| Andrew Cooke | Contents | Latest | RSS | Twitter | Previous | Next

C[omp]ute

Welcome to my blog, which was once a mailing list of the same name and is still generated by mail. Please reply via the "comment" links.

Always interested in offers/projects/new ideas. Eclectic experience in fields like: numerical computing; Python web; Java enterprise; functional languages; GPGPU; SQL databases; etc. Based in Santiago, Chile; telecommute worldwide. CV; email.

Personal Projects

Lepl parser for Python.

Colorless Green.

Photography around Santiago.

SVG experiment.

Professional Portfolio

Calibration of seismometers.

Data access via web services.

Cache rewrite.

Extending OpenSSH.

C-ORM: docs, API.

Last 100 entries

Lepton Decay Irregularity; An Easier Way; Julia's BinDeps (aka How To Install Cairo); Good Example Of Good Police Work (And Anonymity Being Hard); Best Santiago Burgers; Also; Michael Emmerich (Vibrator Translator) Interview (Japanese Books); Clarice Lispector (Brazillian Writer); Books On Evolution; Looks like Ara (Modular Phone) is dead; Index - Translations From Chile; More Emotion in Chilean Wines; Week 7; Aeon Magazine (Science-ish); QM, Deutsch, Constructor Theory; Interesting Talk Transcripts; Interesting Suggestion Of Election Fraud; "Hard" Books; Articles or Papers on depolarizing the US; Textbook for "QM as complex probabilities"; SFO Get Libor Trader (14 years); Why Are There Still So Many Jobs?; Navier Stokes Incomplete; More on Benford; FBI Claimed Vandalism; Architectural Tessellation; Also: Go, Blake's 7; Delusions of Gender (book); Crypto AG DID work with NSA / GCHQ; UNUMS (Universal Number Format); MOOCs (Massive Open Online Courses); Interesting Looking Game; Euler's Theorem for Polynomials; Weeks 3-6; Reddit Comment; Differential Cryptanalysis For Dummies; Japanese Graphic Design; Books To Be Re-Read; And Today I Learned Bugs Need Clear Examples; Factoring a 67 bit prime in your head; Islamic Geometric Art; Useful Julia Backtraces from Tasks; Nothing, however, is lost with less discomfort than that which, when lost, cannot be missed; Article on Didion; Cost of Living by City; British Slavery; Derrida on Metaphor; African SciFi; Traits in Julia; Alternative Japanese Lit; Pulic Key as Address (Snow); Why Information Grows; The Blindness Of The Chilean Elite; Some Victoriagate Links; This Is Why I Left StackOverflow; New TLS Implementation; Maths for Physicists; How I Am 8; 1000 Word Philosophy; Cyberpunk Reading List; Detailed Discussion of Message Dispatch in ParserCombinator Library for Julia; FizzBuzz in Julia w Dependent Types; kokko - Design Shop in Osaka; Summary of Greece, Currently; LLVM and GPUs; See Also; Schoolgirl Groyps (Maths); Japanese Lit; Another Example - Modular Arithmetic; Music from United; Python 2 and 3 compatible alternative.; Read Agatha Christie for the Plot; A Constructive Look at TempleOS; Music Thread w Many Recommendations; Fixed Version; A Useful Julia Macro To Define Equality And Hash; k3b cdrom access, OpenSuse 13.1; Week 2; From outside, the UK looks less than stellar; Huge Fonts in VirtualBox; Keen - Complex Emergencies; The Fallen of World War II; Some Spanish Fiction; Calling C From Fortran 95; Bjork DJ Set; Z3 Example With Python; Week 1; Useful Guide To Starting With IJulia; UK Election + Media; Review: Reinventing Organizations; Inline Assembly With Julia / LLVM; Against the definition of types; Dumb Crypto Paper; The Search For Quasi-Periodicity...; Is There An Alternative To Processing?; CARDIAC (CARDboard Illustrative Aid to Computation); The Bolivian Case Against Chile At The Hague; Clear, Cogent Economic Arguments For Immigration; A Program To Say If I Am Working; Decent Cards For Ill People; New Photo

© 2006-2015 Andrew Cooke (site) / post authors (content).

