https://wiki.chpc.ac.za/ 2026-08-11T16:36:32+00:00 https://wiki.chpc.ac.za/ https://wiki.chpc.ac.za/_media/wiki:favicon.ico text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:abaqus?rev=1639060966&do=diff Abaqus not currently available This page has been archived as the CHPC does not have an Abaqus license at present. If you wish to use Abaqus at the CHPC and you, or your institution, has a current license for Abaqus, please contact us at helpdesk AT text/html 2024-10-09T12:42:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:amber?rev=1728470546&do=diff Amber jobs on non-GPU nodes When running jobs for either AMBER14, AMBER18 or AMBER20 use the easy setup and submission scripts provided on the login node. Note, please first include this module load - even better if your add this line to your .bashrc, then the Easy Scripts should be visible and available: text/html 2023-09-18T08:49:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:amr-wind?rev=1695019776&do=diff Using AMR-Wind at the CHPC AMR-Wind is a massively parallel, block-structured adaptive-mesh, incompressible flow sover for wind turbine and wind farm simulations. It is built on the AMReX framework for massively parallel, block-structured adaptive mesh refinement applications. text/html 2026-07-21T09:03:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:ansys?rev=1784617391&do=diff ANSYS/Fluent Tutorial video - multi-node post-processing Up to v241 it is straightforward to do post-processing on a compute node, using the Mesa software-rendering library. However, from v242 this is only possible with a GPU-equipped visualization node. The process is illustrated in this text/html 2022-03-22T12:20:31+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:ansysmechanical?rev=1647944431&do=diff Ansys Mechanical at the CHPC The Ansys Mechanical sofware is installed together with the CFD solvers in the directory /apps/chpc/compmech/CFD/ansys_inc. There is a separate sub-directory for each version up to v221 although some of the older versions have been removed in order to save storage space. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:aoflagger?rev=1639060966&do=diff AOFlagger AOFlagger-2.10 is available as a module: module load chpc/earth/astro/aoflagger/2.10 will load the appropriate module, as well as the Casacore module upon which it depends. text/html 2025-03-10T13:02:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:approved_schrodinger_users?rev=1741604557&do=diff We need to ensure the following: * That you have an actual userid on Lengau and belong to an active research programme. * That if you are affiliated with a SA Institution. * Add your username to the Schrodinger Linux group on Lengau. * Send you read access to the Sharepoint link via your email. Info is provided here too. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:atat?rev=1639060966&do=diff Running ATAT (The Alloy-Theoretic Automated Toolkit) <http://www.brown.edu/Departments/Engineering/Labs/avdw/atat/> This describes the use of ATAT on Lengau and employs QE (Quantum Espresso 6.1.0). Anton Lopis 11 Jan 2017 Please find the files at /apps/chpc/chem/ATAT/3.36/CHPC_Running including pbs submission/bash script and input files (see below as well). text/html 2023-04-17T12:42:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:bioinformatics.old?rev=1681728144&do=diff OBSOLETE: Bioinformatics at the CHPC Please see <https://wiki.chpc.ac.za/howto:bioinformatics> instead Welcome to the bioinformatics at the CHPC wiki page! This page describes the basic procedures involved in getting your programs running at the CHPC rather than a description of how to do any particular bioinformatics analysis. If anything is unclear please hover your mouse over the superscripts! text/html 2025-05-21T10:50:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:bioinformatics?rev=1747817450&do=diff Bioinformatics at the CHPC Welcome to the bioinformatics at the CHPC wiki page! This page describes the basic procedures involved in getting your programs running at the CHPC rather than a description of how to do any particular bioinformatics analysis. If anything is unclear please hover your mouse over the superscripts! text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:cactus?rev=1639060966&do=diff Cactus at CHPC From its website : “Cactus is an open source problem solving environment designed for scientists and engineers. Its modular structure easily enables parallel computation across different architectures and collaborative code development between different groups text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:casacore?rev=1639060966&do=diff Casacore Casacore-2.4.0 is available by loading the appropriate module: module load chpc/earth/astro/casacore/2.4.0 text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:cdo?rev=1639060966&do=diff Using Climate Data Operator CDO is a collection of command line operators to