Python speed optimization in the real world

I shipped reposurgeon 2.29 a few minutes ago. The main improvement in this version is speed – it now reads in and analyzes Subversion repositories at a clip of more than 11,000 commits per minute. This, is, in case you are in any doubt, ridiculously fast – faster than the native Subversion tools do it, and for certain far faster than any of the rival conversion utilities can manage. It’s well over an order of magnitude faster than when I began seriously tuning for speed three weeks ago. I’ve learned some interesting lessons along the way.

The impetus for this tune-up was the Battle for Wesnoth repository. The project’s senior devs finally decided to move from Subversion to git recently. I wan’t actively involved in the decision myself, since I’ve been semi-retired from Wesnoth for a while, but I supported it and was naturally the person they turned to to do the conversion. Doing surgical runs on that repository rubbed my nose in the fact that code with good enough performance on a repository 500 or 5000 commits long won’t necessarily cut it on a repository with over 56000 commits. Two-hour waits for the topological-analysis phase of each load to finish were kicking my ass – I decided that some serious optimization effort seemed like a far better idea than twiddling my thumbs.

First I’ll talk about some things that didn’t work.

pypy, which is alleged to use fancy JIT compilation techniques to speed up a lot of Python programs, failed miserably on this one. My pypy runs were 20%-30% slower than plain Python. The pypy site warns that pypy’s optimization methods can be defeated by tricky, complex code, and perhaps that accounts for it; reposurgeon is nothing if not algorithmically dense.

cython didn’t emulate pypy’s comic pratfall, but didn’t deliver any speed gains distinguishable from noise either. I wasn’t very surprised by this; what it can compile is mainly control structure. which I didn’t expect to be a substantial component of the runtime compared to (for example) string-bashing during stream-file parsing.

My grandest (and perhaps nuttiest) plan was to translate the program into a Lisp dialect with a decent compiler. Why Lisp? Well…I needed (a) a language with unlimited-extent types that (b) could be compiled to machine-code for speed, and (c) minimized the semantic distance from Python to ease translation (that last point is why you Haskell and ML fans should refrain from even drawing breath to ask your obvious question; instead, go read this). After some research I found Steel Bank Common Lisp (SBCL) and began reading up on what I’d need to do to translate Python to it.

The learning process was interesting. Lisp was my second language; I loved it and was already expert in it by 1980 well before I learned C. But since 1982 the only Lisp programs I’ve written have been Emacs modes. I’ve done a whole hell of a lot of those, including some of the most widely used ones like GDB and VC, but semantically Emacs Lisp is a sort of living fossil coelacanth from the 1970s, dynamic scoping and all. Common Lisp, and more generally the evolution of Lisp implementations with decent alien type bindings, passed me by. And by the time Lisp got good enough for standalone production use in modern environments I already had Python in hand.

So, for me, reading the SBCL and Common Lisp documentation was a strange mixture of learning a new language and returning to very old roots. Yay for lexical scoping! I recoded about 6% of reposurgeon in SBCL, then hit a couple of walls. Once of the lesser walls was a missing feature in Common Lisp corresponding to the __str__ special method in Python. Lisp types don’t know how to print themselves, and as it turns out reposurgeon relies on this capability in various and subtle ways. Another problem was that I couldn’t easily see how to duplicate Python’s subprocess-control interface – at all, let alone portably across common Lisp implementations.

But the big problem was CLOS, the Common Lisp Object System. I like most of the rest of Common Lisp now that I’ve studied it. OK, it’s a bit baroque and heavyweight and I can see where it’s had a couple of kitchen sinks pitched in – if I were choosing a language on purely esthetic grounds I’d prefer Scheme. But I could get comfortable with it, except for CLOS.

But me no buts about multimethods and the power of generics – I get that, OK? I see why it was done the way it was done, but the brute fact remains that CLOS is an ugly pile of ugly. More to the point in this particular context, CLOS objects are quite unlike Python objects (which are in many ways more like CL defstructs). It was the impedance mismatch between Python and CLOS objects that really sank my translation attempt, which I had originally hoped could be done without seriously messing with the architecture of the Python code. Alas, that was not to be. Which refocused me on algorithmic methods of improving the Python code.

Now I’ll talk about what did work.

What worked, ultimately, was finding operations that have instruction costs O(n**2) in the number of commits and squashing them. At this point a shout-out goes to Julien “FrnchFrgg” Rivaud, a very capable hacker trying to use reposurgeon for some work on the Blender repository. He got interested in the speed problem (the Blender repo is also quite large) and was substantially helpful with both patches and advice. Working together, we memoized some expensive operations and eliminated others, often by incrementally computing reverse-lookup pointers when linking objects together in order to avoid having to traverse the entire repository later on.

Even just finding all the O(n**2) operations isn’t necessarily easy in a language as terse and high-level as Python; they can hide in very innocuous-looking code and method calls. The biggest bad boy in this case turned out to be child-node computation. Fast import streams express “is a child of” directly; for obvious reasons, a repository analysis often has to look at all the children of a given parent. This operation blows up quite badly on very large repositories even if you memoize it; the only way to make it fast is to precompute all the reverse lookups and update them when you update the forward ones.

Another time sink (the last one to get solved) was identifying all tags and resets attached to a particular commit. The brute-force method (look through all tags for any with a from member matching the commit’s mark) is expensive mainly because to look through all tags you have to look through all the events in the stream – and that’s expensive when there are 56K of them. Again, the solution was to give each commit a list of back-pointers to the tags that reference it and make sure all the mutation operations update it properly.

It all came good in the end. In the last benchmarking run before I shipped 2.29 it processed 56424 commits in 303 seconds. That’s 186 commits per second, 11160 per minute. That’s good enough that I plan to lay off serious speed-tuning efforts; the gain probably wouldn’t be worth the increased code complexity.

UPDATE: A week later, after more speed-tuning mainly by Julien (because it was still slow on the very large repo he’s working with) analysis speed is up to 282 commits/sec (16920 per minute) and a curious thing has occurred. pypy now actually produces an actual speedup, up to around 338 commits/sec (20280 per minute). We don’t know why, but apparently the algorithmic optimizations somehow gave pypy’s JIT better traction. This is particularly odd because the density of the code actually increased.

120 thoughts on “Python speed optimization in the real world

  1. Has been a pleasure watching hackers at work on irc, and the early warning for the blog post :-)

    – Foo Quuxman

  2. Pingback: Python speed optimization in the real world | dropsafe

  3. Hmmm. I learned a new word today: Memoization. I’ve had few formal programming classes, and none recently. I keep up with programming trends by lurking on various lists–but that often shows me techniques without naming them. Anyways, I regularly “memoize” functions but never knew there was a formal name for it.

  4. Is it 11k commits per second or per minute? First paragraph says second, last paragraph says minute.

  5. >Is it 11k commits per second or per minute? First paragraph says second, last paragraph says minute.

    Typo. I got it right the second time; I’ve fixed the incorrect first instance.

  6. >Anyways, I regularly “memoize” functions but never knew there was a formal name for it.