RXPY Benchmarks

From: andrew cooke <andrew@...>

Date: Sat, 17 Jul 2010 16:48:30 -0400

Much of this is just duplicating the re2 work, and the rest is RXPY-specific,
but even so, these are quite interesting (for me, at least).

Note that the times are relative to the Python re package (log10 in brackets).
Also, the plots are both linear ### and logarithmic [ ].


First, some basic matching.  This is just showing how slow my code is
(hundreds of times slower than the re package).

Match a(.)c against abc
             Backtracking [##########                   ]              95 [2.0]
            Parallel wide [#######################            ]       206 [2.3]
    Parallel wide, hashed [#################################### ]     315 [2.5]
             Parallel seq [#######################            ]       205 [2.3]
     Parallel seq, hashed [###################################  ]     304 [2.5]
            Parallel beam [############################        ]      245 [2.4]
    Parallel beam, hashed [######################################]    339 [2.5]

Match (a)b(?<=(?(1)b|x))(c) against abc
             Backtracking [############                   ]           210 [2.3]
            Parallel wide [#########################          ]       398 [2.6]
    Parallel wide, hashed [#################################    ]     531 [2.7]
             Parallel seq [#########################          ]       400 [2.6]
     Parallel seq, hashed [##################################   ]     546 [2.7]
            Parallel beam [##############################      ]      480 [2.7]
    Parallel beam, hashed [######################################]    622 [2.8]

Match a*b against a^100b
             Backtracking [####################################  ]   1902 [3.3]
            Parallel wide [#################################    ]    1737 [3.2]
    Parallel wide, hashed [####################################  ]   1919 [3.3]
             Parallel seq [################################     ]    1733 [3.2]
     Parallel seq, hashed [####################################  ]   1919 [3.3]
            Parallel beam [###################################  ]    1884 [3.3]
    Parallel beam, hashed [######################################]   2073 [3.3]

Match .*b against a^100b
             Backtracking [#################                 ]       1902 [3.3]
            Parallel wide [###############                   ]       1769 [3.2]
    Parallel wide, hashed [#################                 ]       1927 [3.3]
             Parallel seq [###############                   ]       1757 [3.2]
     Parallel seq, hashed [##################                ]       2015 [3.3]
            Parallel beam [###################################  ]    3825 [3.6]
    Parallel beam, hashed [######################################]   4300 [3.6]

Above is quite interesting because the beam search is suddenly twice as slow,
just by changing from "a*b" to ".*b".  That's because the second expression
has a failure ("." matchs the final "b") and so needs to backtrack.  Because
the initial beam width is 1 that means that the entire search must be repeated
with doubled with.


The next test is a search.

Search .*b against a^100b
             Backtracking [                         ]                1172 [3.1]
            Parallel wide [######################################]  41841 [4.6]
    Parallel wide, hashed [                         ]                1459 [3.2]
             Parallel seq [                         ]                1212 [3.1]
     Parallel seq, hashed [                         ]                1338 [3.1]
            Parallel beam [###                          ]            3764 [3.6]
    Parallel beam, hashed [###                          ]            3688 [3.6]

Above shows the problem with a naive wide parallel approach - there are an
awful lot of different states to store.  Of course, most are duplicates so the
hashing removes the problem (as does sequential or beam search).


The next tests show the exponential explosion problem in Python's matcher.
This is a little more difficult to trigger than in the re2 paper because
Python has a "shortcut" (hack!) that avoids the problem in very simple cases
(but, as we will see below, does nothing to address the underlying issues).

