https://github.com/mmore500/qspool
Dependency-free solution to spool jobs into SLURM scheduler without exceeding queue capacity limits
https://github.com/mmore500/qspool
Last synced: 29 days ago
JSON representation
Dependency-free solution to spool jobs into SLURM scheduler without exceeding queue capacity limits
- Host: GitHub
- URL: https://github.com/mmore500/qspool
- Owner: mmore500
- License: mit
- Created: 2023-01-26T18:18:22.000Z (over 2 years ago)
- Default Branch: master
- Last Pushed: 2024-05-30T07:53:29.000Z (12 months ago)
- Last Synced: 2025-04-30T10:13:05.874Z (29 days ago)
- Language: Python
- Homepage:
- Size: 88.9 KB
- Stars: 4
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
[](https://zenodo.org/doi/10.5281/zenodo.10864602)
[](https://pypi.python.org/pypi/qspool)
[](https://github.com/mmore500/qspool/actions/workflows/CI.yml)
**qspool** is a dependency-free solution to spool jobs into SLURM scheduler without exceeding queue capacity limits.
# Usage
You need to submit more slurm scripts than fit on the queue at once.
```bash
tree .
.
├── slurmscript0.slurm.sh
├── slurmscript1.slurm.sh
├── slurmscript2.slurm.sh
├── slurmscript3.slurm.sh
├── slurmscript4.slurm.sh
├── slurmscript5.slurm.sh
├── slurmscript6.slurm.sh
├── slurmscript7.slurm.sh
├── slurmscript8.slurm.sh
...
```
The `qspool` script will feed your job scripts onto the queue as space becomes available.
```bash
python3 -m qspool *.slurm.sh
```
You can also provide job names via stdin, which is useful for very large job batches.
```bash
find . -maxdepth 1 -name '*.slurm.sh' | python3 -m qspool
```
The `qspool` script creates a slurm job that submits your job scripts.
When queue capacity fills, this `qspool` job will schedule a follow-up job to submit any remaining job scripts.
This process continues until all job scripts have been submitted.
```
usage: qspool.py [-h] [--payload-job-script-paths-infile PAYLOAD_JOB_SCRIPT_PATHS_INFILE] [--job-log-path JOB_LOG_PATH] [--job-script-cc-path JOB_SCRIPT_CC_PATH]
[--queue-capacity QUEUE_CAPACITY] [--qspooler-job-title QSPOOLER_JOB_TITLE]
[payload_job_script_paths ...]
positional arguments:
payload_job_script_paths
What scripts to spool onto slurm queue? (default: None)
options:
-h, --help show this help message and exit
--payload-job-script-paths-infile PAYLOAD_JOB_SCRIPT_PATHS_INFILE
Where to read script paths to spool onto slurm queue? (default: <_io.TextIOWrapper name='' mode='r' encoding='utf-8'>)
--job-log-path JOB_LOG_PATH
Where should logs for qspool jobs be written? (default: ~/joblog/)
--job-script-cc-path JOB_SCRIPT_CC_PATH
Where should copies of submitted job scripts be kept? (default: ~/jobscript/)
--queue-capacity QUEUE_CAPACITY
How many jobs can be running or waiting at once? (default: 1000)
--qspooler-job-title QSPOOLER_JOB_TITLE
What title should be included in qspooler job names? (default: none)
```
# Installation
no installation:
```bash
python3 "$(tmpfile="$(mktemp)"; curl -s https://raw.githubusercontent.com/mmore500/qspool/v0.5.0/qspool.py > "${tmpfile}"; echo "${tmpfile}")" [ARGS]
```
pip installation:
```bash
python3 -m pip install qspool
python3 -m qspool [ARGS]
```
`qspool` has zero dependencies, so no setup or maintenance is required to use it.
Compatible all the way back to Python 3.6, so it will work on your cluster's ancient Python install.
# How it Works
```
qspool
* read contents of target slurm scripts
* instantiate qspooler job script w/ target slurm scripts embedded
* submit qspooler job script to slurm queue
```
⬇️ ⬇️ ⬇️
```
qspooler job 1
* submit embedded target slurm scripts one by one until queue is almost full
* instantiate qspooler job script w/ remaining target slurm scripts embedded
* submit qspooler job script to slurm queue
```
⬇️ ⬇️ ⬇️
```
qspooler job 2
* submit embedded target slurm scripts one by one until queue is almost full
* instantiate qspooler job script w/ remaining target slurm scripts embedded
* submit qspooler job script to slurm queue
```
...
```
qspooler job n
* submit embedded target slurm scripts one by one
* no embedded target slurm scripts remain
* exit
```
# Related Software
[`roll_q`](https://github.com/FergusonAJ/roll_q) uses a similar approach to solve this problem.
`roll_q` differs in implementation strategy.
`roll_q` tracks submission progress via an index variable in a file associated with a job batch.
`qspool` embeds jobs in the submission worker script itself.
# Citing
If qspool is used in scientific publication, please cite it as
> Matthew Andres Moreno (2024). mmore500/qspool. Zenodo. https://doi.org/10.5281/zenodo.10864602
```bibtex
@software{moreno2024qspool,
author = {Matthew Andres Moreno},
title = {mmore500/qspool},
month = mar,
year = 2024,
publisher = {Zenodo},
doi = {10.5281/zenodo.10864602},
url = {https://zenodo.org/doi/10.5281/zenodo.10864602}
}
```
And don't forget to leave a [star on GitHub](https://github.com/mmore500/qspool/stargazers)!