index/suffixarray: add 32-bit implementation

The original index/suffixarray used 32-bit ints on 64-bit machines,
because that's what 'int' meant in Go at the time. When we changed
the meaning of int, that doubled the space overhead of suffix arrays
for all uses, even though the vast majority of them describe less
than 2 GB of text.

The space overhead of a suffix array compared to the text is not
insignificant: there's a big difference for many uses between 4X and 8X.

This CL adjusts names in qsufsort.go so that a global search and
replace s/32/64/g produces a working 64-bit implementation,
and then it modifies suffixarray.go to choose between the 32-bit
and 64-bit implementation as appropriate depending on the input size.
The 64-bit implementation is generated by 'go generate'.

This CL also restructures the benchmarks, to test different
input sizes, different input texts, and 32-bit vs 64-bit.

The serialized form uses varint-encoded numbers and is unchanged,
so on-disk suffix arrays written by older versions of Go will be
readable by this version, and vice versa.

The 32-bit version runs a up to 17% faster than the 64-bit version
on real inputs, but more importantly it uses 50% less memory.

I have a followup CL that also implements a faster algorithm
on top of these improvements, but these are a good first step.

name                                  64-bit speed   32-bit speed    delta
New/text=opticks/size=100K/bits=*-12  4.44MB/s ± 0%  4.64MB/s ± 0%   +4.41%  (p=0.008 n=5+5)
New/text=opticks/size=500K/bits=*-12  3.70MB/s ± 1%  3.82MB/s ± 0%   +3.30%  (p=0.008 n=5+5)
New/text=go/size=100K/bits=*-12       4.40MB/s ± 0%  4.61MB/s ± 0%   +4.82%  (p=0.008 n=5+5)
New/text=go/size=500K/bits=*-12       3.66MB/s ± 0%  3.77MB/s ± 0%   +3.01%  (p=0.016 n=4+5)
New/text=go/size=1M/bits=*-12         3.29MB/s ± 0%  3.55MB/s ± 0%   +7.90%  (p=0.016 n=5+4)
New/text=go/size=5M/bits=*-12         2.25MB/s ± 1%  2.65MB/s ± 0%  +17.81%  (p=0.008 n=5+5)
New/text=go/size=10M/bits=*-12        1.82MB/s ± 0%  2.09MB/s ± 1%  +14.36%  (p=0.008 n=5+5)
New/text=go/size=50M/bits=*-12        1.35MB/s ± 0%  1.51MB/s ± 1%  +12.33%  (p=0.008 n=5+5)
New/text=zero/size=100K/bits=*-12     3.42MB/s ± 0%  3.32MB/s ± 0%   -2.74%  (p=0.000 n=5+4)
New/text=zero/size=500K/bits=*-12     3.00MB/s ± 1%  2.97MB/s ± 0%   -1.13%  (p=0.016 n=5+4)
New/text=zero/size=1M/bits=*-12       2.81MB/s ± 0%  2.78MB/s ± 2%     ~     (p=0.167 n=5+5)
New/text=zero/size=5M/bits=*-12       2.46MB/s ± 0%  2.53MB/s ± 0%   +3.18%  (p=0.008 n=5+5)
New/text=zero/size=10M/bits=*-12      2.35MB/s ± 0%  2.42MB/s ± 0%   +2.98%  (p=0.016 n=4+5)
New/text=zero/size=50M/bits=*-12      2.12MB/s ± 0%  2.18MB/s ± 0%   +3.02%  (p=0.008 n=5+5)
New/text=rand/size=100K/bits=*-12     6.98MB/s ± 0%  7.22MB/s ± 0%   +3.38%  (p=0.016 n=4+5)
New/text=rand/size=500K/bits=*-12     5.53MB/s ± 0%  5.64MB/s ± 0%   +1.92%  (p=0.008 n=5+5)
New/text=rand/size=1M/bits=*-12       4.62MB/s ± 1%  5.06MB/s ± 0%   +9.61%  (p=0.008 n=5+5)
New/text=rand/size=5M/bits=*-12       3.09MB/s ± 0%  3.43MB/s ± 0%  +10.94%  (p=0.016 n=4+5)
New/text=rand/size=10M/bits=*-12      2.68MB/s ± 0%  2.95MB/s ± 0%  +10.39%  (p=0.008 n=5+5)
New/text=rand/size=50M/bits=*-12      1.92MB/s ± 0%  2.06MB/s ± 1%   +7.41%  (p=0.008 n=5+5)
SaveRestore/bits=*-12                  243MB/s ± 1%   259MB/s ± 0%   +6.68%  (p=0.000 n=9+10)

