When I began this project, I thought it would be easy to get libraries for common stuff like matrix math, so I chose to work in Python 3.1- it being the most recent, updated version of the language. Unfortunately, NumPy is only compatible with 2.5 and 2.6 and seems to be the only game in town! Even other stuff that I turned up like gameobjects seemed to be based on NumPy and therefore incompatible with 3.x as well.
Does anyone out there know of a matrix library that is compatible with 3? I need to be able to do the following: matrix add, subtract, multiply, scalar multiply, inverse, transpose, and determinant. I've been looking all day and all roads seem to lead back to NumPy. I even tried this module: http://www.nightmare.com/squirl/python-ext/misc/matrix.py but it too is for 2.x. Even after converting it using the 2to3 tool, I can't get the yarn module that it refers to (and is probably itself 2.x).
Any help is hugely appreciated.
Given that a large portion of those interested in this sort of development are involved in NumPy, and given their schedule for migrating I think the answer is "no, there is nothing yet".
I would advise treating Python 3.x as "still experimental" and start with Python 2.6 instead. Make some small effort to write your code in a such a way that it won't be too hard to migrate in, say, a year or two, when the Python 3.x series really stabilizes, but don't jump there just yet. Other more general questions have answers that may help you decide.
EDIT: PyEuclid has supports matrices, vectors up to 4 dimensions and is designed for geometric operations.
Otherwise, the answer is probably not what you want, but:
use python 2.x instead, do use numpy (which is really good), until numpy supports python 3.x
implement your own Matrix class, since you don't require too much functionality and it's a good exercise to implement. Should be less work than looking a day on the internet.
Related
I am doing my first steps with Cython, and I am wondering how to improve performance even more.
Until now I got to half the usual (python only) execution time, but I think there must be more!
I know cython -a and I already typed my variables. But there is still a lot in yellow in my function. Is this because cython does not recognise numpy or is there something else I am missing?
I believe you can benefit by using math functions from libc as you are calling np.sqrt and np.floor on scalars. This has not only the Python call overhead but there are different code paths in the numpy ufuncs for scalars and arrays. So that involves at least a type switch.
I think it's not a problem, as I've tested with the official tutorial, it's also reported as yellow on every np.* lines, and involves python just the same as your code.
Point 3 at the end of that page should have explained this:
Calling NumPy/SciPy functions currently has a Python call overhead; it would be possible to take a short-cut from Cython directly to C. (This does however require some isolated and incremental changes to those libraries; mail the Cython mailing list for details).
I guess the question speaks for itself. I'm interested in doing some serious computations but am not a programmer by trade. I can string enough python together to get done what I want. But can I write a program in python and have the GPU execute it using CUDA? Or do I have to use some mix of python and C?
The examples on Klockner's (sp) "pyCUDA" webpage had a mix of both python and C, so I'm not sure what the answer is.
If anyone wants to chime in about Opencl, feel free. I heard about this CUDA business only a couple of weeks ago and didn't know you could use your video cards like this.
You should take a look at CUDAmat and Theano. Both are approaches to writing code that executes on the GPU without really having to know much about GPU programming.
I believe that, with PyCUDA, your computational kernels will always have to be written as "CUDA C Code". PyCUDA takes charge of a lot of otherwise-tedious book-keeping, but does not build computational CUDA kernels from Python code.
pyopencl offers an interesting alternative to PyCUDA. It is described as a "sister project" to PyCUDA. It is a complete wrapper around OpenCL's API.
As far as I understand, OpenCL has the advantage of running on GPUs beyond Nvidia's.
Great answers already, but another option is Clyther. It will let you write OpenCL programs without even using C, by compiling a subset of Python into OpenCL kernels.
A promising library is Copperhead (alternative link), you just need to decorate the function that you want to be run by the GPU (and then you can opt-in / opt-out it to see what's best between cpu or gpu for that function)
There is a good, basic set of math constructs with compute kernels already written that can be accessed through pyCUDA's cumath module. If you want to do more involved or specific/custom stuff you will have to write a touch of C in the kernel definition, but the nice thing about pyCUDA is that it will do the heavy C-lifting for you; it does a lot of meta-programming on the back-end so you don't have to worry about serious C programming, just the little pieces. One of the examples given is a Map/Reduce kernel to calculate the dot product:
dot_krnl = ReductionKernel(np.float32, neutral="0",
reduce_expr="a+b",
map_expr="x[i]*y[i]",
arguments="float *x, float *y")
The little snippets of code inside each of those arguments are C lines, but it actually writes the program for you. the ReductionKernel is a custom kernel type for map/reducish type functions, but there are different types. The examples portion of the official pyCUDA documentation goes into more detail.
Good luck!
Scikits CUDA package could be a better option, provided that it doesn't require any low-level knowledge or C code for any operation that can be represented as numpy array manipulation.
