Use Python for Scientific Computing
which would give us a 500x500 element matrix initialized with zeros. We access the real and imaginary parts of each element using:
which would set the value 1+2j into the [0,0] element.
There also are functions to give us more complicated results. These include dot products, inner products, outer products, inverses, transposes, traces and so forth. Needless to say, we have a great deal of tools at our disposal to do a fair amount of science already. But is that enough? Of course not.
Now that we can do some math, how do we get some “real” science done? This is where we start using the features of our second package of interest, scipy. With this package, we have quite a few more functions available to do some fairly sophisticated computational science. Let's look at an example of simple data analysis to show what kind of work is possible.
Let's assume you've collected some data and want to see what form this data has, whether there is any periodicity. The following code lets us do that:
import scipy inFile = file('input.txt', r) inArray = scipy.io.read_array(inFile) outArray = fft(inArray) outFile = file('output.txt', w) scipy.io.write_array(outFile, outArray)
As you can see, reading in the data is a one-liner. In this example, we use the FFT functions to convert the signal to the frequency domain. This lets us see the spread of frequencies in the data. The equivalent C or FORTRAN code is simply too large to include here.
But, what if we want to look at this data to see whether there is anything interesting? Luckily, there is another package, called matplotlib, which can be used to generate graphics for this very purpose. If we generate a sine wave and pass it through an FFT, we can see what form this data has by graphing it (Figures 1 and 2).
We see that the sine wave looks regular, and the FFT confirms this by having a single peak at the frequency of the sine wave. We just did some basic data analysis.
This shows us how easy it is to do fairly sophisticated scientific programming. And, if we use an interactive Python environment, we can do this kind of scientific analysis in an exploratory way, allowing us to experiment on our data in near real time.
Luckily for us, the people at the SciPy Project have thought of this and have given us the program ipython. This also is available at the main SciPy site. ipython has been written to work with scipy, numpy and matplotlib in a very seamless way. To execute it with matplotlib support, type:
The interface is a simple ASCII one, as shown in Figure 3.
If we use it to plot the sine wave from above, it simply pops up a display window to draw in the plot (Figure 4).
The plot window allows you to save your brilliant graphs and plots, so you can show the entire world your scientific breakthrough. All of the plots for this article actually were generated this way.
So, we've started to do some real computational science and some basic data analysis. What do we do next? Why, we go bigger, of course.
So far, we have looked at relatively small data sets and relatively straightforward computations. But, what if we have really large amounts of data, or we have a much more complex analysis we would like to run? We can take advantage of parallelism and run our code on a high-performance computing cluster.
The good people at the SciPy site have written another module called mpi4py. This module provides a Python implementation of the MPI standard. With it, we can write message-passing programs. It does require some work to install, however.
The first step is to install an MPI implementation for your machine (such as MPICH, OpenMPI or LAM). Most distributions have packages for MPI, so that's the easiest way to install it. Then, you can build and install mpi4py the usual way with the following:
python setup.py build python setup.py install
To test it, execute:
mpirun -np 5 python tests/helloworld.py
Joey Bernard has a background in both physics and computer science. This serves him well in his day job as a computational research consultant at the University of New Brunswick. He also teaches computational physics and parallel programming.
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