My Experience at JuliaCon
johnmyleswhite.com
johnmyleswhite.com
Reading between the lines, devectorize.jl and the vectorization framework will make for a heady mix. I am glad that Julia is challenging the traditional mantra of "vectorize (as in the R/Numpy/Matlab sense) the loops". It is heart warming to see that the language designers get it that this style has inherent speed limitations (time is spent filling and copying temporary vectors).
If any Julia core developer is seeing this, just a shout out, (i) to say you are doing awesome work, and (ii) @ macros available in the standard library are not documented well. It would be good to have a page that describes what is available now.
EDIT: Just clarifying my point. Macros as a feature are quite well described in the docs. What I miss is an index of macros that come built in with the standard library. They would help both with pedagogy and with putting them to actual use, for example removing bounds checks. If they are a little more discoverable than they are now that would be very helpful to a newcomer. For a new'ish language the documentation is otherwise quite admirable. @ViralBShah I filed an issue.
Does the Metaprogramming section of the manual not adequately describe macros? It would be great if you submit a pull request or an issue describing what is missing.
http://docs.julialang.org/en/latest/stdlib/base/
The stdlib docs are organized by subject matter. What would the benefit of having a separate index of macros be? If one wants a list of exported macros, that's just a matter of doing
grep @ base/exports.jl
in a Julia repo.I believe the video is heading for their YouTube channel: https://www.youtube.com/user/JuliaLanguage/featured
The point, I think, is not that vectorizing is slow. It's that you don't want to be myopic when you do it. Your point about time spent filling and copying vectors is independent of what Devectorize is trying to do.
Yes, when you vectorize code, you need to have a prologue and an epilogue which gets the data in the correct format for the SIMD operations. This prologue and epilogue has a cost, and if it's larger than the gain from the SIMD operations, then it's not worth vectorizing. (This can happen if, say, you only have 4 elements to vectorize.) However, we have to do this cost-analysis all the time. Figuring out when it's beneficial to vectorize code has been around as long as we've vectorized code.
Devectorize.jl is not about that problem. Rather, it's about when you have a chain of expressions, and the operators in those expressions have implied loops. The naive thing to do is to myopically execute each one of those loops, creating and passing around temporary vectors. The Devectorize framework is given an entire expression, and is able to analyze where the implied loops are, and figures out how to express that computation in a single loop.
We can tell these two concepts are independent because the ideal situation is to first use Devectorize on an expression, and then vectorize the result!
For the record, the approach taken by Devectorize.jl is similar to the problem that expression templates (http://en.wikipedia.org/wiki/Expression_templates) in C++ try to solve. Through template trickery and operator overloading, we can put off evaluating an expression, avoiding the temporaries and unnecessary memory traversal that a naive execution implies. The Boost library uBLAS (micro Base Linear Algebra Subprograms, http://www.boost.org/doc/libs/1_55_0/libs/numeric/ublas/doc/...) uses this technique.
The canonical example of ET and the one that started it all is Blitz++ (unlike its modern descendants it actually handles full n-dimensional tensors). More recent solutions are Blaze, Eigen and Armadillo. I like these over uBLAS (more verbose and not as performant). Blaze is typically the fastest (in this class) as long as you are dealing with 2D arrays and linear algebraic operations. Since Julia is homoiconic and has hygienic macros, one does not have to resort to such syntactically complex ways of doing metaprogramming such as ETs in C++. ET's are great to use, not very pleasant to write the machinery for, although things like Boost::spirit and fusion make it more tolerable. Heaven forbid that you have to understand the error messages though.
Now, to another point, looping is so pathetically slow in R, Numpy and Matlab (in that order) that the traditional solution offered in these languages is to vectorize (in the Matlab/numpy/R sense not in the SIMD sense) the loops into vector-expressions. Often this needs the help of extra prefilled vectors/matrices, (some languages do it smartly with 'broadcasting', some where late to pick it up, looking at you Matlab). Even with broadcasting tricks, the extra stride indirection in the iteration slows down the code from how fast it could have been. That is but one aspect of it, the other is chaining several binary and unary operations together. This also creates temporaries and unnecessary loops (unless you use solutions of somewhat limited scope like numexpr, which BTW is lovely when it is applicable, it also does thread level parallelization as well as SIMD if you can afford to link with intel MKL).
In Julia there is no need to avoid loops because they are inherently fast. In fact they are faster than the vectorized expressions, because of inefficiencies mentioned. However, loops are a lot more verbose than expressions. So this is where devectorize comes in. It transforms those expressions into loops (much like ETs) which can then be JITed to obtain superior performance. Now with SIMD vectorization thrown in on top, one can gain even more, because now one can benefit further from the instruction level parallelism. So yes you devectorize and then vectorize (and you already know this) and the term "vectorization" refer to two different concepts named vectorization , the clash in terminology is rather unfortunate.
EDIT: @scott_s no offense taken and upvoted. As I said, this post was just to offer some clarifications, the clash in terminology indeed gets very confusing. So, thanks for making me improve my comment, if it confused you I am sure it would have confused others as well.
