Tag Archives: Julia

I Like Julia Because It Scales and Is Productive: Some Insights From A Julia Developer

By: Christopher Rackauckas

Re-posted from: http://www.stochasticlifestyle.com/like-julia-scales-productive-insights-julia-developer/

In this post I would like to reflect a bit on Julia. These are my personal views and I have had more than a year developing a lot of packages for the Julia programming language. After roaming around many different languages including R, MATLAB, C, and Python; Julia is finally a language I am sticking to. In this post I would like to explain why. I want to go back through some thoughts about what the current state of the language is, who it’s good for, and what changes I would like to see. My opinions changed a lot since first starting to work on Julia, so I’d just like to share the changed mindset one has after using the language deeply.

Quick Summary

Here’s a quick summary of my views.

  1. Julia is not only a fast language, but what makes it unique is how predictable the performance and the compilation process is.
  2. The language gives you lots of introspection tools to be able to easily isolate issues.
  3. The opt-in type checking and allowing many different architectures to be fast is a strong bonus for software development, especially when scaling to large software ecosystems, over other scripting languages since it allows you to write simple and self-documenting code.
  4. Julia’s unique features make it easy to make packages which are type-generic and parallel.
  5. Most of these benefits will be seen by package developers. “Users” will probably not see as much of a difference in their own codes because the majority of their performance will be determined by the packages they use.
  6. To attract a new wave of users, Julia needs to start taking a “package-first” mentality and push package-level unique features rather than language-level features. Language level is what developers care about, but the majority of programmers are not developers.
  7. We have all of the basics in Julia, but we need to start showing off (and working towards) how we can be different. Every package should be picking some special features and types to support. Speed is just one feature.
  8. Julia can have a bright future, but we may need to start advertising and teaching it differently.

I think that to start, I need to discuss a topic which might be new to newcomers.

Julia’s JiT is not like other JiTs, and it helps package development

LuaJIT is a runtime that just-in-time compiles Lua, so is it the same thing or similar to Julia? What about MATLAB’s JIT? The answer is no, Julia’s compilation strategy is very different. Other JIT setups for scripting languages use something that’s known as a tracing JIT. What these do is they track the commands you are running and then via some algorithm (possibly probabilistic in some setups like LuaJIT) it determines what parts of the code are repetitively ran enough that they warrant compilation, and then code for those specific sets of commands are compiled and when the parser hits those areas again it runs the JIT code.

Julia on the other hand is almost static. When running any Julia function, it will first take your function calls and then auto-specialize it down to concrete types. So f(x::Number)=x^2 will specialize to Float64 when you call it with f(1.0). Using this type information, it has a compile-time stage where it propagates all type information as far as it can go. So if you internally do x^2, it will replace that with ^(::Float64,2) (the 2 is a compile-time constant), and then since it can determine the types of everything, it will push this all the way down to generate clean LLVM IR (and thus clean assembly code) for x^2 on Float64s. It will cache this compiled version of the function so that way f(2.0) uses the same compiled code (notice that the compilation process only needs the type and not the runtime values!). However, when you then call it with f(1), it compiles a separate version for Int.

In some sense, this is very different. The obvious difference is that Julia’s compilation process is deterministic and is open to introspection. If you do

@code_warntype f(1.0)
@code_llvm f(1.0)

Julia will spit back at you its internal AST of the method specialized on Float64, and then the LLVM IR. The nice thing about this is that you can check every step of the process. I never participated in programming language development conversations before working with Julia, but this makes it easy. You see this kick something out, you find out yourself how to optimize it, and then you can easily ask someone “why doesn’t the compiler optimize xyz away here?” and then that leads to code changes (i.e. “oh, array aliasing is preventing compiler optimizations!”), new work on compiler optimizations, and better performance. A recent place where just happened was in this Discourse discussion where a user points out that a separate faster LLVM instruction could be used than the one that is actually omitted.

But what I really like about this process is that it’s clear and deterministic. I can know exactly what my packages are doing and why. This makes it very easy to optimize packages because you always know what’s going on. When trying to piece together 50+ packages like DifferentialEquations.jl, deterministic rules for how to optimize code and easy means of introspection are essential to know what’s going on. This kind of transparency is something that’s really easy to appreciate after working on something like MATLAB where the internals are opaque.

There is a tradeoff though. In order for this process to work well it requires being able to propagate type information. This requires that the types of the variables inside of a function are what’s known as “type-stable” or “type-inferrable”. For example,

function g(a,n)
  x = 0
  for i in 1:n
    x += a

will add a n times. If you call this with g(1.0,10), you’ll notice this is not as fast as you’d hope. The reason is because the type of x starts as a Int, and then Int+Float64 produces a Float64 and so x changes types. Think about writing a C-code for doing this: you can’t just have a variable change types like that? So what Julia does is compile x in a way such that it is dynamically typed, and the lost assumptions associated with doing this is why the performance drops down to that of Python/MATLAB/R since now it has the same amount of dynamicness as a real scripting language: it’s all just a game of how much information is known by the compiler. So the way to think about it is, if your code can be type-stable, Julia will take full advantage of this and make a completely static function and compile that, otherwise it will make the necessary parts dynamic in order to handle the extra features. Together, this is a pretty nifty way to mix ease of use and performance. At any time, you can @code_warntype your function call and it will explicitly highlight which variables are “being dynamic”, and that tells you exactly what to optimize. For example,

  x::UNION{FLOAT64, INT64}
      x::UNION{FLOAT64, INT64} = 0 # line 3:
      SSAValue(2) = (Base.select_value)((Base.sle_int)(1, n::Int64)::Bool, n::Int64, (Base.sub_int)(1, 1)::Int64)::Int64
      #temp#@_5::Int64 = 1
      unless (Base.not_int)((#temp#@_5::Int64 === (Base.add_int)(SSAValue(2), 1)::Int64)::Bool)::Bool goto 29
      SSAValue(3) = #temp#@_5::Int64
      SSAValue(4) = (Base.add_int)(#temp#@_5::Int64, 1)::Int64
      #temp#@_5::Int64 = SSAValue(4) # line 4:
      unless (x::UNION{FLOAT64, INT64} isa Int64)::Bool goto 14
      #temp#@_7::Core.MethodInstance = MethodInstance for +(::Int64, ::Float64)
      goto 23
      unless (x::UNION{FLOAT64, INT64} isa Float64)::Bool goto 18
      #temp#@_7::Core.MethodInstance = MethodInstance for +(::Float64, ::Float64)
      goto 23
      goto 20
      #temp#@_8::Float64 = (x::UNION{FLOAT64, INT64} + a::Float64)::Float64
      goto 25
      #temp#@_8::Float64 = $(Expr(:invoke, :(#temp#@_7), :(Main.+), :(x), :(a)))
      x::UNION{FLOAT64, INT64} = #temp#@_8::Float64
      goto 5