    Oddly enough, my situation was opposite – I knew the word, but how to memoize systematically was something I’d never learned until this last three weeks. I don’t write code that is both performance-critical and compute-bound very often, so I haven’t before had enough use for this technique to nail it down.

  7. Python is faster than a lot of people think it is.

    But not if you code it like you would C.

    You have to figure out how to let most of the looping happen inside C builtins.

    Usually, if it needs to go fast, someone has already made a library.

    Occasionally, I will write C or Pyrex/Cython to speed it up.

    But the last time that happened was in 2003…

  8. Nice writing, although I’m somewhat surprised that you haven’t discovered what I (as someone who frequently works with “big data” setups) have long since determined — that when the going gets slow, it’s time to pull out a profiler and see if some part of your codebase is running -far- more often than you’ve anticipated; a sure sign that something upstream of it is suffering big O problems.

  9. >when the going gets slow, it’s time to pull out a profiler and see if some part of your codebase is running -far- more often than you’ve anticipated; a sure sign that something upstream of it is suffering big O problems.

    I’m well aware of the principle. Unfortunately, my experience is that Python profilers suck rather badly – you generally end up having to write your own instrumentation to gather timings, which is what I did in this case. It helped me find the obscured O(n**2) operations.

  10. > you generally end up having to write your own instrumentation to gather timings, which is what I did in this case.

    Do you deem it good enough to show the rest of the world?

  11. Looks like a classical runtime/memory trade-off. Have you compared the working set size before and after the speedup?

  12. >Looks like a classical runtime/memory trade-off. Have you compared the working set size before and after the speedup?

    It is most certainly that. I didn’t bother measuring the working set because the only metric of that that mattered to me was “doesn’t trigger noticeable swapping”.

  13. >Do you deem it good enough to show the rest of the world?

    Look at the implementation of the “timings” command.

  14. >You want print-object: http://www.lispworks.com/documentation/HyperSpec/Body/f_pr_obj.htm

    “The function print-object is called by the Lisp printer; it should not be called by the user.”

    Anyway, this looks like an analogue of Python repr(), not print – it’s supposed to print a representation that’s invertible (can be fed back to read-eval). I use str() for dumping the fast-import stream representations of objects, which is not invertible by Python itself.

  15. Big O optimization trumps (or at worst equals in lucky cases) any compiler-aware information, because the degrees-of-freedom in the semantics not modeled by the language (and the declared types) is always a superset. Yet another reason why computers will never program themselves creatively and why I think the Singularity is nonsense.

    I don’t know enough about the details of CLOS nor defstructs to grasp the detailed reasons for the claimed impedance mismatch between the CLOS and Python.

    Programmers are rightfully proud when they achieve an order-of-magnitude gain in performance. I don’t see programmers run away from their babies and disappear into thin air without ever bragging to any one of their accomplishment. How lonely that would be otherwise.

  16. Checking to make sure I understand: Memoization is looking up and recording the data you’re likely to keep needing instead of looking it up every time you need it?

  17. >Checking to make sure I understand: Memoization is looking up and recording the data you’re likely to keep needing instead of looking it up every time you need it?

    Correct. It works when the results of an expensive function (a) change slowly, and (b) are small and cheap to store. Also there has to be a way to know when the cached results have become invalid so you can clear the cache.

    Since you’re not a programmer, I’ll add that big-O notation is a way of talking about how your computation costs scale up with the size of your input data. O(1) is constant time, O(n) is linear in the size of the input set, O(n**2) is as the square of the size, O(2**n) as the number of subsets of the data set. Also you’ll see O(log n), typically associated with the cost of finding a specified item in a tree or hash table. And O(n log n) which is the expected cost function of various good sorting algorithms. In general, O(1) < O(log n) < O(n) < O(n log n) < O(n**2) < O(2**n). Normally anything O(n log n) or below is tolerable, O(n**2) is pretty bad, and O(2**n) is unusably slow.

  18. Nancy, it would be more accurate to say you record the results of complex calculations and then reuse the stored result later, rather than recalculate it every time.

  19. > Once of the lesser walls was a missing feature in Common Lisp corresponding to the __str__ special method in Python. Lisp types don’t know how to print themselves, and as it turns out reposurgeon relies on this capability in various and subtle ways.

    Does it also rely on everybody using this and doing it in a sensible, readable way in their classes.

    Also, have you checked Jython?

  20. Rick: all calculations are functions, aren’t they? But if you had to do a look-up which requires expensive/extensive/recurrent parsing, can that be called a calculation?
    It is still good for memoization…

  21. I’m a big believer that a data structure with one-way pointers is vastly inferior to one that includes back-pointers. With back-pointers, you can always traverse the structure in any direction. Without them, you have to do searches, which are always expensive, and progressively more expensive as the structure grows.

    I, too, was unfamiliar with the verb “memoize”, but have made use of the idea behind it many times. At my last job, I wrote some utility programs that had to know where to find some files that weren’t stored in well-known locations (but were very unlikely to move once they’d been put in a given place, because that was a PITA). Since a find is a very expensive operation, I made the utility installer dispatch an at now job to do the find once and cache the result in a specific location that the other utilities knew about.

  22. >Does it also rely on everybody using this and doing it in a sensible, readable way in their classes.

    My code doesn’t assume that every class in the universe has a sensible __str__, but it does assume that almost every class defined in reposurgeon has its own __str__ that is useful for progress/debugging messages, and (this is the key point) the system str() will recurse down through all such methods when told to print an arbitrary structure.

    >Also, have you checked Jython?

    No. Is there any reason I should expect it to be faster than c-python? I thought it was mainly aimed at allowing programmers to use the Java library classes, rather than at performance per se.

  23. “Memoization”; good to know the name for that. I found myself doing that extensively while trying to work through the problems at Project Euler (projecteuler.net), which is a marvelous resource with a series of incrementally more difficult mathematical programming puzzles for those interested in such a thing.

  24. > the system str() will recurse down through all such methods when told to print an arbitrary structure.

    I’m not sure what this means. The closest thing I can think of is the fact that system structure types (such as list/tuple/dict) will call str (or, looks like it’s actually repr at least half the time) on their children.

    That’s a kind of narrow definition of “arbitrary structure” for my taste.

  25. >That’s a kind of narrow definition of “arbitrary structure” for my taste.

    Perhaps I was unclear. I created __str__ methods for all the classes that are parts of Repository – the effect is that when requesting structure dumps for debugging instrumentation I can just say str() on whatever implicit object pointere I have and the intuitively useful thing will happen. I don’t know how to duplicate this effect in CL. What it would probably require is for the system print function to magically call a str generic whenever it reaches a CLOS object.

  26. @The Monster:

    I, too, was unfamiliar with the verb “memoize”, but have made use of the idea behind it many times. At my last job, I wrote some utility programs that had to know where to find some files that weren’t stored in well-known locations (but were very unlikely to move once they’d been put in a given place, because that was a PITA). Since a find is a very expensive operation, I made the utility installer dispatch an at now job to do the find once and cache the result in a specific location that the other utilities knew about.

    Congratulations! You reinvented bash’s command hash. :-)

    But seriously, this is a great idea, and like most great ideas, will have multiple independent inventions by multiple clever people.

