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Goal: Introduction to Slurm and how to start interactive sessions, submit jobs and monitor.

Workload Managers 

  1. Allocates access to appropriate computer nodes specific to your requests.

  2. Framework for starting, executing, monitoring, and even canceling your jobs.

  3. Queue management and job state notification.

ARCC: Slurm: Wiki Pages 

A quick read can be found under: Slurm: Getting Started-Jobs and Nodes

ARCC also hosts a number of more detailed and specific wiki pages:

Interactive Session: salloc

You’re there doing the work.

Suitable for developing and testing over a few hours.

[]$ salloc -–help
[]$ man salloc
# Lots of options. 

# The bare minimum.
# This will provide the defaults of one node, one core and 1G of memory.
[]$ salloc –A <project-name> -t <wall-time>

  • As with other Linux commands, there are typically short and long forms for the options.

    • -A vs --account and -t vs --time.

  • Format for: -t/--time: Acceptable time formats include "minutes", "minutes:seconds", "hours:minutes:seconds", "days-hours", "days-hours:minutes" and "days-hours:minutes:seconds".

Interactive Session: salloc: workshop

You’ll only use the reservation for this (and/or other) workshop.

Once you have an account you typically do not need it.

But there are use cases when we can create a specific reservation for you.

Which itself might require a partition to be defined if you’re using a GPU node (more about that later).

# CPU only compute node.
[]$ salloc –A <project-name> –t 1:00 --reservation=<reservation-name>

# GPU partition/compute node.
[]$ salloc –A <project-name> –t 1:00 --reservation=<reservation-name> --partition=<partition-name>

Interactive Session: squeue: What’s happening?

Use the squeue command to find a list of jobs currently pending/running.

This list can be 10s/100s/1000s of lines long.

Use the -u option with your <username> to specifically look at your jobs.

[]$ salloc -A <project-name> -t 1:00 --reservation=<reservation-name>
salloc: Granted job allocation 13526337
salloc: Nodes m233 are ready for job
# Make a note of the job id.

# Notice the server/node name has changed.
[arcc-t05@m233 intro_to_hpc]$ squeue -u arcc-t05
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
          13526337     moran interact arcc-t05  R       0:19      1 m233
# For an interactive session: Name = interact
# You have the command-line interactively available to you.
[]$ 
...
[]$ squeue -u arcc-t05
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
          13526337     moran interact arcc-t05  R       1:03      1 m233
# Session will automatically time out
[]$ salloc: Job 13526337 has exceeded its time limit and its allocation has been revoked.
slurmstepd: error: *** STEP 13526337.interactive ON m233 CANCELLED AT 2024-03-22T09:36:53 DUE TO TIME LIMIT ***
exit
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.

Interactive Session: salloc: Finished Early?

If you finish using an salloc job before the wall time you requested, you can exit from the command line.

This will stop the interactive session and release its associated resources back to the cluster and make them available for pending jobs.

[]$ salloc -A <project-name> -t 1:00 --reservation=<reservation-name>
salloc: Granted job allocation 13526338
salloc: Nodes m233 are ready for job
[arcc-t05@m233 ...]$ Do stuff…
[]$ exit
exit
salloc: Relinquishing job allocation 13526338

Closing the session will also release the job.

Submit Jobs: sbatch

  • You submit a job to the queue and walk away.

  • Monitor its progress/state using command-line and/or email notifications.

  • Once complete, come back and analyze results.

Submit Jobs: sbatch: Example

The following is an example bash submission script that we will use to submit a job to the cluster.

It uses a short test python file defined here: python script.

#!/bin/bash                               
# Shebang indicating this is a bash script.
# Do NOT put a comment after the shebang, this will cause an error.
#SBATCH --account=<project-name>          # Use #SBATCH to define Slurm related values.
#SBATCH --time=10:00                      # Must define an account and wall-time.
#SBATCH --reservation=<reservation-name>
echo "SLURM_JOB_ID:" $SLURM_JOB_ID        # Can access Slurm related Environment variables.
start=$(date +'%D %T')                    # Can call bash commands.
echo "Start:" $start
module purge
module load gcc/13.2.0 python/3.10.6      # Load the modules you require for your environment.
python python01.py                        # Call your scripts/commands.
sleep 1m
end=$(date +'%D %T')
echo "End:" $end

  • As with salloc, a submission script must at a minimum have an #SBATCH --account and #SBATCH --time defined.

  • Notice we are using the long forms in the example above.

Submit Jobs: squeue: What’s happening?

Remember: Use the squeue command to find a list of your jobs currently pending/running.

[]$ sbatch run.sh
Submitted batch job 13526340
[]$ squeue -u <username>
             JOBID PARTITION     NAME      USER  ST       TIME  NODES NODELIST(REASON)
          13526340     moran   run.sh <username>  R       0:05      1 m233
[]$ ls
python01.py  run.sh  slurm-13526340.out

[]$ cat slurm-13526340.out
SLURM_JOB_ID: 13526340
Start: 03/22/24 09:38:36
Python version: 3.10.6 (main, Oct 17 2022, 16:47:32) [GCC 12.2.0]
Version info: sys.version_info(major=3, minor=10, micro=6, releaselevel='final', serial=0)

[]$ squeue -u <username>
             JOBID PARTITION     NAME       USER ST       TIME  NODES NODELIST(REASON)
          13526340     moran   run.sh <username>  R       0:17      1 m233

  • By default, an output of the form: slurm-<job-id>.out will be generated.