This is spitting back and telling me that x is typed as both Float64 and Int64 which is exactly the problem I identified. But have no fear, Julia is based around typing, so it has ways to handle this. For example, zero(a) gives you a 0 in the type of a, so

function g(a,n)
  x = zero(a)
  for i in 1:n
    x += a

is a good generic type-stable function for any number which has zero and + defined. That’s quite unique: I can put floating point numbers in here, symbolic expressions from SymEngine.jl, ArbFloats from the user-defined ArbFloats.jl fast arbitrary precision library, etc. Since Julia always auto-specializes on the types, no matter what I give it, it will know how to replace zero with whatever it needs to and do so at compile-time since at compile-time there’s enough type information to know what that constant should be, and then it will replace the + with calls to the correct version of +. Thus there is no runtime overhead for handling genericness. All you have to do is remember to write your code in a manner such that the types match what comes in (other helpful functions for this include typeof, eltype, and similar). So Julia is not only built to make generic functions performant, but it also has the right tools for handling types to make this actually easy to do.

There is a little bit more of a cognitive burden here than in other languages. It’s not much, but there are a few things to keep in mind. Tracing JITs will more automatically handle typing by using runtime information, but are harder to introspect and harder to determine when things are going wrong (also, it cannot fully statically compile ahead of time). With Julia, you do need to understand and think about your code in terms of types if you want full performance. But if you do so, then your code isn’t “close to C”, it literally has enough information that it can create and compile a function which is as fast as C (and any speed difference from C is usually due to the fact that you’re using the LLVM (clang) compiler instead of the more standard GCC, or Julia in some cases is missing the ability to add an optimization. Extra compiler optimizations are part of the 1.x milestones. In practice you’ll find that most codes are <2x from C, with the vast majority being close to 1x and then a few being higher due to reasons which already have open issues and many times work in progress PRs scheduled for a 1.x). But this reduction to types and inference has one crucial advantage: it scales really well. This reliance on types (and optional type declarations) makes it easier to scale because Julia gives you lots of information if types don't line up like you think they should. And it's deterministic. While it doesn't do static analysis like C++, type declarations and method dispatch declarations allow your code to throw type warnings when necessary, and the stack trace gives you tons of information about missing methods (this kind of information could be used to give warnings in an IDE though, which is something I'd like to see). From this, it's easy to know when types are wrong. The inability to handle types well is one of the main reasons I see developers having hard times scaling up programs in scripting languages, but it’s not an issue in Julia. So while LuaJIT and other well-designed tracing JITs can in many cases match Julia’s speed with enough work optimizing runtime heuristics, they won’t have the same ease of understanding and predictability as Julia, and won’t have as much of a robust type-checking system to plug into as your program and contributor base grows.

Sure, Numba uses a similar strategy as Julia. If you stick to only using Float64s and a few other basic types (Float32, and some integer types?) you’ll get something very similar to what’s described here. But I’ve described before that making robust generic software with this type-inference approach requires a strong understanding and use of the type system, and I have never found Python+Numba close to matching Julia in its ability to let the user directly handle types, and it’s this combination of the type system + the compilation strategy that makes Julia code scale well. This difference may not be appreciated in one-off scripts, but when building and maintaining robust software I have found it necessary.

But lastly, using this strategy Julia actually can produce static binaries like compiled C or Fortran code, so I think this fact will come in handy for making Julia into a package development language. Basically, you can write packages in Julia, and someday it will be easy to generate a runtime-free binary (like C/Fortran) others can link to. That leads me to my next point.

In some ways, I see Julia actually as a more productive C++ instead of a faster Python. At least as a package developer I tend to use it like that, and a lot of its features essentially give you full generic template programming that you’d attempt in C++, just with a lot less code. I think that for many developers, this is a more appropriate way to consider Julia. But that’s not Julia’s whole audience, which leads to my next point.

You Will See The Most Benefits in Package Development

How much does this language choice actually effect real use cases? Well, I think it depends on who you are. One thing that you’ll notice is that, for the vast majority of users, the performance of your scripts is almost entirely determined by the speed of your packages. This is true in pretty much any scientific computing application that I know of, in Julia, R, MATLAB, Python, etc. If 90% of your time is spent calling functions from DataFrames or JuMP, then the speed of your analysis code really doesn’t impact the final runtime all that much.

So in some sense I don’t believe that Julia’s performance will directly effect most users of the language (and I think that this is true for R/Python/MATLAB as well). However, where it really manifests itself is indirectly through package development productivity. Simply put, a Python package written in pure Python is slow, like really really slow. Same with R and MATLAB. This impacts the development time and resources since all of the major projects like SciPy, NumPy, and Pandas are almost entirely C++ code underneath. And this also impacts features. It’s really hard to make traditional languages handle things like arbitrary precision arithmetic well, and so you’ll see that most functionality in things like SciPy do not support all of the glory that Python allows since it’s not really Python code! Then Python packages are built on SciPy and its limitations, and that just further propagates the impossibility of extending the algorithms to something more generic. Python in fact has so many issues here that projects have had to internally develop their own JITs in order to get the performance, features, and syntax they want. JitCODE and PyDSTool are two ODE solvers which developed DSLs and ways to compile their code. One nice example is this video on PyTorch where the developer describes the tracing JIT they built into their package. I seriously commend these individuals for building such amazing systems, but dear god I do not want to spend my own development time building a compilation scheme for each new scientific project I am involved in! To me, these are language level issues and should be addressed by the language. What the PyTorch developers had to build into their package is what Julia gives you package developers for free, and as a scientist who doesn’t want to write compilers, I am super satisfied.

In Julia, packages can be written in Julia and be performant. As demonstrated above and in this post, they can also be type-agnostic or type-generic and still be performant. This means that it’s much easier/quicker to develop “good” libraries in Julia, and that it’s easy for any of these libraries to support just about any type. An example for this is GenericSVD.jl which just implements an SVD-factorization in Julia, and this compiles to fast code for things which are not supported by common Fortran bindings like BigFloats, ArbFloats, complex numbers, etc. and the code is simple. It’s a great simple package which likely didn’t take much development time but is already something very unique due to its type-genericness and speed.

This makes me think that most users should look at Julia a little differently. To me, Julia is a language which is designed to make it easy to roll your own package and have them be performant. If you want to develop libraries, then Julia is great for you and the benchmarks (among other things like multiple dispatch and type-genericness) show why you should choose Julia over Python/R/MATLAB/etc. To me it’s almost a no-brainer to choose Julia for your next methods project or package. But if you’re a user who uses libraries, you cannot expect a blanket performance difference from your previous language “just” because it’s Julia. For example, Pandas is in Python, but it’s fast because it’s written in C++. Just because you’re switching to Julia you shouldn’t expect functions on data table objects to be faster (in fact, they might not be since Pandas is pretty well-optimized. One place where the package ecosystem is currently not as well-optimized is plotting, where the plotting libraries need some restructuring to improve performance.). What you can expect is that the development of the associated Julia libraries is more transparent (it’s in Julia) and generally performant as well. But also, all of the tools you’d use to help out your own scripts make it easy to find out what’s wrong in a library and contribute some code to speed it up. Going from user to contributor and actually helping package development is super trivial and probably the most underappreciated “feature” (or more, side effect of the design) of Julia.