  27. I would just follow up on esr’s excellent overview of big-O notation above with one point which is often missed by developers. The impact of the algorithm is usually seen as data sets grow larger. For small data sets, the complexity of the operation frequently is overtaken by other concerns.

    To provide a mundane example: a car goes much faster than you can walk, but if you are a city-dweller it’s probably faster to walk to your neighbour’s house than to drive.

  28. > O(1) < O(log n) < O(n) < O(n log n) < O(n**2) < O(2**n)

    While that's theoretically true, It's interesting to note that in practice, O(1) = O(log n). For typical problems, you should just mentally macro expand "log2 n" to 30. The only way you're going to get it different enough from 30 to make any difference is to have n be so small that the operation in question is effectively instant. For example, to shave a mere 1/3 from that "constant" requires n to decrease by three orders of magnitude.

    Maybe you want to work on an atypical problem. For the biggest problem most people could possibly attempt, (log2 n) < 60. For Google, it might be 70. For the crackpot who wants to count every elementary particle in the observable universe, 300 is an upper bound.

  29. Well, looks like the Boston Lisp folks called it. At their last meeting a couple of weeks ago, some of them predicted that you would:

    a) discover that your speed problem is better solved by algorithmic optimization than by switching to a faster language or compiler;

    b) write a post critiquing the shortcomings of Common Lisp.

    They were pretty spot on except they thought you would critique CL’s lack of libraries, not the ugliness of CLOS. :)

  30. >esr’s excellent overview of big-O notation

    Entertainingly, one of the downsides of being an entirely self-taught programmer is that I didn’t learn big-O notation or the associated reflexes until relatively late in my career. It wasn’t intuitive for me until, oh, probably less than five years ago.

  31. >They were pretty spot on except they thought you would critique CL’s lack of libraries, not the ugliness of CLOS. :)

    And I might have gotten to that if I’d gotten around CLOS.

  32. >“The function print-object is called by the Lisp printer; it should not be called by the user.”

    Correct. You define a custom print-object method on your data types, and it is called by the implementation whenever you cause a value of that type to be printed–by calling print, prin1, format, or whatever. Just like you don’t explicitly call __str__.

    > Anyway, this looks like an analogue of Python repr(), not print – it’s supposed to print a representation that’s invertible (can be fed back to read-eval).

    It is used for both, actually. If *print-readably* is T, then it must either print an readable (“invertible”) representation or throw an error–”repr mode”. Otherwise, it can print whatever it wants–”str mode”.

  33. > Once of the lesser walls was a missing feature in Common Lisp corresponding to the >__str__ special method in Python. Lisp types don’t know how to print themselves, and as >it turns out reposurgeon relies on this capability in various and subtle ways. Another >problem was that I couldn’t easily see how to duplicate Python’s subprocess-control >interface

    what about CL’s much hyped ability to have new features added very easily (I’m thinking of Paul Graham’s writings): adding a macro would not have solved your problems? not worth your time? too tricky?

  34. For subprocess control interface — did you mean synchronous execution (waiting for results), or asynchronous? In the first case, UIOP:RUN-PROGRAM does it for you quite portably. In the second case, there is no perfect answer, but EXECUTOR does a decent job on the major implementations (SBCL, CCL and a few more).

    CLOS is ugly but (1) it’s more expressive and powerful than any other object system I’ve heard of (e.g. multiple inheritance, multiple-dispatch, method combinations, accessors, meta-object protocol, etc.), and (2) you can hide the ugly behind suitable macros, and many people have.

    Regarding __str__ and print-method, see John Wiseman’s answer; though in this case you might want to define your own serialize-object method and have a mixin defining a print-object method that wraps a call to that in a print-unreadable-object.

  35. >what about CL’s much hyped ability to have new features added very easily (I’m thinking of Paul Graham’s writings): adding a macro would not have solved your problems? not worth your time? too tricky?

    Dunno. Would have looked into it more deeply, but CLOS blocked the translation. Now that I know SBCL exists, though, I’ll probably do a project in it from scratch sometime and learn these things.

  36. >though in this case you might want to define your own serialize-object method and have a mixin defining a print-object method that wraps a call to that in a print-unreadable-object.

    Yes, I thought the answer would be something much like that.

    Good to know that UIOP:RUN-PROGRAM exists – next time I try something like this I’ll look it up.

  37. >Entertainingly, one of the downsides of being an entirely self-taught programmer is that I didn’t learn big-O notation or the associated reflexes until relatively late in my career. It wasn’t intuitive for me until, oh, probably less than five years ago.

    Weren’t you also a mathematician, at least briefly? My first exposure to the notation was in Real Analysis, after which grasping it in a CS context was almost trivial.

  38. Let’s go up a metalevel. I was mildly surprised you considered switching languages at all before attacking the algorithms’ speed issues. This seems unlike you. How did you get there?

  39. CLOS is ugly but (1) it’s more expressive and powerful than any other object system I’ve heard of (e.g. multiple inheritance, multiple-dispatch, method combinations, accessors, meta-object protocol, etc.), and (2) you can hide the ugly behind suitable macros, and many people have.

    Historically there was T’s object system: as powerful as CLOS but actually beautiful.

    The closest I can find in a modern running Scheme is RScheme’s object system, but RScheme has sadly been lacking in maintenance or interest and is still quite riddled with bugs.

  40. >Let’s go up a metalevel. I was mildly surprised you considered switching languages at all before attacking the algorithms’ speed issues. This seems unlike you. How did you get there?

    You’re right – it was unlike me (on the evidence anyone else has available). I’ve actually been wondering if anyone would notice this and bring it up.

    At the time I began looking at Lisp, I believed – mistakenly – that I had already found and optimized out the stuff that could be attacked that way. In my defense, I will note that the remaining O(n**2) code was pretty well obscured; it took a couple of weeks of concentrated attention by two able hackers to find it, and that was after I’d built the machinery for gathering timings.

  41. >Weren’t you also a mathematician, at least briefly?

    I was, but my concentration was in abstract algebra, logic, and finite mathematics. I didn’t actually learn a lot of real analysis (I had a fondness for topology that was unrelated to my main interests, but I approached it through set and group theory rather than differential geometry). It may also be that big-O notation wasn’t as prominent then (in the 1970s) as it later became, so I’d have been less likely to encounter it even if I had been learning more on the continuous side.

  42. Another note for non-programmers…

    A “profiler” is a tool to determine how much time is spent running different parts of a program. As ESR noted, sometimes it is better to add some code to the program to get the required results. (Such code generally isn’t used/run when not trying to speed up the program.)

    Sometimes, at least as a first try, a programmer can tell from the code where it is worth trying to speed things up.

    In any case, this kind of analysis is very useful. A junior/lousy programmer may attempt to speed up a program by reworking code that obviously can be made to run faster. But if a program takes 10 minutes to run and this code accounts for only 10 seconds of that time, it is a waste of time trying to speed it up. Even if it can be made to run 10 times faster, the program run time goes from 600 (590+10) seconds to 591 (590+1) seconds.

