Friday Links - 2009/12/04

• Incanter Blog - A guy I work with wrote this. It is a statistical package in Clojure. It is currently used by a company that tries to make plane delay predictions.


• Pasteboard HappStack Demo - Here is a little demo of how to write a web app in HappStack. It looks promising.


• Earth's Relative Size - A neat set of videos that demonstrate Earths relative size among other celestial bodies.


• Dirk's Accident - Demonstrates the dangers of magnets! The guy lost part of a finger.

Friday Links - 2009/11/20

• Paaaancaaaakes! - By far the best scene from Cabin Fever


• Part of cat brain simulated - This is part of a cat brain simulated in a computer


• Bowtie - Incredibly fast program for genome assembly against a reference genome

Not too many interesting links this week unfortunately.

My Weaksauce Event Loop In Python

I have been writing a bunch of glorified shell scripts in Python. Like any tool, they start to get more complicated. Originally I was just wrapping up os.system into something with a bit more versatility, like throwing an exception if the program failed. Eventually I started to need to get the output of running programs so I switched to using the subprocess module. Then once again I realized I needed to run multiple programs at once to do some things in a reasonable amount of time. So I took the subprocess code and made it run a list of commands and use select to multiplex. Once again though I have found that I need more versatility. In this case I want to run multiple sequences of commands in parallel and I may not be able to predict what commands I need to run in total. For example, I may want to run a command to mount a drive, then if that succeeds do one thing and if it fails retry or error. So I decided to take my select code and change it a bit.

Rather than taking a list of commands to run, it takes a list of iterables. Each iterable returns a function that, when called, returns a list of streams to be processed and a function to call when all of the streams have been processed. The event loop then goes through handling the streams. When all of the streams for a specific iterable are finished, it calls the clean up function and calls the next iteration, if that is the last iteration for that iterable it removes it from the list.

Combining this with generations in Python makes writing this very easy. Here is some usage example code:

def test():
   import sys
   import random

   def f(id):
       print id
       yield ProgramRunner('date', sys.stdout.write, sys.stderr.write, log=True)
       print id
       yield ProgramRunner('sleep %d' % random.randrange(0, 10), sys.stdout.write, sys.stderr.write, log=True)
       print id
       yield ProgramRunner('date', sys.stdout.write, sys.stderr.write, log=True)
       print id


   runCommandGens([f(v) for v in range(100)])

This defines a generator called f that takes an id. f will run three programs in serial. One just prints out the date, the next sleeps for a random amount of time, and finally prints out the date again. The call to runCommandGens is the event loop. In this case it takes a list of 100 generators. I plan on changing the name of this function because obviously it doesn't need to be a generator, but something iterable.

The object being yielded, in this case a class ProgramRunner implements __call__. The cool thing is you can use whatever you want for this as long as it lives upto the interface required. Eventually having a Sleep instance would be helpful so you can pause reliably. You could also use sockets since the event loop is just selecting on streams. Here is another example:

def test1():
   import sys

   def f1():
       yield ProgramRunner('date', sys.stdout.write, sys.stderr.write, log=True)
       yield ProgramRunner('echo what is up', sys.stdout.write, sys.stderr.write, log=True)
       yield ProgramRunner('sleep 3', sys.stdout.write, sys.stderr.write, log=True)
       yield ProgramRunner('echo that is cool', sys.stdout.write, sys.stderr.write, log=True)

   def f2():
       yield ProgramRunner('sleep 2', sys.stdout.write, sys.stderr.write, log=True)
       yield ProgramRunner('echo this is another thing running concurrently', sys.stdout.write, sys.stderr.write, log=True)


   runCommandGens([f1(), f2()])

As you can see in this case it has iterables that it works through.

The use case for this is if you are mostly planning on doing work in serial and then want to do some work concurrently for a bit and when it is done go back to work in serial. This is mostly a toy at this point (although I do use it for simple things in production). I also want to add more specific versions of ProgramRunner. For example, one that constructs an ssh call or an scp call. I plan on using this for working with clusters of machines, for example on EC2. Often times I need to bring up N many machines and then run through a series of steps to properly set it up. I'll post some example code in the near future.

