Running jobs

An HPC cluster is a multi-user system. This implies that your computations run on a part of the cluster that will be temporarily reserved for you by the scheduler.

Warning

Do not run computationally intensive tasks on the login nodes! These nodes are shared among all active users, so putting a heavy load on those nodes will annoy other users.

Although you can work interactively on an HPC system, most computations are performed in batch mode.

The workflow is straightforward:

1. Create a job script.
2. Submit it as a job to the scheduler.
3. Wait for the computation to run and finish.

Job script

A job script is essentially a Bash script, augmented with information for the scheduler. As an example, consider a file hello_world.pbs as below.

#!/usr/bin/env bash

#PBS -l nodes=1:ppn=1
#PBS -l walltime=00:05:00
#PBS -l pmem=1gb

cd $PBS_O_WORKDIR

module purge
module load Python/3.7.2-foss-2018a

python hello_world.py

We discuss this script line by line.

• Line 1 is a she-bang that indicates that this is a Bash script.
• Lines 3-5 inform the scheduler about the resources required by this job.
  • It requires a single node (nodes=1), and a single core (ppn=1) on that node.
  • It will run for at most 5 minutes (walltime=00:05:00).
  • It will use at most 1 GB of RAM (pmem=1gb).
• Line 7 changes the working directory to the directory in which the job will be submitted (that will be the value of the $PBS_O_WORKDIR environment variable when the job runs).
• Lines 9 and 10 set up the environment by loading the appropriate modules.
• Line 12 performs the actual computation, i.e., running a Python script.

Warning

When running on KU Leuven/UHasselt and Tier-1 infrastructure make sure to specify a credit account as part of your job script, if not, your job will not run.

#PBS -A lp_example

For more information, see credit system basics.

Every job script has the same basic structure.

Note

Although you can use any file name extension you want, it is good practice to use .pbs since that allows support staff to easily identify your job script.

More information is available on

• specifying job resources,
• specifying job names, output files and notifications,
• using the credit system (KU Leuven/UHasselt infrastructure and Tier-1 only),
• using the module system.

Submitting and monitoring a job

Once you have created your job script, and transferred all required input data if necessary, you can submit your job to the scheduler

$ qsub hello_world.pbs
205814.leibniz

The qsub returns a job ID, an unique identifier that you can use to manage your job. Only the number, i.e., 205814 is significant.

Once submitted, you can monitor the status of your job using the qstat command.

$ qstat
Job ID                    Name             User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
205814.leibniz            hello_world.pbs  vsc30140               0 Q q1h

The status of your job is given in the S column. The most common values are given below.

status	meaning
Q	job is queued, i.e., waiting to be executed
R	job is running
C	job is completed, i.e., finished.

More information is available on

• submitting and monitoring your jobs
  • Submitting your job: qsub
    • Starting interactive jobs
  • Viewing your jobs in the queue
    • qstat
    • showq
    • A note on queues
  • Getting detailed information about a job
    • qstat
    • checkjob
  • Deleting a queued or running job: qdel
  • Getting a start time estimate for your job: showstart
  • Checking free resources for a short job: showbf

Job output

By default, the output of your job is saved to two files.

<job_name>.o<jobid>

This file contains all text written to standard output, as well as some information about your job.

<job_name>.e<jobid>

This file contains all text written to standard error, if any. If your job fails, or doesn’t produce the expected output, this is the first place to look.

For instance, for the running example, the output file would be hello_world.pbs.o205814 and contains

===== start of prologue =====
Date : Mon Aug  5 14:50:28 CEST 2019
Job ID : 205814
Job Name : hello_world.pbs
User ID : vsc30140
Group ID : vsc30140
Queue Name : q1h
Resource List : walltime=00:05:00,nodes=1:ppn=1,neednodes=1:ppn=1
===== end of prologue =======

hello world!

===== start of epilogue =====
Date : Mon Aug  5 14:50:29 CEST 2019
Session ID : 21768
Resources Used : cput=00:00:00,vmem=0kb,walltime=00:00:02,mem=0kb,energy_used=0
Allocated Nodes : r3c08cn1.leibniz
Job Exit Code : 0
===== end of epilogue =======

Lines 1 through 10 are written by the prologue, i.e., the administrative script that runs before your job script. Similarly, lines 12 though 19 are written by the epilogue, i.e., the administrative script that runs after your job script.

Line 11 is the actual output of your job script.

Note

The format of the output file differs slightly from cluster to cluster, although the overall structure is the same.

Troubleshooting

• Why doesn't my job start immediately?
• Why does my job fail after a successful start?
  • You ran out of time
  • You ran out of disk space
  • You ran out of memory (RAM)

Advanced topics

• Monitoring memory and CPU usage of programs, which helps to find the right parameters to improve your specification of the job requirements.
• worker quick start: To manage lots of small jobs on a cluster. The cluster scheduler isn’t meant to deal with tons of small jobs. Those create a lot of overhead, so it is better to bundle those jobs in larger sets.
• The Checkpointing framework can be used to run programs that take longer than the maximum time allowed by the queue. It can break a long job in shorter jobs, saving the state at the end to automatically start the next job from the point where the previous job was interrupted.