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Yeah, I am pretty certain you're not right in this understanding. I am not the most knowledgeable, but basically all I know is scientific computing, so here are
by bmer 8y ago
Yeah, I am pretty certain you're not right in this understanding. I am not the most knowledgeable, but basically all I know is scientific computing, so here are my two cents:
Any C-like language does not use the "vector" as its "primitive" (not clear what you mean by primitive, and I am instead interpreting it as "machine type"), since integers, floats, characters, are the "primitives" (machine types), which are the things that the hardware itself "knows" how to store using a consistent system ultimately involving groups of bits.
On top of these primitives, single-type arrays (e.g. basic C arrays) are built, for instance a string is an array of characters.
Using C/typical hardware, a simple array is literally stored in memory "contiguously". An array only needs two pieces of information to define: what is the memory address of the first element, and how many elements are there. Thus, if you want the 6th element, the machine literally finds the first element, and then moves 6 memory "blocks" (C arrays can only have a single type, so each element needs the same amount of space to store) forwards to the 6th element, and then gives you back what it finds there. The simplest/fastest interpretations of a C array don't even care about how many elements there are, so if your array has 5 things, but you ask for the 6th thing, you just get back the data stored where the 6th thing should have been. Typically, this is garbage, but maybe it's super valuable (e.g. the first character of a stored password is put there..."overflow vulnerability"...to get the second character, ask for the 7th element, etc. etc. etc.)
Okay, going off topic. Back to the point.
Other data structures that can be built upon primitives are structs, enums, etc., but the array is important relevant to us because it's easy to think of an array as a linear algebra vector. C does not implement dot products natively, but one can easily write a function called "dot_product" that takes two lists of integers, or floats and returns a scalar integer or float. Some higher level languages (e.g. MATLAB) do exactly this, and save you the work of implementing all of linear algebra again.
Matrices are more tricky: for usual non-parallelized hardware, they are still stored contiguously as an array of primitives, but some extra data might go along with this array to tell you how many elements you have to pass before you're onto the next row. Again, MATLAB just provides this sugar-coating.
So where do GPUs come in?
Well, think of a simple grayscale image on a monitor, and note that it is built up of little pixels: so, this image can be thought of as a matrix of integers that range from 0 to 255 inclusive (256 values total), where the (i, j) corresponds to how light/dark each (i, j) pixel is: if your monitor is a square that contains 1000 pixels by 1000 pixels, you can represent it by a 1000x1000 matrix. Using C-like languages on typical hardware, you are basically representing your 1000x1000 matrix as a 1,000,000 long array. Imagine you want to transform each pixel (independently of the others) by applying some function you have written --- in typical non-parallelized hardware, you would go through each of the million entries in that array, and apply your function, one after the other (serially).
This is the sort of operation you typically have to do when you want to transform images on a screen. You can imagine that doing it serially would get more and more tiresome, as your images get more detailed, your monitors get higher resolution, etc., so purpose built hardware called GPUs were created, which can represent a matrix as a true machine type: a true "primitive", where memory is actually (i, j) addressable. You can pass matrices to the thing, and get matrices back. If you can do matrices, you can also obviously do vectors. Most importantly, you can give the GPU instructions that say "this functions should be applied to each pixel, and it doesn't care about other pixels when transforming one", and the GPU will apply that function in parallel. It will do a 1,000,000 calculations at once (assuming it can store a 1000x1000 matrix, otherwise it might have to get into some other abstractions, but now we are going off topic).
Eventually people figured that any problem that can ultimately be thought of as "I have X data points, and I want to apply a function on each data point independent of the other" could be run efficiently on a GPU.
Machine learning is just one application where you need to deal with lots of matrices.
People have come up with languages that know about matrices as a machine type (early examples being graphics shader languages), and TensorFlow fits in somewhere in this space, with in-built sugar-coating for things the creators thought were "relevant". I have never used TensorFlow though, so someone else can probably give you more detail.
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Some things I have not mentioned:
* vectorization: basically, how to do vector operations "smarter" on non-parallelized hardware, something that many languages (e.g. MATLAB, NumPy) and hardware now support
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Anyway: "transpiling" vector/matrix operations from MATLAB/NumPy to TensorFlow/OpenCL/Cuda is a breeze conceptually (but I bet it's kind of boring problem for advanced programmers). If a transpiler doesn't exist, it's probably because no one has put in the work to open source it. One example of a Python+NumPy to Cuda "transpiler" is Continuum's Numba: http://numba.pydata.org/numba-doc/0.38.0/cuda/index.html http://numba.pydata.org/numba-doc/0.38.0/cuda/index.html
The devs there are also thinking about OpenCL, and some progress was made. This is the current state of that task: https://github.com/numba/numba/pull/582 https://github.com/numba/numba/pull/582
SPIR-V is basically a standardized "middle language" that "transpilers" can use. What you do is translate from language X -> SPIR-V -> OpenCL/Vulkan/whatever -> hardware drivers -> machine language
And SPIR-V is work in progress: https://en.wikipedia.org/wiki/Standard_Portable_Intermediate_Representation https://en.wikipedia.org/wiki/Standard_Portable_Intermediate...