Match (?:a|b)?^2n(?:ab)^n against (ab)^n for n=4
             Backtracking [#############                   ]          573 [2.8]
            Parallel wide [#########                     ]            392 [2.6]
    Parallel wide, hashed [##                      ]                  125 [2.1]
             Parallel seq [#########                     ]            398 [2.6]
     Parallel seq, hashed [##                      ]                  125 [2.1]
            Parallel beam [######################################]   1606 [3.2]
    Parallel beam, hashed [########                      ]            360 [2.6]

Match (?:a|b)?^2n(?:ab)^n against (ab)^n for n=6
             Backtracking [######################################]    637 [2.8]
            Parallel wide [#############################       ]      476 [2.7]
    Parallel wide, hashed [#                 ]                         27 [1.4]
             Parallel seq [#############################       ]      475 [2.7]
     Parallel seq, hashed [#                 ]                         27 [1.4]
    Parallel beam, hashed [##                    ]                     51 [1.7]

Match (?:a|b)?^2n(?:ab)^n against (ab)^n for n=8
    Parallel wide, hashed [##############       ]                       4 [0.6]
     Parallel seq, hashed [##############       ]                       4 [0.6]
    Parallel beam, hashed [######################################]     10 [1.0]

As the number of terms increase, only the hashed approaches are efficient (due
to the explosion in the number of states).  This is as expected.  What is nice
to see is that by n=8 my Python code is oly 4x slower than the re package!
This is because the re backtracker is "exploding", while my code is linear
(but slow).


This is only possible, though, when we can discard duplicate state.  Which
isn't so easy when matching groups:

Match (a|b)?^2n(?:ab)^n against (ab)^n for n=4
             Backtracking [#######                       ]            481 [2.7]
            Parallel wide [#####                       ]              378 [2.6]
    Parallel wide, hashed [#########                      ]           627 [2.8]
             Parallel seq [######                       ]             414 [2.6]
     Parallel seq, hashed [##########                     ]           667 [2.8]
            Parallel beam [##########################          ]     1612 [3.2]
    Parallel beam, hashed [######################################]   2415 [3.4]

Match (a|b)?^2n(?:ab)^n against (ab)^n for n=6
             Backtracking [###########################         ]      512 [2.7]
            Parallel wide [######################             ]       415 [2.6]
    Parallel wide, hashed [######################################]    723 [2.9]
             Parallel seq [######################             ]       418 [2.6]
     Parallel seq, hashed [######################################]    714 [2.9]


And here we do no better than normal backtracking.


The main conclusions, then, are:

1 - Python's re package does suffer from the exponential "explosion" issue,
    while my code (with duplicate state elimination) does not.

2 - My code can also handle groups, but the degrades in performance as
    expected.

So RXPY is both general and, when possible, efficient.  Even if it is terribly
slow.

A secondary conclusion is that the beam search approach does not seem to be
worth the trouble.

Andrew

Future Work

From: andrew cooke <andrew@...>

Date: Sun, 18 Jul 2010 08:53:28 -0400

The following optimisations are needed at some point:

- Branches should test whether there is sufficient remaining text.  This can
  be precomputed by nodes.

- Search should identify (at least) initial sequences and optimise on those.
  See the existing re library code.  RXPY could go better and use non-startign
  sequences with a known lookback to start.

But for now I think I am going to produce a simplified version of the hashed,
wide engine and see how that can work on PyPy.

Andrew

More Benchmarks

From: andrew cooke <andrew@...>

Date: Sun, 25 Jul 2010 11:42:01 -0400

There are some new engines here.  "Simple" is a stripped down engine that does
not support loops or groups.  "Complex" is similar to "Wide hashed", but has
much more care taken in the implementation to reduce overheads.  Finally,
"Quick" uses "Simple" until failure, then changes to "Complex" - this is the
"final" engine.

Also, the "primality" tests are based on '^1?$|^(11+?)\1+$', which repeats
an increasingly large group until match.

Note that for "simple" tests, the overhead of "Quick" is significant.


