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This page is intended as a quick introduction for new users submitting their first job to the HPRC Cluster.Â
In the typical work flow the user:
- Logs into zodiac.hpc.jcu.edu.au
- Prepares a submission script for their jobs
- Submits their jobs to the Job Scheduler
- Monitors their jobs
- Collects the output of their jobs.
A few things that new users should be aware of:
- Typically, jobs are not run in an interactive manner, except when:
- users are running small one off jobs
- evaluating the resources required for bigger jobs
- using graphical applications like MATLAB
- Examples of interactive jobs:
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- HPRC Cluster software is not run in a window on their desktop, neither is it launched by clicking on it in a network drive.
- Users need to log into the cluster and inform the job scheduler about their job and it will run it when it can.
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Logging In
The first step in using the HPRC Cluster is to log in to the login node - zodiac.hpc.jcu.edu.au
.
 Logging into the Cluster
The HPC interactive nodes are accessible via the server named zodiac.hpc.jcu.edu.au. See the relevant tabs below of instructions on how to log in to zodiac. Zodiac is a linux based system. To learn more about the linux shell, see the
Software Carpentry Unix Shell tutorials.
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-
 Install PuTTY
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Starting PuTTY will show this window:
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Enter the hostname (zodiac.hpc.jcu.edu.au) and the port 8822
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The default port for ssh is port 22, which you can use if you are accessing the cluster from on campus, however if you are accessing it from off campus you need to use port 8822.
- Then you will be prompted for your username and password, use your standard JCU credentials (username and password)
- Open the Terminal application:
- In the Terminal window run the ssh command:
ssh <username>@zodiac.jcu.edu.auÂ
(add -p 8822
if you are connecting from outside the JCU network) and you will be asked for your password
- You are now logged in to the HPC interactive node.Â
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Software Packages
The HPRC Cluster uses environment modules to manage the available software packages. This allows multiple versions of the same software to be installed without interfearing with each other. To enable the environment module
system the following command needs to be executed on the command line:
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The software that is available on the HPRC clusted is listed here: HPRC User Software. Alternately you can query the software available on the cluster with the following commands:
Command | Result |
---|
module avail
| A list of available software is displayed |
module help <software>
| Version number and brief synopsis is displayed for <software> |
 Example "module avail" run on the Thu Mar 6 11:19:21 EST 2014
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Running Jobs
To run a job on the cluster create a shell script containing the PBS Directives containing the information required by the scheduler to schedule the job, and the job commands.
Example: paup witth the ML_analysis.nex sample file
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Other Examples
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Job Resources
It is important to match resources requested with the PBS Directives in your script and the resource usage of your job. There can be consequences for incorrectly specifiying these resource requirements
- Walltime: your job can be killed if it exceeds the specified wall time.
- Memory: overusing memory can cause the compute node's memory to be pushed into swap space, slowing down all jobs on that node. This has also killed compute nodes in the past, destroying
- CPUs: using more cpus than requested can slow down all jobs running on that node.
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Furthor Reading
- HPRC Cluster Explained
- HPRC Cluster Job Management Explained
- HPRC PBS script files