  • You can view this file while the job is still running. Only view, do not edit.

Submit Jobs: squeue: What’s happening? Continued

The squeue command only shows pending and running jobs.

If a job is no longer in the queue then it has finished. 

[]$ squeue -u <username>
             JOBID PARTITION     NAME       USER ST       TIME  NODES NODELIST(REASON)
          13526340     moran   run.sh <username>  R       0:29      1 m233
[]$ squeue -u <username>
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)

[]$ cat slurm-13526340.out
SLURM_JOB_ID: 13526340
Start: 03/22/24 09:38:36
Python version: 3.10.6 (main, Oct 17 2022, 16:47:32) [GCC 12.2.0]
Version info: sys.version_info(major=3, minor=10, micro=6, releaselevel='final', serial=0)
End: 03/22/24 09:39:36

  • Finished can mean success, failure, timeout, out-of-memory... It’s just no longer running.

More squeue Information

For more information see the main Slurm squeue page and use.

[]$ squeue --help
[]$ man squeue

For example, using the --Format option you can display additional columns, such as how much time is left from your requested wall time using TimeLeft:

[]$ squeue -u <username> --Format="Account,UserName,JobID,SubmitTime,StartTime,TimeLeft"
ACCOUNT             USER                JOBID               SUBMIT_TIME         START_TIME          TIME_LEFT
<project-name>      <username>          1795458             2024-08-14T10:31:07 2024-08-14T10:31:09 6-04:42:51
<project-name>      <username>          1795453             2024-08-14T10:31:06 2024-08-14T10:31:07 6-04:42:49
<project-name>      <username>          1795454             2024-08-14T10:31:06 2024-08-14T10:31:07 6-04:42:49
...

There are various other time related columns:

  • SubmitTime: The time that the job was submitted at.

  • StartTime: Actual or expected start time of the job or job step. This will be different than the submit time if your job has been pending in the queue.

  • TimeLeft: Time left for the job to execute. This value is calculated by subtracting the job's time used from its time limit.

  • TimeLimit: Time limit for the job.

  • TimeUsed: Time used by the job.

  • EndTime: The time of job termination, actual or expected.

There are lots of other columns that can be defined including ones related to resources (nodes, cores, memory) that have been specifically allocated.

Submission from your Current Working Directory

Remember from Linux, that your current location is your Current Working Directory - abbreviated to CWD.

By default Slurm will look for files, and write output, from the folder you submitted your script from i.e. your CWD.

In the example above, if I called sbatch run.sh from ~/intro_to_modules/ then the Python script should reside within this folder. Any output will be written into this folder.

Within the submission script you can define paths (absolute/relative) to other locations.

You can submit a script from any of your allowed locations /home, /project and/or /gscratch.

But you need to manage and describe paths to scripts, data, output appropriately.

Submit Jobs: scancel: Cancel?

If you have submitted a job, and for what ever reason you want/need to stop it early, then use scancel <job-id>.

This will stop the job at its current point within the computation, and return any associated resources back to the cluster.

[]$ sbatch run.sh
Submitted batch job 13526341
[]$ squeue -u <username>
             JOBID PARTITION     NAME       USER ST       TIME  NODES NODELIST(REASON)
          13526341     moran   run.sh <username>  R       0:03      1 m233
[]$ scancel 13526341
[]$ squeue -u <username>
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)

[]$ cat slurm-13526341.out
SLURM_JOB_ID: 13526341
Start: 03/22/24 09:40:09
Python version: 3.10.6 (main, Oct 17 2022, 16:47:32) [GCC 12.2.0]
Version info: sys.version_info(major=3, minor=10, micro=6, releaselevel='final', serial=0)
slurmstepd: error: *** JOB 13526341 ON m233 CANCELLED AT 2024-03-22T09:40:17 ***

If you know your job no longer needs to be running please cancel it to free up resources - be a good cluster citizen.

Submit Jobs: sacct: What happened?

Use the sacct command to view your jobs that have completed.

By default this will only list jobs from mid night of the that day.

View the -S, --starttime (and -E, --endtime=<end_time>) options to understand how to define a start (and end) time to configure different date/time intervals.