There is also similar work for MATLAB, but its done by the owners: https://www.mathworks.com/matlabcentral/answers/25973-matlab-opencl https://www.mathworks.com/matlabcentral/answers/25973-matlab...
Also, I have to echo other comments about how no one really cares about MATLAB that much in sci-comp, probably because it's proprietary and expensive. Heavy work is usually done in Fortran (legacy code), C/C++, or experimental languages like Julia, or languages that are more flexible/open-source like Python (NumPy/SciPy are just wrappers around lots of C/Fortran).
People who use MATLAB tend to be those who were just "introduced to it" (e.g. through school) and have never hit any limitations that need them to switch to more flexible languages. Or they don't even realize that more flexible languages exist? It's a matter of comfort/goals (I don't advocate that everything should be done in C, and MATLAB is great for quickly doing many things, but many other things that have been done in MATLAB would have been less painful/faster if it used...say, Python+NumPy, because then you can use everything the Python ecosystem has to offer, and aren't limited to the MATLAB ecosystem).
- Koshkin 8y ago> does not use the "vector" as its "primitive" Well, doesn't the SIMD architecture make vectors "primitives", even if in some limited sense?
- bmer 8y agoAs I said: ------------------------------------- Some things I have not mentioned: * vectorization: basically, how to do vector operations "smarter" on non-parallelized hardware[SIMD?], something that many languages (e.g. MATLAB, NumPy) and hardware now support -------------------------------------
- ChrisRackauckas 8y ago>say, Python+NumPy, because then you can use everything the Python ecosystem has to offer, and aren't limited to the MATLAB ecosystem That has an implicit assumption that Python's ecosystem is better for this kind of work than MATLAB which just isn't true in many areas of scientific computing. Take differential equations for example. MATLAB has matcont which is a great bifurcation analysis library which is unrivaled by Python (PyDSTool is a toy in comparison). Python doesn't really have usable DDE solvers. Python's ODE (SciPy, Sundials wrappers, etc) solvers are much less developed than MATLAB's, doing okay since it's wrapping some standard software but with a lot less flexibility than MATLAB. And you can keep going. And to top it off, compilation with Numba or Cython doesn't work well in the case of differential equations since there are a lot of small function calls. So it's not so clear that Python is good at scientific computing at all, and in fact in some regions like differential equations it's quite a step downwards. Generally, the ecosystem in this area is well developed in Julia + the commercial offerings (MATLAB, Maple, Mathematica). That said, Python's ecosystem outside of scientific computing is so much better than MATLAB's. However, at that point I would think Julia is a good choice.
- bmer 8y ago> MATLAB has matcont which is a great bifurcation analysis library which is unrivaled by Python (PyDSTool is a toy in comparison). I know lots of people who work with dynamical systems (math bio), and most people don't use MATLAB's matcont, as it is a toy compared to XPP/AUT. People tolerate XPP/AUT's archaic userface for its power, and can also export data easily to Python for grahping. Also, the DDE thing is no longer true: https://aip.scitation.org/doi/10.1063/1.5019320 https://aip.scitation.org/doi/10.1063/1.5019320 > Python's ODE (SciPy, Sundials wrappers, etc) solvers are much less developed than MATLAB's What do you mean by "much less developed"? ODE solving is an "old problem" in the sense that it has been optimally addressed in C/Fortran/C++ and its just better to make wrappers around that existing code. ODEPACK/SUNDIALS/PETSc are great examples of a cutting edge standard ODE/PDE solvers which have Python wrappers, and if you've got wrappers around them, you're going to be hard pressed to find anything better. Then there are people who are developing new ways of integrating ODEs numerically, and for them, MATLAB is only good as a first pass/prototype thing. A professor I know working on something like this doesn't bother using MATLAB for it (C++/Python). > compilation with Numba or Cython doesn't work well in the case of differential equations since there are a lot of small function calls Again, I have no clue what you mean by this. I just had a paper published which modelled a system involving hundreds of ODEs, with every involved function in the dynamics being compiled using numba's "nopython" mode. The stuff is blazing fast, only about 10 times slower than a C implementation. The structure of the program looked like this: scipy.integrate.odeint -> f -> sub-function ... -> sub-function ... `f` (the function to compute derivatives at each time point) and `sub-function`(s) (which are, I guess, the small function calls you were referring to?) were compiled using numba's nopython mode. It was super easy. You can have a look at the relevant code here: https://github.com/bzm3r/numba-ncc/blob/master/core/dynamics.py#L53 https://github.com/bzm3r/numba-ncc/blob/master/core/dynamics... So I don't get what you mean by "Numba/Cython doesn't work well in the case of DEs since there are a lot of small function calls". Note that MAPLE/Mathematica are not in the same camp as MATLAB, since they are primarily symbolic mathematics engines. Both are fantastic though, I agree. No complaints about Julia. Awesome stuff. Just like Rust. I am not a huge Python fan, in the sense that I am actively moving away from it to "better tools", but I still think Python mostly beats MATLAB.