title	teaching	exercises
Submitting a Job	40	7

:::::::::::::::::::::::::::::::::::::: questions

How do I launch a program to run on a compute node in the cluster?
How do I capture the output of a program that is run on a node in the cluster?
How do I change resource requested or time-limit

::::::::::::::::::::::::::::::::::::::::::::::::

::::::::::::::::::::::::::::::::::::: objectives

Submit a simple script to the cluster.
Monitor the execution of jobs using command line tools.
Inspect the output and error files of your jobs. ::::::::::::::::::::::::::::::::::::::::::::::::

Running a Batch Job

The most basic use of the scheduler is to run a command non-interactively. Any command (or series of commands) that you want to run on the cluster is called a job, and the process of using a scheduler to run the job is called batch job submission.

Basic steps are:

Develop a submission script, a text file of commands, to perform the work
Submit the script to the batch system with enough resource specification
Monitor your jobs
Check script and command output
Evaluate your job

In this episode, we will focus on the first 4 steps.

Preparing a job script

In this case, the job we want to run is a shell script -- essentially a text file containing a list of Linux commands to be executed in a sequential manner.

Our first shell script will have three parts:

On the very first line, add #!/bin/bash. The #! (pronounced "hash-bang" or "shebang") tells the computer what program is meant to process the contents of this file. In this case, we are telling it that the commands that follow are written for the command-line shell.
Anywhere below the first line, we'll add an echo command with a friendly greeting. When run, the shell script will print whatever comes after echo in the terminal.
- echo -n will print everything that follows, without ending the line by printing the new-line character.
On the last line, we'll invoke the hostname command, which will print the name of the machine the script is run on.

nano example-job.sh

#!/bin/bash
echo -n "This script is running on "
hostname

::: challenge

Exercise 1: Run example-job.sh

Run the script. Does it execute on the cluster or just our login node?

:::::: solution

bash example-job.sh

This script is running on slurm-login01.hpc.wehi.edu.au

slurm-login01.hpc.wehi.edu.au may change depending on which node you ssh'ed into to run the script.

:::::: :::

This script ran on the login node, but we want to take advantage of the compute nodes, we need the scheduler to queue up example-job.sh to run on a compute node.

Submit a batch job

To submit this task to the scheduler, we use the sbatch command. This creates a job which will run the script when dispatched to a compute node. The queuing system identified which compute nose is available to perform the work.

sbatch example-job.sh

Submitted batch job 11783863

And that's all we need to do to submit a job. Our work is done -- now the scheduler takes over and tries to run the job for us.

Monitor your batch job

While the job is waiting to run, it goes into a list of jobs called the queue. To check on our job's status, we check the queue using the command squeue -u $USER.

squeue -u $USER

     JOBID    PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
    11783909   regular example- iskander  R       0:06      1 sml-n02

ST is short for status and can be R (RUNNING), PD (PENDING), CA (CANCELLED), or CG (COMPLETING). If the job is stuck in pending, REASON column will reflect the reason, which can be one of the following:

Priority: There are higher priority jobs than yours
Resources: Job is waiting for resources
Dependency: This job is dependent on another and it is waiting for that other job to complete
QOSMaxCpuPerUserLimit: User has used CPUs limit of partition already
QOSMaxMemPerUserLimit: User has used memory limit of partition already

Where's the Output?

On the login node, this script printed output to the terminal -- but now, when the job has finished, nothing was printed to the terminal. Cluster job output is typically redirected to a file in the directory you launched it from. By default, the output file is called slurm-<jobid>.out

Use ls to find and cat to read the file.

::: challenge

Exercise 2: Get output of running example-job.sh in Slurm

List files in your currrent working directory and look for a file Slurm-11783909.out, 11783909 will change according to your job id. And cat the file to see output.

What is the hostname of your job?

