CudaMon: An R Package to Monitor NVIDIA GPUs, Showcased by Monitoring a GPU-accelerated Single-cell Analysis Workflow in R
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arXiv
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| Auteurs principaux: | , , , |
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| Format: | Preprint |
| Publié: |
2026
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| _version_ | 1866916011708514304 |
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| author | Zadenoori, Mohammad Amin Ceccaroni, Riccardo Sales, Gabriele Risso, Davide |
| author_facet | Zadenoori, Mohammad Amin Ceccaroni, Riccardo Sales, Gabriele Risso, Davide |
| contents | NVIDIA GPUs have recently started to be used in computational biology, yet R users lack integrated GPU monitoring tools, forcing reliance on external utilities like nvidia-smi. We introduce CudaMon, an R package providing real-time monitoring of GPU utilization, memory, temperature, and power draw via NVML, along with data export and visualization utilities. Monitoring a GPU-accelerated single-cell RNA-seq pipeline (1M brain cells, RAPIDS workflow) shows that compute-intensive steps (PCA, UMAP, t-SNE) exceed 90% GPU utilization, while data management phases reveal bottlenecks. CudaMon facilitates resource optimization, performance debugging, and reproducibility for GPU-accelerated R workflows. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2605_13928 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | CudaMon: An R Package to Monitor NVIDIA GPUs, Showcased by Monitoring a GPU-accelerated Single-cell Analysis Workflow in R Zadenoori, Mohammad Amin Ceccaroni, Riccardo Sales, Gabriele Risso, Davide Computation NVIDIA GPUs have recently started to be used in computational biology, yet R users lack integrated GPU monitoring tools, forcing reliance on external utilities like nvidia-smi. We introduce CudaMon, an R package providing real-time monitoring of GPU utilization, memory, temperature, and power draw via NVML, along with data export and visualization utilities. Monitoring a GPU-accelerated single-cell RNA-seq pipeline (1M brain cells, RAPIDS workflow) shows that compute-intensive steps (PCA, UMAP, t-SNE) exceed 90% GPU utilization, while data management phases reveal bottlenecks. CudaMon facilitates resource optimization, performance debugging, and reproducibility for GPU-accelerated R workflows. |
| title | CudaMon: An R Package to Monitor NVIDIA GPUs, Showcased by Monitoring a GPU-accelerated Single-cell Analysis Workflow in R |
| topic | Computation |
| url | https://arxiv.org/abs/2605.13928 |