manipulate and analyse Climate and NWP model Data. It has been installed in the directory /apps/chpc/earth/CDO-1.7.1-gcc. Please refer to the CDO home page for more information. A suitable environment should be set up by sourcing a small script: text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:cfd-ace?rev=1639060966&do=diff ESI CFD-Ace The CHPC has an installation of the CFD-Ace suite of software, including Ace, Geom, View and VisCART, but with no license. Approved academic users can use the software on the CHPC cluster, but need to work off their own licenses. Version 2015.0 is currently available on the system. If you need an older version, please contact CHPC support through the CHPC website. text/html 2025-02-21T12:45:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:cfx?rev=1740134755&do=diff ANSYS/CFX The CHPC has an installation of Ansys-CFD along with a limited license for academic use only. The license covers use of the Fluent and CFX solvers, as well as the IcemCFD meshing code. Application Process If you are a full time student or staff at an text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:chem_benchmarking?rev=1639060966&do=diff GAUSSIAN09 CP2K 2.6.2 text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:chimera?rev=1639060966&do=diff Getting CHIMERA to run on CHPC In order to have Chimera run on the CHPC you need to make use of a Visualization Node (viz node). The instructions to get things up and running are provided in the link below: CHIMERA_AT_CHPC text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:coarrayfortran?rev=1639060966&do=diff Using Co-array Fortran Co-array Fortran allows the programmer to develop distributed memory parallel Fortran programs without having to use MPI explicitly. Parallelisation is entirely contained within the Fortran language, using a PGAS (partitioned global address space) approach. In practice, Co-array Fortran is conveniently implemented by using OpenCoarrays, which is an interface built on top of MPI. text/html 2022-08-04T16:28:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:commercial_codes?rev=1659623312&do=diff Commercial Codes (Materials Studio, Gaussian, Schrodinger) The CHPC has National Licenses for the following software packages: * MATERIAL_STUDIO * GAUSSIAN09 and GAUSSIAN16 * SCHRODINGER text/html 2023-10-17T13:26:40+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:compilers?rev=1697542000&do=diff Available Computer Languages and Compilers The options can be seen by listing the available modules: module avail and searching for the compiler that you need. The Lengau cluster is now 6 years old, and as a result has accumulated a very large number of modules, which makes the output of text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:compiling_gcc?rev=1639060966&do=diff Compiling GCC 4.7.1 from Source This guide is written as to aid CHPC users who are struggling to compile the GCC version required for their codes. For the official guide on compiling GCC please visit the GCC website. This guide documents how GCC 4.7.1 would be built on the Sun Tsessbe Cluster login node, after the August 2012 upgrades. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:compiling_octave?rev=1639060966&do=diff Installing Octave 3.6.3 from Source This guide describes how Octave 3.6.3 would be installed from source, under your home directory. This guides follow on after the GCC 4.7.1 and Python 2.7 guides. i.e $ gcc -v ... gcc version 4.7.1 (GCC) $ python -V Python 2.7.3 text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto: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/howto:compiling_python_2_7_3?rev=1639060966&do=diff Installing Python 2.7.3 from Source This guide follows from GCC 4.7.1 install from source Guide, and assumes that your bash environmental are setup accordingly. Building directory $ mkdir -p /tmp/$USER/python_build All libaries and binaries installed in $HOME/local folder, and will require and additional 110M of disk space. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:compiling_r?rev=1639060966&do=diff Install R 2.15 from Source This guide documentation howto install R version 2.15 from Source into your home directory under the $HOME/local folder. This guide follows on for the install GCC 4.7.1, install Python 2.7.3 and install Octave 3.6.3 from source guides. ie text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:compiling_tips_n_tricks?rev=1639060966&do=diff Compiling Tips and Tricks " A technique is what you call any trick you use more than once." Compilers The three dominant compiled languages used in HPC are C, Fortran and C++. " Many people write the first and last as C/C++. That's misleading. C and C++ are separate languages. Confusing them is responsible for many problems. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:cosmomc?rev=1639060966&do=diff COSMOMC at CHPC From its website: “CosmoMC is a Fortran-based Markov-Chain Monte-Carlo (MCMC) engine for exploring cosmological parameter space, together with Fortran and python code for analysing Monte-Carlo samples and importance sampling (plus a suite of scripts for building grids of runs, plotting and presenting results). It can also be compiled as a generic sampler without using any cosmology codes. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:cosmopmc?rev=1639060966&do=diff CosmoPmc Procedure to run CosmoPmc on Sun cluster: The CosmoPmc is installed in the following directory: /opt/gridware/applications/cosmopmc Access is via modules. Firstly, you need to execute this command: module use /opt/gridware/users/nag/modulefiles text/html 2024-08-12T17:15:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:cp2k?rev=1723475735&do=diff CP2K job submission Note, please first include this module load - even better if your add this line to your .bashrc, then the Easy Scripts should be visible and available: module load chpc/easy_scripts Execute qcp2k_2.6.2 or qcp2k_3.0 on login node and follow the prompts. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:data?rev=1639060966&do=diff How to Manage your Data Usage Understand how critical data management is Managing data is an integral part of doing computational analysis work. Scientific applications generally use and create very large amounts of raw data. The graphs and tables that eventually show up in reports, theses and research publications represent this data in post-processed form. However, the raw data generated in the process of may take up several Terabytes of data. Once the raw data has been post-processed, it… text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:datamigration?rev=1639060966&do=diff Moving to the new 3 PB Lustre storage :!: Do not attempt to simply copy all data over. PLAN the transition and read this document first. Background With effect from 1 May 2021, there is a new 3 PB Lustre storage system available. It is mounted on the system as text/html 2024-07-23T14:48:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:dirisa?rev=1721738895&do=diff ` Using DIRISA storage 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 “ text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:discovery_studio?rev=1639060966&do=diff Please Note: CHPC NO LONGER SUPPORTS DISCOVERY STUDIO . . text/html 2024-08-12T13:30:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:dlpoly?rev=1723462233&do=diff DLPOLY job submission There are different versions of DLPOLY currently installed on our system. These include DLPOLY 1.9 (also known as DLPOLY classic), DLPOLY 4.07 and DLPOLY 4.08. As such there are different scripts available on the login node for PBS job creation and submission. To run any or these scripts execute text/html 2022-10-05T13:35:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:fds?rev=1664969721&do=diff Running the open-source Fire Dynamics Simulator FDS on the CHPC system Introduction Please refer to the FDS home page for more information on FDS, an open-source code targeted at fire simulation. There are two installed versions. The older version of the code is 6.7.0, and has been installed in text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:feko?rev=1639060966&do=diff FEKO at the CHPC FEKO is available for use by authorised users. Various versions are installed under the directory /apps/chpc/compmech/altair. Please look at the directory to find the version that suits your purpose. There is a 2017 version under hw2017/altair/feko/, a 2018 version under feko2018 and version 14 under feko14.0. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:fluent?rev=1639060966&do=diff ANSYS/Fluent Page has moved to Ansys/Fluent. text/html 2024-02-09T09:28:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:forte?rev=1707463699&do=diff Ansys Forte at the CHPC Ansys Forte fluid-dynamics software specializes in the simulation of combustion processes in an internal combustion engine, using a highly efficient coupling of detailed chemical kinetics, liquid fuel spray and turbulent gas dynamics. An Ansys Forte simulation solves the full Reynolds-averaged Navier-Stokes (RANS) equations with well established flow turbulence models. Its use on the CHPC cluster is covered by the academic text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:gadget-2?rev=1639060966&do=diff Gadget2 at CHPC From its website: “GADGET computes gravitational forces with a hierarchical tree algorithm (optionally in combination with a particle-mesh scheme for long-range gravitational forces) and represents fluids by means of smoothed particle hydrodynamics (SPH) text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:gadget2?rev=1639060966&do=diff Compiling your own Gadget2 code text/html 2025-10-17T09:51:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:gaussian?rev=1760687501&do=diff Gaussian at CHPC This license can only be used by CHPC registered users, which are