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Using APSIM on the HPC System

To use the APSIM software on the HPC, you will need the following:

  • Access to the HPC system (Contact HPC support if you need an account created).
  • A connection to the HPC System, see Connecting to the Isaac Newton Cluster for information on how to do this.
  • If you plan on using running APSIM in a Graphical environment, you will require a graphical interface to the HPC system.  See Graphical Connection to the HPC System for information on how to do this.

Sample APSIM HPC Scheduler script

By default, when running anything on the CQU HPC systems, you should summit your programs and simulations to the HPC Scheduler.  The Scheduler will check if the requested resources are available.  If they are available, they will execute the job on one of the available compute resources, if no resources are available, the request is "queued", until resources become available.

Thus, running a program interactively on a Login node is perfectly acceptable when developing programs and/or running short tests.  When you wish to execute jobs, especially jobs that run for a reasonable amount of time, you should submit each program to execute on the compute nodes to be run.

If you execute large jobs on a "Login" node, this will slow down usability and will impact other users performance.

The following samples provides details on how to submit a single APSIM job to be executed on the CQUniversity HPC Facilities.

The variable $PBS_O_WORKDIR indicates the directory where the PBS (HPC Scheduler) script file is located and launched from. Replace the example email address provided to your email address. Change the "program name" to the name of the program executable file that you would like to be run on the HPC system.

Note all "[...]" are variables that require defining.

###### Select resources #####
#PBS -N [Job Name]
#PBS -l ncpus=[Number of CPU's requested]
#PBS -l mem=[amount of memory requested]

#### Output File #####
#PBS -o $PBS_O_WORKDIR/[Output File Name].out

#### Error File #####
#PBS -e $PBS_O_WORKDIR/<[Error File Name].err

##### Queue #####
#pbs -q workq

##### Mail Options #####
#PBS -m abe
#PBS -M [your email address]

##### Change to current working directory #####
cd $PBS_O_WORKDIR

##### Execute Program #####
ApsimModel.exe [APSIM File Name].apsim

Real Example

###### Select resources #####
#PBS -N apsim_job_1
#PBS -l ncpus=1
#PBS -l mem=1g

#### Output File #####
#PBS -o $PBS_O_WORKDIR/apsim_job_1.out

#### Error File #####
#PBS -e $PBS_O_WORKDIR/apsim_job_1.err

##### Queue #####
#pbs -q workq

##### Mail Options #####
#PBS -m abe
#PBS -M j.bell@cqu.edu.au

##### Change to current working directory #####
cd $PBS_O_WORKDIR

##### Execute Program #####
ApsimModel.exe BOMPPD5_maize.apsim

Multiple APSIM Job Submission

If you wish to execute multiple 'APSIM' jobs, it is suggest to have a look at the following information guides:

Which "Graphical" connection site should I use?

On the CQUniversity HPC facilities, we provide a number of options when connecting to the HPC system using a graphical user interface.

Using the "Strudel software - see Graphical Connection to the HPC System for instructions", you have a number of selection options.

  • HPC Login Node - Isaac;
  • HPC Login Node - Newton; or
  • GPU Interactive Session;

Users are advised to use one of the "Login Node options", if they are developing a model, or processing a quick model.  If users plan on running long processing jobs, they should select the GPU Interactive Session option.

The benefit for using the "GPU Interactive Session" option, is that the processing occurs on the HPC GPU Compute node, thus not overloading the login nodes.  Additionally, the jobs may be processed faster because of the use of the on-board GPU (Graphical Processing Units) one these specialised Compute nodes.  If you are using "GPU Interactive Session" option, ensure you select the "Stop the Desktop" option, when your modelling/processing has been completed.  This will ensure the resources are freed up for other users to use.