fractal-slurm-tools 0.6.0

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==0.5.0 <entrypoint>
$ uvx --from fractal-slurm-tools==0.5.0 <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>

Environment variables

# Enable compatibility with legacy SLURM (e.g. v15.08.7)
USE_LEGACY_FIELDS=1

# Modify batch size
SACCT_BATCH_SIZE=50

# Token to connect to the Fractal backend
FRACTAL_TOKEN=...

A useful sacct command

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

Development

uv

We use uv to manage the development environment and the dependencies - see https://docs.astral.sh/uv/getting-started/installation/ for methods to install it. From the root folder, you can get started through

# Create a new virtual environment in `.venv`
uv venv

# Install both the required dependencies and the optional dev/docs dependencies
uv sync --frozen --extra dev

# Run a command from within this environment without updating the `uv.lock` file
uv run --frozen fractal-slurm-parse-single-job

Make a release

# Make a release
uv run --frozen bumpver update --patch --dry

Contributors and license

The Fractal project is developed by the BioVisionCenter at the University of Zurich, who contracts eXact lab s.r.l. for software engineering and development support.

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