associated with either South African or SKA partner higher education institutions Gaussian can be run over 1 or 2 nodes (see example below) Easy Gaussian09 and Gaussian16 PBS creation and submission text/html 2024-11-12T09:49:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:geant4?rev=1731397798&do=diff About Geant4 Geant4 <https://https://geant4.web.cern.ch/about/> is a toolkit to create simulations of the passage of particles or radiation through matter. Applications built on Geant4 can simulate any setup or detector and radiation source, and record the chosen output of physical quantities due to source particles and secondaries interacting with the material of the setup. text/html 2024-03-04T12:54:03+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:gizmo?rev=1709549643&do=diff ROOT at CHPC In the realm of High Energy Physics, the preferred framework for handling extensive data analysis tasks has long been CERN’s ROOT framework<https://root.cern/>. ROOT stands as a substantial C++ library, boasting a history predating even that of the STL in certain domains. Additionally, it includes a Just-In-Time (JIT) C++ interpreter named Cling, widely regarded as one of the finest in its field. Notably, the Xeus C++ Kernel for Jupyter is constructed upon the foundation of Cling. … text/html 2025-08-21T09:55:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:globus?rev=1755762915&do=diff Using Globus to transfer data :!: Please note: :!: Due to the previous version of Globus having been “end-of-lifed” at the end of 2023, it has been necessary to update the Globus software version on the CHPC's data transfer node. Unfortunately, this has introduced two additional steps in the process: text/html 2022-09-02T12:57:44+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:gnuplot?rev=1662116264&do=diff Running Gnuplot There are four functional Gnuplot installations: * Version 5.4.3 with qt, X11 or wxt graphics. By default this is intended for a graphics-capable session, such as a VNC session or an interactive PBS session with X-forwarding. You can get access to this version with text/html 2023-09-11T09:22:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:gpu_gromacs?rev=1694416944&do=diff OUTDATED This page refers to the discontinued SUN cluster. See the page Gromacs How To for the new cluster. Gromacs This page describes how to use Gromacs 4.6.5 on the GPU nodes of sun.chpc.ac.za. Basic Usage To use Gromacs add the following lines to your PBS job script: text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:gpu_namd?rev=1639060966&do=diff NAMD This page describes how to use NAMD 2.9 on the GPU nodes of sun.chpc.ac.za. Basic Usage To use NAMD add the following lines to your PBS job script: source /etc/profile.d/modules.sh module add /opt/gridware/applications/gpu/modules/namd/2.9 text/html 2022-03-28T10:27:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:gpu_overview?rev=1648456050&do=diff GPU hardware text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:grace?rev=1639060966&do=diff Running grace A version of the 2D-plotting software Grace, built on top of the GTK+-2 toolkit, has been installed on Lengau. In order to use it, follow these instructions: * Ensure that you have a graphics-capable environment, either by getting an interactive compute node session with X-forwarding (slow), or by getting a text/html 2024-08-12T13:29:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:gromacs?rev=1723462157&do=diff Gromacs The available Easy Scripts (cpu and gpu versions) for Gromacs are: qgromacs_2024-1, qgromacs_2023-1, qgromacs_2022-4, qgromacs_2020-1,qgromacs_2019-4, qgromacs_2018-6, qgromacs_2018-2 and qgromacs_2018 qgromacs_2024-1_gpu, qgromacs_2023-1_gpu, qgromacs_2021-1_gpu, qgromacs_2020-1_gpu, qgromacs_2019-4_gpu and qgromacs_2018-6_gpu text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:java?rev=1639060966&do=diff Using Java Example Java Script /* Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. */ /* * Copyright (c) 2011 Cisco Systems, Inc. All rights reserved. * */ import mpi.*; import java.net.InetAddress; class Hello { static public void main(String[] args) throws MPIException { MPI.Init(args); int myrank = MPI.COMM_WORLD.getRank(); int size = MPI.COMM_WORLD.getSize() ; … text/html 2024-08-12T13:27:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:lammps?rev=1723462053&do=diff LAMMPS You need to ensure that the relevant LAMMPS files are in the directory were you wish to submit your job from. Run qlammps in order to generate a PBS script and submit a job to the cluster. Examples of the script are provided below: Note, please first include this text/html 2025-01-29T09:00:57+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:licensing?rev=1738134057&do=diff Off-site software licensing Introduction Some general background information on software licensing is provided here because it can be tricky to get access to off-site licenses right and it helps to understand some of the general principles and tools that can be used to debug the process. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:liggghts?rev=1639060966&do=diff LIGGGHTS and lammps at the CHPC The LIGGGHTS descreet element method code is installed at the CHPC, although only limited support is available for them at this point. LIGGGHTS version 3.8 is at /apps/chpc/compmech/DEM/LIGGGHTS-3.8, but you can access it by loading the module: text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:list?rev=1639060966&do=diff How To Guides Page moved to How To Guides. text/html 2024-06-21T15:59:47+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:magma?rev=1718978387&do=diff How To Run Magma on the Cluster Magma is accessed by first loading the module module load chpc/math/magma/2.26 and then simply executing the command magma However, Magma is licensed software and only licensed to run on the large memory nodes (usually called the text/html 2026-07-21T12:33:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:material_studio?rev=1784629991&do=diff Material Studio at CHPC This is a package provided by BIOVIA You will need to edit your “hosts.” file (with no extension). The edit is done by copying this hosts file to one of your own dirs such as Documents, edit there, and then copy file back (in the etc\ dir you can't easily edit directly). Do the copy as Administrator (and using Admin elsewhere may help too). text/html 2025-05-22T16:56:58+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:matlab?rev=1747925818&do=diff Matlab Application to Access Matlab is commercial software and the CSIR has a site license which allows for non-commercial use on the CHPC cluster. If you are already a CHPC user: Please send an email to helpdesk@chpc.ac.za to request access to run Matlab M-files on the cluster. Please mention your use case and project. text/html 2025-04-16T12:28:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:mfix?rev=1744799314&do=diff Using MFIX at the CHPC Instructional video: MFix at the CHPC. Introduction MFIX is an open-source multiphase flow solver written in FORTRAN 90. It is used for simulating fluid-solid systems such as fluidized beds. As it appears to have numerous potential uses in chemical engineering and mineral processing applications, a limited level of support for the use of the package is now available at the CHPC. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:mpi?rev=1639060966&do=diff Using and Building MPI Important information on using MPI applications on the CHPC cluster with the PBSPro scheduler. Running MPI Codes Do not use --machinefile option with mpirun or mpiexec. " FIXME Insert examples here of loading an MPI module and launching the the MPI code. text/html 2024-08-12T13:28:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:namd?rev=1723462086&do=diff NAMD You need to ensure that the relevant NAMD files are in the directory were you wish to submit your job from. Run qnamd_2.11 in order to generate a PBS script and submit a job to the cluster. Examples of the script are provided below: Note, please first include this text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:ncview?rev=1639060966&do=diff Running ncview Ncview, a visual browser for netCDF format files, has been installed on the cluster. Set up a suitable environment with module load chpc/earth/ncview/2.1.7-gcc. Please refer to the ncview home page for more information. For interactive graphics, a graphics-enabled environment will be required, therefore refer to the page on text/html 2024-08-12T17:11:28+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:nwchem?rev=1723475488&do=diff NWCHEM job submission Execute qnwchem_6.6 on login node and follow the prompts. This script handles PBS setup and submission. Sets up the mpi environment variables allowing you to run over multiple processors and nodes. Examples of script execution are provided below. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:omnicompiler?rev=1639060966&do=diff Using Omni Compiler Omni Compiler is a collection of programs and libraries that allow users to build code transformation compilers. Omni Compiler can translate C and Fortran programs with XcalableMP and OpenACC directives into parallel code suitable for compiling with a native compiler linked with the Omni Compiler runtime library. Moreover, Omni Compiler supports the XcalableACC programming model for accelerated cluster systems. Please refer to text/html 2026-02-24T13:03:31+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:openfoam?rev=1771931011&do=diff OpenFOAM at CHPC Contents: * Running OpenFOAM * Compiling your own OpenFOAM code * Using the HiSA compressible Solver for OpenFOAM Latest version: OpenFOAM-v2512 The most recent available version is OpenFOAM-v2512. In contrast to previous installations, this has been compiled with Intel's OneAPI compiler and runs under IntelMPI. No