This paragraph made me think you saw a conflict with the two approaches: "Reading between the lines, devectorize.jl and the vectorization framework will make for a heady mix. I am glad that Julia is challenging the traditional mantra of "vectorize (as in the R/Numpy/Matlab sense) the loops". It is heart warming to see that the language designers get it that this style has inherent speed limitations (time is spent filling and copying temporary vectors)."
The difficulty, I think, is what you identified. I was thinking of the classic compiler optimization called "vectorizing".
The problem that Julia solves here is that many scientific programming environments require you to write vectorized code, because they are interpreted and so looping through the elements in a vector incurs massive interpreter overhead. In some cases, this can make your code much more difficult to understand than if you wrote an explicit loop, but even when it does not, it often forces you to give up performance that could be obtained if you could write the code in a devectorized manner.
For example, consider the problem of calculating the variance of a sample. To calculate the variance in MATLAB, one might write:
mu = mean(x)
sum((x - mu).^2) / (length(x) - 1)
Although I don't know the details of how MATLAB optimizes this code, I do know that it has roughly equivalent performance characteristics to Julia code that first computes x - mu, then computes abs2(x - mu), then sums along the result. With an interpreter, you can't do much better, and this is actually how the MATLAB var function does it. In Julia, we compute the variance as: mu = mean(x)
v = 0.
for i = 1:length(x)
v += abs2(x[i] - mu)
end
v / (length(x) - 1)
This is several times faster than MATLAB's included var function, because the computations performed on each element are cheap relative to the cost of memory access. If you wrap the loop in the @simd macro and add @inbounds to eliminate the bounds check when accessing x, the LLVM loop vectorizer will actually take that loop and translate it into SIMD instructions, making it even faster. (The @simd macro is necessary to tell LLVM that it's okay to vectorize, since accumulating into n variables and summing them at the end gives different [but usually more accurate] results compared to accumulating into a single variable due to floating point rounding.)The promise of Devectorize.jl is that you will be able to write the first code fragment and have it transformed to the second, which would be neat indeed.
I understand that your example is entirely pedagogic, but just a cautionary note for the unwary (a) although it is tempting to fold the variance calculation into a single loop (accumulate the totals of x and x^2), (b) neither that obvious single loop version nor the code above are good ways to compute variance if one cares about preserving precision, more so if x has a wide dynamic range. In large scale problems it does raise its ugly head and these bugs are difficult to catch because the code is mathematically correct. Using double mitigates the problem to an extent (but then floats are faster for SIMD vectorization).
Another side note, I have gradually come to realize and appreciate the unique position that Fortran holds. It is not often that you have compiler writers with a background in numerical analysis or vice versa. I BTW have background in none and sorely miss that.
The available version was 0.2 for ages (I see now they offer a pre-release 0.3), and the blog hasn't been updated for 9 months.
Some simple posts every month or so would signal that this is a live, worked-on, language (which it is, and interesting stuff happens all the time).
It was difficult to even find out about JuliaCon -- no banner, no blog post, nothing, just a small link in the main site navigation, that one can easily not notice.
More frequent posts on the main blog would indeed be a good idea. There will certainly be a few GSoC student posts as the summer progresses.
As of a few days ago there is a also Julia blog aggregator highlighting community posts:
I believe we've had 0.3-pre nightlies posted since at least January.
As far as JuliaCon, it was announced on the mailing lists and did show up on HN once I believe. It sold out very quickly, so wasn't really actively promoted after that.
1) RStudio is just such an amazing tool with rmarkdown and pandoc. I run my statistics in a document and can output to html, pdf or Word. I can't tell you how important the ability to print out to Word is in my corporate setting.
2) The libraries and tools are vast (Seems like Linux tons of options but really one or two are perfect for the individual use)
3) 99% of what I do takes less then 2 seconds with R
Personally if I have a need for large datasets I will look to Julia if I can't get a solution with R and data.tables.
Perhaps if MCMC.jl matures, and if it can offer performance competitive with BUGS, JAGS, Stan, etc., I could see Julia's statistical fortunes rise along with Bayesian methods generally. I'm working on a PhD in a discipline that is just now beginning to dip its toes in Bayesian waters. I get the feeling that the adoption surge is yet to come.
Interesting that you're implementing your own MCMC methods mainly. As part of my coursework I did a little bit of that, but perpetually felt like I wasn't smart enough to anything sophisticated--either in terms of exotic sampling methods, or working with very complex posterior distributions. It may just be my frequentist R toolbox experience messing with me, but I know I feel more comfortable with the safety blanket of a framework.
I've wondered what it would take to instrument support for Julia in RStudio. RStudio is open source, but I don't really know how generically it could interface to whatever repl.
Assuming I understand the added requirement of the AGPL, wouldn't RStudio's legal recourse apply only to derived works that didn't release their code?
Like (almost?) all FLOSS dev tools, there's no connection between how the code is written and the ensuing license. Suggesting such (even by way of a comment) is rather unfair.
COIN Cbc/Clp, GNU GLPK, Gurobi, Ipopt, Mosek, NLopt
So you can use it to generate models that are solved in Gurobi if you want. Or you can use the available open source solvers.