If you are a new user to the CHPC, please watch these videos:

• Setting up a cluster password and logging in for the first time
• The CHPC's service nodes and using the module system
• Test running in an interactive PBS session
• Running an application in batch mode under PBS

Tips & tricks for common tasks. Please read this. The information is based on hard won experience.

High-performance computing is closely related to “big data”. Many HPC users both use and generate very large data sets. The CHPC's default recommendation to users is:

• Feel free to use the CHPC's lustre storage as “work space”. It is large, fast and designed for parallel computing.
• Lustre is not a safe space for storing important data sets.
• Expedite post-processing and remove raw data.
• Store post-processed data somewhere safe.

However, the CHPC recognizes that this workflow is not universal. Many research groups own or produce very large data sets that need to be stored safely for sharing or future re-use. This is where the Data Intensive Research Initiative of South Africa comes into play. Like the CHPC, DIRISA is also part of South Africa's National Integrated Cyber Infrastructure System. DIRISA operates storage systems that are designed for long-term safe storage of research data.

DIRISA operates two object stores:

• iRODS is an acronym for Integrated Rule-Oriented Data System
• The Long Term Archive (LTA) is a tape-based system

These storage systems can be accessed by way of DIRISA's web-based Data Deposit Tool. However, the data deposit tool is not well suited to the requirements of a CHPC cluster user. It is intended for smaller quantities of data that are not already stored on NICIS resources.

The DIRISA object stores are directly accessible from the dtn node in the CHPC cluster. The good news is that this data transfer node mounts all the cluster file systems, which makes it possible to transfer data more efficiently to the DIRISA object stores. The bad news is that DIRISA's storage systems differ fundamentally from the cluster's storage:

• The DIRISA systems operate as Object Stores
• The cluster storage is used as

Here are instructions for using Globus to transfer data

A number of computer languages are available on the cluster. The preferred way to set up your environment to use a specific toolset is to load the appropriate modules to activate the needed libraries and set up the paths for the correct binaries.

• Compilers

Commercial software involves dealing with licensing.

• Running Gaussian on the CHPC cluster

• How to use OpenFOAM and build your own code on the CHPC systems
• Using Ansys/Fluent at the CHPC
• Using Ansys/Mechanical at the CHPC
• Using Ansys/CFX at the CHPC
• Using STAR-CCM+ at the CHPC
• Using ESI CFD-Ace at the CHPC
• Running Abaqus on the CHPC
• Using MFIX at the CHPC
• Using LIGGGHTS and lammps at the CHPC
• Using SU2 at the CHPC
• Using the Fire Dynamics Simulator FDS at the CHPC
• Using the discrete element code Rocky DEM at the CHPC
• Using Altair's UltraFluidX LBM code at the CHPC
• Using the lattice-Boltzman code Palabos at the CHPC

• How to use Feko at the CHPC

• How to use pre-installed bioinformatics tools

• COSMOMC
• cosmopmc
• Gadget-2
• Casacore
• AOFlagger

• GPU Cluster overview and generic instructions
• How to run NAMD
• How to run Gromacs

• How to run Gromacs

• dlpoly Material Sciences application

• python
• Running Tensorflow
• ipython_notebook

• Using R on the CHPC cluster

• Using Java on the CHPC cluster

• Using Co-array Fortran on the CHPC cluster

• Using Omni Compiler on the CHPC cluster

• tune

• Installing GCC 4.7.1 from source
• Installing Python 2.7.3 from source
• Installing Octave 3.6.3 from source
• Installing R 2.15.1 from source

• Remote OpenGL visualization with TurboVNC and VirtualGL
• Using Paraview
• Using Gnuplot
• Using ncview
• Using VisIt
• Using grace
• Using p4vasp
• Using Vesta

• Running the WRF model
• Using Climate Data Operator (CDO)