But given the market for who actually chooses Julia, Julia packages do tend to be fast in the end Julia is really top-of-the-class in many disciplines, though that is not true all around. But the fact that development is fast and easy to write scalable packages in means that you can find a lot of odd unique packages: lots of small numerical linear algebra or new optimization algorithm packages which run performantly and just don’t exist anywhere else make up a good chunk of what I find in Julia. To top it off, Julia makes it easy to setup continuous integration in Windows, Mac, and Linux to get your package off the ground and well-tested. Here’s a video that goes through all of that. Again, package-development level features.

Fast Multiparadigms Makes Maintenance Easier

The big thing which has helped me scale packages is that Julia doesn’t care how you program. Looping, vectorization, functional styles with lots of recursion, etc.: it doesn’t care. You can just choose the form that is natural for your problem, write a code which uses that style, and know it’s going to be performant. This is very different than the R/MATLAB/Python mentality of “vectorize everything!”, even if it’s not natural to vectorize. I remember doing some very “fun” hacks in MATLAB and Python specifically in order to make good use of vectorized functions, and having to document inside of comments a step-by-step explanation of what the hell the code is actually doing. Many of those times, a 3 line loop which is almost copy-pasted from the paper’s psudocode would’ve done the trick, but in the name of performance I mangled the code. Julia doesn’t require this, and I have very much appreciated this when reviewing code from others.

This is probably the biggest difference. If you have appropriately vectorized code in MATLAB/Python/R, the performance difference from Julia isn’t actually too big. There’s still a difference because vectorization is particularly wasteful with memory and isn’t actually optimal in most cases, but it’s within an order of magnitude. However, you are required to program in a specific way in these other languages to get here, and if you’re doing anything more than scripting you’ve probably found that this doesn’t scale because, well, sometimes code gets mangled when you force vectorization!

There is Beauty in Using the Full Language

Sure, Python isn’t too bad if for performance you stick to arrays of 64-bit numbers as allowed in NumPy arrays, and you use pre-written functions (C-bindings) in SciPy. But what if you really want to create your own numbers as some object, and you want to build data structures using objects in order to more easily scale your software? This is where this setup begins to take its toll. When saying that a small part of the language is required to be used in order to get good performance, you get pidgeon-holed away from the most intuitive code and have to move towards big arrays of numbers. Instead of “naming” separate arrays, items are thrown into matrices with comments says “1:3 is chemical A, 4:7 is chemical B, …”, which I did not find scales very well.

But in Julia, using types is actually performant. Structs in Julia are value-types, which means that they create structures which inline the type-values instead of using indirection via pointers. This means that a Complex{Float64}, which is a struct of two values (the real and imaginary parts), is in memory as a 128-bit chunk with two numbers. This is as performant as if you implemented some kind of intrinsic type in C. You can use this without worry. And mutable structs, while including pointers, are much more performant than objects in most scripting languages because functions auto-specialize on them. The result is that you can make use of all of the language when building software that needs to be performant, once again making it easier to scale projects.

GPUs and Parallelism is Straightforward and Generic

Serial performance only gets you so far. Scaling up your project means two things: scaling up the size and features of the codebase, and scaling up the computing power. I discussed how Julia excels in the first part, but what about the second? What I have found really great about Julia is that its parallelization is dead simple. Add @threads in front of a loop and done, its multithreaded. @parallel and pmap do distributed parallelism via multiprocessing, and I have shown how in 5 minutes you can parallelize your code across a whole cluster. Explicitly writing GPU kernels and using multiple GPUs is easy.

I cannot forget one of my favorite developments as of late: GPUArrays.jl. Essentially, when you write vectorized (broadcasted) code with a GPUArray, it automatically parallelizes on the GPU. Neat! But this means that any generic function written in this style is already compatible to automatically compile a GPU version. So things like OrdinaryDiffEq.jl (the ODE solvers of DifferentialEquations.jl), even though they don’t have a single piece of GPU-specific code in them, compile performant versions of their solvers for GPUs, automatically, because Julia feels like being nice. Like seriously, once you get a strong understanding about how types and dispatching works, Julia is absolutely mindblowing.

Summary: Julia Is Great For Package Development, But Users Just See Packages

And this leads me to my conclusion. In each of the sections above I note why Julia is great for building packages in. In comparison to the other scripting languages, I find nothing comes close in terms of productivity, scalability, resulting performance, and resulting features. No other languages makes it so easy to make a function which is performant yet doesn’t care what number types you use! And being allowed to use the whole language “correctly” means that your code is much easier to understand and grow. If you’re looking to publish a package along with your algorithm, Julia is definitely the right place to be. In that sense, this group will see Julia as an easier or more productive C++.

But for end users throwing together a 100 line script for a data analysis? I don’t think that this crowd will actually see as much of a difference between other scripting languages if the packages in the other languages they are using are sufficiently performant (this isn’t always true, but let’s assume it is). To people who aren’t “pros” in the language, it will probably look like it just has a different syntax. It will be a little faster than vectorized code in other languages if code is in type-stable functions, but most of the differences a user will notice will come from the mixture of features and performance of packages. Because of this, I am not sure if marketing the features of the language is actually the best way to approach the general audience. The general audience will be convinced Julia is worthwhile only by the package offering.

I want to end though with the fact that, since Julia packages are written in Julia, a Julia user is qualified to write, debug, and contribute to packages. I myself never saw myself becoming a package dev until about a year ago, and this transition only was because Julia makes the change so easy (it wasn’t any different than the Julia development I was already doing!). While this is a good highlight to people who would read a blog post about programming languages, I still think this is a small niche when considering the average programmer. I don’t think that the average programmer sees this as an upside. Most don’t have the time to invest in this kind of development, and see that push that “you can do it all yourself!” as a turn-off (even though it’s “can” instead of “have to”!). It’s a very different crowd to be catered to.

My Recommendations

Package Accessibility and Discoverability

So in the end, I see Julia as in a state of transition. The way it was marketed before in terms of performance benchmarks, the type-system, etc. are all things which appeal to package developers, and Julia already has had great adoption by developers. But now Julia needs to start targeting general audiences by sharing its packages. There are a few things in the Base Julia language like adding noalias scopes that I would like to see, but pretty much everything (other than a few compiler optimizations) I put as “not essential” now. What I see as essential is making packages more accessible.

