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Slurm

NERSC uses Slurm for cluster/resource management and job scheduling. Slurm is responsible for allocating resources to users, providing a framework for starting, executing and monitoring work on allocated resources and scheduling work for future execution.

Additional Resources

Jobs

A job is an allocation of resources such as compute nodes assigned to a user for an amount of time. Jobs can be interactive or batch (e.g., a script) scheduled for later execution.

Tip

NERSC provides an extensive set of example job scripts

Once a job is assigned a set of nodes, the user is able to initiate parallel work in the form of job steps (sets of tasks) in any configuration within the allocation.

When you login to a NERSC system you land on a login node. Login nodes are for editing, compiling, preparing jobs. They are not for running jobs. From the login node you can interact with Slurm to submit job scripts or start interactive jobs.

NERSC's environment is configured to support diverse workload including high-throughput serial tasks, full system capability simulations and complex workflows.

Submitting jobs

sbatch

sbatch is used to submit a job script for later execution. The script will typically contain one or more srun commands to launch parallel tasks.

When you submit the job, Slurm responds with the job's ID, which will be used to identify this job in reports from Slurm.

$ sbatch first-job.sh
Submitted batch job 864933

Slurm will also check your file system usage and reject the job if you are over your quota in your scratch or home file system. See here for more details.

salloc

salloc is used to allocate resources for a job in real time as an interactive batch job. Typically this is used to allocate resources and spawn a shell. The shell is then used to execute srun commands to launch parallel tasks.

srun

srun is used to submit a job for execution or initiate job steps in real time. A job can contain multiple job steps executing sequentially or in parallel on independent or shared resources within the job's node allocation. This command is typically executed within a script which is submitted with sbatch or from an interactive prompt on a compute node obtained via salloc.

Options

At a minimum a job script must include number of nodes, time, type of nodes (constraint), and quality of service (QOS). If a script does not specify any of these options then a default may be applied.

Tip

It is good practice to always set the account option (--account=<NERSC Project>).

Information about available NERSC projects is avaliable on iris and via the iris command on NERSC systems.

The full list of directives is documented in the man pages for the sbatch command (see. man sbatch). Each option can be specified either as a directive in the job script:

#!/bin/bash
#SBATCH -N 2

Or as a command line option when submitting the script:

sbatch -N 2 ./first-job.sh

The command line and directive versions of an option are equivalent and interchangeable. If the same option is present both on the command line and as a directive, the command line will be honored. If the same option or directive is specified twice, the last value supplied will be used.

Also, many options have both a long form, e.g., --nodes=2 and a short form, e.g., -N 2. These are equivalent and interchangable.

Many options are common to both sbatch and srun, for example sbatch -N 4 ./first-job.sh allocates 4 nodes to first-job.sh, and srun -N 4 uname -n inside the job runs a copy of uname -n on each of 4 nodes. If you don't specify an option in the srun command line, srun will inherit the value of that option from sbatch.

In these cases the default behavior of srun is to assume the same options as were passed to sbatch. This is achieved via environment variables: sbatch sets a number of environment variables with names like SLURM_NNODES and srun checks the values of those variables. This has two important consequences:

  1. Your job script can see the settings it was submitted with by checking these environment variables

  2. You should not override these environment variables. Also be aware that if your job script does certain tricky things, such as using ssh to launch a command on another node, the environment might not be propagated and your job may not behave correctly

Commonly Used Options

The below table lists some commonly used sbatch/salloc/srun options as well as their meaning. All the listed options can be used with the sbatch or salloc commands (either on the command line or as directives within a script). Many are also commonly used with srun within a script or interactive job.

The long and short forms of each option are interchangeable, but their formats differ. The long form begins with a double hyphen and includes a word, acronym, or phrase (with words separated by single hyphens) followed by an equals sign and any argument to the option (e.g., --time=10:00:00) while the short form consists a single hyphen and a single letter, followed by a space and any argument to the option (e.g., -t 10:00:00). For clarity, we recommend using the long form for Slurm directives in a script -- this makes it easier to understand what options are being set on each line.

