fractal-slurm-tools 0.3.0

Shared tools for parsing&processing SLURM data

fractal-slurm-tools

You can run a version of this tool from PyPI or GitHub, either via pipx or uvx.

Examples (the CLI entrypoint must be one of fractal-slurm-aggregate fractal-slurm-parse-bulk or fractal-slurm-parse-single-job):

# Latest PyPI release
$ pipx run --spec fractal-slurm-tools <entrypoint>
$ uvx --from fractal-slurm-tools <entrypoint>

# Specific PyPI release
$ pipx run --spec fractal-slurm-tools==0.1.0 <entrypoint>
$ uvx --from fractal-slurm-tools==0.1.0 <entrypoint>

# Latest git commit on the default branch
$ pipx run --spec git+https://github.com/fractal-analytics-platform/fractal-slurm-tools.git <entrypoint>
$ uvx --from git+https://github.com/fractal-analytics-platform/fractal-slurm-tools.git <entrypoint>

# Specific git commit
$ pipx run --spec git+https://github.com/fractal-analytics-platform/fractal-slurm-tools.git@3faeefd0eac0f53c6c73d2e3179b10ff2a111793 <entrypoint>
$ uvx --from git+https://github.com/fractal-analytics-platform/fractal-slurm-tools.git@3faeefd0eac0f53c6c73d2e3179b10ff2a111793 <entrypoint>

# Specific git branch
$ pipx run --spec git+https://github.com/fractal-analytics-platform/fractal-slurm-tools.git@main <entrypoint>
$ uvx --from git+https://github.com/fractal-analytics-platform/fractal-slurm-tools.git@main <entrypoint>

A useful sacct command

sacct --format='JobID%18,JobName%18,State,ReqMem,MaxRSS,AveRSS,Elapsed,NCPUS,CPUTimeRaw,MaxDiskRead,MaxDiskWrite' -j XXXX

Development

$ python -m venv venv
$ source venv/bin/activate
$ python -m pip install -e .[dev]
[...]
$ pre-commit install
pre-commit installed at .git/hooks/pre-commit

# Run mypi
$ python -m mypy ./src

# Make a release
$ bumpver update --patch --dry

Contributors and license

Fractal was conceived in the Liberali Lab at the Friedrich Miescher Institute for Biomedical Research and in the Pelkmans Lab at the University of Zurich by @jluethi and @gusqgm. The Fractal project is now developed at the BioVisionCenter at the University of Zurich and the project lead is with @jluethi. The core development is done under contract by eXact lab S.r.l..

Unless otherwise specified, Fractal components are released under the BSD 3-Clause License, and copyright is with the BioVisionCenter at the University of Zurich.