As someone well-aware of the packages which are available, I can tell you that “lack of packages” isn’t really a problem with the ecosystem: you can find a great package that does what you’re looking for. In fact, this weird idea that Julia doesn’t have packages yet leads to some silly chatroom discussions where a newcomer joins the Gitter channel and asks “I wanna contribute to the language… has x been done yet?”, give back 10 example, “y?”, give back 5 examples, “z?”, 5 examples, “oh, I’m surprised how much is already done!”.

This chat happens quite often, which is fine, but it points to a problem. We really need to work more on “discoverability” and “noob-friendly docs”, both items which I’m not entirely sure what the easiest way to handle are. But, I think that this is what is required for Julia to grow (word choice is on purpose: grow instead of succeed, because Julia to me is clearly already successful enough to sustain a development community and thus invest your own time in it, though the community could grow much more). If we think of newcomers as coming in waves: wave 1 brought in language devs and was extremely successful (as evidenced by the over 500 committers to just the Base language, more than projects like Cython has ever had!), wave 2 brought in package devs and has been very successful as well, but now we need to gear up for wave 3: the package users. This means that package discoverability is what will bring in the third wave.

Package Uniqueness

Julia packages should spend more time on their unique parts. Everyone has optimization packages, and people in Python are using things written in C/C++/Fortran like NLopt and IPOPT and so the performance difference is essentially nil in these well-developed cases. But a native Julia package can have other advantages as well. Working out of the box with complex and arbitrary precision numbers, using autodifferentiation, being compatible with DistributedArrays and GPUArrays to allow these forms of parallelism without having to transfer back to the CPU for the optimizer’s parts. These features are huge for large classes of researchers (I know that quantum physicists want better complex number support everywhere!) and this is where Julia’s packages shine: genericness. Supporting genericness and parallelism should be front and center with every big Julia package, and it should have unique examples to show it off.

We already have very strong libraries in quite a few domains of scientific computing. Here’s what Julia sounds like when, instead of saying “Julia can do ______”, you say some unique things about the libraries:

  1. Constrainted optimization and mathematical programming. JuMP‘s DSL automatically defines Jacobians and Hessians via autodifferentiation. Its solver independence makes it easy to switch between libraries to choose the most efficient one for the problem.
  2. Numerical linear algebra. Not only does th standard library expose more of BLAS and LAPACK via special matrix types than other languages, there are many special-purpose libraries for linear solving. IterativeSolvers.jl allows you to use any LinearMap, meaning that by passing a lazy LinearMap it automatically works as matrix-free preconditioned GMRES etc., and there are many (and a growing number) of methods to choose from. This library also supported complex and arbitrary precision numbers. In case you were wondering, there does exist PETSc.jl is a binding to the infamous PETSc library, and it is compatible with MPI.
  3. Differential equations. I’ve already discussed the feature set of DifferentialEquations.jl.
  4. Autodifferentiation. With ForwardDiff.jl and its operator overloading approach, pretty much any Julia code can use forward-mode autodifferentiation without any modifications, including the Base library. This means there’s almost no reason to use numerical differentiation of any pure-Julia code! Reverse-mode autodifferentiation exists as well, but I’ll leave a note pointing to the future Cassette.jl.

I’m not an image processing guy but Images.jl is a large library developed by Tim Holy which must have some unique points. A major contributor to Julia is Steven Johnson, the creator of FFTW (and NLopt which has a Julia binding), the widely used FFT library, is a big Julia contributor and there has been discussions about building a generic FFT library in Julia. In addition, many applied mathematicians are pointing to mixed-precision algorithms as a big possibility for increasing the performance of scientific applications, and Julia’s strong control over types and specialization on types is perfect for handling such algorithms.

The main thing is that, if we only talk about “Python does this, does Julia do _____?”, then we can only talk about speed. We have lots of unique developments already, so we should change the conversation to highlight the things that packages in Julia can do that other packages cannot.

Package Distributions and Branding

Another thing I think we should be doing is bundling together packages as distributions. We somewhat do this with the organizations (JuliaStats, JuliaOpt, etc.), but it’s not the same as having a single cohesive documentation. People know and respect SciPy. It’s a hodgepodge of different things, but you know who’s going to look at your bug reports and you’ve other parts of SciPy and that’s why over time you respect it. It’s very hard to get that kind of respect for a lone 5 star github package. I think cohesive documentation for orgs and metapackages, much like I have done with DifferentialEquations.jl is required in order to get big “mainstream” packages that users can know and trust.

“User”-focused Tutorials

I think Julia can become big since it gives package developers so many tools to make big performant package ecosystems with ease. But this has made most people in the community focused on talking to other “developers”. We should reach out to “users” with simple examples and tutorials, and understand that most people don’t want to contribute to a package or anything like that, but really just want to add a package and use a function to spit out a plot as fast as possible. For the next wave of Julia users, we should show should how the package ecosystem enables this kind of usage, and that’s how Julia will grow.

I believe that we should target teaching resources directly to them, similar to what’s seen in other languages. I see workshops for “learn how to do regression in R!”, “learn how to build websites with Shiny!”, “learn how to use Pandas!”, but for Julia I only seem to see “let’s learn Julia in depth: how to write fast code and the type system”. We should instead run workshops directly on Optim, JuMP, DifferentialEquations, etc. at various universities where we are already “teaching Julia”, and have it setup as “direct to skill” for specific disciplines instead of teaching fancy language-level features. Although it’s hard because I too am a purist in “learn the language and you can do it all!”, I think we need to reach out more to those who only want to do a very specific thing, and train them in Julia for psychology research, Julia for climate models, etc. And honestly, I can’t think off of the top of my head a good tutorial that says “here’s how to do scientific computing in Julia”, and works through some specific issues and skills that piece together a few important libraries. We need to write some resources along these lines.

At least, that’s what I think. Feel free to agree/disagree in the comments below.

The post I Like Julia Because It Scales and Is Productive: Some Insights From A Julia Developer appeared first on Stochastic Lifestyle.

A Comparison Between Differential Equation Solver Suites In MATLAB, R, Julia, Python, C, Mathematica, Maple, and Fortran

By: Christopher Rackauckas

Re-posted from: http://www.stochasticlifestyle.com/comparison-differential-equation-solver-suites-matlab-r-julia-python-c-fortran/

Many times a scientist is choosing a programming language or a software for a specific purpose. For the field of scientific computing, the methods for solving differential equations are what’s important. What I would like to do is take the time to compare and contrast between the most popular offerings.
This is a good way to reflect upon what’s available and find out where there is room for improvement. I hope that by giving you the details for how each suite was put together (and the “why”, as gathered from software publications) you can come to your own conclusion as to which suites are right for you.

(Full disclosure, I am the lead developer of DifferentialEquations.jl. You will see at the end that DifferentialEquations.jl does offer pretty much everything from the other suite combined, but that’s no accident: our software organization came last and we used these suites as a guiding hand for how to design ours.)

