Data Analysis via Slurm | Nero User Documentation

Slurm Concept Basics

Warning: Login nodes are not for computing
Login nodes are shared among many users and therefore must not be used to run computationally intensive tasks. Those should be submitted to the Slurm scheduler which will dispatch them on an available compute node.

Nero uses Slurm, an open-source resource manager and job scheduler, used by many of the world’s supercomputers and computer clusters.

The Slurm scheduler provides three key functions:

it allocates access to resources (compute nodes) to users for some duration of time so they can perform work.
it provides a framework for starting, executing, and monitoring work (typically a parallel job such as MPI) on a set of allocated nodes.
it arbitrates contention for resources by managing a queue of pending jobs.

Slurm supports a variety of job submission techniques. Slurm will match appropriate compute resource based on user resource criteria, such as, CPUs, GPUs and memory.

Tip: Wait times in queue
As a quick rule of thumb, it’s important to keep in mind that the more resources your job requests (CPUs, GPUs, memory, nodes, and time), the longer it may have to wait in queue before it could start.
In other words, accurately requesting resources to match your job’s needs will minimize your wait times.

Verify you are logged into nero.compute.stanford.edu

Review steps for logging into nero.compute.stanford.edu

Components of a Slurm Job

A job consists in two parts: resource requests and job steps.: Resource requests describe the amount of computing resource (CPUs, GPUs, memory, expected run time, etc.) that the job will need to successfully run.; Job steps describe tasks that must be executed.

Slurm Interactive Session

Interactive session on a compute node is to use srun to execute a shell through the scheduler. For instance, to start a bash session on a compute node, with the default resource requirements (one core for 2 hours), you can run:

$ srun --pty bash

You can then see you session via

cdoane@nero-login-1:~$ squeue -u cdoane
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
             29613    normal     bash   cdoane  R       4:13      1 nero-4

Slurm Batch scripts

Note: Overview of batch script options can be found here: Slurm jobscript template.

The typical way of creating a job is to write a job submission script. A submission script is a shell script (e.g. a Bash script) whose first comments, if they are prefixed with #SBATCH, are interpreted by Slurm as parameters describing resource requests and submissions options.

The submission script itself is a job step. Other job steps are created with the srun command.

For instance, the following script would request one task with one CPU for 10 minutes, along with 2 GB of memory, in the default partition:

#!/bin/bash
#
#SBATCH --job-name=test
#
#SBATCH --time=10:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=2G

srun hostname
srun sleep 60

When started, the job would run a first job step srun hostname, which will launch the command hostname on the node on which the requested CPU was allocated. Then, a second job step will start the sleep command.

You can create this job submission script on Nero using a text editor such as nano or vim, and save it as submit.sh.

Warning: Slurm directives must be at the top of the script
Slurm will ignore all #SBATCH directives after the first non-comment line. Always put your #SBATCH parameters at the top of your batch script.

Job submission

Once the submission script is written properly, you can submit it to the scheduler with the sbatch command. Upon success, sbatch will return the ID it has assigned to the job (the jobid).

$ sbatch submit.sh
Submitted batch job 1377

Check the job

Once submitted, the job enters the queue in the PENDING state. When resources become available and the job has sufficient priority, an allocation is created for it and it moves to the RUNNING state. If the job completes correctly, it goes to the COMPLETED state, otherwise, its state is set to FAILED.

You’ll be able to check the status of your job and follow its evolution with the squeue -u $USER command:

$ squeue -u cdoane
     JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
      1377    normal     test   cdoane  R       0:12      1 slurm-gpu-compute-7t8jf

The scheduler will automatically create an output file that will contain the result of the commands run in the script file. That output file is named slurm-<jobid>.out by default, but can be customized via submission options. In the above example, you can list the contents of that output file with the following commands:

$ cat slurm-1377.out
slurm-gpu-compute-7t8jf

Congratulations, you’ve submitted your first batch job on Nero!

Check Overall Utilization

You can quickly see the resources you’re using across Slurm for certain time period. Use the following to see your cpu,mem,and gpu utilization statistics. This example would return with information across the month of November:

$ sreport cluster UserUtilizationByAccount -T GRES/gpu,cpu,Mem Start=2019-11-1T00:00:00 End=2019-11-30T23:59:59 user=SUNetID

Replace the time period for the Start and End months if you want to change the time range. Also, make sure to also replace SUNetID with your own Stanford SUNetID.

What’s next?

Actually, quite a lot. Although you now know how to submit a simple batch job, there are many other options. You can get the complete list of parameters by referring to the sbatch manual page (man sbatch).

Overview of GPU Resources and Slurm GPU Specific Examples