https://wiki.chpc.ac.za/ 2026-09-14T07:56:55+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/acelab:adding_new_nodes?rev=1639060966&do=diff All nodes are configured with BMC ip address. Below is the table with all IP address (Including the compute nodes of the Power Edge M1000e) Add main switch to Bright Cluster Manager Adding Dell Networking N2048 Switch management IP address. This is the BMC network all nodes will be using for IPMI communications. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:administration_guide?rev=1639060966&do=diff Administration Guide Bright Scheduler NFS Lustre text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:application_benchmarks?rev=1639060966&do=diff Software setup GCC OpenMPI Synthetic HPCC HPCG Phoronix Test Suite Application GADGET-2 GIZMO OpenFOAM WRF LAMMPS NAMD GROMACS Amber Quantum ESPRESSO text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:build_document?rev=1639060966&do=diff CMC Build PowerVault PV Setup Bright Node Categories and Images Define Networks Adding New Nodes Infiniband Install and Configure Storage NFS Configuration Intel Enterprise for Lustre Scheduler PBSPro text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:change_management_control_cluster?rev=1639060966&do=diff Change Management Control Documentation Change Management Control (CMC) is a continuous process of ensuring system change is introduced in a controlled and coordinated manner to minimise service disruptions. As part of implementing CMC the CHPC formulated a Cluster Usage Evaluation team to analyse system usage, propose improvements and approve changes. The test cluster is the platform where CMC actions are evaluated in order to gather enough information to submit a change request for the produc… text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:change_report?rev=1639060966&do=diff Submitting A Change Report Change Reports are linked to Change Requests, Click here to view Change Requests. It is required to submit a Change Report after working on the CMC Cluster. This report is used when making a decision about the project to be implemented on text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:change_request?rev=1639060966&do=diff Submitting A Change Request Click Here to submit real Change Request [CMC Change Request Landing Page] When submitting a change request, all fields need to be filled. We encouraged to describe the project and the activities fully. This information will be used in the decision process of approval, scheduling and in preparation of the bright images. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:cmc_workflow?rev=1639060966&do=diff Background Change Management Control (CMC) is a continuous process of ensuring system changes are introduced in a controlled and coordinated manner to minimise service disruptions. The implementation and maintenance of lengau involves integrating many elements e.g. compute nodes, parallel file systems, fast networks, provisioning and configuration systems. The CHPC needed a platform to text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:define_networks?rev=1639060966&do=diff Name Base address Domain Name externalnet 10.128.24.0 brightcomputingipminet 172.17.0.0 ipmi.cluster internalnet 172.18.0.0 eth.cluster ibnet 172.20.0.0 ib.cluster During bright cluster manager installation, network information can be provided and automatically configured. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:gadget-2?rev=1639060966&do=diff General Info GADGET is a freely available code for cosmological N-body/SPH simulations on massively parallel computers with distributed memory. GADGET uses an explicit communication model that is implemented with the standardized MPI communication interface. The code can be run on essentially all supercomputer systems presently in use, including clusters of workstations or individual PCs. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:gcc?rev=1639060966&do=diff Guide to install GCC 4.x.x and 5.x.x sudo su cd /data/scratch Download the source required from the following FTP servers: GCC: <http://ftp.gnu.org/gnu/gcc/> Install repo dependencies: yum install glibc-devel.i686 glibc glibc-devel glibc-static Setup GCC prerequisites: tar -xf gcc-x.x.x.tar.gz cd gcc-x.x.x ./contrib/download_prerequisites text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:gizmo?rev=1639060966&do=diff General Info The simulation code GIZMO is a flexible, multi-method magneto-hydrodynamics+gravity code. The code lets you solve the hydrodynamic equations using a variety of different methods -- whatever is best for the problem at hand. In particular, it introduces a couple of new, Lagrangian Godunov-type methods, that allow you to solve the fluid equations with a moving particle distribution that is automatically adaptive in resolution and avoids the advection errors, angular momentum conservat… text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:gromacs?rev=1639060966&do=diff General Info GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological syste… text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:hpcc?rev=1639060966&do=diff General Info HPC Challenge is a benchmark suite comprising 7 micro benchmarks designs to assess a number of HPC system characteristics. The suite includes HPL, DGEMM and FFT which test floating point performance. STREAM and RandomAccess are included to access memory performance. PTRANS and 'Communication bandwidth and latency' are used to assess network performance. