Hi, 2014-04-10 13:05 GMT-04:00 Martin A. Brown <mar...@linux-ip.net>:
> > Hi there Gabriele, > > : I have a program that is reading near 600000 elements from a > : file. For each element it performs 200 times a particular > : mathematical operation (a numerical interpolation of a function). > : Now these process takes near 8 hours. > > Sounds fun! Here are some thoughts (though I may not have any solid > answers, I hope these pointers are useful): > > Are you sure (from profiling) that the numerical interpolation > is the bottleneck? > > I see that the time needed by the code increase when I increase the number of these operation. It's the only thing I do in the code. (I'm sorry but I don't know very well what profiling is) > What is the numerical operation? > 1: Is the function implemented in Numpy? [0] > 2: How about SciPy? [1] > > Is interp1d from scipy.interpolate. I think is the best one > Is there a domain-specific Python library that already does the > computation you want to achieve? If so, then you have "only" the > format question--how to put your data into the format required by > the library. If not, then on to the next question you ask ... > > No, interp1d do exactly what I want. > : Creating a C function and calling it from the code could improve > : the speed? It could be useful that it contains both the > : mathematical operation and the for loop or only the mathematical > : operation? > : > : If it is a reasonable solution to try decreasing the > : computational time how can I implement this C function? > > It is certainly an option! In the event that you cannot find > something that is fast enough in Python already and you cannot find > any C library that has Python bindings, then, whether you have to > write your own, or you have a third party C library, you have > several options for writing bindings. > You can write your Python bindings using: > > * ctypes: https://docs.python.org/2/library/ctypes.html > * cffi: http://cffi.readthedocs.org/en/release-0.8/ > * cython: http://www.cython.org/ > * roll your own C! > > Do you know if does a C library exist with an already implemented function like interp1d? I use Anaconda, is there an already implemented mode to do it in Anaconda? Cython? > It might be beyond the scope of this list (certainly beyond my > capabilities) to provide recommendations on which avenue to > take--but if you are asking, you may already have the tools you need > to assess for yourself. There is, however, quite a bit of > experience loitering around this list, so perhaps somebody else will > have a suggestion. > > -Martin > > [0] http://www.numpy.org/ > [1] http://www.scipy.org/ > > -- > Martin A. Brown > http://linux-ip.net/ >
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