Add dask-cuda LocalCUDACluster support and VesselFM benchmark rule

[Copilot]

VesselFM uses GPUs but was limited to the threaded Dask scheduler. This adds dask-cuda integration via a new "cuda" scheduler option and introduces benchmark rules to profile VesselFM performance across different chunk sizes and thread counts.

Changes

dask_setup.py

• New "cuda" scheduler branch using dask_cuda.LocalCUDACluster(threads_per_worker=threads_per_worker) with a dask.distributed.Client

with get_dask_client("cuda", snakemake.threads):
    # workers are now GPU-backed via LocalCUDACluster

vesselfm.py

• Uses config["dask_scheduler"] instead of hardcoded "threads", enabling GPU-accelerated inference

snakebids.yml

• --dask_scheduler now accepts cuda as a valid choice
• New vesselfm_benchmark config block with default chunk_sizes and thread_counts for benchmark sweeps

vessels.smk

• run_vesselfm gains a benchmark: directive for automatic timing
• New benchmark_run_vesselfm rule: parameterizes chunk_size and thread_count as wildcards, runs each combination 3× via repeat()
• New all_benchmark_vesselfm aggregate target expanding over all configured chunk/thread combinations

# Run benchmark sweep across all chunk_size × thread_count combinations
snakemake all_benchmark_vesselfm --cores all

Warning

Firewall rules blocked me from connecting to one or more addresses (expand for details)

I tried to connect to the following addresses, but was blocked by firewall rules:

• pixi.sh
  • Triggering command: /usr/bin/curl curl -fsSL REDACTED (dns block)

If you need me to access, download, or install something from one of these locations, you can either:

• Configure Actions setup steps to set up my environment, which run before the firewall is enabled
• Add the appropriate URLs or hosts to the custom allowlist in this repository's Copilot coding agent settings (admins only)

---

💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.