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Russ Cox 6ca324f283 index/suffixarray: index 3-10X faster in half the memory 
This CL changes the index/suffixarray construction algorithm from QSufSort to SAIS.

For an N-byte input, QSufSort runs in O(N log N) time and requires
an N-int temporary work space in addition to the N-int output.

In contrast, SAIS runs in O(N) time and, for essentially all real inputs,
is able to use the N-int output buffer as its temporary work space.
(In pathological cases, SAIS must allocate a temporary work space of
at most N/2 ints. There exist more complex variants that guarantee
to avoid the work space in all cases, but they hardly seem worth the cost
given how rare these pathological cases are.)

The SAIS code therefore uses 50% of the memory across the board.
It also runs 3-10X faster on real input text.

This CL also adds more extensive algorithmic tests, including an
exhaustive test over small inputs to catch corner case problems.

name                                   old speed      new speed        delta
New/text=opticks/size=100K/bits=32-12  6.15MB/s ± 1%   26.79MB/s ± 1%   +335.89%  (p=0.008 n=5+5)
New/text=opticks/size=100K/bits=64-12  5.90MB/s ± 2%   27.29MB/s ± 2%   +362.23%  (p=0.008 n=5+5)
New/text=opticks/size=500K/bits=32-12  4.99MB/s ± 3%   25.37MB/s ± 2%   +408.01%  (p=0.008 n=5+5)
New/text=opticks/size=500K/bits=64-12  4.88MB/s ± 1%   25.66MB/s ± 4%   +425.52%  (p=0.008 n=5+5)
New/text=go/size=100K/bits=32-12       5.81MB/s ± 1%   26.49MB/s ± 2%   +355.85%  (p=0.008 n=5+5)
New/text=go/size=100K/bits=64-12       5.76MB/s ± 2%   26.65MB/s ± 3%   +362.60%  (p=0.008 n=5+5)
New/text=go/size=500K/bits=32-12       4.91MB/s ± 1%   25.12MB/s ± 2%   +411.86%  (p=0.008 n=5+5)
New/text=go/size=500K/bits=64-12       4.83MB/s ± 2%   25.79MB/s ± 2%   +434.44%  (p=0.008 n=5+5)
New/text=go/size=1M/bits=32-12         4.62MB/s ± 2%   24.87MB/s ± 2%   +438.78%  (p=0.008 n=5+5)
New/text=go/size=1M/bits=64-12         4.39MB/s ± 2%   24.61MB/s ± 2%   +460.68%  (p=0.008 n=5+5)
New/text=go/size=5M/bits=32-12         2.85MB/s ± 2%   24.78MB/s ± 7%   +768.33%  (p=0.008 n=5+5)
New/text=go/size=5M/bits=64-12         2.28MB/s ± 1%   18.70MB/s ± 7%   +719.63%  (p=0.008 n=5+5)
New/text=go/size=10M/bits=32-12        2.08MB/s ± 1%   21.04MB/s ± 6%   +909.60%  (p=0.008 n=5+5)
New/text=go/size=10M/bits=64-12        1.83MB/s ± 1%   16.64MB/s ± 2%   +809.18%  (p=0.008 n=5+5)
New/text=go/size=50M/bits=32-12        1.51MB/s ± 0%   10.58MB/s ± 1%   +602.52%  (p=0.008 n=5+5)
New/text=go/size=50M/bits=64-12        1.34MB/s ± 4%    9.00MB/s ± 1%   +569.35%  (p=0.008 n=5+5)
