dask-awkward
awkward
dask-awkward | awkward | |
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1 | 4 | |
56 | 793 | |
- | 0.6% | |
9.3 | 9.6 | |
4 days ago | about 2 hours ago | |
Python | Python | |
BSD 3-clause "New" or "Revised" License | BSD 3-clause "New" or "Revised" License |
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dask-awkward
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Awkward: Nested, jagged, differentiable, mixed type, GPU-enabled, JIT'd NumPy
Hi! I'm the original author of Awkward Array (Jim Pivarski), though there are now many contributors with about five regulars. Two of my colleagues just pointed me here—I'm glad you're interested! I can answer any questions you have about it.
First, sorry about all the TODOs in the documentation: I laid out a table of contents structure as a reminder to myself of what ought to be written, but haven't had a chance to fill in all of the topics. From the front page (https://awkward-array.org/), if you click through to the Python API reference (https://awkward-array.readthedocs.io/), that site is 100% filled in. Like NumPy, the library consists of one basic data type, `ak.Array`, and a suite of functions that act on it, `ak.this` and `ak.that`. All of those functions are individually documented, and many have examples.
The basic idea starts with a data structure like Apache Arrow (https://arrow.apache.org/)—a tree of general, variable-length types, organized in memory as a collection of columnar arrays—but performs operations on the data without ever taking it out of its columnar form. (3.5 minute explanation here: https://youtu.be/2NxWpU7NArk?t=661) Those columnar operations are compiled (in C++); there's a core of structure-manipulation functions suggestively named "cpu-kernels" that will also be implemented in CUDA (some already have, but that's in an experimental stage).
A key aspect of this is that structure can be manipulated just by changing values in some internal arrays and rearranging the single tree organizing those arrays. If, for instance, you want to replace a bunch of objects in variable-length lists with another structure, it never needs to instantiate those objects or lists as explicit types (e.g. `struct` or `std::vector`), and so the functions don't need to be compiled for specific data types. You can define any new data types at runtime and the same compiled functions apply. Therefore, JIT compilation is not necessary.
We do have Numba extensions so that you can iterate over runtime-defined data types in JIT-compiled Numba, but that's a second way to manipulate the same data. By analogy with NumPy, you can compute many things using NumPy's precompiled functions, as long as you express your workflow in NumPy's vectorized way. Numba additionally allows you to express your workflow in imperative loops without losing performance. It's the same way with Awkward Array: unpacking a million record structures or slicing a million variable-length lists in a single function call makes use of some precompiled functions (no JIT), but iterating over them at scale with imperative for loops requires JIT-compilation in Numba.
Just as we work with Numba to provide both of these programming styles—array-oriented and imperative—we'll also be working with JAX to add autodifferentiation (Anish Biswas will be starting on this in January; he's actually continuing work from last spring, but in a different direction). We're also working with Martin Durant and Doug Davis to replace our homegrown lazy arrays with industry-standard Dask, as a new collection type (https://github.com/ContinuumIO/dask-awkward/). A lot of my time, with Ianna Osborne and Ioana Ifrim at my university, is being spent refactoring the internals to make these kinds of integrations easier (https://indico.cern.ch/event/855454/contributions/4605044/). We found that we had implemented too much in C++ and need more, but not all, of the code to be in Python to be able to interact with third-party libraries.
If you have any other questions, I'd be happy to answer them!
awkward
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Efficient Jagged Arrays
there's a whole ecosystem in Python originally developed for high energy physics data processing: https://github.com/scikit-hep/awkward all because Numpy demands square N-dimensional array
Same technique used everywhere, here's a simple Julia pkg for the same thing: https://github.com/JuliaArrays/ArraysOfArrays.jl/blob/3a6f5b...
But Julia at least has the decency to just support ragged Vector{Vector} out of the box, and it's not that slow
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The hand-picked selection of the best Python libraries released in 2021
Awkward Array.
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Awkward: Nested, jagged, differentiable, mixed type, GPU-enabled, JIT'd NumPy
Numba's @vectorize decorator (https://numba.pydata.org/numba-doc/latest/user/vectorize.htm...) makes a ufunc, and Awkward Array knows how to implicitly map ufuncs. (It is necessary to specify the signature in the @vectorize argument; otherwise, it won't be a true ufunc and Awkward won't recognize it.)
When Numba's JIT encounters a ctypes function, it goes to the ABI source and inserts a function pointer in the LLVM IR that it's generating. Unfortunately, that means that there is function-pointer indirection on each call, and whether that matters depends on how long-running the function is. If you mean that your assembly function is 0.1 ns per call or something, then yes, that function-pointer indirection is going to be the bottleneck. If you mean that your assembly function is 1 μs per call and that's fast, given what it does, then I think it would be alright.
If you need to remove the function-pointer indirection and still run on Awkward Arrays, there are other things we can do, but they're more involved. Ping me in a GitHub Issue or Discussion on https://github.com/scikit-hep/awkward-1.0
What are some alternatives?
xarray - N-D labeled arrays and datasets in Python
sqlmodel - SQL databases in Python, designed for simplicity, compatibility, and robustness.
Apache Arrow - Apache Arrow is a multi-language toolbox for accelerated data interchange and in-memory processing
DearPyGui - Dear PyGui: A fast and powerful Graphical User Interface Toolkit for Python with minimal dependencies
stumpy - STUMPY is a powerful and scalable Python library for modern time series analysis
uproot5 - ROOT I/O in pure Python and NumPy.
Optimus - :truck: Agile Data Preparation Workflows made easy with Pandas, Dask, cuDF, Dask-cuDF, Vaex and PySpark
django-ninja - 💨 Fast, Async-ready, Openapi, type hints based framework for building APIs
numba-dpex - Data Parallel Extension for Numba
skweak - skweak: A software toolkit for weak supervision applied to NLP tasks
AugLy - A data augmentations library for audio, image, text, and video.
dpbench - Benchmark suite to evaluate Data Parallel Extensions for Python