alphafold2
array
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alphafold2 | array | |
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1 | 5 | |
1,501 | 189 | |
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0.0 | 6.9 | |
over 1 year ago | 5 months ago | |
Python | C++ | |
MIT License | Apache License 2.0 |
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alphafold2
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A basic introduction to NumPy's einsum
* Example: https://github.com/lucidrains/alphafold2/blob/d59cb1ea536bc5...
array
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Einsum in 40 Lines of Python
I wrote a library in C++ (I know, probably a non-starter for most reading this) that I think does most of what you want, as well as some other requests in this thread (generalized to more than just multiply-add): https://github.com/dsharlet/array?tab=readme-ov-file#einstei....
A matrix multiply written with this looks like this:
enum { i = 2, j = 0, k = 1 };
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Benchmarking 20 programming languages on N-queens and matrix multiplication
I should have mentioned somewhere, I disabled threading for OpenBLAS, so it is comparing one thread to one thread. Parallelism would be easy to add, but I tend to want the thread parallelism outside code like this anyways.
As for the inner loop not being well optimized... the disassembly looks like the same basic thing as OpenBLAS. There's disassembly in the comments of that file to show what code it generates, I'd love to know what you think is lacking! The only difference between the one I linked and this is prefetching and outer loop ordering: https://github.com/dsharlet/array/blob/master/examples/linea...
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A basic introduction to NumPy's einsum
If you are looking for something like this in C++, here's my attempt at implementing it: https://github.com/dsharlet/array#einstein-reductions
It doesn't do any automatic optimization of the loops like some of the projects linked in this thread, but, it provides all the tools needed for humans to express the code in a way that a good compiler can turn it into really good code.
What are some alternatives?
einops - Flexible and powerful tensor operations for readable and reliable code (for pytorch, jax, TF and others)
optimizing-the-memory-layout-of-std-tuple - Optimizing the memory layout of std::tuple