New/text=zero/size=100K/bits=32-12     4.17MB/s ± 0%  157.56MB/s ± 1%  +3678.42%  (p=0.016 n=4+5)
New/text=zero/size=100K/bits=64-12     4.19MB/s ± 2%  162.72MB/s ± 2%  +3783.63%  (p=0.008 n=5+5)
New/text=zero/size=500K/bits=32-12     3.72MB/s ± 5%  159.17MB/s ± 1%  +4176.57%  (p=0.008 n=5+5)
New/text=zero/size=500K/bits=64-12     3.77MB/s ± 3%  164.95MB/s ± 4%  +4277.60%  (p=0.008 n=5+5)
New/text=zero/size=1M/bits=32-12       3.46MB/s ± 3%  158.42MB/s ± 1%  +4476.08%  (p=0.008 n=5+5)
New/text=zero/size=1M/bits=64-12       3.41MB/s ± 4%  163.70MB/s ± 2%  +4700.65%  (p=0.008 n=5+5)
New/text=zero/size=5M/bits=32-12       3.12MB/s ± 2%  151.92MB/s ± 4%  +4775.48%  (p=0.008 n=5+5)
New/text=zero/size=5M/bits=64-12       3.09MB/s ± 2%  166.19MB/s ± 2%  +5274.84%  (p=0.008 n=5+5)
New/text=zero/size=10M/bits=32-12      2.97MB/s ± 1%  157.75MB/s ± 1%  +5211.38%  (p=0.008 n=5+5)
New/text=zero/size=10M/bits=64-12      2.92MB/s ± 1%  162.75MB/s ± 2%  +5473.77%  (p=0.008 n=5+5)
New/text=zero/size=50M/bits=32-12      2.67MB/s ± 1%  144.43MB/s ± 5%  +5305.39%  (p=0.008 n=5+5)
New/text=zero/size=50M/bits=64-12      2.61MB/s ± 1%  125.19MB/s ± 2%  +4700.33%  (p=0.016 n=5+4)
New/text=rand/size=100K/bits=32-12     8.69MB/s ± 6%   27.60MB/s ± 1%   +217.73%  (p=0.008 n=5+5)
New/text=rand/size=100K/bits=64-12     8.92MB/s ± 1%   26.37MB/s ± 4%   +195.50%  (p=0.008 n=5+5)
New/text=rand/size=500K/bits=32-12     7.11MB/s ± 2%   25.23MB/s ± 2%   +254.78%  (p=0.008 n=5+5)
New/text=rand/size=500K/bits=64-12     7.08MB/s ± 1%   25.45MB/s ± 2%   +259.56%  (p=0.008 n=5+5)
New/text=rand/size=1M/bits=32-12       6.45MB/s ± 2%   24.47MB/s ± 3%   +279.11%  (p=0.008 n=5+5)
New/text=rand/size=1M/bits=64-12       6.09MB/s ± 4%   23.00MB/s ± 4%   +277.85%  (p=0.008 n=5+5)
New/text=rand/size=5M/bits=32-12       3.68MB/s ± 3%   10.34MB/s ± 5%   +181.08%  (p=0.008 n=5+5)
New/text=rand/size=5M/bits=64-12       3.25MB/s ± 1%    6.23MB/s ± 1%    +91.93%  (p=0.008 n=5+5)
New/text=rand/size=10M/bits=32-12      3.03MB/s ± 1%    5.61MB/s ± 2%    +85.28%  (p=0.008 n=5+5)
New/text=rand/size=10M/bits=64-12      2.80MB/s ± 1%    4.29MB/s ± 2%    +53.40%  (p=0.008 n=5+5)
New/text=rand/size=50M/bits=32-12      2.11MB/s ± 0%    2.45MB/s ± 1%    +16.23%  (p=0.029 n=4+4)
New/text=rand/size=50M/bits=64-12      2.04MB/s ± 1%    2.24MB/s ± 1%    +10.03%  (p=0.016 n=5+4)
SaveRestore/bits=32-12                  327MB/s ± 5%     319MB/s ± 2%       ~     (p=0.310 n=5+5)
SaveRestore/bits=64-12                  306MB/s ± 3%     306MB/s ± 2%       ~     (p=0.841 n=5+5)

