High Performance Computing (HPC) at Center for Information Communication and Technology in UTM

1. High Performance Computing (HPC) at Center for Information Communication and Technology in UTM

2. Definition • High-performance computing (HPC) uses supercomputers and/or computer clusters to solve advanced computation problems. • 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.

3. CICT HPC Infrastructure • SUN Cluster: • 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

4. CICT HPC Infrastructure • 2) IBM Cluster: • 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

5. CICT HPC Networking Worldwide Grid Computing

6. CICIT HPC Connected to Worldwide Grids

7. Software on CICT HPC Installed: • OpenMPI - Message Passing Interface (MPI) library • Abaqus • For finite element analysis and computer-aided engineering. • 3 Cores. • MatlabDistributed 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.

8. 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.

9. Services Provided by CICT HPC 1) CPU 2) Storage 3) Software

10. Policy on CICT HPC User Account: • Each user is required to have ACID account before applying to use the HPC and Grid. • Every application needs to be included letter of support supervisor. • This facility is provided according to the duration of the project application. Storage: • 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. • Saving running result (output) in the storage is temporary. Users need to quickly download the output results after job has been processed. • Data which is no longer used need to be removed immediately.

11. 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. • 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. • 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.

12. Policy on CICT HPC Software: 1) Install software/tool in your user directory • 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. • Users need to download the software and install it by theirselves. 2) Install software / tool in directory which requires superuser access: • 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.

13. Policy on CICT HPC Acknowledgment: • 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.

14. Access CICT HPC Clients / Users CICT HPC INTERNET / VPN / LAN

15. Access CICT HPC Clients / Users CICT HPC Manager Manager

16. Access CICT HPC Apply user account: • Grid User Account • Example form • HPC User Account • http://hpc.utm.my/registration.php

17. Procedure to Apply Grid User Accounts

18. 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 • Using Putty software • To submit jobs and give Linux/Unix commands • Download at • http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html • Using WinSCP software • To upload and download files/folders • Download at • http://winscp.net/eng/download.php

19. Access CICT HPC Using Putty to access CICT HPC

20. Access CICT HPC Using WinSCP to access CICT HPC

21. Thank you