Quick Summary Table

If you just want a quick summary, I created a table which has all of this information. You can find it here (click for PDF):

Comparison Of Differential Equation Solver Software

MATLAB’s Built-In Methods

Due to its popularity, let’s start with MATLAB’s built in differential equation solvers. MATLAB’s differential equation solver suite was described in a research paper by its creator Lawerance Shampine, and this paper is one of the most highly cited SIAM Scientific Computing publications. Shampine also had a few other papers at this time developing the idea of a “methods for a problem solving environment” or a PSE. The idea is pretty simple: users of a problem solving environment (the examples from his papers are MATLAB and Maple) do not have the same requirements as more general users of scientific computing. Instead of focusing on efficiency, they key for this group is to have a clear and neatly defined (universal) interface which has a lot of flexibility.

The MATLAB ODE Suite does extremely well at hitting these goals. MATLAB documents its ODE solvers very well, there’s a similar interface for using each of the different methods, and it tells you in a table in which cases you should use the different methods.

But the modifications to the methods goes even further. Let’s take for example the classic ode45. That method just works and creates good plots, right? Well, Shampine added a little trick to it. When you solve an equation using ode45, the Runge-Kutta method uses a “free” interpolation to fill in some extra points. So between any two steps that the solver takes, it automatically adds in 4 extra points using a 4th order interpolation. This is because high order ODE solvers are good enough at achieving “standard user error tolerances” that they actually achieve quite large timesteps, and in doing so step too infrequently to make a good plot. Shampine’s scheme is a good quick fix to this problem which most people probably never knew was occurring under the hood!

There’s quite a bit of flexibility here. The methods allow you to use complex numbers. You’re given access to the “dense output function” (this is the function which computes the interpolations). There’s a few options you can tweak. Every one of these methods is setup with event handling, and there are methods which can handle differential-algebraic equations. There are also dde23 and ddesd for delay differential equations, and in the financial toolbox there’s an Euler-Maruyama method for SDEs.

While MATLAB does an excellent job at giving a large amount of easily available functionality, where it lacks is performance. There’s a few reasons for this. For one thing, these modifications like adding extra points to the solution array can really increase the amount of memory consumed if the ODE system is large! This actually has an impact in other ways. There’s a very good example of this in ode45. ode45 is based on the Dormand-Prince 5(4) pair. However, in 1999, the same year the MATLAB ODE Suite was published, Shampine released a paper with a new 5(4) pair which was more efficient than the Dormand-Prince method. So that begs the question, why wasn’t this used in the MATLAB ODE Suite (it’s clear Shampine new about it!)? (I actually asked him in an email) The reason is because its interpolation requires calculating some extra steps, so it’s less efficient if you are ALWAYS interpolating. But since ode45 is always interpolating in order to make the plots look nicer, this would get in the way. Essentially, it can be more efficient, but MATLAB sets things up for nice plotting and not pure efficiency.

But there are other areas where more efficient methods were passed up during the development phase of the ODE suite. For example, Hairer’s benchmarks in his book Solving Ordinary Differential Equations I and II (the second is for stiff problems), along with the benchmarks from the Julia DifferentialEquations.jl suite, consistently show that high order Runge-Kutta methods are usually the most efficient methods for high accuracy solving of nonstiff ODEs. These benchmarks both consistently show that, for the same error, high order Runge-Kutta methods (like order >6) can solve the equation much faster than methods like Adams methods. But MATLAB does not offer high order Runge-Kutta methods and only offers ode113 (an Adams method) for high-accuracy solving.

Some of this is due to a limitation within MATLAB itself. MATLAB’s ODE solver requires taking in a user-defined function, and since this function is defined in MATLAB its function calls are very inefficient and expensive. Thus MATLAB’s ODE solver suite can become more efficient by using methods which reduce the number of function calls (which multistep methods do). But this isn’t the only case where efficient methods are missing. Both Hairer and the JuliaDiffEq benchmarks show that high-order Rosenbrock methods are the most efficient for low-medium accuracy stiff ODEs, but MATLAB doesn’t offer these methods. It does offer ode23s, a low-order Rosenbrock method, and ode15s which is a multistep method. ode15s is supposed to be the “meat and potatoes of the MATLAB Suite”, but it cannot handle all equations of since its higher order methods (it’s adaptive order) are not L-stable (and not even A-stable). For this reason there’s a few other low order SDIRK methods (ode23tb, an ESDIRK method for highly stiff problems) which are recommended to fill in the gaps, but none of the higher order variants which are known to be more efficient for many equations.

This pattern goes beyond the ODE solvers. The DDE solvers are all low order, and in the case of ddesd, it’s a low accuracy method which is fast for getting plots correct but not something which converges to many decimal places all too well since it doesn’t explicitly track discontinuities. This is even seen in the paper on the method which shows the convergence only matches dde23 to graphical accuracy on a constant-delay problem. Again, this fits in with the mantra of the suite, but may not hit all demographics. Shampine specifically made a separate version of ddesd for Fortran for people who are interested in efficiency, which is another way of noting that the key of ddesd is features and automatic usage, and not hardcore scientific computing efficiency. The mentioned SDE solver from the financial toolbox is only order 0.5 and thus requires quite a small dt to be accurate.

And I can keep going, but I think you get the moral of the story. This suite was created with one purpose in mind: to make it very easy to solve a wide array of differential equations and get a nice plot out. It does a very good job at doing so. But it wasn’t made with efficiency in mind, and so it’s missing a lot of methods that may be useful if you want high efficiency or high accuracy. Adding these wouldn’t make sense to the MATLAB suite anyways since it would clutter the offering. MATLAB is about ease of use, and not efficiency, and it does extremely well at what it set out to do. For software that was first made before the Y2K crisis with just a few methods added later, it still holds up very well.

Hairer’s Solvers (Fortran)

Next I want to bring up some Fortran solvers because they will come up later. Hairer’s Fortran solvers are a set methods with similar interfaces that were designed with efficiency in mind. Many of these methods are classics: dopri5, dop853, radau, and rodas will specifically show up in many of the suites which are discussed later. These methods are not too flexible: they don’t allow event handling (though with enough gusto you can use the dense output to write your own), or numbers that aren’t double-precision floating point numbers (it’s Fortran). They have a good set of options for tweaking parameters to make the adaptive timestepping more efficient, though you may have to read a few textbooks to know exactly what they do. And that’s the key to them: they will solve an ODE, stiff or non-stiff, and they will do so pretty efficiently, but nothing more. But even then, they show some age which don’t make them “perfectly efficient”. These solvers include their own linear algebra routines which don’t multithread like standard BLAS and LINPACK implementations, meaning that they won’t make full use of modern CPU architectures. The computations don’t necessarily SIMD or use FMA. But most of all, to use it directly you need to use Fortran which would be turn off for many people.

