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

The goal is to learn how to request resources that match the needs of a job

💬 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

💬 A serial program can only use one core (CPU)

One should request only a single core from Slurm
The job does not benefit from additional cores
Excess cores are wasted since they will not be available to other users

💬 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

Go to the /scratch directory of your project:

cd /scratch/<project>      # replace <project> with your CSC project, e.g. project_2001234

Now your input (and output) will be on a shared disk that is accessible to the compute nodes.

💡 You can list your projects with csc-projects

💡 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)

Create a file called my_serial.bash e.g. with the nano text editor:

nano my_serial.bash

Copy the following batch script there and change <project> to the CSC project you actually want to use:

#!/bin/bash
#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

Submit the job to the batch queue and check its status with the commands:

sbatch my_serial.bash
squeue -u $USER

💬 In the batch job example above we are requesting

one core (--ntasks=1)
for two minutes (--time=00:02:00)
from the test queue (--partition=test)

💬 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

💬 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

By default, the output is written to a file named slurm-<jobid>.out where <jobid> is a unique job ID assigned to the job by Slurm
Check the efficiency of the job compared to the reserved resources by issuing the command seff <jobid> (replace <jobid> with the actual Slurm job ID)

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

🗯 A submitted job can be cancelled using the command scancel <jobid>

More information

💡 FAQ on CSC batch jobs in Docs CSC

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