Match . against a
             Backtracking [#############                 ]             49 [1.7]
            Parallel wide [#######################           ]         82 [1.9]
    Parallel wide, hashed [############################       ]        97 [2.0]
             Parallel seq [########################          ]         84 [1.9]
     Parallel seq, hashed [##########################         ]        92 [2.0]
            Parallel beam [#################################    ]     114 [2.1]
    Parallel beam, hashed [###################################  ]     122 [2.1]
          Parallel simple [##################################   ]     117 [2.1]
         Parallel complex [######################################]    135 [2.1]
                    Quick [##################################   ]     120 [2.1]

Match a(.)c against abc
             Backtracking [####                     ]                  60 [1.8]
            Parallel wide [#########                    ]             124 [2.1]
    Parallel wide, hashed [###############                 ]          193 [2.3]
             Parallel seq [##########                   ]             126 [2.1]
     Parallel seq, hashed [################                ]          201 [2.3]
            Parallel beam [############                   ]           159 [2.2]
    Parallel beam, hashed [#################                ]         214 [2.3]
         Parallel complex [###################               ]        240 [2.4]
                    Quick [######################################]    473 [2.7]

Match a*b against a^100b
             Backtracking [######################################]   1605 [3.2]
            Parallel wide [################################     ]    1384 [3.1]
    Parallel wide, hashed [####################################  ]   1519 [3.2]
             Parallel seq [################################     ]    1385 [3.1]
     Parallel seq, hashed [####################################  ]   1517 [3.2]
            Parallel beam [###################################  ]    1513 [3.2]
    Parallel beam, hashed [######################################]   1662 [3.2]
          Parallel simple [##############                   ]         630 [2.8]
         Parallel complex [############################        ]     1202 [3.1]
                    Quick [##############                   ]         624 [2.8]

Match .*b against a^100b
             Backtracking [##################                ]       1461 [3.2]
            Parallel wide [###############                   ]       1273 [3.1]
    Parallel wide, hashed [##################                ]       1444 [3.2]
             Parallel seq [################                  ]       1295 [3.1]
     Parallel seq, hashed [#################                 ]       1401 [3.1]
            Parallel beam [####################################  ]   2896 [3.5]
    Parallel beam, hashed [######################################]   3108 [3.5]
          Parallel simple [######                        ]            581 [2.8]
         Parallel complex [#############                    ]        1100 [3.0]
                    Quick [#######                       ]            585 [2.8]

Search .*b against a^100b
             Backtracking [                        ]                  846 [2.9]
            Parallel wide [######################################]  29364 [4.5]
    Parallel wide, hashed [                         ]                1011 [3.0]
             Parallel seq [                        ]                  730 [2.9]
     Parallel seq, hashed [                        ]                  818 [2.9]
            Parallel beam [##                          ]             2462 [3.4]
    Parallel beam, hashed [##                          ]             2110 [3.3]
          Parallel simple [                     ]                     335 [2.5]
         Parallel complex [                       ]                   690 [2.8]
                    Quick [                     ]                     335 [2.5]

Match (.*) (.*) (.*)  against abc abc abc
             Backtracking [#################                 ]        601 [2.8]
            Parallel wide [#############                   ]          465 [2.7]
    Parallel wide, hashed [#################                 ]        592 [2.8]
             Parallel seq [#############                   ]          450 [2.7]
     Parallel seq, hashed [################                 ]         568 [2.8]
            Parallel beam [################################     ]    1087 [3.0]
    Parallel beam, hashed [######################################]   1328 [3.1]
         Parallel complex [#############                   ]          471 [2.7]
                    Quick [####################              ]        706 [2.8]


Search .*?a*b against a^10b
             Backtracking [#                      ]                   109 [2.0]
            Parallel wide [######################################]   1991 [3.3]
    Parallel wide, hashed [####                       ]               242 [2.4]
             Parallel seq [########                      ]            441 [2.6]
     Parallel seq, hashed [###                       ]                222 [2.3]
            Parallel beam [#                      ]                   118 [2.1]
    Parallel beam, hashed [##                      ]                  129 [2.1]
          Parallel simple [#                     ]                    101 [2.0]
         Parallel complex [###                       ]                200 [2.3]
                    Quick [#                     ]                    101 [2.0]