:::::: solution

cat slurm-11783863.out

This script is running on sml-n02.hpc.wehi.edu.au

:::::: :::

Customising a Job

The job we just ran used all of the scheduler's default options. In a real-world scenario, that's probably not what we want. Chances are, we will need more cores, more memory, more/less time, among other special considerations. To get access to these resources we must customize our job script.

The default parameters on Milton is 2 CPU, 10MB Ram, 48-hours time-limit and runs on the regular partition

After your job has completed, you can get details of the job using sacct command.

sacct -j 11783909 -ojobid,jobname,ncpus,reqmem,timelimit,partition -X

JobID           JobName      NCPUS     ReqMem  Timelimit  Partition
------------ ---------- ---------- ---------- ---------- ----------
11783909     example-j+          2        10M 2-00:00:00    regular

We can change the resource specification of the job by two ways:

Adding extra options to the sbatch command

sbatch --job-name hello-world --mem 1G --cpus-per-task 1 --time 1:00:00 example-job.sh

Modifying the submission script

#!/bin/bash
#SBATCH --job-name hello-world
#SBATCH --mem 1G
#SBATCH --cpus-per-task 1
#SBATCH  --time 1:00:00
echo -n "This script is running on "
hostname

Submit the job and monitor its status:

$ sbatch example-job.sh
Submitted batch job 11785584
$ squeue -u $USER
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
          11785584   regular hello-wo iskander  R       0:01      1 sml-n20

Comments in shell scripts (denoted by #) are typically ignored, but there are exceptions. Schedulers like SLURM have a special comment used to denote special scheduler-specific options. Though these comments differ from scheduler to scheduler, SLURM's special comment is #SBATCH. Anything following the #SBATCH comment is interpreted as an instruction to the scheduler. These SBATCH commands are also know as SBATCH directives.

Remember Slurm directives must be at the top of the script, below the "hash bang". No command can come before them, nor in between them.

Resource Requests

One thing that is absolutely critical when working on an HPC system is specifying the resources required to run a job. This allows the scheduler to find the right time and place to schedule our job. As we have seen before, if you do not specify requirements, you will be stuck with default resources, which is probably not what you want.

The following are several key resource requests:

--time or -t : Time (wall-time) required for a job to run. The part can be omitted. default = 48 hours on the regular queue
--mem: Memory requested per node in MiB. Add G to specify GiB (e.g. 10G). There is also --mem-per-cpu. default = 10M
--nodes or -N: Number of nodes your job needs to run on. default = 1
--cpus-per-task or -c Number of CPUs for each task. Use this for threads/cores in single-node jobs.
--partition or -p: the partition in which your job is placed. default = regular
--ntasks or -n : Number of tasks (used for distributed processing, e.g. MPI workers). There is also --ntasks-per-node. default = 1
--gres: special resources such as GPUs. To specify gpus, use gpu::, for example, gres=gpu:P100:1, and you must specify the correct queue (gpuq or gpuq_large)

Note that just requesting these resources does not make your job run faster, nor does it necessarily mean that you will consume all of these resources. It only means that these are made available to you. Your job may end up using less memory, or less time, or fewer nodes than you have requested, and it will still run. It's best if your requests accurately reflect your job's requirements.

In summary, the main parts of a SLURM submission script

1. #! line:

This must be the first line of your SBATCH/Slurm script.

#!/bin/bash

2. Resource Request:

This is to set the amount of resources required for the job.

#SBATCH --job-name=TestJob
#SBATCH --time=00:10:00
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=500M

3. Job Steps

Specify the list of tasks to be carried out. It may include an initial load of all the modules that the project depends on to execute. For example, if you are working on a python project, you’d definitely require the python module to run your code.

module load python
echo "Start process"
hostname
sleep 30
python myscript.py
echo "End"

All the next exercises will use scripts saved in the exercise folder which you should have moved to your current directory.

::: challenge

Exercise 3: Setting appropriate wall-time

List then run job1.sh script in the batch system. What is the output? Is there an error? How to fix it?