This code is also quite limited currently, in that it only allows output streams. In reality, this is the reverse of what I would like it to look like. What would be really cool is, rather than each iterator yielding something with a bunch of callbacks is if they could do:

def f():
    for event in ProgramRunner(...):
        process_event(event)

In this case, processing events would be no different than just iterating over a source of events. This is what Meijer appears to be going after in Meijer on .NET Reactive Framework. I really like the idea of what he was going for there.

Here is the code for runCommandGens. I'll probably be posting the complete code somewhere when I get a chance and if there is interest. Bear in mind this is just something I'm playing with, comments, criticisms and suggestions are welcome.

def runCommandGens(generators):
    """
    This takes a list of generators and runs through each of them
    in parallel running the commands.

    Each iteration of a generator must return something that is callable and returns a tuple that looks like:
    (oncomplete, [(stream1, function), (stream2, function), ... (streamn, function)])

    Where 'oncomplete' is a function that gets called when all streams have been exhausted
    and each stream has an associated function that gets called with the output
    """

    ##
    # contain objects being worked on from generator
    states = [(g, None) for g in ctorGenerators(generators)]

    ##
    # start initial commends:
    states = nextIteration(states)

    outputStreams = dict(activeOutputStreams(states))

    while outputStreams:
        input, _output, _error = select(outputStreams.keys(), [], [])

        iterateAndBuild = False
        for s in input:
            line = s.readline()

            if line:
                callStreamF(s, line, states[outputStreams[s]])
            else:
                iterateAndBuild = True
                            
                ##
                # removeStream returns True if this was the last stream to be removed
                # which means we need to try to start up the next iteration
                # and recreate outputStreams
                if not removeStream(s, states[outputStreams[s]]):
                    state = states[outputStreams[s]]
                    f = getOnComplete(state)
                    ##
                    # Finished with this one, call onComplete
                    f()
                    # Set the second portion to None, nextIteration uses that to know
                    # when to get the next iteration
                    states[outputStreams[s]] = (state[0], None)

        # If any of our streams are completely done, lets get new ones and rebuild
        if iterateAndBuild:
            states = nextIteration(states)
            outputStreams = dict(activeOutputStreams(states))

Friday links - 2009/11/13

Smashing the Mega-d/Ozdok botnet in 24 hours - Pretty neat story of taking down a large botnet

3D Mandelbrot Set - purdy pictures

Google can render LaTeX math - Very nice feature to easily get proper mathematical equations in your webpages

Interview with John Hughes - John Hughes talking about Erlang and Haskell, I need to check out QuickCheck it sounds rad. I really like the end of this when he asks where the next order of magnitude in decreasing code size will come from.

Python Language Moratorium - A moratorium has been put on the Python language so that other implementations can catch up. This might mean we'll get an implementation that makes some aggressive optimizations

Cool Haskell Function - Shows off how simple and powerful Haskell can be

Philosophizing about Programming - MarkCC talks about his experiences with Haskell and why he thinks functional languages are great for building large systems

Google Go Language - Another MarkCC post. Go has made a lot of noise this week, it looks like it has promise

Friday Links - 2009/11/06

I thought I'd add a weekly list of links that I found interesting over the course of the week. Here is the first installment. Some of these links may be old, they are presented in the week that I get to them, not necessarily the week they hit the 'tubes.

Blue Brain Project - A project to simulate a brain, pretty neat.

Where smoking kills most people - In developed countries, surpriiiiiiiise.

Shazam - Not Magic After All - How that Shazam program works, pretty neat.

F# and workflows - A short blurb + links about F# and workflows (which are monads). F# seems to have some pretty neat stuff.

Algae and Light Help Injured Mice Walk Again - Pretty amazing article on 'optigenetics".

