pathml
cunumeric
pathml | cunumeric | |
---|---|---|
2 | 9 | |
364 | 594 | |
3.0% | -0.2% | |
8.0 | 8.5 | |
about 1 month ago | 7 days ago | |
Python | Python | |
GNU General Public License v3.0 only | Apache License 2.0 |
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pathml
- Hilo Semanal de Consultas IT - Asesoría Técnica, Desarrollo Profesional y Aprendizaje
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Dask – a flexible library for parallel computing in Python
We have been using dask to support our computational pathology workflows [1], where the images are so big that they cannot be loaded in memory, let alone analyzed (standard pathology whole slide images are ~1GB; some microscopy techniques generate images >1TB). We divide each image into a bunch of smaller tiles and process each tile independently. The dask.distributed scheduler lets us scale up by distributing the tile processing across a cluster.
Benefits of dask.distributed: easy to get up and running, and has support for spinning up clusters on lots of different computing platforms (local machines, HPC cluster, k8s, etc.)
One difficulty is optimizing performance - there are so many configuration details (job size, number of workers, worker resources, etc. etc.) that it's been hard to know what is best.
[1] https://github.com/Dana-Farber-AIOS/pathml
cunumeric
- Announcing Chapel 1.32
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Is Parallel Programming Hard, and, If So, What Can You Do About It? [pdf]
I am biased because this is my research area, but I have to respectfully disagree. Actor models are awful, and the only reason it's not obvious is because everything else is even more awful.
But if you look at e.g., the recent work on task-based models, you'll see that you can have literally sequential programs that parallelize automatically. No message passing, no synchronization, no data races, no deadlocks. Read your programs as if they're sequential, and you immediately understand their semantics. Some of these systems are able to scale to thousands of nodes.
An interesting example of this is cuNumeric, which allows you to take sequential Python programs that use NumPy, and by changing one line (the import statement), run automatically on clusters of GPUs. It is 100% pure awesomeness.
https://github.com/nv-legate/cunumeric
(I don't work on cuNumeric, but I do work on the runtime framework that cuNumeric uses.)
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GPT in 60 Lines of NumPy
I know this probably isn't intended for performance, but it would be fun to run this in cuNumeric [1] and see how it scales.
[1]: https://github.com/nv-legate/cunumeric
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Dask – a flexible library for parallel computing in Python
If you want built-in GPU support (and distributed), you should check out cuNumeric (released by NVIDIA in the last week or so). Also avoids needing to manually specify chunk sizes, like it says in a sibling comment.
https://github.com/nv-legate/cunumeric
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Julia is the better language for extending Python
Try dask
Distribute your data and run everything as dask.delayed and then compute only at the end.
Also check out legate.numpy from Nvidia which promises to be a drop in numpy replacement that will use all your CPU cores without any tweaks on your part.
https://github.com/nv-legate/legate.numpy
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Learning more about HPC as a python guy
Something for the HPC tools category: https://github.com/nv-legate/legate.numpy
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Unifying the CUDA Python Ecosystem
You might be interested in Legate [1]. It supports the NumPy interface as a drop-in replacement, supports GPUs and also distributed machines. And you can see for yourself their performance results; they're not far off from hand-tuned MPI.
[1]: https://github.com/nv-legate/legate.numpy
Disclaimer: I work on the library Legate uses for distributed computing, but otherwise have no connection.
- Legate NumPy: An Aspiring Drop-In Replacement for NumPy at Scale