name                               64-bit alloc/op  32-bit alloc/op  delta
New/text=opticks/size=100K/bits=*-12    1.62MB ± 0%    0.81MB ± 0%  -50.00%  (p=0.000 n=5+4)
New/text=opticks/size=500K/bits=*-12    8.07MB ± 0%    4.04MB ± 0%  -49.89%  (p=0.008 n=5+5)
New/text=go/size=100K/bits=*-12         1.62MB ± 0%    0.81MB ± 0%  -50.00%  (p=0.008 n=5+5)
New/text=go/size=500K/bits=*-12         8.07MB ± 0%    4.04MB ± 0%  -49.89%  (p=0.029 n=4+4)
New/text=go/size=1M/bits=*-12           16.1MB ± 0%     8.1MB ± 0%  -49.95%  (p=0.008 n=5+5)
New/text=go/size=5M/bits=*-12           80.3MB ± 0%    40.2MB ± 0%     ~     (p=0.079 n=4+5)
New/text=go/size=10M/bits=*-12           160MB ± 0%      80MB ± 0%  -50.00%  (p=0.008 n=5+5)
New/text=go/size=50M/bits=*-12           805MB ± 0%     402MB ± 0%  -50.06%  (p=0.029 n=4+4)
New/text=zero/size=100K/bits=*-12       3.02MB ± 0%    1.46MB ± 0%     ~     (p=0.079 n=4+5)
New/text=zero/size=500K/bits=*-12       19.7MB ± 0%     8.7MB ± 0%  -55.98%  (p=0.008 n=5+5)
New/text=zero/size=1M/bits=*-12         39.0MB ± 0%    19.7MB ± 0%  -49.60%  (p=0.000 n=5+4)
New/text=zero/size=5M/bits=*-12          169MB ± 0%      85MB ± 0%  -49.46%  (p=0.029 n=4+4)
New/text=zero/size=10M/bits=*-12         333MB ± 0%     169MB ± 0%  -49.43%  (p=0.000 n=5+4)
New/text=zero/size=50M/bits=*-12        1.63GB ± 0%    0.74GB ± 0%  -54.61%  (p=0.008 n=5+5)
New/text=rand/size=100K/bits=*-12       1.61MB ± 0%    0.81MB ± 0%  -50.00%  (p=0.000 n=5+4)
New/text=rand/size=500K/bits=*-12       8.07MB ± 0%    4.04MB ± 0%  -49.89%  (p=0.000 n=5+4)
New/text=rand/size=1M/bits=*-12         16.1MB ± 0%     8.1MB ± 0%  -49.95%  (p=0.029 n=4+4)
New/text=rand/size=5M/bits=*-12         80.7MB ± 0%    40.3MB ± 0%  -50.06%  (p=0.008 n=5+5)
New/text=rand/size=10M/bits=*-12         161MB ± 0%      81MB ± 0%  -50.03%  (p=0.008 n=5+5)
New/text=rand/size=50M/bits=*-12         806MB ± 0%     403MB ± 0%  -50.00%  (p=0.016 n=4+5)
SaveRestore/bits=*-12                   9.47MB ± 0%    5.28MB ± 0%  -44.29%  (p=0.000 n=9+8)

https://perf.golang.org/search?q=upload:20190126.1+|+bits:64+vs+bits:32

Fixes #6816.

Change-Id: Ied2fbea519a202ecc43719debcd233344ce38847
Reviewed-on: https://go-review.googlesource.com/c/go/+/174097
Run-TryBot: Russ Cox <rsc@golang.org>
TryBot-Result: Gobot Gobot <gobot@golang.org>
Reviewed-by: Brad Fitzpatrick <bradfitz@golang.org>

src/index/suffixarray/gen64.go

@@ -0,0 +1,31 @@
+// Copyright 2019 The Go Authors. All rights reserved.
+// Use of this source code is governed by a BSD-style
+// license that can be found in the LICENSE file.
+
+// +build ignore
+
+// Gen64 generates qsufsort64.go from qsufsort.go by s/32/64/g.
+package main
+
+import (
+	"bytes"
+	"io/ioutil"
+	"log"
+)
+
+func main() {
+	log.SetPrefix("gen64: ")
+	log.SetFlags(0)
+
+	data, err := ioutil.ReadFile("qsufsort.go")
+	if err != nil {
+		log.Fatal(err)
+	}
+
+	data = bytes.Replace(data, []byte("\n\n"), []byte("\n\n// Code generated by gen64.go; DO NOT EDIT.\n//go:generate go run gen64.go\n\n"), 1)
+	data = bytes.Replace(data, []byte("32"), []byte("64"), -1)
+
+	if err := ioutil.WriteFile("qsufsort64.go", data, 0666); err != nil {
+		log.Fatal(err)
+	}
+}

src/index/suffixarray/qsufsort.go

@@ -24,26 +24,28 @@
 
 package suffixarray
 
-import "sort"
+import (
+	"sort"
+)
 
-func qsufsort(data []byte) []int {
+func qsufsort32(data []byte) []int32 {
 	// initial sorting by first byte of suffix
-	sa := sortedByFirstByte(data)
+	sa := sortedByFirstByte32(data)
 	if len(sa) < 2 {
 		return sa
 	}
 	// initialize the group lookup table
 	// this becomes the inverse of the suffix array when all groups are sorted
-	inv := initGroups(sa, data)
+	inv := initGroups32(sa, data)
 