special settings or parameters outside of the source script OF2512 are required. Here is an example job script: text/html 2026-02-26T15:22:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:orca?rev=1772112130&do=diff ORCA is available on Lengau, but we require users to be licensed/registered with the developers. Once we have proof of this, the user can be added to the orca Linux group on Lengau. ORCA job submission Execute qorca_6.1.0 on login node and follow the prompts (we should also have text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:p4vasp?rev=1639060966&do=diff p4vasp P4vasp is a plotting utility for Vasp data, there is more information available on the p4vasp homepage. To set up an environment for p4vasp type in the command load module chpc/compmech/p4vasp-0.3.30. Please note that p4vasp has been compiled for use on either chpclic1 or chpcviz1, and will not run on a compute node. It may be necessary to use the TurboVNC and VirtualGL interface as described text/html 2022-05-13T14:59:30+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:palabos?rev=1652446770&do=diff Using the Lattice-Boltzman code Palabos The following instructions are courtesy of Dr. Muaaz Bhamjee of the University of Johannesburg. Introduction Palabos is an open source CFD package based on the Lattice Boltzmann Method (LBM). Palabos is effectively a C++ library that can be used to develop CFD applications. More information can be obtained at the text/html 2025-04-14T10:59:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:paraview?rev=1744621183&do=diff Running Paraview Video tutorial - Parallel ParaView in client / server mode Watch this video tutorial Alternative method - ParaView using GPUs in the cluster Introduction Paraview is an extremely capable open-source programme for visualising simulation results. It supports a wide variety of file formats and is used in many different scientific and engineering disciplines. The code is designed to make effective use of parallel processing in order to process extremely large datasets. The… text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:pbs-pro_job_submission_diagnostics?rev=1639060966&do=diff Job Status Diagnostics A job submitted to the queue is not running Look at the job status with qstat. The next to last line of the output is a comment describing the job status. Possible outputs include: qstat -f yourjobid Job run at date at time on hostname text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:pbs-pro_job_submission_examples?rev=1639060966&do=diff PBSPro Job Submission Examples See the Quick Start Guide . text/html 2023-10-10T13:37:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:pbsdsh?rev=1696937828&do=diff pbsdsh There is a major problem with using GNU parallel directly on the PBSPro cluster: it uses the ssh transport and not momd which means that the PBS does not know about the tasks. This prevents PBSPro from properly monitoring or cleaning up node(s) when a job ends. Especially if that job ends from error or walltime ending. text/html 2025-08-18T10:37:52+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:port_issues?rev=1755506272&do=diff Intermittent Port Issues Affecting Materials Studio and Schrodinger Software If you are obtaining error messages or warnings related to licenses not accessible or similar, the info below should be useful. The nmap tests may also be useful to you anyway. text/html 2024-11-11T10:55:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:pythia8?rev=1731315333&do=diff About Pythia8 PYTHIA <https://https://pythia.org/> is a program for the generation of high-energy physics collision events, i.e. for the description of collisions at high energies between electrons, protons, photons and heavy nuclei. It contains theory and models for a number of physics aspects, including hard and soft interactions, parton distributions, initial- and final-state parton showers, multiparton interactions, fragmentation and decay. It is largely based on original research, but also… text/html 2024-08-12T17:12:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:quantum_espresso?rev=1723475573&do=diff QUANTUM ESPRESSO job submission Please see this info regarding quantum_espresso_checkpointing_restarting in order to allow your job to continue if it runs out of walltime or fails. Execute qesp_6.3.0 or qesp_6.4.0 qesp_6.4.1 qesp_6.4.1_gnu qesp_6.5_gnu or qesp_6.6 on the login node and follow the prompts. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:quantum_espresso_checkpointing_restarting?rev=1639060966&do=diff Checkpoint or Restarting a Failed QE Calculation Most codes permit a checkpoint file to be created so that one's job can be continued from the point shortly before it failed. Since QE 5.1 restarting from an arbitrary point of the code is no more supported. Instead it is possible to write out only one checkpoint file at a user specified time. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:r?rev=1639060966&do=diff Using R R has been installed in /apps/chpc/bio/R/? and is compiled using openmpi and the GNU compilers. R modules have been created so simply adding: module add chpc/R/3.2.3-gcc5.1.0 to your scripts will set up the appropriate paths to R, the compilers (if you want to add your own R packages) and the mpi libraries. Note that there may be several versions of R installed and can be seen by running the: text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:remote_viz?rev=1639060966&do=diff Visualisation servers The visualization servers are intended for single-process pre- and post-processing only, as well as GUI monitoring of running jobs. These servers are NOT intended for parallel processing or running compute tasks. The system administrators will terminate processes that do not fit the above description without warning. text/html 2024-04-03T14:42:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:rocky_dem?rev=1712148153&do=diff Running the commercial discrete element code Rocky DEM on the CHPC system Introduction Please refer to the Rocky DEM home page for more information on Rocky, a commercial code targeted at discrete element modelling. The current version of the code is v241, and has been installed in text/html 2024-11-11T13:33:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:root?rev=1731324788&do=diff About ROOT ROOT <https://https://root.cern/about/CERN> is a software framework born at CERN, at the heart of the research on high-energy physics. Physicists use ROOT applications to analyze their data or to perform simulations. Installing ROOT in a Python Virtual Environment on LENGAU text/html 2026-07-21T13:31:41+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:schrodinger?rev=1784633501&do=diff Schrodinger at CHPC This is a package provided by SCHRODINGER This license can only be used by CHPC registered users, which are associated with South African higher education institutions To gain access to Schrodinger you need to contact us via HelpDesk page text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:sharefiles?rev=1639060966&do=diff How To Share Files Research is a collaborative endeavour and you will likely want to share your files on the cluster with a colleague at some time during your project. This How-To describes how to use the standard Linux file permissions to: * share files in a sub-directory within your home directory or your Lustre work directory, or text/html 2022-06-24T10:56:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:singularity?rev=1656060981&do=diff Singularity in a Nutshell Singularity is a container solution created for scientific and application-driven workloads. This solution provides users with full control of their environments for developing software, libraries and scientific workflows. The other benefit is that it would allow users already invested in Docker containers to easily import their images without the need to install and configure Docker on HPC clusters. These benefits can be summarised into 4 points as follows: text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:sphgr?rev=1639060966&do=diff SPHGR at CHPC SPHGR is a multi-purpose data reduction suite designed to read and then process GADGET, TIPSY, or HDF5 binary outputs from GADGET. Then general idea is to be a one-stop-shop to simulation analysis and data access. The resulting data is saved to the disk in distinct object files which allows for easy examination/plotting. See the documentation here: text/html 2026-07-13T14:11:45+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:starccm?rev=1783944705&do=diff STAR-CCM+ NOTE on license tunnels Use 1999@chpclic1 for the license, the dtn node is not currently available for this. New procedure for versions from 19.02.009 onwards There has been a major change to the underlying dependencies of versions of STAR-CCM+ released from 2024, starting with 19.02.009. Specifically, the software now requires glibc-2.28 or higher. This is not compatible with the CentOS-7 operating system used on the Lengau cluster. The workaround is to package the software ins… text/html 2026-02-24T10:42:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:start?rev=1771922545&do=diff How To Guides Video tutorials for newcomers 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 and Tricks Tips & tricks for common tasks. :!: Please read this. The information is based on hard won experience. :!: If you need more memory text/html 2022-11-02T16:10:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:su2?rev=1667398237&do=diff Running the open-source code SU2 on the CHPC system Introduction Please refer to the SU2 home page for more information on SU2, an open-source code targeted at aerodynamics and adjoint shape development. The current version of the code is 6.2.0, and has been installed in text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:tau?rev=1639060966&do=diff