https://wiki.chpc.ac.za/ 2026-07-30T17:39:34+00:00 https://wiki.chpc.ac.za/ https://wiki.chpc.ac.za/_media/wiki:favicon.ico text/html 2026-06-18T23:46:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:bitvise_keys?rev=1781819168&do=diff Setting up keys in BitVise The BitVise client can be downloaded from the BitVise website. The software has a client key manager menu for setting up new keys or importing existing keys. Please refer to the last section of the Windows ssh-keys tutorial video for a demonstration. text/html 2025-10-12T12:31:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:cloud?rev=1760265068&do=diff CHPC Cloud Resources * Overview * Getting Started * User Guide * IAC (Advanced) * Best Practice and Policies * Glossary of Terms * FAQs How can I use an OpenStack cloud? As an OpenStack cloud end user, you can provision your own resources within the limits set by cloud administrators. The examples in this guide show you how to perform tasks by using the following methods: text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:compiling?rev=1639060966&do=diff Compiling Compilers The following is a list of C, C++ and Fortran compilers available on the CHPC cluster: Intel * icc (for C and C++) * ifort GNU Compiler Collection * gcc * g++ * gfortran Environment module Command The module command provides a convenient mechanism for managing which environment variables are set in your shell session. The following is a list of the basic usage of the module command: text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:compiling_gcc?rev=1639060966&do=diff Page moved to Compiling gcc from source. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:compiling_octave?rev=1639060966&do=diff Compiling Octave 3.4.3 from Source This guide is written for the Sun Tsessbe Cluster. The reader is advise to read through the INSTALL file located in the Octave Source Folder before proceeding with this guide. Also it recommended to make use of temporary or scratch directory to do all the compilation in (i.e. ~/scratch or /tmp/$USER), as to save disk space in your home directory. This guide assumes GCC 4.6.2 has been installed in your home directory as in text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:compiling_octave_3_2_4?rev=1639060966&do=diff Compiling Octave 3.2.4 from Source This guide is written as to aid CHPC users in compiling Octave version 3.2.4 from source on the Sun Tsessbe Cluster. Its recommended that you make you use of temporary or scratch directory to do all the compilation in (i.e. ~/scratch or /tmp/$USER), as to save disk space in your home directory. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:compiling_python_2_7_3?rev=1639060966&do=diff Page moved to Installing Python from source. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:compiling_r?rev=1639060966&do=diff Installing R 2.14 from Source This guide is written fun the Sun Tsessbe Cluster, login node. Its recommended that you make you use of temporary or scratch directory to do all the compilation in (i.e. ~/scratch or /tmp/$USER), as to save disk space in your home directory. Note that for this guide, all binary and libraries are installed home directory, i.e prefix=$HOME. text/html 2026-06-18T19:45:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:connect?rev=1781804754&do=diff Connecting to the CHPC The CHPC hosts a supercomputer comprising: * 1008 regular compute nodes with 24 cores and 128 GiB of RAM each; * 360 regular computes nodes with 24 cores and 64 GiB of RAM each; * 4 large memory nodes with 56 cores and 1TiB of RAM each; text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:dell?rev=1639060966&do=diff Dell Cluster Overview The Dell cluster consists of 240 Dell C6100 nodes (12 cores, two sockets, Intel Xeon 2.93 GHz, 36GB RAM, QDR ConnectX2 Infiniband) which are linked into the pre-existing cluster ethernet network and infiniband fabric. These nodes are: text/html 2026-04-16T09:18:12+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:feedback?rev=1776323892&do=diff Principal Investigator Feedback Guide While it is possible to save an incomplete form by clicking on the “Save” button it is also advisable to keep a backup copy of the longer fields as you fill in your feedback form in case there is a problem with your browser and the save facility fails. text/html 2026-05-18T13:11:51+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:filesystems?rev=1779102711&do=diff File Systems :!: To prevent data loss the CHPC has to be strict about its 90 day life time policy for files on Lustre. Please manage your data carefully and always keep off site backups on all needed files. The primary file systems available to users are: text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:glossary?rev=1639060966&do=diff Glossary High Performance Computing * The use of parallel processing for running advanced application programs efficiently, reliably and quickly. Supercomputer * A system that performs at or near the currently highest operational rate for computers. Some supercomputers work at over half a petaflop or 10 text/html 2025-08-07T12:51:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:gpu?rev=1754563892&do=diff GPU Nodes Upgraded: more GPUs added. The Lengau cluster at the CHPC includes 9 GPU compute nodes with a total of 30 Nvidia V100 GPU devices. There are 6 gpu200n nodes with 3 GPUs in each, and 3 gpu400n nodes with 4 GPUs in each. GPU Node CPU Cores text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:induction?rev=1639060966&do=diff CHPC Induction This short practical hands-on course is provided for new users to the CHPC. Prerequisite Skills Linux command line interface. You should be familiar with Linux basics: * files and subdirectories: cd, mkdir, pwd, cp, mv, etc. * text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:induction1?rev=1639060966&do=diff CHPC Induction This is an introduction to the practical aspects of using the CHPC Lengau cluster. This page is an abbreviated overview of the full short course. More details will be delivered by the lecturer. " Links to slides and videos will be added later. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:intelphi?rev=1639060966&do=diff Using the Intel Xeon Phi nodes at CHPC Jargon The Phi cards are known officially as “Intel® Xeon Phi™” and will be referred to simply as “Phi”. Generally, the chip that is the Phi is called MIC (for Many Integrated Core architecture) and hence many programming tools will refer to text/html 2026-06-25T13:14:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:linux_keys?rev=1782386075&do=diff Linux * Open a terminal on your Linux system. * Generate a new key: ssh-keygen -t ed25519 -C "your_username@lengau" * Press Enter to accept the default file location. * Keep the private key safe in: ~/.ssh/id_ed25519 * Show your public key: text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:lustre?rev=1639060966&do=diff The Lustre Parallel File System :!: There is a new Lustre parallel file system mounted on /mnt/lustre3p. The old Lustre on /mnt/lustre will be decommissioned after 1 June 2021 and so you must copy over the files you will need by 31 May 2021. See the text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:m9000?rev=1639060966&do=diff Using the SUN M9000 SMP This guide explains how to use the M9000 massive multi-core shared memory super computer. Hardware M9000 CPU 64× SPARC64 VII quad-core CPU clock 2.88 GHz CPU cores 256 (512 threads available) Memory 2 048 GB (2 TB) text/html 2026-06-25T13:15:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:macos_keys?rev=1782386107&do=diff macOS * Open Terminal on your Mac. * Generate a new key: ssh-keygen -t ed25519 -C "your_username@lengau" * Press Enter to accept the default file location. * Keep the private key safe in: ~/.ssh/id_ed25519 * Show your public key: cat ~/.ssh/id_ed25519.pub text/html 2026-06-18T13:57:38+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:mfa?rev=1781783858&do=diff Multi Factor Authentication Access to the CHPC User Portal is now controlled by using your email address as user name and a password along with a code sent to your email address. After logging in using your email address and password you will need to enter the MFA code sent to your email address. Once this is done, you will have full access to your user profile. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:moab?rev=1639060966&do=diff A Guide to the Moab Job Scheduler at the CHPC To submit jobs to run on CHPC systems, you must write a shell script that will run your job, and then use msub to put it on the queue. msub needs information, like which cluster to run your code on, and where to put any errors or output from the job. This extra information can be put within the script, disguised from the shell as special comments, or put on the command line when submitting the job. text/html 2026-07-14T11:09:51+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:mobaxterm_keys?rev=1784020191&do=diff Windows MobaXterm Use the "Installer" version of MobaXterm :!: IMPORTANT There are two downloadable versions of the MobaXterm home edition - An “installer” version and a “portable” version. Do not use the portable one, it creates home directories that are not persistent. Use text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:pbspro?rev=1639060966&do=diff FIXME " This page in intended to supplement Job submission using PBSPro which will be simplified to the basics." PBSPro Scheduler The CHPC's Lengau cluster uses the PBSPro scheduler to manage both interactive and batch access to the compute resources (compute nodes). Building a New MPI Library text/html 2022-06-13T11:58:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:python?rev=1655114314&do=diff Python There are a number of python versions installed on Lengau compiled with either gcc or the intel compiler, including Python 2.7.11 to 2.7.15, Python 3.5-3.7 and anaconda installs for Python 2 and 3. Use this command to get a full list: module avail chpc/python text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:r?rev=1639060966&do=diff R on the Cluster Modules Interactive R Rscript for Job Scripts R Packages text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:scaling?rev=1639060966&do=diff Scaling Using Fewer Cores than Available There are several reasons why you would want to request more cores than you need, and they all depend on the hardware limits of the compute nodes. Core Frequencies A standard compute node on Lengau has two chips with 12 cores in each for a total of 24 cores. Each chip is limited by its text/html 2026-07-14T12:47:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:sshkeys?rev=1784026076&do=diff Setting up ssh Key Access to the Cluster Why access is now through keys only A major weakness of using passwords for security is that passwords have to be stored permanently on the remote system. You may have noticed that there is a recent movement towards text/html 2026-06-15T14:22:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:start?rev=1781526124&do=diff Users' Guide * Connecting to the CHPC * Setup CHPC VPN * File Systems * Compiling * GPU computing * Libraries * Development tools * python * tensorflow Instructions for building common tools can be found in the How To Guides section: * Compiling GCC 4.6.3 from source * Installing Python from source * Installing Octave 3.2.4 from source * Installing Octave 3.4.3 from source * Installing R from source text/html 2025-04-23T14:19:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:tensorflow?rev=1745410749&do=diff TensorFlow If you are making use of Jupyter notebook to write your python scripts then you first need to make sure you export the .py file from Jupyter and then copy it onto the cluster Also ensure job is copied to /mnt/lustre/users/YOURUSERNAME or subdirectories thereunder. text/html 2026-07-02T10:08:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:vpn?rev=1782979734&do=diff CHPC VPN The CHPC requires all access to the cluster to use the CHPC Wireguard VPN server. This adds an essential additional security layer to protect the internal network and your connection. The Wireguard VPN is fast and uses modern advanced encryption to protect your connection. text/html 2026-06-25T13:14:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/guide:windowscommandshell_keys?rev=1782386043&do=diff Windows command shell * Open a local terminal on your system. * Generate a new key: ssh-keygen -t ed25519 -C "your_username@lengau" * Press Enter to accept the default file location. * Keep the private key safe in: C:\Users\<your-user>\\.ssh\\id_ed25519