I was wondering the same thing and carried a few searches. I found the article linked below which seems to answer your question. However, you asked this back in 2014 and the Nvidia article does not have a date.
https://developer.nvidia.com/how-to-cuda-python
The video goes through the set up, an initial example and, quite importantly, profiliing. However, I do not know if you can implement all of the usual general compute patterns. I would think you can because as far as I could there are no limitations in NumPy.
I wrote a number crunching python code. The calculations involved can take hours. Is it possible somehow to compile it to binary?
Thanks
Not in any useful (for you) way, but moving the calculations into NumPy or Cython will speed them up.
First you can try psyco, that may give you a speed up as much as 10x, but 2x is more typical
If you can post the code up somewhere, perhaps someone can point out how to leverage numpy.
If your task doesn't map well only numpy then cython is a good choice to convert a intensive function or two into C code just by adding a few cdefs.
If you can show us the code (even just the hot spots) we can probably give you better advice.
Perhaps you can modify your algorithm
Shedskin might be worth a try.
From their front page blurb:
Shed Skin is an experimental compiler,
that can translate pure, but
implicitly statically typed Python
programs into optimized C++. It can
generate stand-alone programs or
extension modules that can be imported
and used in larger Python programs.
Besides the typing restriction,
programs cannot freely use the Python
standard library (although about 20
common modules, such as random and re,
are currently supported). Also, not
all Python features, such as nested
functions and variable numbers of
arguments, are supported (see the
tutorial for details).
For a set of 44 non-trivial test
programs (at over 10,000 lines in
total (sloccount)), measurements show
a typical speedup of 2-40 times over
Psyco, and 2-220 times over CPython.
Because Shed Skin is still in an early
stage of development, however, many
other programs will not compile
out-of-the-box.
I want to compute magnetic fields of some conductors using the Biot–Savart law and I want to use a 1000x1000x1000 matrix. Before I use MATLAB, but now I want to use Python. Is Python slower than MATLAB ? How can I make Python faster?
EDIT:
Maybe the best way is to compute the big array with C/C++ and then transfering them to Python. I want to visualise then with VPython.
EDIT2: Which is better in my case: C or C++?
You might find some useful results at the bottom of this link
http://wiki.scipy.org/PerformancePython
From the introduction,
A comparison of weave with NumPy, Pyrex, Psyco, Fortran (77 and 90) and C++ for solving Laplace's equation.
It also compares MATLAB and seems to show similar speeds to when using Python and NumPy.
Of course this is only a specific example, your application might be allow better or worse performance. There is no harm in running the same test on both and comparing.
You can also compile NumPy with optimized libraries such as ATLAS which provides some BLAS/LAPACK routines. These should be of comparable speed to MATLAB.
I'm not sure if the NumPy downloads are already built against it, but I think ATLAS will tune libraries to your system if you compile NumPy,
http://www.scipy.org/Installing_SciPy/Windows
The link has more details on what is required under the Windows platform.
EDIT:
If you want to find out what performs better, C or C++, it might be worth asking a new question. Although from the link above C++ has best performance. Other solutions are quite close too i.e. Pyrex, Python/Fortran (using f2py) and inline C++.
The only matrix algebra under C++ I have ever done was using MTL and implementing an Extended Kalman Filter. I guess, though, in essence it depends on the libraries you are using LAPACK/BLAS and how well optimised it is.
This link has a list of object-oriented numerical packages for many languages.
http://www.oonumerics.org/oon/
NumPy and MATLAB both use an underlying BLAS implementation for standard linear algebra operations. For some time both used ATLAS, but nowadays MATLAB apparently also comes with other implementations like Intel's Math Kernel Library (MKL). Which one is faster by how much depends on the system and how the BLAS implementation was compiled. You can also compile NumPy with MKL and Enthought is working on MKL support for their Python distribution (see their roadmap). Here is also a recent interesting blog post about this.
On the other hand, if you need more specialized operations or data structures then both Python and MATLAB offer you various ways for optimization (like Cython, PyCUDA,...).
Edit: I corrected this answer to take into account different BLAS implementations. I hope it is now a fair representation of the current situation.
The only valid test is to benchmark it. It really depends on what your platform is, and how well the Biot-Savart Law maps to Matlab or NumPy/SciPy built-in operations.
As for making Python faster, Google's working on Unladen Swallow, a JIT compiler for Python. There are probably other projects like this as well.
As per your edit 2, I recommend very strongly that you use Fortran because you can leverage the available linear algebra subroutines (Lapack and Blas) and it is way simpler than C/C++ for matrix computations.
If you prefer to go with a C/C++ approach, I would use C, because you presumably need raw performance on a presumably simple interface (matrix computations tend to have simple interfaces and complex algorithms).
If, however, you decide to go with C++, you can use the TNT (the Template Numerical Toolkit, the C++ implementation of Lapack).
Good luck.
If you're just using Python (with NumPy), it may be slower, depending on which pieces you use, whether or not you have optimized linear algebra libraries installed, and how well you know how to take advantage of NumPy.