#!/bin/bash
#SBATCH -t 00:01:00 

echo -n "This script is running on "
sleep 80 # time in seconds
hostname

:::::: solution

After 1 minute the job ends and the output is similar to this

cat slurm-11792811.out

This script is running on Slurmstepd: error: *** JOB 11792811 ON sml-n24 CANCELLED AT 2023-05-13T20:41:10 DUE TO TIME LIMIT ***

To fix it, change the script to

#!/bin/bash
#SBATCH -t 00:01:20 # timeout in HH:MM

echo -n "This script is running on "
sleep 70 # time in seconds
hostname

Try running again.

:::::: :::

Resource requests are typically binding. If you exceed them, your job will be killed.

The job was killed for exceeding the amount of resources it requested. Although this appears harsh, this is actually a feature. Strict adherence to resource requests allows the scheduler to find the best possible place for your jobs. Even more importantly, it ensures that another user cannot use more resources than they've been given. If another user messes up and accidentally attempts to use all of the cores or memory on a node, Slurm will either restrain their job to the requested resources or kill the job outright. Other jobs on the node will be unaffected. This means that one user cannot mess up the experience of others, the only jobs affected by a mistake in scheduling will be their own.

::: challenge

Exercise 4: Setting appropriate Slurm directives

List then run job2.sh script in the batch system. What is the output? Is there an error? How can you fix it?

#!/bin/bash
#SBATCH -t 00:01:00
#SBATCH --gres gpu:P100:1
#SBATCH  --mem 1G
#SBATCH --cpus-per-task 1

#This is  a job that needs GPUs
echo -n "This script is running on "
hostname

:::::: solution

When submitting to Slurm, you get an error

sbatch job2.sh

sbatch: error: Batch job submission failed: Requested node configuration is not available

This is because a GPU was requested without specifying the correct GPU partition, so the regular partition was used which has no GPUs. To fix it, change the script to

#!/bin/bash
#SBATCH -t 00:01:00
#SBATCH -p gpuq
#SBATCH --gres gpu:P100:1
#SBATCH  --mem 1G
#SBATCH --cpus-per-task 1

#This is  a job that needs GPUs
echo -n "This script is running on "
hostname

Try running again.

:::::: :::

::: challenge

Exercise 5

Make alignment job (job3.sh) work.

:::::: solution

Add the correct Slurm directives to the start of the script

#SBATCH --job-name=Bowtie-test.Slurm
#SBATCH --ntasks=1
#SBATCH -t 0:15:00
#SBATCH --mem 20G

:::::: :::

::: challenge

Exercise 6: Run job3.sh again and monitor progress on the node .

Run job3.sh again and monitor progress on the node. You can do this by sshing to the node and running top.

:::::: solution

Run the job
Get which node it is running on from squeue -u $USER
ssh into the node
use top -u $USER

:::::: :::

We can have a live-demo on how to monitor a running job on the compute node, using top, iotop and nvtop for GPU nodes

Cancelling a Job

Sometimes we'll make a mistake and need to cancel a job. This can be done with the scancel command. Let's submit a job and then cancel it using its job number.

sbatch example-jobwithsleep.sh
Submitted batch job 11785772
$ squeue -u $USER
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
          11785772   regular example- iskander  R       0:10      1 sml-n20
$ scancel 11785772
$ squeue -u $USER
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
$

We can also cancel all of our jobs at once using the -u option. This will delete all jobs for a specific user (in this case, yourself). Note that you can only delete your own jobs.

Try submitting multiple jobs and then cancelling them all.

::: challenge

Exercise 7: Submit multiple jobs and then cancel them all.

:::::: solution

sbatch job1.sh
sbatch job1.sh
sbatch job1.sh
sbatch job1.sh

Check what you have in the queue

squeue -u $USER

             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
          11792908   regular  job1.sh iskander  R       0:13      1 sml-n23
          11792909   regular  job1.sh iskander  R       0:13      1 sml-n23
          11792906   regular  job1.sh iskander  R       0:16      1 sml-n23
          11792907   regular  job1.sh iskander  R       0:16      1 sml-n23

Cancel the jobs

$ scancel -u $USER

Recheck the queue

$ squeue -u $USER
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)

And the queue is empty.