 	// the index starts 1-ordered
-	sufSortable := &suffixSortable{sa: sa, inv: inv, h: 1}
+	sufSortable := &suffixSortable32{sa: sa, inv: inv, h: 1}
 
-	for sa[0] > -len(sa) { // until all suffixes are one big sorted group
+	for sa[0] > -int32(len(sa)) { // until all suffixes are one big sorted group
 		// The suffixes are h-ordered, make them 2*h-ordered
-		pi := 0 // pi is first position of first group
-		sl := 0 // sl is negated length of sorted groups
-		for pi < len(sa) {
+		pi := int32(0) // pi is first position of first group
+		sl := int32(0) // sl is negated length of sorted groups
+		for pi < int32(len(sa)) {
 			if s := sa[pi]; s < 0 { // if pi starts sorted group
 				pi -= s // skip over sorted group
 				sl += s // add negated length to sl
@@ -67,12 +69,12 @@ func qsufsort(data []byte) []int {
 	}
 
 	for i := range sa { // reconstruct suffix array from inverse
-		sa[inv[i]] = i
+		sa[inv[i]] = int32(i)
 	}
 	return sa
 }
 
-func sortedByFirstByte(data []byte) []int {
+func sortedByFirstByte32(data []byte) []int32 {
 	// total byte counts
 	var count [256]int
 	for _, b := range data {
@@ -84,20 +86,20 @@ func sortedByFirstByte(data []byte) []int {
 		count[b], sum = sum, count[b]+sum
 	}
 	// iterate through bytes, placing index into the correct spot in sa
-	sa := make([]int, len(data))
+	sa := make([]int32, len(data))
 	for i, b := range data {
-		sa[count[b]] = i
+		sa[count[b]] = int32(i)
 		count[b]++
 	}
 	return sa
 }
 
-func initGroups(sa []int, data []byte) []int {
+func initGroups32(sa []int32, data []byte) []int32 {
 	// label contiguous same-letter groups with the same group number
-	inv := make([]int, len(data))
-	prevGroup := len(sa) - 1
+	inv := make([]int32, len(data))
+	prevGroup := int32(len(sa)) - 1
 	groupByte := data[sa[prevGroup]]
-	for i := len(sa) - 1; i >= 0; i-- {
+	for i := int32(len(sa)) - 1; i >= 0; i-- {
 		if b := data[sa[i]]; b < groupByte {
 			if prevGroup == i+1 {
 				sa[i+1] = -1
@@ -114,13 +116,13 @@ func initGroups(sa []int, data []byte) []int {
 	// This is necessary to ensure the suffix "a" is before "aba"
 	// when using a potentially unstable sort.
 	lastByte := data[len(data)-1]
-	s := -1
+	s := int32(-1)
 	for i := range sa {
 		if sa[i] >= 0 {
 			if data[sa[i]] == lastByte && s == -1 {
-				s = i
+				s = int32(i)
 			}
-			if sa[i] == len(sa)-1 {
+			if sa[i] == int32(len(sa))-1 {
 				sa[i], sa[s] = sa[s], sa[i]
 				inv[sa[s]] = s
 				sa[s] = -1 // mark it as an isolated sorted group
@@ -131,31 +133,31 @@ func initGroups(sa []int, data []byte) []int {
 	return inv
 }
 
-type suffixSortable struct {
-	sa  []int
-	inv []int
-	h   int
-	buf []int // common scratch space
+type suffixSortable32 struct {
+	sa  []int32
+	inv []int32
+	h   int32
+	buf []int32 // common scratch space
 }
 
-func (x *suffixSortable) Len() int           { return len(x.sa) }
-func (x *suffixSortable) Less(i, j int) bool { return x.inv[x.sa[i]+x.h] < x.inv[x.sa[j]+x.h] }
-func (x *suffixSortable) Swap(i, j int)      { x.sa[i], x.sa[j] = x.sa[j], x.sa[i] }
+func (x *suffixSortable32) Len() int           { return len(x.sa) }
+func (x *suffixSortable32) Less(i, j int) bool { return x.inv[x.sa[i]+x.h] < x.inv[x.sa[j]+x.h] }
+func (x *suffixSortable32) Swap(i, j int)      { x.sa[i], x.sa[j] = x.sa[j], x.sa[i] }
 
-func (x *suffixSortable) updateGroups(offset int) {
+func (x *suffixSortable32) updateGroups(offset int32) {
 	bounds := x.buf[0:0]
 	group := x.inv[x.sa[0]+x.h]
 	for i := 1; i < len(x.sa); i++ {
 		if g := x.inv[x.sa[i]+x.h]; g > group {
-			bounds = append(bounds, i)
+			bounds = append(bounds, int32(i))
 			group = g
 		}
 	}
-	bounds = append(bounds, len(x.sa))
+	bounds = append(bounds, int32(len(x.sa)))
 	x.buf = bounds
 
 	// update the group numberings after all new groups are determined
-	prev := 0
+	prev := int32(0)
 	for _, b := range bounds {
 		for i := prev; i < b; i++ {
 			x.inv[x.sa[i]] = offset + b - 1