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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 analyz
by rosej 5y ago
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 https://github.com/Dana-Farber-AIOS/pathml
- gsteinb88 5y agoJust FYI, Amazon and most other providers offer instances that go up to many TB of ram — the largest listed on EC2 right now is 24TB. Depending on your workload, you may get far better throughput not worrying about distributing the work and data