Sbatchpy is a python package allowing easy sbatch job script creation and submissions on hpc clusters, directly from python.
Project description
SbatchPy
A python package that allows easy sbatch
job script creation and submissions on hpc clusters
, directly from python
.
Installation
# to install latest PyPI release
pip install sbatchpy
# to install latest GitHub commit
pip install --upgrade git+https://github.com/killiansheriff/sbatchpy
Usage
An example on how to run a python script called my_script.py
taking 2 arguments var1
and var2
as inputs, and using the base
environement is provided below. A complete example with outputs can be found here.
from sbatchpy import run
config = {
"mem": "1gb",
"time": "00:01:00",
"account": "myaccount",
"cpus-per-task": "5",
"partition": "shared",
"ntasks-per-node": "1",
"nodes": "1",
}
for var1, var2 in zip([1, 2, 3], ["A", "B", "C"]):
config["job-name"] = f"myjob_{var1}var1_{var2}var2.sh"
config["output"] = f"out/myjob_{var1}var1_{var2}var2.out"
run(
config,
code=f"source activate base \n python my_script.py {var1} {var2}",
)
By default, sbatchpy will check that config["output"]
's directory folder exists. If it doesn't, you will be notified and the job will not run.
Additionally, each sbatch submission script is saved inside the f"{os.getcwd()}/.job"
folder. Another saving folder can be chosen by passing job_directory=my_saving_directory_path
to the run
function which is responsible of creating the submission script and running it using sbatch job_directory/config["job-name"]
.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file sbatchpy-1.0.0.tar.gz
.
File metadata
- Download URL: sbatchpy-1.0.0.tar.gz
- Upload date:
- Size: 2.8 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.2 CPython/3.9.17
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | 54a4ebaabd90ec7e7a93441c5124cbe9a5d8ebafb7b77ac488f9193facf3645a |
|
MD5 | e2775f3299a04eb1001766030536b038 |
|
BLAKE2b-256 | 1791b7f0e1e6d2364f6adf7a55373c8a6027cb114ff78666bcf81cd9c300f277 |
Provenance
File details
Details for the file sbatchpy-1.0.0-py3-none-any.whl
.
File metadata
- Download URL: sbatchpy-1.0.0-py3-none-any.whl
- Upload date:
- Size: 3.0 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/4.0.2 CPython/3.9.17
File hashes
Algorithm | Hash digest | |
---|---|---|
SHA256 | da7424c0dd9f1d1086c57c7e89621f1792ede29c12ae61a41429b3f945afa321 |
|
MD5 | 90c45b1327101a7c309175203c38f2e3 |
|
BLAKE2b-256 | 3e0bc4ff3b250c98a6875c2ac3b7bf30af9e7ec102b2395588b9162a86237a0f |