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.

You’re there doing the work.

Suitable for developing and testing over a few hours.

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[]$ salloc: Job 13526337 has exceeded its time limit and its allocation has been revoked.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.

[]$ 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

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=arccanetrain<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:" $start
module loadpurge
module load gcc/1214.2.0 python/3.10.6      # Load the modules you require for your environment.
python python01.py                        # Call your scripts/commands.
sleep 1m
end=$(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.

The squeue command only shows pending and running jobs.

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

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 arcc-t05<username> --Format="Account,UserName,JobID,SubmitTime,StartTime,TimeLeft"
[salexan5@mblog1 ~]$ squeue -u vvarenth --Format="Account,UserName,JobID,SubmitTime,StartTime,TimeLeft"
ACCOUNT             ACCOUNT             USER                JOBID               SUBMIT_TIME         START_TIME          TIME_LEFT
arccantrain<project-name>         arcc-t05  <username>          1795458             2024-08-14T10:31:07 2024-08-14T10:31:09 6-04:42:51
arccantrain<project-name>      <username>   arcc-t05            1795453             2024-08-14T10:31:06 2024-08-14T10:31:07 6-04:42:49
arccantrain<project-name>      <username>   arcc-t05            1795454             2024-08-14T10:31:06 2024-08-14T10:31:07 6-04:42:49
...

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.

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, Sep  3 2024, 15:13:56) [GCC 14.2.0]
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.

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    JOBID PARTITION     NAME1     USER ST1000M CANCELLED+ 2024-03-22T09:40:08   00:00:09

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

[]$ sacct 

--help
[]$ 

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         1  COMPLETED      0:0 13526340    # Request specific memory needs.
run.sh   #SBATCH --mem-per-cpu=10G
#SBATCH --mail-type=ALL   moran arccanetr+          1  COMPLETED # Get email notifications of 0:0the 13526341state of the job.
#SBATCH --mail-user=<email-address>
   run.sh#SBATCH --output=<prefix>_%A.out      moran arccanetr+ # Define a named output file postfixed with the 1 CANCELLED+      0:0

# Lots more information
[]$ sacct --help
[]$ man sacct

# Display more columns:
[]$ sacct -u arcc-t05 --format="JobID,Partition,nnodes,NodeList,NCPUS,ReqMem,State,Start,Elapsed" -X
JobIDjob 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.

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

#!/bin/bash             Partition   NNodes        NodeList      NCPUS 
#SBATCH --account=<project-name>
 ReqMem      State #SBATCH --time=10:00
#SBATCH --reservation=<reservation-name>

#SBATCH --job-name=pytest
#SBATCH --nodes=1              Start    Elapsed ------------ ---------- -------- --------------- ---------- ---------- ---------- ------------------- ----------
13526337     
#SBATCH --cpus-per-task=1               
#SBATCH --mail-type=ALL                 
#SBATCH --mail-user=<email-address>
#SBATCH --output=slurms/pyresults_%A.out      

echo "SLURM_JOB_ID:" $SLURM_JOB_ID       moran # Can access Slurm related Environment  1  variables.
start=$(date +'%D %T')          m233          1# Can call bash commands.
echo 1000M"Start:" $start
module purge
TIMEOUT 2024-03-22T09:35:25   00:01:28
13526338module load gcc/14.2.0 python/3.10.6      # Load the modules you require moranfor your environment.
python  python01.py   1            m233         # 1Call your scripts/commands.
sleep 1m
 1000M  COMPLETED 2024-03-22T09:37:41   00:00:06
13526340          moran        1            m233          1      1000M  COMPLETED 2024-03-22T09:38:35   00:01:01
13526341          moranend=$(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

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

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.