1 2 3 4 5 6 7 8 9
Julia
<lang julia>intfile = open("/tmp/mmap.bin", "r+")
arr = Mmap.mmap(intfile, Vector{Int64}, (div(stat(intfile).size, 8))) # Int64 is 8 bytes
sort!(arr) </lang>
Perl
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. <lang perl>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 () {
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} = $lowest->{fh}->getline();
}
__DATA__ 432 345 321 543 987 456 678 123 765 567 876 654 789 234</lang>
- Output:
123 234 321 345 432 456 543 567 654 678 765 789 876 987
Phix
Slight variation on Stream_Merge <lang Phix>include builtins/pqueue.e include builtins/pfile.e -- write_lines() - not [yet] documented
procedure add(integer fn, pq)
object line = gets(fn)
if line=-1 then
close(fn)
else
pq_add({fn,line}, pq)
end if
end procedure
procedure sort_files(sequence filenames)
for i=1 to length(filenames) do
sequence lines = get_text(filenames[i],GT_LF_STRIPPED),
sorted = sort(lines)
printf(1,"%s:%v => %v\n",{filenames[i],lines,sorted})
if write_lines(filenames[i],sorted)!=1 then ?9/0 end if
end for
end procedure
procedure merge_files(integer outfn, sequence filenames)
integer pq = pq_new()
for i=1 to length(filenames) do
add(open(filenames[i], "r"),pq)
end for
while not pq_empty(pq) do
{integer fn, string line} = pq_pop(pq)
puts(outfn,line)
add(fn, pq)
end while
pq_destroy(pq)
end procedure
procedure test()
integer nf = rand(5), -- number of files
lp = 3 -- lines per file
sequence filenames = {},
lines = shuffle(tagset(nf*lp))
for i=1 to nf do
string filename = sprintf("file%d.txt",i)
filenames = append(filenames,filename)
integer fn = open(filename,"w")
for l=1 to lp do
printf(fn,"Line %02d\n",lines[l])
end for
lines = lines[lp+1..$]
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()</lang>
- 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
A technique demonstrated with a short string character data. <lang python>
- ! /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()
</lang>
Raku
(formerly Perl 6) Borrowing from Stream_Merge here. Temporary files are automatically deleted when program is done, so no explicit clean-up required. <lang perl6>use File::Temp;
sub merge_streams ( @streams ) {
my @s = @streams.map({ hash( STREAM => $_, HEAD => .get ) }).grep({ .<HEAD>.defined });
return gather while @s {
my $h = @s.min: +*.<HEAD>;
take $h<HEAD>;
$h<HEAD> := $h<STREAM>.get
orelse @s .= grep( { $_ !=== $h } );
}
}
sub store (@values) {
my ($filename,$filehandle) = tempfile(:prefix('external-sort.'));
$filehandle.say: join "\n", @values.sort: +*;
$filename
}
- we're going to pretend that this is a long stream of input from stdin...
my (@chunk,@files); for (<43 2 45 32 15 4 3 -9 45 66 0 42 78 123 -11 76 55 87 -2 64 92 34>) {
@chunk.push: $_; @files.push: store(@chunk) and @chunk = () if @chunk.elems == 4; # limit of records per merge file
} @files.push: store(@chunk) if @chunk;
say join ' ', merge_streams @files».&open;</lang>
- Output:
-11 -9 -2 0 2 3 4 15 32 34 42 43 45 45 55 64 66 76 78 87 92 123
REXX
Programming note: the method used to generate the input file is to create the file with 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. <lang rexx>/*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 @.j==@.; 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; y=@.; z=0 /*find the lowest value for N values.*/
do k=1 for j /*traipse through the stemmed @ array.*/
if @.k==@. then call rdr k /*Not defined? Then read a file record*/
if @.k<<y then do; y=@.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; @.a=@.; 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</lang>
Wren
A bit simpler than the Go version as we use fixed length integers which (together with a following space) can be sorted as strings. <lang ecmascript>import "io" for File import "random" for Random import "/dynamic" for Struct import "/sort" for Sort import "/str" for Str