    Sometimes this kind of improvement is worse than a waste of time. The code may be written in a way that makes it obvious what it is supposed to do and that it is, in fact, doing it. Reworking code that makes unimportant improvements but also makes the code obscure and subtle is bad practice.

  43. > Also you’ll see O(log n), typically associated with the cost of finding a specified item in a tree or hash table.

    Small correction: hash table insertion and lookup are expected O(1), not O(lg n).

    (At worst, they are O(n), but this degenerate case hardly ever happens unless you piss off a cryptographer.)

  44. @Adam:

    It’s interesting to note that in practice, O(1) = O(log n). For typical problems, you should just mentally macro expand “log2 n” to 30. The only way you’re going to get it different enough from 30 to make any difference is to have n be so small that the operation in question is effectively instant. For example, to shave a mere 1/3 from that “constant” requires n to decrease by three orders of magnitude.

    Why are you claiming that 300% efficiency increase is irrelevant (equivalent to constant) in the presence of iterations that range over 3 orders-of-magnitude?

    log n is still log n, not constant.

    Are you claiming that no such cases occur?

  45. @esr:

    You’re right – it was unlike me (on the evidence anyone else has available). I’ve actually been wondering if anyone would notice this and bring it up.

    I had assumed that you wanted to test out whether there was a fundamental advantage of your long-lost love over your new one. I have observed that you favor continuity of code bases over other considerations, so I should have realized I was wrong. Perhaps I was distracted.

  46. JustSaying: I think the point is that going from 30 to 1 is almost never enough improvement to be worth doing, and it’s effectively linear (when you have a 2**30 scale factor on input producing scale factor of 30 on output, there are much bigger fish to fry).

  47. >I will note that the remaining O(n**2) code was pretty well obscured; it took a couple of weeks of concentrated attention by two able hackers to find it

    Are there any O(n**2) traps within Python itself we can avoid that you found, or was this all your algorithms’ fault?

  48. Did you consider profiling reposurgeon for performance bottlenecks, rewriting the relevant pieces of code in C/C++ and using bindings? I personally like boost-python.

    Maybe if you keep 90% of code written in Python and rewrite 10% of performance-critical code in C, you can approach the speed of a C program.

  49. almost never

    That is why I asked if there are no cases. I can’t think of a case at the moment, but I am skeptical of saying there are none. I think log n is still log n and I should remember it as that, while also factoring in that it might nearly always be too low of a priority. All of us experienced programmers, I am sure share BRM’s experience that obfuscating code for insignificant efficiency gains is myopic.

  50. @JustSaying
    ” I think log n is still log n and I should remember it as that, while also factoring in that it might nearly always be too low of a priority.”

    O(log n) vs O(n) corresponds to [c1 * log(n) + d1] N. In practice the constants may be so large that n > N is out of your reach.

    So, your implementation might indeed scale as O(log n), but it could still run much slower for practical n.

  51. Sorry, html filter messed up my comment:

    @JustSaying
    ” I think log n is still log n and I should remember it as that, while also factoring in that it might nearly always be too low of a priority.”

    O(log n) vs O(n) corresponds to [c1 * log(n) + d1] LT [c2 * n + d2] for some n GT N. In practice the constants may be so large that n GT N is out of your reach.

    So, your implementation might indeed scale as O(log n), but it could still run much slower for practical n.

  52. Of course lg n isn’t *really* a constant, but it’s often useful to think of it that way. It’s also useful at times to assume a spherical cow.

    They say that premature optimization is the root of all evil. If you need to sort the items in a dropdown box, you’re probably fine to use an n^2 sort. Those are fast and easy to code up, which means fewer bugs. It’s a dropdown box, so your user experience will be crap if you have more that a few dozen items anyway. At most, you’ll add a few milliseconds, which isn’t noticeable. When “n” is small enough, even the difference between O(n) and O(n^2) doesn’t matter. An extra lg n is completely irrelevant. That’s one of Knuth’s “small efficiencies”.

    However, some optimizations aren’t premature. If you have lists of a billion items, n^2 sorts are out of the question. Lets say you’re typically sorting a billion items. Then lg n is 30. Assume that once in a while, you need to sort 10 billion items. Then lg n is a hair over 33. That adds 11% to your runtime. Instead of spending 10x longer processing 10x more items, you’ll have to spend 11x longer. The difference is negligible: An order of magnitude change of the input size in either direction affects your total runtime over by only 11% over an O(n) algorithm. Given a gigantic three orders of magnitude change of input size, the lg n factor results in only 66%. That’s not nothing, but it’s also not the real problem. You’ll need more memory before you’ll need more CPU.

    In short, when “lg n” really varies, “n” is small enough that the entire operation doesn’t matter. When “n” is large enough to matter, “lg n” varies so little that the variation doesn’t matter. Not much anyway.

    You could improve your spherical cow model by making it an oblate spheroid, adding another smaller one as a head, and adding four cylindrical legs — but that won’t change the air resistance enough to stop the cow from making a big mess when it hits the ground.

  53. >Are there any O(n**2) traps within Python itself we can avoid that you found, or was this all your algorithms’ fault?

    I don’t know that yet. It was probably all my code, but there could be O(n**2) traps within Python as well.

  54. >Did you consider profiling reposurgeon for performance bottlenecks, rewriting the relevant pieces of code in C/C++ and using bindings?

    Yes, for about a half-second. Then I realized how ridiculous the idea was and abandoned it.

    That strategy only works when the stuff you need to do fast fits in C’s type ontology without incurring so much code complexity that you end up with more problems than you started with. There was no chance that would be true of reposurgeon’s internals – none at all.

  55. @JustSaying:

    I work with filesystems for a living. When you have a large on-disk data structure you need to search, loading another block off of disk is a big cost. OTOH, searching that block in memory is comparatively cheap. For some of our data structures we use binary or hash trees to locate the block we need, but then pack the block as an array. This avoids extra pointers and allows us to cram a few more entries per block. In these cases, cutting the number of block loads from 20 to 10 can be a big savings if the operation must occur in real-time for a client (as opposed to a background processing operation). Spinning rust is slow …

  56. @esr:

    O(1) is constant time [...] O(log n), typically associated with the cost of finding a specified item in a tree or hash table.

    O(1) is typically associated with the cost of accessing a specified item in an array by index.

    @Winter: O(log n) vs O(n) corresponds to [c1 * log(n) + d1] LT [c2 * n + d2]

    @Adam:

    In short, when “lg n” really varies, “n” is small enough that the entire operation doesn’t matter.

    That is only if c1 is small relative to d1 and the “universe”.

    The curve for log(n) flattens faster than even sqrt.

    The sacrosanct rule to not do premature optimization appears to be deprecated under open-extension, because profiling isn’t available.

    If your caller must to call you a billion times (perhaps deep in some nested function hierarchy), and you are employing a log(n) tree or hash instead of an array, then the difference in application performance can 300% n = 1000, 400% n = 10,000, 500% n = 100,000, etc.

    So log(n) is never the same as constant. The cow is never spherical except when we “touch him only one way” — Steve Jobs.

  57. @esr: “…I didn’t bother measuring the working set because the only metric of that that mattered to me was “doesn’t trigger noticeable swapping”.”