Search .*?a*b against a^100b
             Backtracking [                         ]                1026 [3.0]
    Parallel wide, hashed [##                          ]             2542 [3.4]
             Parallel seq [######################################]  33381 [4.5]
     Parallel seq, hashed [##                          ]             2264 [3.4]
            Parallel beam [                         ]                1055 [3.0]
    Parallel beam, hashed [                         ]                1162 [3.1]
          Parallel simple [                        ]                  781 [2.9]
         Parallel complex [#                          ]              1922 [3.3]
                    Quick [                        ]                  780 [2.9]

Search .*?a*b against a^1000b
             Backtracking [##############                    ]       8137 [3.9]
    Parallel wide, hashed [######################################]  21470 [4.3]
     Parallel seq, hashed [###################################   ]  19550 [4.3]
            Parallel beam [################                   ]      9044 [4.0]
    Parallel beam, hashed [#################                  ]      9792 [4.0]
          Parallel simple [###########                      ]        6512 [3.8]
         Parallel complex [#############################        ]   16108 [4.2]
                    Quick [###########                      ]        6679 [3.8]


Match (a|b)?^2n(?:ab)^n against (ab)^n for n=4
             Backtracking [#######                       ]            492 [2.7]
            Parallel wide [#####                       ]              358 [2.6]
    Parallel wide, hashed [##########                     ]           615 [2.8]
             Parallel seq [#####                       ]              354 [2.5]
     Parallel seq, hashed [#########                      ]           597 [2.8]
            Parallel beam [########################            ]     1485 [3.2]
    Parallel beam, hashed [######################################]   2343 [3.4]
         Parallel complex [###                        ]               261 [2.4]
                    Quick [####                        ]              310 [2.5]

Match (a|b)?^2n(?:ab)^n against (ab)^n for n=6
             Backtracking [############################        ]      514 [2.7]
            Parallel wide [#####################             ]        401 [2.6]
    Parallel wide, hashed [######################################]    712 [2.9]
             Parallel seq [#####################             ]        396 [2.6]
     Parallel seq, hashed [######################################]    718 [2.9]
         Parallel complex [#################                ]         331 [2.5]
                    Quick [##################               ]         338 [2.5]


Match (?:a|b)?^2n(?:ab)^n against (ab)^n for n=4
             Backtracking [##############                   ]         597 [2.8]
            Parallel wide [#########                     ]            394 [2.6]
    Parallel wide, hashed [##                      ]                  127 [2.1]
             Parallel seq [#########                     ]            386 [2.6]
     Parallel seq, hashed [##                       ]                 141 [2.2]
            Parallel beam [######################################]   1619 [3.2]
    Parallel beam, hashed [########                      ]            366 [2.6]
          Parallel simple [                    ]                       58 [1.8]
         Parallel complex [##                      ]                  120 [2.1]
                    Quick [                    ]                       55 [1.7]

Match (?:a|b)?^2n(?:ab)^n against (ab)^n for n=6
             Backtracking [######################################]    628 [2.8]
            Parallel wide [############################        ]      457 [2.7]
    Parallel wide, hashed [#                 ]                         26 [1.4]
             Parallel seq [############################        ]      453 [2.7]
     Parallel seq, hashed [#                 ]                         26 [1.4]
    Parallel beam, hashed [##                    ]                     50 [1.7]
          Parallel simple [            ]                               10 [1.0]
         Parallel complex [                 ]                          23 [1.4]
                    Quick [            ]                               10 [1.0]

Match (?:a|b)?^2n(?:ab)^n against (ab)^n for n=8
    Parallel wide, hashed [##############       ]                       4 [0.6]
     Parallel seq, hashed [##############       ]                       4 [0.6]
    Parallel beam, hashed [######################################]     10 [1.0]
          Parallel simple [##]#                                         1 [0.1]
         Parallel complex [############      ]                          3 [0.5]
                    Quick [#]##                                         1 [0.1]

Match a?^na^n against a^n for n=8
    Parallel wide, hashed [##############                 ]           136 [2.1]
     Parallel seq, hashed [##############                 ]           132 [2.1]
    Parallel beam, hashed [######################################]    361 [2.6]
          Parallel simple [####                    ]                   49 [1.7]
         Parallel complex [###########                   ]            105 [2.0]
                    Quick [#####                    ]                  51 [1.7]


