idmtools-platform-slurm

• Introduction
• Setting Up Virtual Environment
• Development Tips
• Manually run a script as a Slurm job
• Use SlurmJob to run a script as a Slurm job
• With SlurmPlatform to run a script as a Slurm job
• Folder structure:

Introduction

SlurmPlatform is a platform designed to facilitate the execution of experiments and simulations in slurm cluster.

Setting Up Virtual Environment

To set up a virtual environment for SlurmPlatform, follow these steps:

1. Install Python

   Ensure you have Python 3.8+ installed on your system.

2. Create Virtual Environment

   There are multiple ways to create a virtual environment. Below is an example using venv:

   python -m venv slurm_env
   

3. Activate Virtual Environment

   • On Windows:

     slurm_env\Scripts\activate
     

   • On Linux:

     source slurm_env/bin/activate
     

4. Install SlurmPlatform

   pip install idmtools-platform-slurm
   

5. Install Dependencies

   pip install -r requirements.txt
   

6. Optional(No need step #4 and #5), Install all slurm platform related packages

   pip install idmtools[slurm]
   

Development Tips

There is a Makefile file available for most common development tasks. Here is a list of commands

clean       -   Clean up temproary files
lint        -   Lint package and tests
test        -   Run All tests
coverage    -   Run tests and generate coverage report that is shown in browser

On Windows, you can use pymake instead of make

Manually run a script as a Slurm job

Preparation

(1).Have target script ready, say my_script.py, suppose you have folder structure like::

script_folder
    my_script.py
    ......

(2). Created a virtual environment and activated it.

Steps

1. within the target script folder, create a batch file 'sbatch.sh' (without quote) with content:

#!/bin/bash

#SBATCH --partition=b1139
#SBATCH --time=10:00:00
#SBATCH --account=b1139

#SBATCH --output=stdout.txt
#SBATCH --error=stderr.txt

# replace with your script file
python3 my_script.py
    
exit $RESULT

Note: the content here is based on Northwestern University QUEST Slurm system. For general case, above content (required #SBATCH parameters) may be a little bit different.

2. run your target script as SLURM job execute the following commands from console (under virtual environment):

   cd path_to_script_folder

   sbatch sbatch.sh

Note: any output information from my_script.py is stored in file stdout.txt under the current folder. For example, if my_script.py kicks out another Slurm job, then its Slurm id information can be found in file stdout.txt.

Use SlurmJob to run a script as a Slurm job

The example can be simple as the following:

--script.py--

   from idmtools.core.platform_factory import Platform
   from idmtools_platform_slurm.utils.slurm_job.slurm_job import SlurmJob

   script = '<user script path>'
   # script = 'example_path/python_sim_slurm.py'   # example
   platform = Platform('SLURM_LOCAL', job_directory='<job_directory>')
   sj = SlurmJob(script_path=script, platform=platform)
   sj.run()

With SlurmPlatform to run a script as a Slurm job

We have SlurmJob integrated into SlurmPlatform and any Python script can run as a Slurm job simply doing:

--script.py--

   from idmtools.entities.command_task import CommandTask
   from idmtools.entities.experiment import Experiment
   from idmtools.core.platform_factory import Platform
   
   platform = Platform('SLURM_LOCAL', job_directory='<job_directory>')
   # Define task
   command = "echo 'Hello, World!'"
   task = CommandTask(command=command)
   # Run an experiment
   experiment = Experiment.from_task(task, name="example")
   experiment.run(platform=platform)

Folder structure:

See Folder Structure