CSC Computing Environment

Batch job tutorial - Serial jobs

In this tutorial we’ll get familiar with the basic usage of the Slurm batch queue system at CSC

πŸ’¬ A batch job consists of two parts: resource requests and the job step(s)

☝🏻 Examples are done on Puhti. If using the web interface, open a login node shell.

Serial jobs

πŸ’¬ A serial program can only use one core (CPU)

πŸ’¬ Within the job (or allocation), the actual program is launched using the command srun

☝🏻 If you use a software that is pre-installed by CSC, please check its documentation page; it might have a batch job example with useful default settings.

Launching a serial job

  1. Go to the /scratch directory of your project:
cd /scratch/<project>      # replace <project> with your CSC project, e.g. project_2001234

πŸ’‘ You can list your projects with csc-projects

πŸ’‘ Note! If you’re using a project with other members (like the course project), first make a subdirectory for yourself (e.g. mkdir $USER and then move there (cd $USER) to not clutter the /scratch root of your project)

  1. Create a file called my_serial.bash e.g. with the nano text editor:
nano my_serial.bash
  1. Copy the following batch script there and change <project> to the CSC project you actually want to use:
#SBATCH --account=<project>      # Choose the billing project. Has to be defined!
#SBATCH --time=00:02:00          # Maximum duration of the job. Upper limit depends on the partition. 
#SBATCH --partition=test         # Job queues: test, interactive, small, large, longrun, hugemem, hugemem_longrun
#SBATCH --ntasks=1               # Number of tasks. Upper limit depends on partition. For a serial job this should be set 1!

srun hostname                    # Run hostname-command
srun sleep 60                    # Run sleep-command
  1. Submit the job to the batch queue and check its status with the commands:
sbatch my_serial.bash
squeue -u $USER

πŸ’¬ In the batch job example above we are requesting

πŸ’¬ We want to run the program hostname that will print the name of the Puhti compute node that has been allocated for this particular job

πŸ’¬ In addition, we are running the sleep program to keep the job running for an additional 60 seconds, in order to have time to monitor the job

Checking the output and the efficiency

πŸ’­ You can get a list of all your jobs that are running or queuing with the command squeue -u $USER

πŸ—― A submitted job can be cancelled using the command scancel <jobid>

More information

πŸ’‘ FAQ on CSC batch jobs in Docs CSC