There is some flexibility in the offering. There are symplectic solvers for second order ODEs, the stiff solvers allow for solving DAEs in mass matrix form, there’s a constant-lag nonstiff delay differential equation solver (RETARD), there is a fantastic generalization of radau to stiff state-dependent delay differential equations (RADAR5), and there’s some solvers specifically for some “mechanical ODEs” commonly found in physical problems. Of course, to get this all working you’ll need to be pretty familiar with Fortran, but this is a good suite to look at if you are.

ODEPACK and Netlib ODE Solvers (Fortran)

ODEPACK is an old set of ODE solvers which accumulated over time. You can learn a bit about its history by reading this interview with Alan Hindenmarsh. I also bundle the Netlib suite together with it. There’s a wide variety of methods in there. There’s old Runge-Kutta methods due to Shampine, some of Shampine’s old multistep methods ddebdf and ddeabm, etc. The reason why this pack is really important though is because of the Lawarance Livermore set of methods, specifically LSODE and its related methods (LSODA, LSODR, VODE, etc.). It includes methods for implicit ODEs (DAEs) as well. These are a group of multistep methods which are descendent from GEAR, the original BDF code. They are pretty low level and thus allow you to control the solver step by step, and some of them have “rootfinding capabilities”. This means that you can use these to add event handling, though an event handling interface will take some coding. There’s lots of options and these are generally pretty performant for a large array of problems, but they do show their age in the same way that the Hairer codes do. Their linear algebra setups do not make use of modern BLAS and LINPACK, which in practical terms means they don’t make full use of modern computer architectures to speed things up. They don’t always make use of SIMD and other modern CPU acceleration features. They are the vanilla ODE solvers which have existed through time. In particular, LSODA is popular because this is the most widely distributed method which automatically detects stiffness and swtiches between integration methods, though it should be pointed out that there is a performance penalty from this feature.

Sundials and ARKCODE (C++ and Fortran)

Sundials‘ CVODE is a re-write of VODE to C which is a descendent of LSODE which is a descendent itself of the original GEAR multistep code. Yes, this has a long history. But you should think of it as “LSODE upgraded”: it makes use of modern BLAS/LINPACK, and also a bunch of other efficient C/Fortran linear solvers, to give a very efficient Adams and BDF method. Its solver IDA is like CVODE but handles implicit ODEs (DAEs). The interface for these is very similar to the ODEPACK interface, which means you can control it step by step and use the rootfinding capabilities to write your own event handling interface. Since the Adams methods handle nonstiff ODEs and the BDF methods handle stiff ODEs, this performance plus flexibility makes it the “one-stop-shop” for ODE solving. Many different scientific computing software internally are making use of Sundials because it can handle just about anything. Well, it does have many limitations. For one, this only works with standard C++ numbers and arrays. There’s no stochasticity or delays allowed. But more importantly, Hairer and DifferentialEquations.jl’s show that these multistep methods are usually not the most efficient methods since high order Rosenbrock, (E)SDIRK, and fully implicit RK methods are usually faster for the same accuracy for stiff problems, and high order Runge-Kutta are faster than the Adams methods for the same accuracy. Multistep methods are also not very stable at their higher orders, and so at higher tolerances (lower accuracy) these methods may fail to have their steps converge on standard test problems (see this note in the ROBER tests), meaning that you may have to increase the accuracy (and thus computational cost) due to stiffness issues. But, since multistep methods only require a single function evaluation per step (or are implicit in only single steps), they are the most efficient for asymptotically hard problems (i.e. when the derivative calculation is very expensive or the ODE is a large 10,000+ system). For this reason, these methods excel at solving large discretizations of PDEs. To top it off, there are parallel (MPI) versions for using CVODE/IDA for HPC applications.

I also want to note that recently Sundials added ARKCODE, a set of Runge-Kutta methods. These include explicit Runge-Kutta methods and SDIRK methods, including additive Runge-Kutta methods for IMEX methods (i.e. you can split out a portion to solve explicitly so that the implicit portion is cheaper when you know your problem is only partly or semi stiff). This means that it covers the methods which I mentioned earlier are more efficient in many of the cases (though it is a bit lacking on the explicit tableaus and thus could be more efficient, but that’s just details).

If you are using C++ or Fortran and want to write to only one interface, the Sundials suite is a great Swiss Army knife. And if you have an asymtopically large problem or very expensive function evaluations, this will be the most efficient as well. Plus the parallel versions are cool! You do have to live with the limitations of low-level software forcing specific number and array types, along with the fact that you need to write your own event handling, but if you’re “hardcore” and writing in a compiled language this suite is a good bet.

SciPy’s Solvers (Python)

Now we come to SciPy’s suite. If you look at what it offers, the names should now start to sound familiar: LSODA, VODE, dopri5, dop853. That is write: SciPy is simply a wrapper over Hairer’s and ODEPACK’s methods. Because it writes a generic interface though, it doesn’t have the granularity that is offered by ODEPACK, meaning that you don’t have step-by-step control and no event handling. The tweaking options are very basic as well. Basically, they let you define a function in Python, say what timeframe to solve it on, give a few tolerances, and it calls Fortran code and spits back a solution. It only has ODE solvers, no differential-algebraic, delay, or stochastic solvers. It only allows the basic number types and does no event handling. Super vanilla, but gets the job done? As with the methods analysis, it has the high order Runge-Kutta methods for efficient solving of nonstiff equations, but it’s missing Rosenbrock and SDIRK methods entirely, opting to only provide the multistep methods.

I should note here that it has the same limitation as MATLAB though, namely that the user’s function is Python code. Since the derivative function is where the ODE solver spends most of its time (for sufficiently difficult problems), this means that even though you are calling Fortran code, you will lose out on a lot of efficiency. Still, if efficiency isn’t a big deal and you don’t need bells and whistles, this suite will do the basics.

deSolve Package (R)

There’s not much to say other than that deSolve is very much like SciPy’s suite. It wraps almost the same solvers, has pretty much the same limitations, and has the same efficiency problem since in this case it’s calling the user-provided R function most of the time. One advantage is that it does have event handling. Less vanilla with a little bit more features, but generally the same as SciPy.

PyDSTool (Python)

PyDSTool is an odd little beast. Part of the software is for analytic continuation (i.e. bifurcation plotting). But another part of it is for ODE solvers. It contains one ODE solver which is written in Python itself and it recommends against actually using this for efficiency reasons. Instead, it wraps some of the Hairer methods, specifically dopri5 and radau, and recommends these. But it’s different than SciPy in that it takes in the specification of the ODE as a string, and compiles it to a C function, and uses this inside the ODE solver. By doing so, it’s much more efficient. We still note that its array of available methods is small and it offers radau which is great for high accuracy ODEs and DAEs, but is not the most efficient at lower accuracy so it would’ve been nice to see Rosenbrock and ESDIRK methods. It has some basic event handling and methods for DDEs (again as wrappers to a Hairer method). This is a pretty good suite if you can get it working, though I do caution that getting the extra (non-Python) methods setup and compiled is nontrivial. One big point to note is that I find the documentation spectacularly difficult to parse. Together, it’s pretty efficient and has a good set of methods which will do basic event handling and solve problems at double precision.

