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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) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
| Node |
|---|
| Names | Total |
|---|
Total Amount of Memory (GB)
Compute Nodes
| Number | Mem per |
|---|
Medium Memory Nodes
108
216
9
| No Format |
|---|
(n005-n009,n010-n012,n019) |
12
24
| node | Cores per node | Processor Type |
|---|
Small Memory Nodes
48
48
4
| No Format |
|---|
(n001-n004) |
12
12
1
Intel(R) Xeon(R) CPU X5650 @ 2.67GHz
| GPU card | |||||||
|---|---|---|---|---|---|---|---|
gc-prd-hpcn001 gc-prd-hpcn002 gc-prd-hpcn003 gc-prd-hpcn004 gc-prd-hpcn005 gc-prd-hpcn006 | 6 | 192GB | 72 | 2x Intel Xeon 6140 | |||
| n061 (gpu node) | 1 | 500 GB | 96 | 2X AMD EPYC 7413 24-Core Processor | 5 X A100 NVIDIA A100 80GB PCIe | ||
| n060 (gpu node) | 1 | 380 GB | 72 | Intel(R) Xeon(R) Gold 6140 CPU |
@ 2. |
Large Memory Nodes
72
288
6
| No Format |
|---|
(n013-n018) |
12
48
30GHz | 8 X V100 NVIDIA V100-PCIE-32GB |
2.2 Old Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Node Type | Total Number of Cores | Total Amount of Memory (GB) | Compute Nodes | Cores Per node | Mem per Node (GB) | Memory per Core | Processor Type | ||
|---|---|---|---|---|---|---|---|---|---|
Small Memory Nodes | 48 | 48 |
| 4 | 12 | 1 | Intel(R) Xeon(R) CPU X5650 @ 2.67GHz | ||
Extra Large Memory Nodes with Medium Memory Nodes | 108 | 216 | 9
| 12 | 24 | 2 | Intel(R) Xeon(R) CPU X5650 @ 2.67GHz | ||
Large Memory Nodes | 72 | 288 | 6
| 12 | 48 | 4 | Intel(R) Xeon(R) CPU X5650 @ 2.67GHz | ||
Extra Large Memory Nodes with GPU (see table below for more details about GPU) | 48 | 384 | 4
| 12 | 96 | 8 | Intel(R) Xeon(R) CPU X5650 @ 2.67GHz | ||
Extra Large Memory Nodes (no GPU) | 96 | 768 | 8
| 12 | 96 | 8 | Intel(R) Xeon(R) CPU X5650 @ 2.67GHz | ||
Special Nodes (no GPU) | 64 | 128 | 16
| 16 | 32 | 2 | Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz | ||
Special Large Memory Nodes (no GPU) | 64 | 1024 | 8
| 16 | 256 | 16 | Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz | ||
Special Large Memory Nodes (no GPU) | 192 | 1536 | 24
| 16 | 128 | 8 | Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz |
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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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Support staff may be contacted via:
Griffith Library and IT help 3735 5555 or X55555
email support: 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: 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.
| Anchor | ||||
|---|---|---|---|---|
|
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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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 . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . . . . ..
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7.3 Delete Jobs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
| No Format |
|---|
qdel <jobID>
|
7.4 Check the current status of the cluster .. . . . . . . . . . . . . . . . . . . . . . . . .
pbsnodes
pbsjobs
pbsqueues
| No Format |
|---|
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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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-32GBHPE 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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