    Sure, for your current number commits. Now, using caching, the design trades off runtime for an upper limit based on the memory of the box.

  58. >Now, using caching, the design trades off runtime for an upper limit based on the memory of the box.

    Indeed so. It’s easier to buy memory than more processor speed these days.

  59. @JustSaying

    The constants for O(log n) tend to be larger than for O(n), else you would have tried the log n algorithm first. And indeed, log n matters if n is in the billions. But at that point, you are tweaking all algorithms.

  60. > Looks like a classical runtime/memory trade-off. Have you compared the working set size before and after the speedup?

    TL,DR: see below

    In fact, I should tell that before I worked on refactoring for speed, I began searching for ways to cut a lot the memory used by reposurgeon. Most of the gain was obtained by using __slots__ on most instanciated structures, but I did some dict eviction and copy on write optimization on a really memory hungry part: the filemaps.

    Reposurgeon already was optimized in that regard (Eric had already implemented a rather good COW scheme for PathMaps), but the fact that PathMap’s snapshotting required a new dictionnary each time — to be able to replace later an entry by its copy — was taking its toll… So I devised a tweek to take snapshots even less often, then a further optimization which is a real memory usage/code complexity tradeoff.

    Returning to simpler structures would probably gain some speed too, but the fact is that on my machine, reposurgeon still tops at 75% of my 4GB of RAM when converting the blender repository — and I suspect Battle for Westnoth to be such a contender too. Sure, one can trade computationnal cost and even code readability for memory, but the bargain is not the same when you can trade 200MB temporary memory for a O(n**2) to expected O(n) reduction — e.g. store previous hits in a set/dict instead of searching them backwards in the “already seen” list — than when you trade 2GB of memory used through the whole import for only a constant factor — one of the costs of the smart COW PathMap over a list of dicts is that built-in types don’t have interpreter overhead, and in fact run at C-speed, but that’s only a constant factor rather that a whole new complexity class.

    As for the optimization itself, it is amusing to note that Eric and I actually started optimizing for speed each in his corner without concerting… At first we were doing orthogonal changes, then as the set of molasses reduced we began stepping on each other’s toes^W^W^W^W^W collaborating more ;-) Also note that while Eric says to have driven his optimizations by profiling, I was less smart and just wandered in the code searching for unpythonic or unpretty code to my eyes — to the risk of premature or over- optimization. I was more seeking refactors for clarity and code compactess — and iterators galore because I love them too much for my own good — than real speed optimizations; it just happens that I seem to find ugly O(n**2) code.

    The last thing that can explain why Eric didn’t find the places to optimize at first sight is that reposurgeon is big and its internal structures have been made to mirror the fast-import format at first. This legacy still shows a lot. While that decision was sane at the time when reposurgeon was less complex and able than now, and while there still are several tangible benefits to this similarity — like the ability of reposurgeon to round-trip fast-import streams to the exact character, over the course of time — and especially in the few last weeks where Eric and I started to optimize — internal objects like Commits track more and more their relationships with their surrondings, to the point that now they collectively maintain in memory the whole DAG, in both directions.

    At first, Commits only stored the marks to their parents. To find parents a sweep over the complete set of events was needed, because a mark is only a string containing a colon and a number, and marks aren’t even necessarily consecutive… Eric made that computation to remember its results, then swapped altogether to storing the commits objects instead, diverging from fast-import towards a graph representation. For children, I first memoized the function searching for all commits whose parents contained self, then replaced that altogether by code that stores the children list on commits but keeps them synchronized at all times with parent lists. And for tags/resets, Eric and I both tried to make commits know which tags/resets pointed to them, always kept in sync with the information on tags telling where they point to.

    TL,DR: Some of the innefficiencies were hidden, but most of them were due to the lack of informations stored. Some loops that were only O(n) were actually called O(n) times by another function — which in a codebase that dense is not easy to spot — and it was not possible to make tho inner loop more efficient short of doing large refactors… All these problems combined tend to make a poor human’s brain automatically sweep over and search some other more palatable optimization. The needed refactors were difficult to do, not because the end result isn’t known but because the transition must be painless, and that’s difficult when there are tricky corner cases everywhere.

    Keeping commits very small and ensuring each state was correct was an imperative goal for me. Kudos for Eric and his approach to writing code, documentation, and test suites at the same time, or else none of these refactorings could have happened for fear of breaking everything… And I broke a lot of things… but noticed right away. Some parts of the code were actually relying on some invariants that came from the fact that parent and children lists were generated at first ! Finding those was hard and a blocker for the refactorings.

    I already said far too much for a small comment, sorry for that :-(

  61. BRM said: Sometimes this kind of improvement is worse than a waste of time. The code may be written in a way that makes it obvious what it is supposed to do and that it is, in fact, doing it. Reworking code that makes unimportant improvements but also makes the code obscure and subtle is bad practice.

    True fact.

    “Premature optimization” is a related problem.

    First, see if it’s slow.

    Then, see what part of it’s actually making it slow,

    Then fix that part.

    (And if, as in the quote above, the speed improvement is minor compared to the added complexity, don’t fix it.)

  62. >(Eric had already implemented a rather good COW scheme for PathMaps)

    Actually that code wasn’t mine. Somebody named Greg Hudson wrote it in an attempt to reduce memory footprint, and in so doing enabled me to solved a fiendishly subtle bug in branch processing that had stalled the completion of the Subversion reader for six months. To invoke it, the repository had to contain a Subversion branch creation, followed by a deletion, followed by a move of another branch to the deleted name.

    I still don’t know what exactly was wrong with my original implementation, but a small generalization of Hudson’s code (from CoW filepath sets to CoW filepath maps) enabled me to use it to remove a particular O(n**2) ancestry computation in which I suspected the bug was lurking. Happily that suspicion proved correct.

  63. By the way, Eric, what profiler did you try to use, and what you are missing in it? What features would you like to see in profiler?

  64. >By the way, Eric, what profiler did you try to use, and what you are missing in it? What features would you like to see in profiler?

    The stock Python profiler. Unfortunately, it’s pretty bad about assigning time to method calls! I’ve always thought this was odd given that the standard style is so OO.

  65. BTW, SBCL has SB-SPROF for profiling, which is quite informative, though it is not obvious at first how to read the results.

  66. (Also, if you do complex shell pipes or string substitutions, INFERIOR-SHELL:RUN is a richer front-end on top of UIOP:RUN-PROGRAM. A implementation of it on top of EXECUTOR:RUN-PROGRAM or IOLIB:SPAWN would be nice, but hasn’t been done yet.)

  67. >Entertainingly, one of the downsides of being an entirely self-taught programmer

    Actually I think the standard schoolish way of learning theory, then hands-on experience, then more work experience, is not useful at all in the two fields I was taught, programming/database design and business administration. We memorize and barf back theoretical definitions which we don’t care about because we have no idea what they are good for, and are often too formal to seem really useful, take an exam, forget them, and later on it is hard to apply it to practical problems, or even realize that the problems we face have anything to do with them.

    It would be better to do hands-on practice first, try to figure out solutions, usually fail, then being told to do it X way without an explanation, and then learn the theory why we were told so.