:::::: :::

You can check how busy the queue is through the Milton dashboards

Slurm Event notification

You can use --mail-type and --mail-user to set SLURM to send you emails when certain events occurs, e.g. BEGIN, END, FAIL, REQUEUE, ALL

#SBATCH --mail-type BEGIN
#SBATCH --mail-user iskander.j@wehi.edu.au

Adding the above two lines to a submission script will make Slurm send me an email when my job starts running.

Slurm Output files

By default both standard output and standard error are directed to a file of the name "slurm-%j.out", where the "%j" is replaced with the job id. The file will be saved in the submission directory as we saw before. You can choose where the output files is saved and also separate standard output from standard error using --output and --error

--output can be used to change the standard output filename and location.
--error can be used to specify where the standard output file shall be saved. If not specified, it will be directed to the standard output file.

In the file names you can use:

%j for job id
%N for host name
%u for user name
%x for job name

For example, running the following

sbatch --error=/vast/scratch/users/%u/slurm%j_%N_%x.err --output=/vast/scratch/users/%u/slurm%j_%N_%x.out job1.sh will write error to slurm12345678_sml-n01_job1.sh.err and output to slurm12345678_sml-n01_job1.sh.out in the directory /vast/scratch/users/<username>, i.e. the following will be created:

a standard output file /vast/scratch/users/iskander.j/slurm11795785_sml-n21_job1.sh.out and
an error files /vast/scratch/users/iskander.j/slurm11795785_sml-n21_job1.sh.err.

Bonus QoS and preemption

Before we move to our next lesson, let's breiflt talk about the bonus QoS. We have discussed before the limits of each partition. So what if you have run many jobs and hit the limit on the regular partition but when you look at the dashboards you observe that there are still free resources that can be used?

Can you make use of them as long as no one else needs them? Yes you can!

You can use --qos=bonus.

This will run your job in a preemptive mode, which means other users can terminate your job, if Slurm couldn't find other resources for their jobs and they are using the normal QoS.

This is useful for jobs that can be resumed or restart is not an issue.

::::::::::::::::::::::::::::::::::::: keypoints

sbatch is used to submit the job
squeue is used to list jobs in the Slurm queue
- passing the -u <username> option will show jobs for just that user.
sacct is used to show job details
#SBATCH directives are used in submission scripts to set Slurm directives
Setting up job resources is a challenge and you might not get the first time

::::::::::::::::::::::::::::::::::::::::::::::::

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06-submit.md

06-submit.md

Running a Batch Job

Preparing a job script

Exercise 1: Run example-job.sh

Submit a batch job

Monitor your batch job

Where's the Output?

Exercise 2: Get output of running example-job.sh in Slurm

Customising a Job

Resource Requests

Exercise 3: Setting appropriate wall-time

Exercise 4: Setting appropriate Slurm directives

Exercise 5

Exercise 6: Run job3.sh again and monitor progress on the node .

Cancelling a Job

Exercise 7: Submit multiple jobs and then cancel them all.

Slurm Event notification

Slurm Output files

Bonus QoS and preemption

Files

06-submit.md

Latest commit

History

06-submit.md

File metadata and controls

Running a Batch Job

Preparing a job script

Exercise 1: Run example-job.sh

Submit a batch job

Monitor your batch job

Where's the Output?

Exercise 2: Get output of running example-job.sh in Slurm

Customising a Job

Resource Requests

Exercise 3: Setting appropriate wall-time

Exercise 4: Setting appropriate Slurm directives

Exercise 5

Exercise 6: Run job3.sh again and monitor progress on the node .

Cancelling a Job

Exercise 7: Submit multiple jobs and then cancel them all.

Slurm Event notification

Slurm Output files

Bonus QoS and preemption