Machine Learning - Stanford - Videos of Stanford course on Machine Learning (according to klafka the best part of stats).

One of those amazing Harvard Uni cell biology videos

Suggestions On Debugging Distributed Apps?

So far distributed apps seem to be the best use case for why it is important to be able to walk through code and do it by hand with a pencil and paper. I have been writing analytics code that runs on a cluster for close to a year and still have not been able to figure out a good way of debugging the code that runs on it.

Being able to bring it down to a testcase works well in some situations but I have found it ineffective in the long run. When you are dealing with a few terabytes of data it can be difficult to cut the problem down to a few megs of input data that you can reason about. While the framework I am using lets me run code on a single process so I can debug it, it is again not always possible to bring the input data down small enough that it is manageable on a single process. On top of that, the behavior you are trying to debug may not show up on such a simple case. It's pretty impossible to use a traditional debugger if the bug only shows up in a few megs of data when you are dealing with a terabyte, how can you step through a 6 hour run if it only shows up on a small portion of that data? How do you predict what machine that bad data will run on if you don't even know what the bad data is?

I have so far been using three methods to debug a distributed app.

• If I have some idea what the bad data looks like, I'll look for some approximation of it in the input data and throw an exception with the debugging info I'm interested in. Exceptions make their way back to the main console of where the jobs are run from so I can see them easy enough.


• Use standard IO. The annoying part is the framework I use only logs this out to local files on the machine it ran on, so I have to wrap the grep in an ssh call to each machine. It's also sometimes difficult to know what to even print out. Too much printing can also significantly reduce performance and even fill up the disk with logging data. Logging data as big as the input data is not any easy to comb through.


• Just reading through the code by hand and working it out with pencil and paper. This has only really worked if I can get a good mental image of what the input is like. If I have a terabyte of input from untrusted sources it can be quite freeform and difficult to reason about as I walk through the code by hand.

Right now I am experiencing a bug that I have been unsuccessful in tracking down. The problem is it only shows up when I use it on huge amounts of data. I have two ways of doing the same thing. One of them takes way too long and the other takes a very short time, and the short way is not producing the same numbers as the long way. It is off by only about 500 million in 5 billion rows of input and it is being a very frustrating bug to track down. The main problem is that I cannot produce a smaller set of input files to cause the issue. Runs take over 6 hours with the input file I need, so a single test can take almost my entire work day. If anyone has any suggestions, please let me know.

Sneaking Complexity - Being Asynchronous

I went out to lunch with some coworkers last week and we got to talking about the project they are working on. They had done a great job of implementing the app which pretty much makes up the backbone of our company. They rewrote it in Java and have gotten orders of magnitude better performance. The app needs access to various pieces of persistent data quickly and they have created several data-clusters that perform amazingly. And the code is very clean and easy to read. The problem they are running into though is the client code for the data-clusters.

One of the main reasons that Java was selected as a language to write in is the simplicity of reading and writing it. It is fairly easy to jump into a method and, with a good IDE, figure out what it is doing. It is simple. The problems they are running into, though, is when doing things Teh Java Way isn't working out for the volume and latency they are trying to reach. Specifically, they are hitting issues when they query the data-cluster. Generally when they decide they need to hit the data-cluster they do a query and if they don't get a response back in some timeout period they go on as if they have a new record. In this case, being correct about the data all the time is not very important. But they are getting over the number of timed out queries they feel comfortable with (there is also a concern that the timeouts on the library they are using are not working properly). What they would like to do is handle hitting the data-cluster asynchronously. When they think they are going to need data, they send their query in, go do some more processing, then check to see if the data is there and continue on as if a new record if the timeout is reached. The problem is, this really sucks so far in Java. Being asynchronous is hard if you haven't designed your application around it in the first place. You pretty much have to fire up a new thread for every one of these queries you want to do. When considering a single case, this doesn't sound too bad, but the JVM uses OS threads so if you are already pushing your app to the limit, in the worst case doubling or tripling the number of threads it needs is not going to help. You also have increased the complexity of your application. Most of the threading in this application doesn't really need to share any data, each request is off doing its own thing and rarely hitting shared objects. But in this case, sharing the result of the query will need to share some data. It may not be much but it is added complexity. On top of that, there might be a performance hit in terms of GC. I'm not an expert in the JVM GC but shared memory means you might have to walk the entire heap in order to clean up the objects created by the query thread.