    Example: I remember memorizing, not really understanding, taking an exam of, and then promptly forgetting database normalization: 3NF, BCNF, 4NF. Then years later actually designing databases, figuring out a common sense way of doing it, then realizing this actually sounds something like BCNF. Then I went back to the textbook, looked up 4NF and actually my design got better. And then – realizing it is all too slow and we have to denormalize for speed :-)

    Same with business administration, only after many years of work I got the philosophy of accounting and going back to the textbook they started to make sense.

    What would be a world like in which every construction engineer would first work as a mason and carpenter?

  68. It would be nice if you told us more about your dissatisfaction with CLOS. I can think of lack of dot notation and therefore somewhat inconvenient slot access, although it doesn’t bother me very much, and for situations when it does there are with-slots and with-accessors. Maybe decorators for classes/generic functions/methods would not harm, too (macrology and MOP helps, but in some situations I would indeed prefer decorators as they’re easier to combine and using MOP may switch off compiler optimizations for CLOS). Other than that, is the problem reduced to the fact that CLOS is unlike Python’s object model? If so, I’m not sure whether it’s a problem of CLOS or one of Python. I for one often miss CLOS when I write Python or JavaScript code. Besides multimethods/MOP/etc. there are other good sides to it, for instance using (func object) instead of object.method notation makes completion and call tips work much better; also, CLOS is very well suited for “live editing”, when you make modifications without restarting your program – that’s usually hard to achieve in JS and very hard in Python.

  69. >It would be nice if you told us more about your dissatisfaction with CLOS.

    Dot notation would have been nice, but that’s just syntax and un-Lispy (though you should look into e7 if any documentation for it is still on the web). I think the “feature” that stuck most in my craw was having to declare stub generics on penalty of a style warning from the compiler. Bletch! I dislike the requirement that all methods be globally exposed. too.

    For this particular translation, I wanted a class system that simulated Python behavior more closely. I’m sure this could be done with sufficiently complex macro wrappers but that seemed like a forbidding amount of work and possibly dangerous to maintainability.

  70. > It’s easier to buy memory than more processor speed these days.

    The original driver for 64-bit architectures was people who wanted to cache their entire database in RAM, and the 32-bit machines couldn’t address enough memory to do that.

  71. What would be a world like in which every construction engineer would first work as a mason and carpenter?

    My dad served as a mentor to a couple of UConn mech eng students a few years back for their senior project. His big complaint was that while they were smart and knew their physics, they didn’t know how to machine at all. He thought it terribly important that an engineer gain experience as a machinist, since a technical drawing is basically a set of instructions to the machinist who will actually make the part.

  72. > Actually I think the standard schoolish way of learning theory, then hands-on
    >experience, then more work experience, is not useful at all in the two fields I
    >was taught, programming/database design and business administration.

    This was my constant complaint about my CS classes. They taught plenty of theory of the various modern programming techniques, but there was so little practical application, and what little there was was so contrived (a square is a rectangle is a shape for class inheritance for example) that while I could give you the reasons why you would want to do these things on an intellectual level, I had no gut understanding of why you would go through the extra work.

  73. Tangential to the matter at hand, but…

    Probably anyone who is into database design has heard this one, but…

    1NF, 2NF and 3NF can be described as:
    “The key, the whole key and nothing but the key”

  74. > [...] what little there was was so contrived (a square is a rectangle is a shape for class inheritance for example) [...]

    Particullary because square / rectangle relationship is just a bad fit and bad example of OOP inheritance (where more specialized class is usually extended, not limited).

  75. @Jakub:

    where more specialized class is usually extended, not limited

    That’s a really good observation.

  76. “where more specialized class is usually extended, not limited”
    “That’s a really good observation.”

    Yes, but it just goes to show that while OOP is a good fit for many problems, it doesn’t make things much easier. Coming up with a really good set of classes, with the right ‘responsibilities’ is difficult. Finding hidden gotchas in the inheritance hierarchy is difficult. It’s only after you’ve struggled quite a while with these issues that you end up with a good set of classes that make the actual program construction easy.

    This is not really an OOP thing. If you’re doing plain old procedural programming, the hard part is figuring out how to partition the problem. Once you do that, everything seems to fall into place.

    Either way, what you are doing is actually trying to understand the problem you are trying to solve. That’s the hard part.

  77. ESR wrote “Dot notation [for CLOS] would have been nice, but that’s just syntax and un-Lispy ”

    It’s not what you’re looking for, but you might at least be amused that I often use a macro DEF.STRUCT which is a fairly thin layer over stock CL:DEFSTRUCT which, among other things, makes accessor names use #\. instead of #\- as the separator between structure class name and slot name. (E.g., after (DEF.STRUCT PLANAR-POINT X Y), PLANAR-POINT.X is the name of an accessor function.)

    More seriously, when you talked earlier about the apparent limitations of CL for printing objects, my impression is that the CL printer is more powerful and flexible than in most languages. It has some ugly misfeatures in its design (e.g., making stream printing behavior depend too much on global special variables instead of per-stream settings). It tends to be slow. But it is fundamentally functional and flexible enough that on net I’d list it as an advantage of CL vs. most other languages in something like Peter Norvig’s chart. The feature I’ve pushed hardest on is *PRINT-READABLY* coupled with complementary readmacros to allow the object to be read back in. In CL, these hooks are expressive enough to let me do tricks like writing out a complex cyclic data structure at the REPL, and later scrolling back in the REPL or even in the transcript of a previous session, cutting out the printed form, pasting it into my new REPL prompt, and getting “the same” thing. (Of course the implementor of the readmacros needs to decide how “the same” copes with technicalities like shared structure, e.g. by memoization or not.) I am not an expert in Python 2.x or Ocaml or Haskell, but I’ve read about them and written thousands of lines of each, and it’s not clear to me that their printer/reader configurability is powerful enough to support this.

  78. >More seriously, when you talked earlier about the apparent limitations of CL for printing objects, my impression is that the CL printer is more powerful and flexible than in most languages.

    You may well be right. It wouldn’t surprise me if you were.

    But you’re falling into a trap here that I find often besets Lisp advocates (and as I criticize, remember that I love the language myself). You’re confusing theoretical availability with practicality to hand. As you note, and as I had previously noticed, print behavior has ugly dependencies on global variables. Separately, supposing your “more powerful” is really there, it is difficult to use, requiring arcane and poorly documented invocations. Contrast this with Python str(), which ten minutes after you’ve first seen it looks natural enough that any fool can use it.

    Programming languages should not be tavern puzzles. The Lispy habit of saying “yes, you can do X provided you’re willing to sacrifice a goat at midnight and then dance widdershins around a flowerpot” is one of the reasons Lisp advocates are often dismissed as semi-crackpots. Yes, LISP has tremendous power, but it also has terrible affordances. Also see why I didn’t program in it outside of Emacs for 30 years.

  79. Those of you who are concerned about software patents have reason to celebrate: Uniloc just got handed its ass in their patent suit against Rackspace. In the very same East Texas district court that patent trolls venue-shop for to get patent-troll-friendly rulings. Uniloc is a notorious, and heretofore rather successful, patent troll; basically if you do any sort of license verification for a piece of proprietary software, expect to be sued by Uniloc.