var MinHeapNode = Struct.create("MinHeapNode", ["element", "index"])
class MinHeap {
construct new(nodes) {
_nodes = nodes
var start = ((_nodes.count-1)/2).floor
for (i in start..0) minHeapify(i)
}
left(i) { 2*i + 1 }
right(i) { 2*i + 2 }
nodes { _nodes }
min { _nodes[0] }
replaceMin(x) {
_nodes[0] = x
minHeapify(0)
}
minHeapify(i) {
var l = left(i)
var r = right(i)
var smallest = i
var heapSize = _nodes.count
if (l < heapSize && Str.lt(_nodes[l].element, _nodes[i].element)) smallest = l
if (r < heapSize && Str.lt(_nodes[r].element, _nodes[smallest].element)) smallest = r
if (smallest != i) {
_nodes.swap(i, smallest)
minHeapify(smallest)
}
}
}
// Merge k sorted files: es0,es1 etc. var mergeFiles = Fn.new { |outputFile, k, e|
var inp = List.filled(k, null)
var offset = List.filled(k, 0) // current offset for each input file
for (i in 0...k) {
var fileName = "es%(i)"
inp[i] = File.open(fileName)
}
var out = File.create(outputFile)
var nodes = List.filled(k, null)
for (i in 0...k) nodes[i] = MinHeapNode.new(0, 0)
var i = 0
while (i < k) {
var bytes = inp[i].readBytes(e)
if (bytes.count < e) break // end of file reached
nodes[i].element = bytes
nodes[i].index = i
offset[i] = offset[i] + e
i = i + 1
}
var hp = MinHeap.new(nodes[0...i])
var count = 0
while (count != i) {
var root = hp.min
out.writeBytes(root.element)
var bytes = inp[root.index].readBytes(e, offset[root.index])
if (bytes.count < e) { // end of file reached
root.element = "999999 "
count = count + 1
} else {
root.element = bytes
offset[root.index] = offset[root.index] + e
}
hp.replaceMin(root)
}
for (j in 0...k) inp[j].close()
out.close()
}
// Create initial runs, divide them evenly amongst the output files // and then merge-sort them. var createInitialRuns = Fn.new { |inputFile, numWays, runSize, elementSize|
var inp = File.open(inputFile)
var offset = 0
for (i in 0...numWays) {
var fileName = "es%(i)" // es0, es1 etc.
var bytes = inp.readBytes(runSize * elementSize, offset)
offset = offset + runSize * elementSize
var numbers = Str.chunks(bytes, elementSize)
numbers = Sort.merge(numbers)
File.create(fileName) { |f| f.writeBytes(numbers.join("")) }
}
inp.close()
}
var externalSort = Fn.new { |inputFile, outputFile, numWays, runSize, elementSize|
createInitialRuns.call(inputFile, numWays, runSize, elementSize) mergeFiles.call(outputFile, numWays, elementSize)
}
// Create a small test file of 40 random 6 digit integers and split it into 4 files // of 10 such integers each. var numWays = 4 var runSize = 10 var elementSize = 7 // 6 digits + a following space var inputFile = "external_sort_input.txt" var outputFile = "external_sort_output.txt" var inp = File.create(inputFile) var rand = Random.new() var min = 100000 var max = 999999 for (i in 0...numWays*runSize) inp.writeBytes("%(rand.int(min, max).toString) ") inp.close() externalSort.call(inputFile, outputFile, numWays, runSize, elementSize) // remove temporary files for (i in 0...numWays) {
var fileName = "es%(i)" File.delete(fileName)
}</lang>
- Output:
Sample run:
Contents of external_sort_input.txt: 195387 279593 270645 457221 187563 459521 984067 443317 890630 986820 357072 302605 354825 295908 541221 273855 318978 913819 961359 776939 337617 640070 100140 266938 597987 305187 731698 449166 388165 121283 516001 256453 197931 660491 785453 544828 346520 532447 688793 194774 Contents of external_sort_output.txt: 100140 121283 187563 194774 195387 197931 256453 266938 270645 273855 279593 295908 302605 305187 318978 337617 346520 354825 357072 388165 443317 449166 457221 459521 516001 532447 541221 544828 597987 640070 660491 688793 731698 776939 785453 890630 913819 961359 984067 986820