This brings me to something that is so great about Erlang. Accomplishing this is trivial. Since messages in Erlang are asynchronous, you simply send your message to query the data-cluster at the beginning of your block, then do whatever work you'd like, and receive it when you are good and ready. A receive block can take a timeout so you don't have any issues there. Doing things asynchronously is how Erlang works pretty much from the get-go. Erlang processes also have their own heap so cleaning up after one is fairly light on the GC, just throw away that process's heap.

To be fair, I am certain that had they implemented this in Erlang they would have run into their own fair share of issues. No language is perfect and Erlang certainly is no exception. But the application in question is basically what Erlang was designed for and is good at. There are also other issues that we talked that they would benefit from had they used Erlang too that I did not talk about. But this is a pattern that seems common in my short career as a developer. People look at the project they are solving, then look at whatever tools solve all the easy problems fast but in the end leave them in a worse state when it comes to solving the harder problems. Those tools that get you 70% of the way there have forced you to design your app so that it even harder to solve that 30%. This happened at my previous employer. A framework was chosen that implemented all the simple things they wanted to solve but they had now inherited this framework whose design was not made to solve the more complex problems. In the end they had to rewrite a bunch of the framework to get what they wanted. I'm sure that my coworkers are going to be able to solve this problem in Java (they have no choice) and perhaps there is a Java-way that this should have been done and I am sure that had they implemented this in Erlang there would still be problems being discussed over lunch. But I feel confident that they would be frustration Erlang records, or syntax, or strings, not with the sneaking complexity of trying to get it to do things asynchronously (and don't even get me started on fault-tolerance).

Lorenz Attractor In R

I spent much of this weekend trying to figure out how to graph Chua's Circuit for a homework assignment. I ended up using R since I don't have or know MATLAB and I don't really want to learn Octave. It took me longer than it should have mostly because I don't know much of anything about differential equations. The implementation required two extra R packages, deSolve and scatterplot3d. The fun thing about working on this project is the whole point is to graph it so you get to see some neat visual output.

After finishing the circuit I decided to do a little extra and graph the Lorenz Attractor, which comes up quite often in class. This is a pretty famous structure in the realm of chaos theory. The term 'butterfly effect' comes from look of the attractor.

My solution uses the deSolve package in R. The function ode is used to solve the three equations that make up the attractor. With some minor understanding of R it should be pretty easy to play with. The settings I have in there give this pretty image:

library(deSolve)
library(scatterplot3d)

##
# Parameters for the solver
pars <- c(alpha = 10,
          beta = 8/3,
          c = 25.58)

##
# In initial state
yini <- c(x = 0.01, y = 0.0, z = 0.0)


lorenz <- function(Time, State, Pars) {
  with(as.list(c(State, Pars)), {
    xdot <- alpha * (y - x)
    ydot <- x * (c - z) - y
    zdot <- x*y - beta*z
    return(list(c(xdot, ydot, zdot)))
  })
}

runIt <- function(times) {
  out <- as.data.frame(ode(func = lorenz, y = yini, parms = pars, times = times))

  scatterplot3d(x=out[,2],
                y=out[,3],
                z=out[,4],
                type="l",
                box=FALSE,
                highlight.3d=TRUE,
                xlab="x",
                ylab="y",
                zlab="z",
                main="3d Plot of Lorenz Oscillator")

}

##
# Run a default value
runAll <- function() {
  runIt(seq(0, 100, by=0.01))
}

Impressed with Haskell's concurrency

I have been playing with both Ocaml and Haskell* lately. In Ocaml, I have been rewriting a lot of simple Python scripts I use at work to see how they compare. They tend to be faster and more trustworthy. Ocaml, though, has pretty bad concurrency support. They have some thread library that wraps the OS threads, no real good message passing interface. Even the guys at Jane St have listed that as a complaint**.