    The defense cited not only In re Bilski but two other, more recent cases: Cybersource v. Retail Decisions and Dealertrack v. Huber, which establish that for purposes of the “machine or transformation test” of patentability, a general-purpose computer is not a specific enough machine, and transformation of data is not sufficient transformation.

    Given the way the sausage that is law gets made in Murka, I’m not going to say it’s game over for software patentholders yet. But their job just got a whole lot harder.

  80. > You’re confusing theoretical availability with practicality to hand

    Writing the equivalent of simple __str__ and __repr__ methods in Lisp is very easy, it’s not some theoretically-powerful-but-practically-difficult beast. You just have to know that print-object and *print-readably* exist, like you have to know that __str__ and __repr__ exist.

    If you want to support pretty-printing or printing cyclic data structures in a way that they can be read back in, then you need to learn some more Lisp, but that’s actually not hard either (well, except pretty-printing–that can be a beast). As far as I know neither is even possible in Python using the standard for printing & reading.

  81. Programming languages should not be tavern puzzles. The Lispy habit of saying “yes, you can do X provided you’re willing to sacrifice a goat at midnight and then dance widdershins around a flowerpot” is one of the reasons Lisp advocates are often dismissed as semi-crackpots.

    s/Programming languages/Operating systems/g

    s/Lisp/Linux/g

  82. @John Wiseman:

    If you want to support pretty-printing or printing cyclic data structures in a way that they can be read back in, then you need to learn some more Lisp, but that’s actually not hard either (well, except pretty-printing–that can be a beast). As far as I know neither is even possible in Python using the standard for printing & reading.

    In the general case, there is usually no real reason to worry about printing for round-tripping in Python, because pickle handles things like circular references quite nicely.

    As far as the other goes, there are several ways to pretty print things, including leveraging the standard str() functions by providing your own __str__.

  83. @esr
    > Unfortunately, my experience is that Python profilers suck rather badly

    Whatever happened to “batteries included”?

    Improving the performance of anything beyond a trivial program without a profiler is like painting a portrait wearing a blindfold. It is a plain observable fact that programs don’t spend their time where programmers think they do. It is much more fun to write a cool optimization than an effective one.

    Nonetheless, it sounds like you recognize this and implemented a custom, rube goldberg profiler. Which reminds me of the aphorism that those who don’t use UNIX are deemed to reinvent it, badly.[*]

    One more reason not to do Python, as if there weren’t enough already.

    [*] BTW, I know that isn’t actually what Henry Spencer said, but I didn’t want to use the real one since plainly ESR is not lacking understanding here, just tools.

  84. >Whatever happened to “batteries included”?

    It’s a question I’ve wondered about myself in this case. There aren’t many places where Python fails to live up to its billing; this is one. Actually, the most serious one I can think of offhand.

    >Nonetheless, it sounds like you recognize this and implemented a custom, rube goldberg profiler.

    That’s too negative. What I did is often useful in conjunction with profilers even when they don’t suck – I sampled a timer after each phase in my repo analysis and reported both elapsed time and percentages. When several different phases call (for example) the same lookup-commit-by-mark code, custom instrumentation of the phases can tell you things that function timings alone will not.

  85. >s/Lisp/Linux/g

    Linux is not even within orders of magnitude as bad as Lisp is this way – they’re really not comparable. The real-world evidence for that is penetration levels.

  86. >Jessica, what is *your* weapon of choice for the problem space Python occupies?

    I’m curious about that myself. I would rate Ruby approximately as good (though with weaker library support) Perl somewhat inferior due to long-term maintainability issues, and nothing else anywhere near as good.

  87. I’m curious about that myself. I would rate Ruby approximately as good (though with weaker library support) Perl somewhat inferior due to long-term maintainability issues, and nothing else anywhere near as good.

    Given Jessica’s putative requirements (must be statically typed and work with the .NET framework), Boo would be the closest thing to Python; but really, C# is a good enough language that few people working within those constraints have a reason to switch away from it.

  88. I’m not really sure what “problem space” Python occupies. It seems to me that “every programming problem” is its domain, according to its advocates.

    Nonetheless, as I have said here a number of times as a general programming language I think C# is the best system I have used (system including all the peripheral items that make a language usable.)

    The problem space Eric is referring too, what I want to call “batch” tools, I find C# excellent for that kind of work.

    I doubt you love that answer, but there it is.

    Most of my programming is done in C# and JavaScript. FWIW, you all should totally check out angularjs as an helper for javascript. It is super cool, very useful, and has probably tripled my speed in writing browser side code.

    I have never used Ruby, but I have read a little about it and know someone who has a lot of expertise. Anything that describes itself as “the good parts of perl” is unlikely to be appealing to me – because I don’t think perl has any good parts.

  89. @esr
    > That’s too negative. What I did is often useful in conjunction with profilers even when they don’t suck – I sampled a timer after each phase in my repo analysis and reported both elapsed time and percentages.

    I didn’t read your code, but FWIW, a sampling profiler is more than adequate for 95% of profiling needs. Seems to me that you just created the batteries required, assuming you made it general enough.

    Certainly for optimizing what you need is “show me the top five places my code spends most of its time”, which is what that gives you. So Rube Goldberg be damned, sounds like a great tool you built.

  90. @esr:

    It’s a question I’ve wondered about myself in this case. There aren’t many places where Python fails to live up to its billing; this is one. Actually, the most serious one I can think of offhand.

    In my experience, one of the stock profilers (cProfile) works quite well. But you do have to take into consideration the number of calls that are made to a given method (this data is reported as well as total time spent in each call). An attribute lookup for a call is quite properly assigned to the calling function.

    @Jessica Boxer:

    The problem space Eric is referring too, what I want to call “batch” tools, I find C# excellent for that kind of work.

    I agree that C# is a good language. Like Python, its domain space is huge, so it’s worthwhile honing your abilities on a general purpose tool like either one of these rather than remembering arcane batch syntax.

    But I’m not going to use a Microsoft OS and I’m not going to use a non-Microsoft implementation of C#, so I’m not using C#.

  91. You have a performance problem, and your first instinct is to rewrite the code in a different language, rather than find algorithmic bottlenecks? Maybe you should stop hating on computer science education, and start taking some CS classes?

  92. >You have a performance problem, and your first instinct is to rewrite the code in a different language, rather than find algorithmic bottlenecks? Maybe you should stop hating on computer science education, and start taking some CS classes?

    How do you pack that many misconceptions into two sentences? It must take both native talent and a lot of practice.

  93. >A combination of clojure and jython is one possibility

    Intriguing thought. I may try it on a future project.

  94. I have a ready-made C# project that I could hack on if I felt the need…though something tells me that diving into a 500 KLOC package as an introduction to a language may not be that good an idea…after all, I learned to hate C++ from diving into a then-800 KLOC package…

  95. Jessica, I’d say Python’s problem space is that group of programs for which an interpreted language is good enough, little to no bit-bashing is needed, and its I/O capabilities are good enough. yeah, that’s a pretty wide domain, but by no means “every programming problem”.