name                                   old alloc/op   new alloc/op     delta
New/text=opticks/size=100K/bits=32-12     811kB ± 0%       401kB ± 0%    -50.51%  (p=0.008 n=5+5)
New/text=opticks/size=100K/bits=64-12    1.62MB ± 0%      0.80MB ± 0%    -50.51%  (p=0.008 n=5+5)
New/text=opticks/size=500K/bits=32-12    4.04MB ± 0%      2.01MB ± 0%    -50.37%  (p=0.008 n=5+5)
New/text=opticks/size=500K/bits=64-12    8.07MB ± 0%      4.01MB ± 0%    -50.36%  (p=0.016 n=4+5)
New/text=go/size=100K/bits=32-12          811kB ± 0%       401kB ± 0%       ~     (p=0.079 n=4+5)
New/text=go/size=100K/bits=64-12         1.62MB ± 0%      0.80MB ± 0%    -50.50%  (p=0.008 n=5+5)
New/text=go/size=500K/bits=32-12         4.04MB ± 0%      2.01MB ± 0%       ~     (p=0.079 n=4+5)
New/text=go/size=500K/bits=64-12         8.07MB ± 0%      4.01MB ± 0%    -50.36%  (p=0.000 n=4+5)
New/text=go/size=1M/bits=32-12           8.07MB ± 0%      4.01MB ± 0%    -50.36%  (p=0.008 n=5+5)
New/text=go/size=1M/bits=64-12           16.1MB ± 0%       8.0MB ± 0%    -50.36%  (p=0.008 n=5+5)
New/text=go/size=5M/bits=32-12           40.2MB ± 0%      20.0MB ± 0%    -50.18%  (p=0.008 n=5+5)
New/text=go/size=5M/bits=64-12           80.3MB ± 0%      40.0MB ± 0%    -50.18%  (p=0.008 n=5+5)
New/text=go/size=10M/bits=32-12          80.2MB ± 0%      40.0MB ± 0%    -50.09%  (p=0.000 n=5+4)
New/text=go/size=10M/bits=64-12           160MB ± 0%        80MB ± 0%    -50.09%  (p=0.000 n=5+4)
New/text=go/size=50M/bits=32-12           402MB ± 0%       200MB ± 0%    -50.29%  (p=0.000 n=5+4)
New/text=go/size=50M/bits=64-12           805MB ± 0%       400MB ± 0%    -50.29%  (p=0.000 n=5+4)
New/text=zero/size=100K/bits=32-12       1.46MB ± 0%      0.40MB ± 0%    -72.46%  (p=0.008 n=5+5)
New/text=zero/size=100K/bits=64-12       3.02MB ± 0%      0.80MB ± 0%    -73.45%  (p=0.008 n=5+5)
New/text=zero/size=500K/bits=32-12       8.66MB ± 0%      2.01MB ± 0%       ~     (p=0.079 n=4+5)
New/text=zero/size=500K/bits=64-12       19.7MB ± 0%       4.0MB ± 0%    -79.63%  (p=0.008 n=5+5)
New/text=zero/size=1M/bits=32-12         19.7MB ± 0%       4.0MB ± 0%       ~     (p=0.079 n=4+5)
New/text=zero/size=1M/bits=64-12         39.0MB ± 0%       8.0MB ± 0%    -79.48%  (p=0.000 n=5+4)
New/text=zero/size=5M/bits=32-12         85.2MB ± 0%      20.0MB ± 0%    -76.52%  (p=0.008 n=5+5)
New/text=zero/size=5M/bits=64-12          169MB ± 0%        40MB ± 0%    -76.27%  (p=0.008 n=5+5)
New/text=zero/size=10M/bits=32-12         169MB ± 0%        40MB ± 0%    -76.26%  (p=0.000 n=5+4)
New/text=zero/size=10M/bits=64-12         333MB ± 0%        80MB ± 0%    -75.99%  (p=0.008 n=5+5)
New/text=zero/size=50M/bits=32-12         739MB ± 0%       200MB ± 0%    -72.93%  (p=0.000 n=4+5)
New/text=zero/size=50M/bits=64-12        1.63GB ± 0%      0.40GB ± 0%    -75.42%  (p=0.008 n=5+5)
New/text=rand/size=100K/bits=32-12        807kB ± 0%       401kB ± 0%    -50.25%  (p=0.008 n=5+5)
New/text=rand/size=100K/bits=64-12       1.61MB ± 0%      0.80MB ± 0%    -50.25%  (p=0.008 n=5+5)
New/text=rand/size=500K/bits=32-12       4.04MB ± 0%      2.01MB ± 0%       ~     (p=0.079 n=4+5)
New/text=rand/size=500K/bits=64-12       8.07MB ± 0%      4.01MB ± 0%       ~     (p=0.079 n=4+5)
New/text=rand/size=1M/bits=32-12         8.07MB ± 0%      4.01MB ± 0%    -50.36%  (p=0.000 n=5+4)
New/text=rand/size=1M/bits=64-12         16.1MB ± 0%       8.0MB ± 0%    -50.36%  (p=0.008 n=5+5)
New/text=rand/size=5M/bits=32-12         40.3MB ± 0%      20.0MB ± 0%    -50.35%  (p=0.029 n=4+4)
New/text=rand/size=5M/bits=64-12         80.7MB ± 0%      40.0MB ± 0%       ~     (p=0.079 n=4+5)
New/text=rand/size=10M/bits=32-12        80.7MB ± 0%      40.0MB ± 0%    -50.41%  (p=0.008 n=5+5)
New/text=rand/size=10M/bits=64-12         161MB ± 0%        80MB ± 0%    -50.44%  (p=0.029 n=4+4)
New/text=rand/size=50M/bits=32-12         403MB ± 0%       200MB ± 0%    -50.36%  (p=0.000 n=5+4)
New/text=rand/size=50M/bits=64-12         806MB ± 0%       400MB ± 0%       ~     (p=0.079 n=4+5)
SaveRestore/bits=32-12                   5.28MB ± 0%      5.28MB ± 0%       ~     (p=1.000 n=5+5)
SaveRestore/bits=64-12                   9.47MB ± 0%      9.47MB ± 0%       ~     (p=0.286 n=5+5)

https://perf.golang.org/search?q=upload:20190426.1

Fixes #15480.

Change-Id: I0790f6edf67f5a9c02b4462632b4942e0c37988b
Reviewed-on: https://go-review.googlesource.com/c/go/+/174100
Run-TryBot: Russ Cox <rsc@golang.org>
TryBot-Result: Gobot Gobot <gobot@golang.org>
Reviewed-by: Eric Roshan-Eisner <edre@google.com>
Reviewed-by: Brad Fitzpatrick <bradfitz@golang.org>
2019-05-13 18:50:32 +00:00
..
example_test.go
gen.go index/suffixarray: index 3-10X faster in half the memory 2019-05-13 18:50:32 +00:00
sais2.go index/suffixarray: index 3-10X faster in half the memory 2019-05-13 18:50:32 +00:00
sais.go index/suffixarray: index 3-10X faster in half the memory 2019-05-13 18:50:32 +00:00
suffixarray_test.go index/suffixarray: index 3-10X faster in half the memory 2019-05-13 18:50:32 +00:00
suffixarray.go index/suffixarray: index 3-10X faster in half the memory 2019-05-13 18:50:32 +00:00