Option (long form) Option (short form) Meaning Use with sbatch/salloc? Use with srun?
--time -t maximum walltime Y N
--time-min (none) minimum walltime Y N
--nodes -N number of nodes Y Y
--ntasks -n number of MPI tasks Y Y
--cpus-per-task -c number of processors per MPI task Y Y
--constraint -C constraint (e.g., type of resource) Y N
--qos -q quality of service (QOS) Y N
--account -A project to charge for this job Y N
--licenses -L licenses (filesystem required for job) Y N
--job-name -J name of job Y N

Writing a Job Script

A clear job script will include at least the number of nodes, walltime, type of nodes (constraint), and quality of service (QOS). These options could be specified on the command line, but for clarity and to establish a record of the job submission we recommend including all these options (and more) in your job script.

A Slurm job script begins with a shell invocation (e.g., #!/bin/bash) followed by lines of directives, each of which begins with #SBATCH. After these directives, users then include the commands to be run in the script, including the setting of environment variables and the setup of the job. Usually (but not always) the script includes at least one srun command, launching a parallel job onto one or more nodes allocated to the job.

#!/bin/bash
#SBATCH --nodes=<nnodes>
#SBATCH --time=hh:mm:ss
#SBATCH --constraint=<architecture>
#SBATCH --qos=<QOS>
#SBATCH --account=<project_name>

# set up for problem & define any environment variables here

srun -n <num_mpi_processes> -c <cpus_per_task> a.out

# perform any cleanup or short post-processing here

The above script is easily applied only to the simplest of cases and is not widely generalizable. In this simple case, a user would replace the items between < > with specific arguments, e.g., --nodes=2 or --qos=debug. The format for the maximum walltime request is number of hours, number of minutes, and number of seconds, separated by colons (e.g., --time=12:34:56 for 12 hours, 34 minutes, and 56 seconds).

There are many factors to consider when creating a script for your particular job. In our experience, we find that determining the correct settings for number of CPUs per task, process affinity, etc. can be tricky. Consequently, we recommend using the Job Script Generator to generate the correct #SBATCH directives, srun arguments, and process affinity settings for you.

The job script generator will provide the correct runtime arguments for your job, but may not adequately demonstrate a way to run jobs that fits your particular workflow or application. To help with this, we have developed a curated collection of example job scripts for users to peruse for inspiration.

Defaults

If you do not specify the following options in your script, defaults will be assigned.

Option Cori
nodes 1
time 10 minutes
qos debug
account set in Iris

There is no default architecture

Jobs not specifying the "constraint" will be rejected.

Debugging issues

If there are issues with job submission check:

Available memory for applications on compute nodes

Some memory on compute nodes is reserved for the operating system.

Architecture Total Memory Available to Applications
Haswell 128 GB 118 GB
KNL 96 GB 87 GB

Quota Enforcement

Users will not be allowed to submit jobs if they are over quota in their scratch or home directories. This quota check is performed twice, first when the job is submitted and again when the running job invokes srun. This could mean that if you went over quota after submitting the job, the job could fail when it runs. Please check your quota regularly and delete or archive data as needed.

Queue Wait Times

Queue wait times for past jobs can be a useful guide in estimating wait times of current jobs. The wait time depends on the quality of service (QOS), requested resources (nodes, time, filesystems, etc), jobs in the queue, your other jobs and other jobs from the same NERSC project.

For active jobs in queue, you can monitor start time by using squeue --start option. In example below job 1448935 can't start because user has exceeded max jobs per QOS limit. Slurm will report N/A for start time estimation if the job has not been scheduled with reserved nodes. You can periodically check the job to see if there is a job estimate.

$ squeue --start -j 1448935
             JOBID PARTITION     NAME     USER ST          START_TIME  NODES SCHEDNODES           NODELIST(REASON)
           1448935    bigmem   dummy     elvis PD                 N/A      1 (null)               (QOSMaxJobsPerUserLimit)

Tip

sqs is an alias to squeue with predefined helpful options, including --start.

In most, cases jobs will be pending because of priority, you will see a Reason=Priority is in the output as shown below.

For more details on job state and reasons codes see:

Further reading about jobs

Additional Constraints

Currently it is not possible for users to run a single job which includes multiple types of nodes (e.g. Haswell and KNL nodes in a single job).