Primality 32
             Backtracking [#                      ]                   146 [2.2]
            Parallel wide [###########################         ]     2157 [3.3]
    Parallel wide, hashed [######################################]   3115 [3.5]
             Parallel seq [###########################         ]     2143 [3.3]
     Parallel seq, hashed [##################################### ]   2994 [3.5]
            Parallel beam [######                       ]             516 [2.7]
    Parallel beam, hashed [########                      ]            672 [2.8]
         Parallel complex [########                      ]            683 [2.8]
                    Quick [#########                      ]           754 [2.9]

Primality 37
             Backtracking [##                        ]                444 [2.6]
            Parallel wide [#######                        ]          1305 [3.1]
    Parallel wide, hashed [##########                      ]         1852 [3.3]
             Parallel seq [#######                        ]          1302 [3.1]
     Parallel seq, hashed [##########                      ]         1811 [3.3]
            Parallel beam [#############################        ]    4956 [3.7]
    Parallel beam, hashed [######################################]   6709 [3.8]
         Parallel complex [#                        ]                 378 [2.6]
                    Quick [#                        ]                 409 [2.6]

Primality 128
             Backtracking [                     ]                     401 [2.6]
            Parallel wide [#############################        ]   21910 [4.3]
    Parallel wide, hashed [######################################]  28511 [4.5]
             Parallel seq [############################         ]   21262 [4.3]
     Parallel seq, hashed [######################################]  29158 [4.5]
         Parallel complex [####                          ]           3876 [3.6]
                    Quick [####                          ]           3910 [3.6]

Primality 131
             Backtracking [####                        ]              563 [2.8]
            Parallel wide [#############################        ]    3298 [3.5]
    Parallel wide, hashed [######################################]   4397 [3.6]
             Parallel seq [############################        ]     3220 [3.5]
     Parallel seq, hashed [######################################]   4466 [3.6]
         Parallel complex [####                        ]              585 [2.8]
                    Quick [####                        ]              586 [2.8]

Primality (eager) 32
             Backtracking [                       ]                   313 [2.5]
            Parallel wide [########                        ]         2224 [3.3]
    Parallel wide, hashed [############                     ]        3068 [3.5]
             Parallel seq [########                        ]         2198 [3.3]
     Parallel seq, hashed [###########                      ]        2965 [3.5]
            Parallel beam [##############################       ]    7542 [3.9]
    Parallel beam, hashed [######################################]   9658 [4.0]
         Parallel complex [##                        ]                677 [2.8]
                    Quick [##                         ]               749 [2.9]

Primality (eager) 37
             Backtracking [##                        ]                534 [2.7]
            Parallel wide [######                        ]           1387 [3.1]
    Parallel wide, hashed [#########                       ]         1882 [3.3]
             Parallel seq [######                        ]           1370 [3.1]
     Parallel seq, hashed [#########                       ]         1854 [3.3]
            Parallel beam [##############################       ]    5855 [3.8]
    Parallel beam, hashed [######################################]   7586 [3.9]
         Parallel complex [#                        ]                 396 [2.6]
                    Quick [#                        ]                 436 [2.6]

Primality (eager) 128
             Backtracking [                       ]                   351 [2.5]
            Parallel wide [#############################        ]    8833 [3.9]
    Parallel wide, hashed [######################################]  11640 [4.1]
             Parallel seq [#############################        ]    8685 [3.9]
     Parallel seq, hashed [######################################]  11709 [4.1]
         Parallel complex [####                         ]            1590 [3.2]
                    Quick [####                          ]           1600 [3.2]

Primality (eager) 131
             Backtracking [####                         ]             631 [2.8]
            Parallel wide [###########################         ]     3310 [3.5]
    Parallel wide, hashed [##################################### ]   4419 [3.6]
             Parallel seq [###########################         ]     3244 [3.5]
     Parallel seq, hashed [######################################]   4692 [3.7]
         Parallel complex [####                        ]              586 [2.8]
                    Quick [####                        ]              596 [2.8]

Comment on this post