To make it faster, there are a few things you can do. There is a tool called Cython that allows you to add type declarations to Python code and translate it into a Python extension module in C. How much benefit this gets you depends a bit on how diligent you are with your type declarations - if you don't add any at all, you won't see much of any benefit. Cython also has support for NumPy types, though these are a bit more complicated than other types.
If you have a good graphics card and are willing to learn a bit about GPU computing, PyCUDA can also help. (If you don't have an nvidia graphics card, I hear there is a PyOpenCL in the works as well). I don't know your problem domain, but if it can be mapped into a CUDA problem then it should be able to handle your 10^9 elements nicely.
And here is an updated "comparison" between MATLAB and NumPy/MKL based on some linear algebra functions:
http://dpinte.wordpress.com/2010/03/16/numpymkl-vs-matlab-performance/
The dot product is not that slow ;-)
I couldn't find much hard numbers to answer this same question so I went ahead and did the testing myself. The results, scripts, and data sets used are all available here on my post on MATLAB vs Python speed for vibration analysis.
Long story short, the FFT function in MATLAB is better than Python but you can do some simple manipulation to get comparable results and speed. I also found that importing data was faster in Python compared to MATLAB (even for MAT files using the scipy.io).
I would also like to point out that Python (+NumPy) can easily interface with Fortran via the F2Py module, which basically nets you native Fortran speeds on the pieces of code you offload into it.
Are parts of NumPy and/or SciPy programmed in C/C++?
And how does the overhead of calling C from Python compare to the overhead of calling C from Java and/or C#?
I'm just wondering if Python is a better option than Java or C# for scientific apps.
If I look at the shootouts, Python loses by a huge margin. But I guess this is because they don't use 3rd-party libraries in those benchmarks.
I would question any benchmark which doesn't show the source for each implementation (or did I miss something)? It's entirely possible that either or both of those solutions are coded badly which would result in an unfair appraisal of either or both language's performance. [Edit] Oops, now I see the source. As others have pointed out though, it's not using the NumPy/SciPy libraries so those benchmarks are not going to help you make a decision.
I believe the vast majority of NumPy and SciPy is written in C and wrapped in Python for ease of use.
It probably depends what you're doing in any of those languages as to how much overhead there is for a particular application.
I've used Python for data processing and analysis for a couple of years now so I would say it's certainly fit for purpose.
What are you trying to achieve at the end of the day? If you want a fast way to develop readable code, Python is an excellent option and certainly fast enough for a first stab at whatever it is you're trying to solve.
Why not have a bash at each for a small subset of your problem and benchmark the results in terms of development time and run time? Then you can make an objective decision based on some relevant data ...or at least that's what I'd do :-)
There is a better comparison here (not a benchmark but shows ways of speeding up Python). NumPy is mostly written in C. The main advantage of Python is that there are a number of ways of very easily extending your code with C (ctypes, swig,f2py) / C++ (boost.python, weave.inline, weave.blitz) / Fortran (f2py) - or even just by adding type annotations to Python so it can be processed to C (cython). I don't think there are many things comparably easy for C# or Java - at least that so seemlessly handle passing numerical arrays of different types (although I guess proponents would argue since they don't have the performance penalty of Python there is less need to).
A lot of it is written in C or fortran. You can re-write the hot loops in C (or use one of the gazillion ways to speed python up, boost/weave is my favorite), but does it really matter?
Your scientific app will be run once. The rest is just debugging and development, and those can be much quicker on Python.
Most of NumPy is in C, but a large portion of the C code is "boilerplate" to handle all the dirty details of the Python/C interface. I think the ratio C vs. Python is around 50/50 ATM for NumPy.
I am not too familiar with vm-based low-level details, but I believe the interface cost would be higher because of the restrictions put on the jvm and the .clr. One of the reason why numpy is often faster than similar environments is the memory representation and how arrays are shared/passed between functions. Whereas most environments (Matlab and R as well I believe) use Copy-On-Write to pass arrays between functions, NumPy use references. But doing so in e.g. the JVM would be hard (because of restrictions on how to use pointer, etc...). It is doable (an early port of NumPy for Jython exists), but I don't know how they solve this issue. Maybe C++/Cli would make this easier, but I have zero experience with that environment.
It always depends on your own capability to handle the langue, so the language is able to generate fast code. Out of my experience, numpy is several times slower then good .NET implementations. And I expect JAVA to be similar fast. Their optimizing JIT compilers have improved significantly over the years and produce very efficient instructions.
numpy on the other hand comes with a syntax wich is easier to use for those, which are attuned to scripting languages. But if it comes to application development, those advantages often turn to obstacles and you will yearn for typesafety and enterprise IDEs. Also, the syntactic gap is already closing with C#. A growing number of scientific libraries exist for Java and .NET.Personally I tend towards C#, bacause it provides better syntax for multidimensional arrays and somehow feels more 'modern'. But of course, this is only my personal experience.