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Getting started with the Sleep Revolution slurm cluster
Slurm is a workload manager/scheduler system
The cluster is a linux environment, connect with SSH
Terminal connection :
Open a terminal to log-in ssh <myUser>@cheetah.sleep.ru.is
About the user environment :
Each user has his home folder, the path is [/mount/home/<username>]
- The first step for users is to make sure their working environment fits their needs.
User can install different version of Python and all necessary modules for their work.
For those who are using Python, we recommend, for ease of use, using a Python virtual environment
- However user can setup and install their Python modules locally without a Python virtual environment, by using Pip3 install <Module>
- Each user directory has a few files an readMe.lst file and template (slurm) script file (exampleJob.sh)
Every user needs to use a script file for instructing the cluster what to do
- The cluster gives users access to memory, cpu and GPU. To execute your job on the cluster, first update exampleJob.sh to run your code (or make a copy)
Then submit your job to the queue with command sbatch exampleJob.sh
Your template script file (exampleJob.sh) looks like this
#!/bin/bash
#SBATCH --account=staff
#SBATCH --job-name=runJob
#SBATCH --gpus-per-node=1
#SBATCH --mem-per-cpu=2G
#SBATCH --partition=main
#SBATCH --output=aSlurm.log
Useful commands
cmd | Descr |
---|---|
sbatch <exampleJob.sh> | Submit job |
sacct | My jobs |
squeue | Show all jobs on the queue |
sinfo | Information about the cluster |
srun | Run job interactively |
scancel <id> | kill job with <id> |
Examples of Python virtual environment
Python venv
Miniconda
Aaconda