High Performance Computing (HPC) at
Center for Information Communication
and Technology in UTM
Definition
1) High-performance computing
(HPC) uses supercomputers
and/or computer clusters to solve
advanced computation problems.
2) A computer cluster is a group of
linked computers, working together
closely thus in many respects
forming a single computer.
Clusters are usually deployed to
improve performance and
availability over that of a single
computer.
CICT HPC Infrastructure
1) SUN Cluster:
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CPU Types = 2 AMD Opteron 2356 (2.3Ghz)
The Number of Nodes (Machine) = 8 units
Memory Size for Each Node = 8GB
The Number of CPUs for Each Node = 6 CPUs
Total Number of CPUs = 8 x 6 = 48 CPUs
Total Storage Size = 11TB
Connections = High Speed Infiniband
Operation Systems = Scientific Linux 5.4
Middleware = Glite 3.2
CICT HPC Infrastructure
2) IBM Cluster:
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CPU Types = Intel Xeon DP (3.0GHz)
The Number of Nodes (Machine) = 16 Units
Memory Size on Each Node = 3GB
The Number of CPUs for Each Node = 4
CPUs
Total Number of CPUs = 4 x 16 = 64 CPUs
Total Storage Size = 800GB
Connections = High Speed Myrinet
Operation Systems = Scientific Linux 5.5
Middleware = Glite 3.2
CICT HPC Networking
Worldwide Grid Computing
CICIT HPC Connected to Worldwide
Grids
Installed:
Software on CICT HPC
• OpenMPI - Message Passing Interface (MPI) library
• Abaqus
– For finite element analysis and computer-aided
engineering.
– 3 Cores.
• Matlab Distributed Computing Server 5
– Allows users to submit sequential or parallel Matlab code
from their personal machine to a cluster.
– 120 Concurrent Users (Basic).
– 16 Cores.
• BNFinder-0.2.1 – For Bayesian Network reconstruction in
dynamic and static networks.
• Intel Fortran Composer XE 2011 - Build high-performance
serial and parallel applications for multicore.
Software on CICT HPC
Will be installed soon:
• OpenFoam-2.0.0 – Computational fluid dynamics toolbox.
• Blast - Basic local alignment search tool.
• ANSYS/Fluent:
– Computational fluid dynamics for optimization of product
development and processes.
– 5 concurrent license, includes 25 Ansys Academic Research HPC
licenses.
– Number of node limits (CFX & Fluent) : limited by hardware License
server.
• Abaqus
– For finite element analysis and computer-aided engineering.
– 24 Cores.
– Packaged for 20 users with unlimited research license.
• Gromacs-4.5.4 - A molecular dynamics package primarily designed for
biomolecular systems.
Services Provided by CICT HPC
1) CPU
2) Storage
3) Software
Policy on CICT HPC
User Account:
1. Each user is required to have ACID account before applying to
use the HPC and Grid.
2. Every application needs to be included letter of support
supervisor.
3. This facility is provided according to the duration of the project
application.
Storage:
a. The CICT did not provide large storage to users. So, this storage
space is limited to processes related to their applications, like
data, programs and software.
b. Saving running result (output) in the storage is temporary. Users
need to quickly download the output results after job has been
processed.
c. Data which is no longer used need to be removed immediately.
Policy on CICT HPC
Submit and Run Jobs:
•
Job that you wish to submit is only the job that related to the
projects in Universiti Teknologi Malaysia and gives benefits to the
university. If the job is submitted does not related to the university,
we are entitled to terminate your use of HPC and Grid facilities.
•
Maximum 1 running job is one week. If more, need to ask special
request.
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Maximum for each user, can submit only 10 jobs on a particular time.
•
Consumer need to always check the job status to prevent a long
pending job in case of the job has an error.
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Output stored in storage is for temporary, the users need to
immediately store the output backups on elsewhere after the job
processing has been completed. CICT will not be responsible on
output and backups loss.
Policy on CICT HPC
Software:
1) Install software/tool in your user directory
a. Users are allowed to install their own software in their own
respective directories on the condition of installed software is
related to applications that use or wish to be used.
b. Users need to download the software and install it by theirselves.
2) Install software / tool in directory which requires superuser access:
a.
b.
Users have to fill up and complete an installing software application
form that could be downloaded online. This form contains complete
information about the software that wish to be installed such as,
software name, version, website and so on.
Users need to download the software and installation guide before
handing over the next task of installing it to the CICT party.
Policy on CICT HPC
Acknowledgment:
1. Please put CICT UTM name in your publication that used
CICT HPC services as follows (for example):
We would like to thank Center for Information and
Communication Technology (CICT) in Universiti Teknologi
Malaysia for supporting and providing facilities and
services of high performance computing.
Access CICT HPC
Clients / Users
CICT HPC
INTERNET
/ VPN /
LAN
Access CICT HPC
Clients / Users
Job 1
Job 2
Job 3
Heavy
job 1
CICT HPC
Manager
Manager
Processing Job 1
Processing Job 2
Processing Job 3
Processing Sub-Job 1
Processing Sub-Job 1
Processing Sub-Job 1
Access CICT HPC
Apply user account:
1) Grid User Account
• Example form
2)HPC User Account
• http://hpc.utm.my/registration.php
Procedure to Apply Grid User
Accounts
Access CICT HPC
Option 1: Address to access (grid user): ui.utmgrid.utm.my
Option 2: Address to access (HPC user): ce.utmgrid.utm.my
1) Using Putty software
• To submit jobs and give Linux/Unix commands
• Download at
http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html
2) Using WinSCP software
• To upload and download files/folders
• Download at
http://winscp.net/eng/download.php
Access CICT HPC
Using Putty to access CICT HPC
Access CICT HPC
Using WinSCP to access CICT HPC
Thank you