JiTCODE and JiTCSDE (Python)

JiTCODE is another Python library which makes things efficient by compiling the function that the user provides. It uses the SciPy integrators and does something similar to PyDSTool in order to get efficiency. I haven’t tried it out myself but I’ll assume this will get you as efficient as though you used it from Fortran. However, it is lacking in the features department, not offering advanced things like arbitrary number types, event handling, etc. But if you have a vanilla ODE to solve and you want to easily do it efficiently in Python, this is a good option to look at.

Additionally, JiTCDDE is a version for constant-lag DDEs similar to dde23. JiTCSDE is a version for stochastic differential equations. It uses the high order (strong order 1.5) adaptive Runge-Kutta method for diagonal noise SDEs developed by Rackauckas (that’s me) and Nie which has been demonstrated as much more efficient than the low order and fixed timestep methods found in the other offerings. It employs the same compilation setup as JitCODE so it should create efficient code as well. I haven’t used this myself but it would probably be a very efficient ODE/DDE/SDE solver if you want to use Python and don’t need events and other sugar.

Boost ODEINT Solver Library (C++)

The Boost ODEINT solver library has some efficient implementations of some basic explicit Runge-Kutta methods (including high order RK methods) and some basic Rosenbrock methods (including a high order one). Thus it can be pretty efficient for solving the most standard stiff and nonstiff ODEs. However, its implementations do not make use of advanced timestepping techniques (PI-controllers and Gustofsson accleration) which makes it require more steps to achieve the same accuracy as some of the more advanced software, making it not really any more efficient in practice. It doesn’t have event handling, but it is flexible with the number and array types you can put in there via C++ templates. It and DifferentialEquations.jl are the only two suites that are mentioned that allow for solving the differential equations on the GPU. Thus if you are familiar with templates and really want to make use of them, this might be the library to look at, otherwise you’re probably better off looking elsewhere like Sundials.

GSL ODE Solvers (C)

To say it lightly, the GSL ODE solvers are kind of a tragedy. Actually, they are just kind of weird. When comparing their choices against what is known to be efficient according to the ODE research and benchmarks, the methods that they choose to implement are pretty bizarre like extrapolation methods which have repeatedly been shown to not be very efficient, while not included other more important methods. But they do have some of the basics like multistep Adams and BDF methods. This, like Boost, doesn’t do all of the fancy PI-controlled adaptivity and everything though, so YMMV. This benchmark, while not measuring runtime and only uses function evaluations (which can be very very different according to more
sophisticated benchmarks like the Hairer and DifferentialEquations.jl ones!), clearly shows that the GSL solvers can take way too many function evaluations because of this and thus, since it’s using methods similar to LSODA/LSODE/dopri5, probably have much higher runtimes than they should.

Mathematica’s ODE Solvers

Mathematica’s ODE solvers are very sophisticated. It has a lot of explicit Runge-Kutta methods, including newer high order efficient methods due to Verner and Shampine’s efficient method mentioned in the MATLAB section. These methods can be almost 5x faster than the older high order explicit RK methods which themselves are the most efficient class of methods for many nonstiff ODEs, and thus these do quite well. It
includes interpolations to make their solutions continuous functions that plot nicely. Its native methods are able to make full use of Mathematica and its arbitrary precision, but sadly most of the methods it uses are wrappers for the classic solvers. Its stiff solvers mainly call into Sundials or LSODA. By using LSODA, it tends to be able to do automatic stiffness detection by default. It also wraps Sundials’ IDA for DAEs. It uses a method of steps implementation over its explicit Runge-Kutta methods for solving nonstiff DDEs efficiently, and includes high order Runge-Kutta methods for stochastic differential equations (though it doesn’t do adaptive timestepping in this case). One nice feature is that all solutions come with an interpolation to make them continuous. Additionally, it can use the symbolic form of the user-provided equation in order to create a function for the Jacobian, and use that (instead of a numerical differentiation fallback like all of the previous methods) in the stiff solvers for more accuracy and efficiency. It also has symplectic methods for solving second order ODEs, and its event handling is very expressive. It’s very impressive, but since it’s using a lot of wrapped methods you cannot always make use of Mathematica’s arbitrary precision inside of these numerical methods. Additionally, its interface doesn’t give you control over all of the fine details of the solvers that it wraps.

Maple’s ODE Solvers

Maple’s ODE solvers are pretty basic. It defaults to a 6th order explicit RK method due to Verner (not the newer more efficient ones though), and for stiff problems it uses a high order Rosenbrock method. It also wraps LSODE like everything else. It has some basic event handling, but not much more. As another symbolic programming language, it computes Jacobians analytically to pass to the stiff solvers like Mathematica, helping it out in that respect, but its offerings pale in comparison to Mathematica.

FATODE (Fortran)

is a set of methods written in Fortran. It includes explicit Runge-Kutta methods, SDIRK methods, Rosenbrock methods and fully implicit RK methods. Thus it has something that’s pretty efficient for pretty much every case. What makes it special is that it includes the ability to do sensitivity analysis calcuations. It can’t do anything but double-precision numbers and doesn’t have event handling, but the sensitivity calculations makes it quite special. If you’re a FORTRAN programmer, this is worth a look, especially if you want to do sensitivity analysis.

DifferentialEquations.jl (Julia)

Okay, time for DifferentialEquations.jl. I left it for last because it is by far the most complex of the solver suites, and pulls ideas from many of them. While most of the other suite offer no more than about 15 methods on the high end (with most offering about 8 or less), DifferentialEquations.jl offers 200+ methods and is continually growing. Like the standard Python and R suites, it offers wrappers to Sundials, ODEPACK, and Hairer methods. However, since Julia code is always JIT compiled, its wrappers are more akin to PyDSTool or JiTCODE in terms of efficiency. Thus all of the standard methods mentioned before are available in this suite.

But then there are the native Julia methods. For ODEs, these include explicit Runge-Kutta methods, (E)SDIRK methods, and Rosenbrock methods. In each of these categories it has a huge amount of variety, offering pretty much every method from the other suites along with some unique methods. Some unique methods to point out are that it has the only 5th order Rosenbrock method, it has the efficient Verner methods discussed in the Mathematica part, it has newer 5th order methods (i.e. it includes the Bogacki-Shampine method discussed as an alternative to ode45’s tableau, along with an even newer tableau due to Tsitorious which is even more efficient). It has methods specialized to reduce interpolation error (the OwrenZen methods), and methods which are strong-stability presurving (for hyperbolic PDEs). It by default the solutions as continuous functions via a high order interpolation (though this can be turned off to make the saving more efficient). Each of these implementations employ a lot of extra tricks for efficiency. For example, the interpolation is “lazy”, meaning that if the method requires extra function evaluations for the continuous form, it will only do those extra calculations when the continuous function is used (so when you directly ask for it or when you plot). This is just a peak at the special things the library does to gain an edge.