  96. A combination of clojure and jython is one possibility

    Holy crap, if you thought CL had warts — wait till you get a load of Clojure. I tried wrapping my head around it for a “joke project”. I’d been joking around on Reddit about L33tStart — a fictional init(1) replacement written in ClojureScript and running on Node — and decided that such a blasphemous thing should really, actually exist.

    It didn’t take much exposure to Clojure(Script) for me to discover that I was allergic. That combined with Clojure’s community of twenty-something naïfs (“holy shit, guys, Rich Hickey is such a genius! Check out this talk of his (only available in embedded video with no transcript) — he’s discovered that if you minimize side effects and code in strictly functional style, your programs become simpler and more tractable!”) is enough to turn me right off the language and actively discourage other smart folks from adopting it.

    Anyway, Clojure is strictly only as powerful as JScheme or Kawa — so if you like Scheme you can use one of those and gain all of Clojure’s java-interop advantages, plus the awesomeness of working directly in (a somewhat reduced form of) Scheme.

  97. So you find the algorithmic bottlenecks and fix them in Python. Then you begin a failed translation to Lisp for no reason?

  98. rrenaud – you’ve messed up your reading comprehension somewhere, or just didn’t read through the comments from before your initial post – he _thought_ he found them, then attempted a rewrite, then found more.

    As he said March 25 at 4:06 pm: “””At the time I began looking at Lisp, I believed – mistakenly – that I had already found and optimized out the stuff that could be attacked that way. In my defense, I will note that the remaining O(n**2) code was pretty well obscured; it took a couple of weeks of concentrated attention by two able hackers to find it, and that was after I’d built the machinery for gathering timings.”””

  99. rrenaud: Why do you think I said that was unlike Eric? Unlike you, apparently, I do know him personally and have what I think is a decent grasp on his hacking style, and the idea that he’d commence a port for performance reasons before making sure every last drop of speed was wrung out of it algorithmically is something that he’d normally ridicule with vigor.

  100. >the idea that he’d commence a port for performance reasons before making sure every last drop of speed was wrung out of it algorithmically is something that he’d normally ridicule with vigor.

    Indeed. But to be fair, I didn’t actually give enough information in the OP to exclude the following two theories: (1) Eric had a momentary attack of brain-damage and behaved in a way he would normally ridicule, (2) Eric had a momentary attack of “oooh, look at the shiny Lisp” and put more effort into thinking about a port to that specific language than the evidence justified.

    Neither theory is true, mind you. But I can’t entirely blame anyone for entertaining them, because I didn’t convey the whole sequence of events exactly.

    rrenaud’s biggest mistake was to suppose that I hate CS education; in fact, while I have little use for the version taught everywhere but a handful of excellent schools like MIT/CMU/Stanford, “mild contempt” would be a far better description than “hate”. If these places were doing their job properly, hackers at my skill level and above wouldn’t be rara aves – and I wish that were the case, because there’s lots of work to go around.

    His funniest mistake was that he thought CS education would fix the mistake he believed me to be making. See above…

  101. 2) was the theory I’d come up with…figuring you had a sudden need to connect with your roots or something. Like I occasionally fire up a CP/M system.

  102. And CS education, to me, seems to be a good way to train people to be computing theorists, which is almost entirely orthogonal to hacking ability. I’ve never had a single CS course, have no plans to do so, and my hacking abilities are at a level I consider adequate to get the job done.

  103. My experience with performance tuning is that you get the greatest gains by starting with a really bad algorithm. Fortunately, there are a lot of those lying around.

  104. It would be interesting to see the performance of pypy on the post optimization version. The question being, did the algorithmic optimization that was done help or hurt the relative performance of pypy?

  105. >It would be interesting to see the performance of pypy on the post optimization version. The question being, did the algorithmic optimization that was done help or hurt the relative performance of pypy?

    It’s easy enough to run that test that I’m doing it now. Timing stock Python on the 56K-commit benchmark repo, 270sec (208 commits/sec). Same with pypy 178sec (315 commits/sec) That’s interesting – actually a significant speedup this time. I wasn’t seeing that when I wrote the OP, quite the reverse in fact. Something Julien or I did in the last six days has made a significant difference – might be worth running a bisection to find out what.

  106. Warning: Jay and Jessica, if you fail to appreciate Python as the transcendent language of the gods, you will be replaced by a small Python script after the Singularity!

  107. >Warning: Jay and Jessica, if you fail to appreciate Python as the transcendent language of the gods, you will be replaced by a small Python script after the Singularity!

    “There is another theory which states this has already occurred.”

  108. Go see the people in the PyPy channel on Freenode about why your code is slow. Slowness is considered to be a bug, unless you your code is too short to overcome warmup.

  109. Warning: Jay and Jessica, if you fail to appreciate Python as the transcendent language of the gods, you will be replaced by a small Python script after the Singularity!

    Any singularity based on Python will itself meet a day of reckoning with the Gods of the Copybook Headings, who insist that bugs caught at runtime are orders of magnitude more expensive to fix than bugs caught at compile time.

    Traceback (most recent call last):
    File “/usr/bin/singularity.py”, line 8643, in run_ai
    File “/usr/lib/python2.7/dist-packages/ai/ai.py”, line 137406, in get_neuron_state:
    File “/usr/lib/python2.7/dist-packages/ai/neuralnet.py”, line 99205, in query_neuron
    File “/usr/lib/python2.7/dist-packages/ai/neuron.py”, line 20431, in query_synapse
    TypeError: expected object of type ‘SynapseConfiguration’, got ‘NoneType’

    Strong static typing systems are not put into languages just to make your lives miserable, folks.

  110. @Jeff Read: Strong typing does not necessarily mean static typing, ask ML (or Haskell, I’m not sure which), with its implied types (and correctness checking that can discover errors in an algorithm by type mismatch).

  111. @Jakub Narebski:

    There are actually three different things that get conflated on typing:

    strength
    static/dynamic
    explicit/implicit

    Python has reasonably strong typing that is dynamic and implicit.
    Some newer languages have strong typing that is static and implicit.
    Typing on older languages is usually explicit. Even C#, which has “implicit” local variables, still requires variable declarations for those. You tell the compiler — here’s a variable, figure it out based on its use.

    Strong is usually good. Static is usually good. Implicit is usually good. It wasn’t until recently that you could have all three.

  112. Strong typing does not necessarily mean static typing, ask ML (or Haskell, I’m not sure which), with its implied types (and correctness checking that can discover errors in an algorithm by type mismatch).

    Never said it did. I chose the phrase “strong static typing” specifically to contrast with weak static typing (e.g., C) and strong dynamic typing (e.g., Python, Lisp).

    Also, both Haskell and ML support type inference.

  113. I’m well aware of the principle. Unfortunately, my experience is that Python profilers suck rather badly – you generally end up having to write your own instrumentation to gather timings, which is what I did in this case. It helped me find the obscured O(n**2) operations.

    Did you use any profiling tools at all ? I’m interested to hear if there are any ready made tools that can run against your Python code and suggest meaningful improvements.

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