SLURM

The SLURM platform allows use of the Simple Linux Utility for Resource Management (SLURM). “Slurm is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for large and small Linux clusters.”, as quoted from (https://slurm.schedmd.com/overview.html). For high-level architecture information about SLURM, see (https://slurm.schedmd.com/quickstart.html#arch). For architecure and included packages information about idmtools and SLURM, see (Architecture and packages reference).

Prerequisites

  • Linux client

  • SLURM cluster access and general understanding

  • Python 3.7, or 3.8 64-bit (https://www.python.org/downloads/release)

  • Python virtual environments

    Python virtual environments enable you to isolate your Python environments from one another and give you the option to run multiple versions of Python on the same computer. When using a virtual environment, you can indicate the version of Python you want to use and the packages you want to install, which will remain separate from other Python environments. You may use virtualenv, which requires a separate installation, but venv is recommended and included with Python 3.3+.

Configuration

The Slurm platform requires you to provide some configuration elements to define its operation.

You can define these parameters in your idmtools.ini file by adding a configuration block for Slurm.

idmtools.ini example:

[SLURM_LOCAL]
type = SLURM
job_directory = /home/userxyz/experiments
You can also do this directly from code by passing the minimum requirements

Python script example:

Platform('SLURM_LOCAL', job_directory='/home/userxyz/experiments')

Configuration Options

Title

Parameter

Description

job_directory

This defines the location that idmtools will use to manage experiments on the SLURM cluster. The directory should be located somewhere that is mounted on all SLURM nodes at the same location. If you are unsure, ask your SLURM server administrator for guidance.

mode

Allows you to control the operational mode for idmtools. There are two modes currently supported. * - local * - bridged Bridged mode is required if you are running from within a Singularity container. See :ref:Operation Modes for details.

Note

Bold parameters are required

Operation Modes

The SLURM platform supports two modes of operation, Local and Bridged. Local is the default mode.

Bridged

Bridged mode allows you to utilize the emodpy/idmtools Singularity environment containers. This is accomplished through a script that manages the communication to Slurm outside the container.

Bridged mode requires the package idmtools-slurm-utils.

To use bridged mode, before running your container you must run the bridge script outside the container:

idmtools-slurm-bridge

If you plan on using the same terminal, you may want to run the bridge in the background:

idmtools-slurm-bridge &

Once you have the bridge running, you can now run idmtools scripts from within Singularity containers. Ensure your platform is configured to use bridged mode:

singularity exec idmtools_1.6.8 bash
$ python my_script.py

Tips

When using the slurm-bridge, there are a few tips for use

  1. When you background the process by running:

    idmtools-slurm-bridge &

    You will need to run:

    fg

    See [Foreground and Background Processes](https://www.linuxshelltips.com/foreground-and-background-process-in-linux/) in Linux

  2. You may need to load modules before executing the bridge. See [Modules documentation](https://curc.readthedocs.io/en/latest/compute/modules.html) for more details.

Local

Local operation is meant to be executed directly on a SLURM cluster node.

Recommendations

  • Simulation results and files should be backed up

Getting started

After you have installed idmtools (Basic installation or Developer installation) and met the above listed prerequisites, you can begin submitting and running jobs to your SLURM cluster with idmtools. First verify your SLURM platform is running. Then submit a job with the included example Python script.

Verify SLURM platform is running

Type the following at a terminal session to verify that SLURM platform is running:

sinfo -a

This will list your available partitions, and status. You should see output similar to the following:

PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
LocalQ*      up   infinite      1   idle localhost

Submit a job

Run the following included Python script to submit and run a job on your SLURM cluster:

/examples/native_slurm/python_sims.py

Note

workitems and AssetCollection are not supported on the SLURM platform with idmtools. If you’ve used the COMPS platform with idmtools you may have scripts using these objects. You would need to update these scripts without using these objects in order to run them on the SLURM platform.