Tuning and Analysis Utilities (TAU) text/html 2025-03-19T15:20:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:tipsandtricks?rev=1742390401&do=diff Tips and Tricks Fault finding - Check your ssh keys Parallel computing relies on passwordless ssh access between compute nodes. If passwordless ssh does not work, nothing else will. Therefore, if you find yourself with jobs that simply won't run, or even provide helpful error messages, first check that your ssh keys are correct. You can do this very simply be testing if you can ssh from the login node into another service node without supplying a password: text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:tune?rev=1639060966&do=diff User Guide For Tuning and Analysis Tools on the CHPC Lengau System Author: M.S Mabakane Date: November, 30 2018 TAU (Tuning and Analysis Utilities) is a portable profiling and tracing tool that analyse the performance of parallel models written in C, C++, Python and FORTRAN. It is further used to identify performance bottlenecks incurred during the simulation of the parallel program. TAU users can obtain performance information such as execution time of the objects (e.g. modules, routines, sub… text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:tuxedo?rev=1639060966&do=diff Under construction text/html 2022-03-29T16:23:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:ultrafluidx?rev=1648563815&do=diff Altair UltraFluidX Introduction UltraFluidX is a Lattice Boltzman solver that is part of Altair's suite of CFD codes. The CHPC hosts a license on behalf of the Mechanical engineering department at Nelson Mandela University. This license is access-controlled and available to users from the this department only. If you are interested in using any of the Altair fluid dynamics solvers, please contact text/html 2022-03-18T12:12:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:umask?rev=1647598354&do=diff umask The CHPC cluster uses CentOS as its operating system and follows the user private group convention for user accounts. This means that each user has a username (UID) and a corresponding group (GID). This scheme allows for easier set up of shared directories on the various file systems (home or Lustre) that users have access to. text/html 2024-08-12T17:12:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:vasp?rev=1723475543&do=diff P4vasp Please also see P4vasp for postprocessing etc. http://wiki.chpc.ac.za/howto:p4vasp VASP NOTE: The CHPC does NOT hold a license for VASP and the software is only accessible to those who have a valid license of their own. You need to ensure that the relevant VASP files are in the directory were you wish to submit your job from. Run text/html 2022-12-01T14:40:07+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:vesta?rev=1669898407&do=diff Using Vesta The visualization code Vesta-3.4.6 is available. In order to access it, load the appropriate module: module load chpc/compmech/vesta-3.4.6 Vesta can then be loaded with the command VESTA However, it is necessary to work in a graphics-enabled session to do this. This can be obtained with a text/html 2022-05-23T11:52:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:visit?rev=1653299521&do=diff Running VisIt There are three versions of VisIt installed on Lengau: * Visit-2.10.2 * Visit-2.13.3 * Visit-3.1.1 All three versions are available as modules. Use the command module avail 2>&1 | grep VisIt to find the module names. Please refer to the text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:vmd?rev=1639060966&do=diff Getting VMD to run on CHPC In order to have VMD run on the CHPC you need to make use of a Visualization Node (viz node). The instructions to get things up and running are provided in the link below: VMD_AT_CHPC text/html 2024-04-17T22:39:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:windows?rev=1713386348&do=diff Running Windows applications Fortunately, open-source scientific software applications, even those with Graphical User Interfaces, are most often developed on Linux. Those that have been developed on other operating systems generally also have build configurations for Linux. However, there are some applications that are only available on Windows. For the most part, these should be used on personal workstations or laptop computers. However, there are some exceptional circumstances where it m… text/html 2022-10-27T18:42:34+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/howto:wrf?rev=1666888954&do=diff Running ARW / WRF at the CHPC NEW: Howto video There are several versions of WRF, using different combinations of compiler and MPI implementation, installed on the filesystem in /apps/chpc/earth/. The latest version is WRF-4.2, built with the Intel compiler. Tests have indicated a very large benefit from using the Intel compiler and MPI rather than Gnu compiler and OpenMPI or MPICH. MPICH versions need the mpirun argument