It too has a --format option allowing you to display additional columns:

[]$ sacct -u <username> -X
JobID           JobName  Partition    Account  AllocCPUS      State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
13526337     interacti+      moran arccanetr+          1    TIMEOUT      0:0
13526338     interacti+      moran arccanetr+          1  COMPLETED      0:0
13526340         run.sh      moran arccanetr+          1  COMPLETED      0:0
13526341         run.sh      moran arccanetr+          1 CANCELLED+      0:0

[]$ sacct -u <username> --format="JobID,Partition,nnodes,NodeList,NCPUS,ReqMem,State,Start,Elapsed" -X
JobID         Partition   NNodes        NodeList      NCPUS     ReqMem      State               Start    Elapsed
------------ ---------- -------- --------------- ---------- ---------- ---------- ------------------- ----------
13526337          moran        1            m233          1      1000M    TIMEOUT 2024-03-22T09:35:25   00:01:28
13526338          moran        1            m233          1      1000M  COMPLETED 2024-03-22T09:37:41   00:00:06
13526340          moran        1            m233          1      1000M  COMPLETED 2024-03-22T09:38:35   00:01:01
13526341          moran        1            m233          1      1000M CANCELLED+ 2024-03-22T09:40:08   00:00:09

For more information see the main Slurm sacct page and use:

[]$ sacct --help
[]$ man sacct

Submit Jobs: sbatch: Options

Here are some of the common options available:

[]$ sbatch –-help
#SBATCH --account=<prohect-name>        # Required: account/time
#SBATCH --time=72:00:00
#SBATCH --job-name=workshop             # Job name: Help to identify when using squeue.
#SBATCH --nodes=1                       # Options will typically have defaults.
#SBATCH --tasks-per-node=1              # Request resources in accordance to how you want
#SBATCH --cpus-per-task=1               # to parallelize your job, type of hardware partition
#SBATCH --partition=mb                  # and if you require a GPU.
#SBATCH --gres=gpu:1
#SBATCH --mem=100G                      # Request specific memory needs.
#SBATCH --mem-per-cpu=10G
#SBATCH --mail-type=ALL                 # Get email notifications of the state of the job.
#SBATCH --mail-user=<email-address>
#SBATCH --output=<prefix>_%A.out        # Define a named output file postfixed with the job id.

  • Both salloc and sbatch have 10s of options, in both short and long form.

  • Some options mimic functionality, for example -G/--gpus can work the same as --gres=gpu:1.

  • Please consult the command --help and man pages and/or web links to discover further options not listed.

Submit Jobs: sbatch: Options: Applied to Example

Let’s take the previous example, and add some of the additional options:

#!/bin/bash                               
#SBATCH --account=<project-name>
#SBATCH --time=10:00
#SBATCH --reservation=<reservation-name>

#SBATCH --job-name=pytest
#SBATCH --nodes=1                       
#SBATCH --cpus-per-task=1               
#SBATCH --mail-type=ALL                 
#SBATCH --mail-user=<email-address>
#SBATCH --output=slurms/pyresults_%A.out      

echo "SLURM_JOB_ID:" $SLURM_JOB_ID        # Can access Slurm related Environment variables.
start=$(date +'%D %T')                    # Can call bash commands.
echo "Start:" $start
module purge
module load gcc/13.2.0 python/3.10.6      # Load the modules you require for your environment.
python python01.py                        # Call your scripts/commands.
sleep 1m
end=$(date +'%D %T')
echo "End:" $end

Notice:

  • I’ve given the job a specific name and have requested email notifications.

  • The output is written to a sub folder slurm/ with a name of the form pytest_<jobid>.out

Extended Example: What Does the Run look Like?

With the above settings (written into a file called run.sh), a submission will look something like the following:

 Example Flow and Output:
# Submit the job:
[intro_to_modules]$ sbatch run.sh
Submitted batch job 1817260

# Notice the NAME is now 'pytest'
[intro_to_modules]$ squeue -u salexan5
             JOBID PARTITION     NAME       USER ST       TIME  NODES NODELIST(REASON)
           1817259        mb   pytest <username>  R       0:58      1 mbcpu-002

# I can view the output while the job is running.
# The output is now in a sub folder under slurm/
# It also uses the name 'pyresults_<job_id>.out'
[intro_to_modules]$ cat slurms/pyresults_1817260.out
SLURM_JOB_ID: 1817260
Start: 08/14/24 14:48:38
Python version: 3.10.6 (main, Apr 30 2024, 11:23:04) [GCC 13.2.0]
Version info: sys.version_info(major=3, minor=10, micro=6, releaselevel='final', serial=0)

[intro_to_modules]$ squeue -u <username>
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)

[intro_to_modules]$ cat slurms/pyresults_1817260.out
SLURM_JOB_ID: 1817260
Start: 08/14/24 14:48:38
Python version: 3.10.6 (main, Apr 30 2024, 11:23:04) [GCC 13.2.0]
Version info: sys.version_info(major=3, minor=10, micro=6, releaselevel='final', serial=0)
End: 08/14/24 14:49:38

In my inbox, I also received two emails with the subjects:

  1. medicinebow Slurm Job_id=1817260 Name=pytest Began, Queued time 00:00:00

    1. This will have no text within the email body.

  2. medicinebow Slurm Job_id=1817260 Name=pytest Ended, Run time 00:01:01, COMPLETED, ExitCode 0

    1. The body of this email contained the seff results.

 

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Intro to Job Scheduling

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Slurm: Workflows and Best Practices

 

 

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