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Development Notes

Setup friction encountered on this fork during GPU development — kept here separately so the main README stays clean. Not universal microsim guidance, just what was hit on this machine.

GPU backend (cupy) setup

  1. numpy version conflict — microsim's metadata pins numpy<2.0, but cupy-cuda12x requires numpy>=2.0. In practice, numpy 2.4.6 worked fine at runtime with this version of microsim despite the metadata warning — if pip flags the conflict, it's likely safe to ignore, but verify by running a real simulation before trusting it.

  2. CUDA headers not found (RuntimeError: Failed to find CUDA headers) — if your system has multiple CUDA toolkit installs (common after driver updates over time), cupy's JIT compiler may not find headers even with CUDA_PATH set correctly. Installing the toolkit extra directly into the venv sidesteps the problem:

   pip install "cupy-cuda12x[ctk]"
  1. zarr / numcodecs mismatch (ImportError: cannot import name 'cbuffer_sizes' from 'numcodecs.blosc') — zarr 2.17.x expects an older numcodecs API:
   pip install "numcodecs<0.13"
  1. COSEM data fetching — loading real segmentation data (e.g. the cosem example) requires the optional extra:
   pip install "microsim[cosem]"

None of these are bugs in microsim itself, except where already filed as upstream PRs (#140, #141) — mostly environment/dependency friction from multiple existing CUDA/Python installs on a dev machine.