The native Julia methods benchmark very well as well, and all of the benchmarks are openly available. Essentially, these methods make use of the native multithreading of modern BLAS/LINPACK, FMA, SIMD, and all of the extra little compiler goodies that allows code to be efficient, along with newer solver methods which theoretically reduce the amount of work that’s required to get the same error. They even allow you to tweak a lot of the internals and swap out the linear algebra routines to use parallel solvers like PETSc. The result is that these methods usually outperform the classic C/Fortran methods which are wrapped. Additionally, it has ways to symbolically calculate Jacobians like Mathematica/Maple, and instead of defaulting to numerical differentiation the stiff solvers fall back to automatic differentiation which is more efficient and has much increased accuracy.

Its event handling is the most advanced out of all of the offerings. You can change just about anything. You can make your ODE do things like change its size during the solving if you want, and you can make the event handling adjust and adapt internal solver parameters. It’s not a hyperbole to say that the user is given “full control” since the differential equation solvers themselves are written as essentially a method on the event handling interface, meaning that anything it can do internally you can do.

The variety of methods is also much more diverse than the other offerings. It has symplectic integrators like Harier’s suite, but has more high and low order methods. It has a range of Runge-Kutta Nystrom methods for efficiently solving second order ODEs. It has the same high order adaptive method for diagonal noise SDEs as JiTCSDE, but also includes high order adaptive methods specifically for additive noise SDEs. It also has methods for stiff SDEs in Ito and Stratanovich interpretations, and allows for event handling in the SDE case (with the full flexibility). It has DDE solvers for constant-lag and state-dependent delays, and it has stiff solvers for each of these cases. The stiff solvers also all allow for solving DAEs in mass matrix form (though fully implicit ODEs are possible, but can only be solved using a few methods like a wrapper to Sundials’ IDA and doesn’t include event handling here quite yet).

It allows arbitrary numbers and arrays like Boost. This means you can use arbitrary precision numbers in the native Julia methods, or you can use “array-like” objects to model multiscale biological organisms instead of always having to use simple contiguous arrays. It has addons for things like sensitivity analysis and parameter estimation. Also like Boost, it can solve equations on the
GPU by using a GPUArray.

It hits the strong points of each of the previously mentioned suites because it was designed from the get-go to do so. And it benchmarks extremely well. The only downside is that, because it is so feature and performance focused, its documentation is heavy. The beginning tutorial will give you the basics (making it hopefully as easy as MATLAB to pick up), but pretty much every control knob is available, making the extended portion of the documentation a long read.


Let’s take a step back and summarize this information. DifferentialEquations.jl objectively has the largest feature-set, swamping most of the others while wrapping all of the common solvers. Since it also features solvers for the non-ordinary differential equations and its unique Julia methods also benchmarks well, I think it’s clear that DifferentialEquations.jl is by far the best choice for “power-users” who are looking for a comprehensive suite.

As for the other choices from scripting languages, MATLAB wasn’t designed to have all of the most efficient methods, but it’ll handle basic equations with delays and events and output good plots. R’s deSolve is similar in most respects to MATLAB. SciPy’s offering is lacking in comparison to MATLAB and R’s due to the lack of event handling. But MATLAB/Python/R all have efficiency problems due to the fact that the user’s function is written in the scripting language. JiTCODE and PyDSTool are two Python offerings make the interface to the Fortran solvers more efficient than straight SciPy. Mathematica and Maple will do symbolic pre-calculations to speed things up and can JiT compile functions, along with offering pretty good event handling, and thus their wrappers are more like DifferentialEquations.jl in terms of flexibility and efficiency (and Mathematica had a few non-wrapper goodies mentioned as well). So in a pinch when not all of the bells and whistles are necessary, each of these scripting language suites will get you by. Behind DifferentialEquations.jl, I would definitely put Mathematica’s suite second for scripting languages with everything else much further behind.

If you’re already hardcore and writing in C++/Fortran, Sundials is a pretty good “one-stop-shop” to get everything you need, especially when you add in ARKCODE. Still, you’re going to have to write a lot of stuff yourself to make the rootfinding into an event handling interface, but if you put the work in
this will do you well. Hairer’s codes are a great set of classics which cover a wide variety of equations, and FATODE is the only non-DifferentialEquations.jl suite which offers a way to calculate sensitivity equations (and its sensitivity equations are more advanced). Any of these will do you well if you want to really get down-and-dirty in a compiled language and write a lot of the interfaces yourself, but they will be a sacrifice in productivity with no clear performance gain over the scripting language methods which also include some form of JIT compilation. With these in mind, I don’t really see a purpose for the GSL or Boost suites, and the ODEPACK methods are generally outdated.

I hope this review helps you make a choice which is right for you.

The post A Comparison Between Differential Equation Solver Suites In MATLAB, R, Julia, Python, C, Mathematica, Maple, and Fortran appeared first on Stochastic Lifestyle.

Solving the code lock riddle with Julia

By: perfectionatic

Re-posted from: http://perfectionatic.org/?p=494

I came across a neat math puzzle involving counting the number of unique combinations in a hypothetical lock where digit order does not count. Before you continue, please watch at least the first minute of following video:

The rest of the video describes two related approaches for carrying out the counting. Often when I run into complex counting problems, I like to do a sanity check using brute force computation to make sure I have not missed anything. Julia is fantastic choice for doing such computation. It has C like speed, and with an expressiveness that rivals many other high level languages.

Without further ado, here is the Julia code I used to verify my solution the problem.

  1. function unique_combs(n=4)
  2.     pat_lookup=Dict{String,Bool}()
  3.     for i=0:10^n-1
  4.         d=digits(i,10,n) # The digits on an integer in an array with padding
  5.         ds=d |> sort |> join # putting the digits in a string after sorting
  6.         get(pat_lookup,ds,false) || (pat_lookup[ds]=true)
  7.     end
  8.     println("The number of unique digits is $(length(pat_lookup))")
  9. end

In line 2 we create a dictionary that we will be using to check if the number fits a previously seen pattern. The loop starting in line 3, examines all possible ordered combinations. The digits function in line 4 takes any integer and generate an array of its constituent digits. We generate the unique digit string in line 5 using pipes, by first sorting the integer array of digits and then combining them in a string. In line 6 we check if the pattern of digits was seen before and make use of quick short short-circuit evaluation to avoid an if-then statement.