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This document is loosely modeled after “A Beginner's Guide to the Barrine Linux HPC Cluster” written by Dr. David Green (HPC manager, UQ) , ICE Cluster User Guide written by Bryan Hughes and Wiki pages of the City University of New York (CUNY) HPC Center (see reference for further details).

2. Gowonda Overview

2.1 Hardware

2.1.1 Hardware (2024 upgrade) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

2.1.2 Hardware (2019 upgrade) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

(n001-n004)

(n005-n009,n010-n012,n019)

192GB

2x Intel Xeon 6140 

NVIDIA A100 80GB PCIe

(n013-n018)

2.2 Old Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

(n001-n004)

(n005-n009,n010-n012,n019)

(n013-n018)

(n020-n023)

(n031-n038)

(n039-n042)

(n044-n047)

(aspen01-aspen12)

Please note that each of the Extra Large nodes (n020,n021, n022 and n023) have 2 nvidia tesla C-2050 GPU cards.

(n020-n023)

Special Administrative Nodes (Not used for computing purposes)

More information about the Intel(R) Xeon(R) CPU X5650 processor can be obtained here.

In addition to the above, there is a special windows HPC node.

n029

Instructions for using the Windows HPC is given in a separate user guide

2.

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3 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

The operating system on gowonda is RedHat Enterprise Linux (RHEL) 6.1 updated with SGI foundation-2.4 suite and accelerate-1.2 support package. The queuing system used is PBS Pro 11 . The exception is the Windows HPC node which runs Windows 2008 R2 with Windows HPC pack and Windows HPCS job scheduler. Gowonda has the following compilers and parallel library software. Much more detail on each can be found below.

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The following third party applications are currently installed or will be installed shortly. The Gowonda HPC Center staff will be happy to work with any user interested in installing additional applications, subject to meeting that application's license requirements.

module load cuda/4.0

module load gaussian/g03

module load gaussian/g09

module load gromos/1.0.0

module load matlab/2009b,module load matlab/2011a 

module load python/2.7.1

module load python/2.7.1

module load R/2.13.0

module load python/2.7.1

The following graphics, IO, and scientific libraries are also supported.

 module load ATLAS/3.9.39

  module load fftw/3.3-alpha-intel 

 module load  module load gsl/gsl-1.15 

 e.g. module load NetCDF/4.1.2

3 Support

3.1 Hours of Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ..

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Users with further questions or requiring immediate assistance in use of the systems should send an email to:

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submit a ticket here

Support staff may be contacted via:
Griffith Library and IT help 3735 5555 or X55555
email support: hpc-services@gi.griffith.edu.au Submit form 
You can log cases on service desk (category: eResearch services.HPC)

eResearch Services, Griffith University
Phone: +61 - 7 - 373 56649 (GMT +10 Hours)
Email:  hpc-services@gi.griffith.edu.au  Submit a Question to the HPC Support Team
Web: eresearch. griffith.edu.au/eresearch-services

3.3 Service Alerts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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In addition to the home directory, users have access to a /scratch directory. A soft link to this scratch directory is also provided in the home directory. Files on system temporary and scratch directories are not backed up. All files older than 15 days will be deleted from the /scratch/<snumber> directory.

4 Access

4.1 Request an account on gowonda

Please fill out this form:
https://conf-ers.griffith.edu.au/display/GHCD/Griffith+HPC+AccountSupport+Request+Form?src=contextnavpagetreemode
A staff from the gowonda HPC cluster team will contact you to provide you with login details.

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To log in to the cluster, ssh to

gowondagc-prd-hpclogin1.rcs.griffith.edu.au

You will need to be connected to the Griffith network (either at Griffith or through vpn from home).

Please check VPN installation instruction here:

https://intranet.secure.griffith.edu.au/computing/remote-access/accessing-resources/virtual-private-network

ssh on windows platform . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . ..

To use X11 port forwarding, Install Xming X Server for Windows first.
See instructions here

If X11 forwading is not needed (true for most cases), do not install it.

To install a ssh client e.g. putty, please follow this instruction

ssh on Linux platform and mac platform . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . ..

ssh -Y gowonda-Y gc-prd-hpclogin1.rcs.griffith.edu.au

Once you are on the system, have a look around. Your home directory is stored in:
/exports/home/<SNumber>

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 Warning
Do not run jobs on the login node "gowondagc-prd-hpclogin1.rcs.grifithgriffith.edu.au" Please use it for compilation and small debugging runs only. 

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7.1 Submit Jobs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

qsub <pbscriptFile> 

A pbs simple script file is as follows:

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7.3 Delete Jobs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

qdel <jobID>

7.4 Check the current status of the cluster  .. . . . . . . . . . . . . . . . . . . . . . . . .

pbsnodes

pbsjobs

pbsqueues

To view the current cluster status, you use the elinks text browser on the login node to view the status like below:

pbsnodes   (elinks http://localhost:3000/nodes)

pbsjobs (elinks http://localhost:3000/jobs)

pbsqueues (elinks http://localhost:3000/queues)

(You can press "Q" to quit from the below text-based browsers

8 Examples

8.1 Intel MPI and Compiler with Interactive Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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http://confluence.rcs.griffith.edu.au:8080/display/GHPC/Windows+HPC+User+Guide

Update: This facility has been removed and is no longer available on gowonda

10 Acknowledgements

We encourage you to acknowledge significant support you have received from the Griffith University eResearch Services University eResearch Service & Specialised Platforms Team in your publications.

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"We gratefully acknowledge the support of the Griffith University eResearch Services University eResearch Service & Specialised Platforms Team and the use of the High Performance Computing Cluster "Gowonda" to complete this research."

If you need to give hardware specifics for readers to reproduce results, it is:

• Intel(R) Xeon

  CPU X5650 processor@2.67GHzQDR 4 x

  (R) Gold 6140 CPU @ 2.30GHz

• 
  

  EDR InfiniBand Interconnect

For more technical information, please check here

If you need to give hardware specifics of the gpu node for readers to reproduce results, it is:

• Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz

• EDR InfiniBand Interconnect

• GPU card: Tesla V100-PCIE-32GB

• HPE Proliant HPE XL270d Gen 10 Node CTO server

Please advise us of this acknowledgment by emailing us at eresearch-services@griffith.edu.au for our record keeping.

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