So I decided to check out Haskell again. With Haskell I have always thought it was a great language, but could never grok it. That sounds a little weird, but reading Haskell code is simply great. When you figure out what it does, it tends to be very expressive and flexible. After looking at what Haskell offers for concurrency, I think that in theory it could give Erlang a serious run for its money. Here's why:

- Haskell, in general and in my opinion, is a safer language to write code in than Erlang. One can do a lot of work with Dialyzer to verify their code, but they are still somewhat limited. Haskells type system is very expressive and powerful. Haskell also has ADT's, which as far as I know Erlang still does not. For an idea of why ADT's are so powerful when it comes to writing safe code, see the Caml Trading video. And in this case, by 'safe' I mean writing correct code.

- Haskell produces generally fast code. GHC does some impressive optimizations, and supercompilation*** is most likely getting going to be part of GHC in the near future. It should noted that while Haskell can produce fast results, its lazyness can also be unpredictable in the optimizations (both speed and memory) that it performs. This is believed, by many, to be a big drawback to Haskell. I haven't done enough work in Haskell to really say how bad this is but Real World Haskell does give a complete chapter to diagnosing performance problems and optimizing them.

- Haskell's threading implementation uses green threads with a many-to-one mapping to OS threads. This means you can take advantage of multiple cores without modifying your Haskell code. The Erlang VM does this too, with SMP support. The greenthread implementation also appears to be blazing fast. Haskell is number one in the threadring solution on the language shootout. Erlang is about 4x slower. Take from that what you will.

- You can implement Erlang-like best-case programming in Haskell, from what I can tell. Haskell supports Exceptions, and you can throw exceptions to other threads using asynchronous exceptions. This gives you a way to 'link' threads like you can link Erlang processes. It is still programmer driven, so you can make a mistake, point for Erlang.

- STM, while I haven't read up on this, it seems like a pretty great way to handle synchronization between threads.

- Monads. When reading up on concurrency in Haskell, monads seemed to often come up as valuable in ensuring correctness. For example, in an STM transaction, one wants to restrict the transaction from doing things that cannot be rolled back, such as IO. This is done by the 'atomically' function taking an STM monad as input and wrapping the output in an IO monad. What this all means is one can't do IO in the atomically block unless it's unsafe. The ability to restrict what the user can do, when one wants to, with the type system is quite powerful.

That being said, Haskell does have some clear losses next to Erlang. The biggest drawback is the lack of a distributed model. There is distributed Haskell, I have not researched it much but I'm under the impression it is not 'there' yet. Erlang is easy to learn, very easy. Haskell is not. I have found that, in order to write really good Haskell code, one has to keep a lot of stuff in their head at once. Perhaps this is just because I am new but I have found Haskell better to read than to write. Erlang is not like this, while the syntax has some peculiarities to it, it is not hard to pick up and start writing good Erlang. I think Ocaml shares more in common to Erlang in this regard. The hump one needs to get over in order to write solid Haskell code is a real and legitimate reason to not choose Haskell.


All that being said, I admittedly am fairly new to Haskell so these opinions will change over time, I'm planning on putting more effort into writing real projects in Haskell to see how it goes. Needless to say, I am impressed by what Haskell has to offer for concurrency. If I'm factually wrong on anything here, please correct me, this is all based on some reading research I've been doing on Haskell, not my actual experiences.

* When I say Haskell, I really mean GHC here

** Yaron Minsky's Caml Trading lecture, very good! Makes a great, practical argument, for Ocaml - http://ocaml.janestreet.com/?q=node/61

*** Supercompilation http://community.haskell.org/~ndm/downloads/slides-supercompilation_for_haskell-03_mar_2009.pdf