Design question: use of OO for scientific simulation...

Discussion in 'Ruby' started by Egg, Jul 12, 2005.

  1. Egg

    Egg Guest

    Hi all,

    I have a slightly embarassingly naive question or set of questions.(I
    am not posting the code because this iteration is in Python--but Ruby
    is next and you all are better OO folks too.)

    I am writing a class to do Lee Carter demographic projection of
    mortality (write me if you care about the details): basically involves
    a bunch of 30 x 100 x 18 float matrices, a little linear algebra, and
    some simple monte carlo simulation.

    Here are parts of the problem:

    * We need to organize storage of a bunch of 3-d matrices and derived
    parameters (which take lots of time to calculate, so want to retain
    them for later). Various dimensions of the matrices correspond to
    various things, like years of step ahead, age, simulation run, etc, so
    keeping track of that would be good too. I think this stuff belongs in
    an instance class.

    * We have several parameter-finding and simulation-running algorithms,
    taking big matrices and returning big matrices. I think these should
    be written as functions which don't retain state across calls--then
    they are more testable since they don't require an instantiation of

    * Each instance needs to display itself in a number of different views
    including graphics and text, often for webservers (so in html), but
    also text for command line use.

    * Long term storage, both for command line playing and to put into part
    of a web service (probably run as part of a queue and stored for later

    * The basic sequence of interaction is: 1, store some death rates. 2,
    infer some parameters from them. 3, run some simulations. 4, infer
    some more parameters from those simulations. 5, display it all in a
    couple of different ways.

    Anyway, I was wondering if anyone has done anything that they liked
    with a situation like this, and could share a pattern or two. The
    closest design problem might be analysing and simulating genetic
    sequences, if that matters.
    Egg, Jul 12, 2005
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  2. Egg

    Phil Tomson Guest

    Sorry, my advice isn't pattern related. You mention matrices, so I wanted
    to recommend Narray if you haven't already looked at it. It'll speed
    things up.

    Phil Tomson, Jul 13, 2005
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  3. Sounds reasonable. But since you'll still need instances of the matrices
    to be converted, you could put these functions into a Module and have
    the matrices transform themselves.
    I'd write an abstract Displayer class, with subclasses to produce each
    type of output. Having a class display itself with a to_s() method is
    fair enough, but for the number and complexity of display types that you
    propose, I think that a separate class is justified.
    Ruby's serialization (Marshal module) should work fine here.
    jason r tibbetts, Jul 13, 2005
  4. Egg

    Alan Chen Guest

    I don't know how long it takes for your simulation to execute, but I
    run simulations (aerospace) which can take anywhere from under a minute
    to days on end. In my case the simulation itself is C++, but we've
    implemented a lot of utilities in ruby -- input parameter permutation,
    queue execution, post-process, and automated post process, plot
    generation and packaging). Even if your core sim is in ruby, I think it
    is often worth splitting up the actual simulation core from your pre
    and post analysis tools.

    If your organization doesn't mind you opening ports and running
    webservers, a wiki is nice to post simulation data to, and it's easy to
    annotate the output pages with notes. I'll mention RuWiki as a blatant
    plug for the wiki that I started and Austin Zeigler has really picked
    up and carried along (Project page at and demo at RuWiki may actually be nice for you as
    it has a fairly simple file system backend for which you could directly
    write simulation output pages. I'm sure many other wiki's both in Ruby
    and other languages would give you a nice ranges of choices.

    Depending on how simple the inputs for your simulation are, you could
    even try a fitnesse style operation, where the inputs are entered into
    a wiki page and the server will come along and execute the scenario. If
    your simulation model is anything like mine in complexity though, this
    isn't really a feasable option though...


    - alan
    Alan Chen, Jul 13, 2005
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