atria-gpu-rs 0.1.0

CUDA-required GPU build of the Ablatio Triadum (ATria) centrality algorithm as a PluMA plugin
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atria-gpu-rs

CUDA-required GPU build of the Ablatio Triadum (ATria) centrality algorithm, packaged as a PluMA plugin.

Rust License: MIT Cargo

Relationship to atria-rs

The upstream atria-rs crate ships three computational backends — CPU, wgpu, and CUDA — selected at runtime via ComputeBackend. This crate is a thin wrapper that:

  1. Depends on atria-rs with the cuda feature compiled in.
  2. Forces ComputeBackend::Cuda at construction time and never exposes a setter that could switch it back to CPU.
  3. Exports a different PluMA-FFI prefix (ATriaGPU_plugin_*) so it can coexist with the canonical ATria plugin in the same PluMA tree under plugins/ATriaGPU/libATriaGPUPlugin.so.
  4. Emits a log::warn! if the CUDA runtime is unavailable and the underlying atria-rs silently degrades to CPU — surfacing the fallback rather than letting users be surprised by slower-than-expected wall clock.

Algorithm + output semantics are byte-for-byte identical to atria-rs >= 1.4.0. The same corrP.never.csv reference run through ATriaGPU produces output sort-identical to the upstream C++ ATria plugin's corrP.never.ATria.noa.expected reference file, including the tie-handling at ranks #4 / #4 / #4 / #7.

Requirements

  • An NVIDIA GPU exposed to the host (visible via nvidia-smi).
  • CUDA toolkit installed and nvcc reachable through $CUDA_PATH / $CUDA_ROOT. The cudarc build script auto-detects the toolkit version (CUDA 11.4 through 13.x are supported).
  • PluMA built with --with-rust (see FIUBioRG/PluMA#13) for the loader to be active.

Build

git clone https://github.com/quinnjr/atria-gpu-rs.git
cd atria-gpu-rs
CUDA_PATH=/opt/cuda cargo build --release
# → target/release/libATriaGPUPlugin.so

Install into PluMA

cd /path/to/PluMA/plugins
mkdir -p ATriaGPU
ln -sfn /path/to/atria-gpu-rs/target/release/libATriaGPUPlugin.so \
        ATriaGPU/libATriaGPUPlugin.so
ln -sfn /path/to/atria-gpu-rs/Cargo.toml ATriaGPU/Cargo.toml

Pipeline config

Prefix plugins/ATriaGPU/example/
Plugin ATriaGPU inputfile corrP.never.csv outputfile corrP.never.ATriaGPU.noa

Test against PluMA's harness

cd /path/to/PluMA
python3 testPluMA.py ATriaGPU
# Testing ATriaGPU...                              [PASS]
# Passing Rate: 100.0%

The bundled example/corrP.never.csv is the canonical 126-node oral-microbiome correlation network from the upstream ATria fixture; example/corrP.never.ATriaGPU.noa.expected is the upstream C++ ATria plugin's actual output. A passing test certifies that the CUDA backend produces the same ranks (including ties) as the C++ original.

Performance notes

The Floyd-Warshall step is dominated by n³ work where n = 2 * GSIZE (GSIZE is the number of nodes; the split-vertex expansion doubles it). On the reference 126-node network, that's 126·2 = 252-wide matrix — small enough that PCIe transfer overhead can dominate. CUDA payoff is expected on larger networks where the n³ cubic factor dwarfs the fixed transfer cost.

License

MIT — see LICENSE.md.

References