Advanced Computing

The High Performance Computing (HPC) research infrastructure was established in Monash University Malaysia to support research, providing powerful computing services that can reduce computing jobs taking several days to just a few hours.

It is composed of one master node (2×8 Core E5-2650 v2, 48GB Memory), twelve compute nodes (2×8 Core E5-2650 v2, 256GB Memory) with a total of 192 processor cores, and is efficiently coupled with a disk storage system of 115 TB in capacity.

The infrastructure aims to support multidisciplinary research in the natural and social sciences such business, medicine, pharmacy, information technology and engineering.

It is currently used for research in the (but not limited to) following fields of study, i.e., from computer vision, image processing, optical network, machine learning, pattern recognition, combustion, turbulent flow, nanomaterials, genomes analysis, to disease association studies.

Getting Started

Introduction

As a new user, when you registered a HPC account, the first thing you want to know may include one or more of the following:

  • How can you login and what is the best ways to access the host remotely?
  • How to transfer files between the host and your PC or another Unix system in your lab?
  • After you login to one of the host, which directories can you use to run your jobs?
  • What are the batch LSF queues for running long hours computing jobs?

This introductory guide is to answer those questions. Together with the relevant links provided, we hope that it will help you to get started smoothly.

At HPC, all systems are managed by the LSF (load sharing facility). With the LSF commands, you can submit your jobs to different hosts with different features, capabilities and limitations. You can monitor your jobs while they are running or check the load and status of each host to chose your submission queues and hosts. Therefore, before you start your work, do check the User Guide in HPC home page or read the man pages (type man followed by the command) for different commands to familiarize yourself with LSF commands and the queues and hosts used in the LSF environment. The recommendation is to submit all compute intensive jobs as batch jobs through the LSF.

Some users are new to the Linux operating system. To learn more about Linux, you can read books on Linux; or simply type a “linux commands” in the internet search engines to search, you will get dozens of web pages with listing and explanation of Linux commands. A compiled list of the Linux commands is also available here for your reference, click here to download.

Register HPC

  • HPC resources are open to all MUM staff and post graduate students
  • User need  to request access for their HPC accounts.
  • They will need to fill up the HPC requisition form from ITS intranet and submit it. Click here to register.
  • Once the request is approved by HPC Director, your HPC account will be ready within 3 - 4 working days.

 

Login to HPC

Monash Malaysia HPC cluster can be access as follow:

  1. Web Browser
    • Require a browser that support Java. eg: Firefox
    • Java plug-in - latest Java version
    • Enter the site address or click here
    • Enter your HPC User Name and Password

      HPC Web Browser
    • Upon successful login

      HPC Login
  1. SSH client
      • Use PuTTY
      • SSH to 59.191.192.119 (mum-soe-hpchn1)
      • Home directory: /home/
        E.g: /home/testhpc

    SSH Client

  1. File Transfer Utility
    • Download and install WinSCP
    • Run and connect to 59.191.192.119

      WinSCP
    • Login with your HPC User Name and Password
    • Upon successful login

      WinSCP Interface

Job Submission

User can submit their job by using the existing template in HPC web portal or by using command. Please refer to below guide

How to submit job in HPC Web Portal

Please refer to this guide here.

How to submit jo in HPC using command

Please refer to this guide here.

 

Application Software

Compilers and Libraries

Name Description
GCC GNU compilers colletions for C/C++ and Fortran programs
Java Java Development Kit and Java Runtime Environment
Python High-level, general-purpose, interpreted, dynamic programming language compile
R R compiler

Life Science/ Molecular Modeling and Visualisation

Name Description
AmberTools A set of molecular mechanical force fields for the simulation of biomolecules
Biovia Discovery Studio Molecular Simulation and Drug Design
LAMMPS Molecular Dynamics Simulator
MrBayes A software performs Bayesian inference of phylogeny
GROMACS A versatile package to perform molecular dynamics

Computational Fluid Dynamics

Name Description
Ansys Fluent General purpose CFD package
Ansys Workbench General-purpose preprocessor for CFD analysis, default for CFX
Open Foam Open source CFD software package

Numerical and Symbolics Tools

Name Description
Elmerfem A finite element software for numerical solution of partial differential equations.
Mathematica Interactive tool for technical computing
Octave Octave is a high-level language, primarily intended for numerical computations.

 

Contact US

Research & HPC Enquiries

A/Prof Edwin Tan Chee Pin 
HPC Director

Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

Wan Mohd Azreen
Research IT Operations Lead

Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Tel: +603 5515 9770

ITS Administration Office, Building 9, Level 5

The HPC server is located within ITS Data Center in Building 9, Level 5

A wholly owned subsidiary of Monash University Malaysia