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Using SLURM on HiPerGator

HiPerGator and most other supercomputers are not used the same way as personal desktops/laptops/workstations. The massive amount of computing power requires a sophisticated approach to scheduling workloads to make sure that hardware resources are used efficiently, allocation limits are honored, and users and groups have a fair chance of using the resources without interfering with each other.

Software called a resource manager and a scheduler are required to fulfill the above and other functions and conditions. on HiPerGator we use Slurm for managing hardware resources and scheduling workloads whether those submitted directly to the scheduler via job scripts or behind the scenes of more convenient interfaces like Open OnDemand, Galaxy, or JupyterHub.

Slurm is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for large and small Linux clusters. Slurm requires no kernel modifications for its operation and is relatively self-contained. As a cluster workload manager, Slurm has three key functions.

  • First, it allocates exclusive and/or non-exclusive access to resources (compute nodes) to users for some duration of time so they can perform work.
  • Second, it provides a framework for starting, executing, and monitoring work (normally a parallel job) on the set of allocated nodes.
  • Finally, it arbitrates contention for resources by managing a queue of pending work.

Optional plugins can be used for accounting, advanced reservation, gang scheduling (time sharing for parallel jobs), backfill scheduling, topology optimized resource selection, resource limits by user or bank account, and sophisticated multifactor job prioritization algorithms.

Submitting a SLURM Job

The first step to submitting a SLURM job is writing your own SLURM script. This script will setup important scheduler options such as resource allocation and also hold your actual execution commands. Please see our Sample SLURM Scripts page for example scripts you can use to start.

First, your script will set the #SBATCH options to specify how many CPUs, nodes, and how much memory your job will use. Next, you'll load any required modules or applications. Finally, you'll add the commands or programs you want the job to run.

Once your script is made, you can run your script using: sbatch your_script.sh

For interactive sessions, please visit the Development and Testing and Open OnDemand pages.

SLURM Commands

Please visit our SLURM Commands to learn more about the commands available to control and monitor your jobs. Again, SLURM is highly customizable and allows user's to select what resources are being used for their computation. In addition, there are multiple commands used to track the status of your job in real-time.

Avoiding Session Interruption

It is possible to have multiple sessions running simultaneously. HiPerGator offers options for terminal multiplexing. See Persistent Terminal Sessions for more details.