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Paul Khuong: some Lisp

Retrospective on Binary Search and Comp{ress,ilat}ion

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I never know whether to prefer closure or fresh questions, in research. I got a little of both lately. First, closure on searching in permutations of sorted arrays, and second, more avenues on the compilation as compression angle.

Array Layouts for Comparison-Based Searching

In July 2012, I started really looking into searching in static sorted sets, and found the literature disturbingly useless. I reviewed a lot of code, and it turned out that most binary searches out there are not only unsafe for overflow, but also happen to be badly micro-optimised for small arrays with simple comparators. That lead to Binary Search eliminates Branch Mispredictions, a reaction to popular assertions that binary search has bad constant factors (compared to linear search or a breadth first layout) on modern microarchitecture, mostly due to branch mispredictions. That post has code for really riced up searches on fixed array sizes, so here’s the size generic inner loop I currently use.

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const uint32_t x = ...;
const uint32_t *base = ...;
size_t n = ...;
size_t half;

while ((half = n / 2) > 0) {
    const uint32_t *mid = &base[half];
    base = (*mid < x) ? mid : base;
    n -= half;
}

The snippet above implements a binary search, instead of dividing by three to avoid aliasing issues. That issue only shows up with array sizes that are (near) powers of two. I know of two situations where that happens a lot:

  1. bad benchmarks;
  2. data structures built around powers of two (e.g., Saxe & Bentley dynamisation).

The fix for the first case is to do proper benchmarking on a wide range of input sizes. Ternary or offset binary search are only really useful in the second case. There’s actually a third case: when I’m about to repeatedly search in the same array, I dispatch to unrolled ternary searches, with one routine for each power of two. I can reduce any size to a power of two with one initial iteration on an off-center “midpoint.” Ternary search has a high overhead for small arrays, unless we can precompute offsets by unrolling the whole thing.

My work on binary search taught me how to implement binary search not stupidly–unlike real implementations–and that most experiments on searching in array permutations seem broken in their very design (they focus on full binary trees).

I don’t think I ever make that explicit, but the reason I even started looking into binary search is that I wanted to have a fast implementation of searching in a van Emde Boas layout! However, none of the benchmarks (or analyses) I found were convincing, and I kind of lost steam as I improved sorted arrays: sortedness tends to be useful for operations other than predecessor/successor search.

Some time in May this year, I found Pat Morin’s fresh effort on the exact question I had abandoned over the years: how do popular permutations work in terms of raw CPU time? The code was open, and even good by research standards! Pat had written the annoying part (building the permutations), generated a bunch of tests I could use to check correctness, and avoided obvious microbenchmarking pitfalls. He also found a really nice way to find the return value for BFS searches from the location where the search ends with fast bit operations (j = (i + 1) >> __builtin_ffs(~(i + 1));, which he explains in the paper).

I took that opportunity to improve constant factors for all the implementations, and to really try and explain in detail the performance of each layout with respect to each other, as well as how they respond to the size of the array. That sparked a very interesting back and forth with Pat from May until September (!). Pat eventually took the time to turn our informal exchange into a coherent paper. More than 3 years after I started spending time on the question of array layouts for implicit search trees, I found the research I was looking for… all it took was a bit of collaboration (:

Bonus: the results were unexpected! Neither usual suspects (B-tree or van Emde Boas) came out on top, even for very large arrays. I was also surprised to see the breadth-first layout perform much better than straight binary search: none of the usual explanations made sense to me. It turns out that the improved performance (when people weren’t testing on round, power of two, array sizes) was probably an unintended consequence of bad code! Breadth-first is fast, faster than layouts with better cache efficiency, because it prefetches well enough to hide latency even when it extracts only one bit of information from each cache line; its performance has nothing to do with cachability. Our code prefetches explicitly, but slower branchy implementations in the wild get implicit prefetching, thanks to speculative execution.

Conclusion: if you need to do a lot of comparison-based searches in > L2-sized arrays, use a breadth-first order and prefetch. If you need sorted arrays, consider sticking some prefetches in a decent binary search loop. If only I’d known that in 2012!

Comp{ress,ilat}ion

A couple months ago, I found LZ77-like Compression with Fast Random Access by Kreft and Navarro. They describe a Lempel-Ziv approach that is similar to LZ77, but better suited to decompressing arbitrary substrings. The hard part about applying LZ77 compression to (byte)code is that parses may reuse any substring that happens to appear earlier in the original text. That’s why I had to use Jez’s algorithm to convert the LZ77 parse into a (one word) grammar.

LZ-End fixes that.

Kreft and Navarro improve random access decompression by restricting the format of “backreferences” in the LZ parse. The parse decomposes the original string into a sequence of phrases; concatenating the phrases yields the string back, and phrases have a compact representation. In LZ77, phrases are compressed because they refer back to substrings in prior phrases. LZ-End adds another constraint: the backreferences cannot end in the middle of phrases.

For example, LZ77 might have a backreference like

[abc][def][ghi]
   ---------

to represent “cdefg.” LZ-End would be forced to end the new phrase at “f”

[abc][def][ghi]
   -------

and only represent “cdef.” The paper shows that this additional restriction has a marginal impact on compression rate, and uses the structure to speed up operations on compressed data. (The formal definition also forbids the cute/annoying self-reference-as-loop idiom of LZ77, without losing too much compression power!)

We can apply the same idea to compress code. Each phrase is now a subroutine with a return at the end. A backreference is a series of calls to subroutines; the first call might begin in the middle, but matches always end on return, exactly like normal code does! A phrase might begin in the middle of a phrase that itself consists of calls. That’s still implementable: the referrer can see through the indirection and call in the middle of the callee’s callee (etc.), and then go back to the callee for a suitably aligned submatch.

That last step looks like it causes a space blowup, and I can’t bound it (yet).

But that’s OK, because I was only looking into compressing traces as a last resort. I’m much more interested in expression trees, but couldn’t find a way to canonicalize sets (e.g., arguments to integer +) and sequences (e.g., floating point *) so that similar collections have similar subtrees… until I read Hammer et al’s work on Nominal Adapton, which solves a similar problem in a different context.

They want a tree representation for lists and tries (sets/maps) such that a small change in the list/trie causes a small change in the tree that mostly preserves identical subtrees. They also want the representation to be a deterministic function of the list/trie. That way, they can efficiently reuse computations after incremental changes to inputs.

That’s exactly my sequence/set problem! I want a tree-based representation for sequences (lists) and sets (tries) such that similar sequences and sets have mostly identical subtrees for which I can reuse pre-generated code.

Nominal Adapton uses a hash-based construction described by Pugh and Teitelbaum in 1989 (Incremental computation via function caching) to represent lists, and extends the idea for tries. I can “just” use the same trick to canonicalise lists and sets into binary trees, and (probabilistically) get common subexpressions for free, even across expressions trees! It’s not perfect, but it should scale pretty well.

That’s what I’m currently exploring when it comes to using compression to reduce cache footprint while doing aggressive specialisation. Instead of finding redundancy in linearised bytecode after the fact, induce identical subtrees for similar expressions, and directly reuse code fragments for subexpressions.

More to come

I thought I’d post a snippet on the effect of alignment and virtual memory tricks on TLBs, but couldn’t find time for that. Perhaps later this week. In the meantime, I have to prepare a short talk on the software transactional memory system we built at AppNexus. Swing by 23rd Street on December 15 if you’re in New York!

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