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:hpcg?rev=1639060966&do=diff General Info The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark. The computational and data access patterns of HPL are no longer driving computer system designs in directions that are beneficial to many important scalable applications. HPCG is designed to exercise computational and data access patterns that more closely match a broad set of important ap… text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:hpl_cuda?rev=1639060966&do=diff General Info This guide describes how to configure and run High Performance LinPACK on CUDA compatible GPUs. The HPL benchmark is run ONLY on the GPUs in this guide, however then are simple steps to take in order to distribute work between both CPUs and GPUs. A CPU (x86) only version of the HPL benchmark is performed by HPCC, presented in this guide: text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:install_and_configure?rev=1639060966&do=diff * Verify that the server has Mellanox network adapter installed (HCA/NIC) [root@bright1 OFED]# lspci -v|grep Mellanox 02:00.0 Network controller: Mellanox Technologies MT27500 Family [ConnectX-3] Subsystem: Mellanox Technologies Device 0067 [root@bright1 OFED]# text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:intel_enterprise_for_lustre?rev=1639060966&do=diff 1. Install all packages that are needed [root@oss01 ~]# yum install device-mapper device-mapper-devel device-mapper-multipath kpartx [root@oss01 ~]# yum install sg3_utils sg3_utils-devel 2. Start multipath service [root@oss01 ~]# service multipathd start Starting multipathd daemon: [ OK ] [root@oss01 ~]# chkconfig multipathd on [root@oss01 ~]# text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:lammps?rev=1639060966&do=diff General Info LAMMPS (“Large-scale Atomic/Molecular Massively Parallel Simulator”) is a molecular dynamics program from Sandia National Laboratories. LAMMPS makes use of MPI for parallel communication and is free, open-source software, distributed under the terms of the GNU General Public License. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:namd?rev=1639060966&do=diff General Info NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 500,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build… text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:nfs_configuration?rev=1639060966&do=diff On the Host servers [nfs01 and nfs02] Device Mapper Multipathing Devices (DMMP) - Scan for virtual disks - Display the multipath device topology - Create a partition on a multipath device node - Add a partition to Device Mapper(DM) - Crate a file systems on a Device Mapper partition text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:node_categories_and_images?rev=1639060966&do=diff Node Categories Software Images Nodes compute compute-image cnode[01-16] login login-image login[01-02] scheduler sched-image sched iml iml-image imlnode mds mds-image text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:openfoam?rev=1639060966&do=diff General Info OpenFOAM is an Open-Source Computational Fluid Dynamics (CFD) is a C++ toolbox for the development of customized numerical solvers, and pre-/post-processing utilities for the solution of continuum mechanics problems. The code is typically memory bandwidth limited, such that memory channels are more useful than sheer core count. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:openmpi?rev=1639060966&do=diff Guide to install OpenMPI with GCC and ICS sudo yum install zlib-devel binutils-devel Intel: ./configure CC=icc CXX=icpc F77=ifort FC=ifort --with-verbs --with-mxm=/opt/mellanox/mxm --prefix=/opt/openmpi-1.x.x GCC: ./configure --with-verbs --with-mxm=/opt/mellanox/mxm --prefix=/opt/openmpi-1.x.x text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:opennebula_sr-iov_vmm_driver?rev=1639060966&do=diff OpenNebula KVM SR-IOV Driver With the release of an OFED which supports SR-IOV on Infiniband HCAs it is now possible to use verbs from inside a VM. This VMM driver supports these Infiniband HCAs, and any other SR-IOV network device, in OpenNebula. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:pbspro?rev=1639060966&do=diff Get software from Altair customer webportal 1. License Installation [root@sched ~]# ./altair_licensing_13.0.0.linux_x64.bin -i console Default Install Folder: /usr/local/altair/licensing13.0 License file ...... 2. Copy the license file and restart the license server service text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:phoronix_test_suite?rev=1639060966&do=diff General Info The Phoronix Test Suite is the most comprehensive testing and benchmarking platform available that provides an extensible framework for which new tests can be easily added. The software is designed to effectively carry out both qualitative and quantitative benchmarks in a clean, reproducible, and easy-to-use manner. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:pv_setup?rev=1639060966&do=diff Powervault MDSM guide Setup and Connection: * Open PowerVault MDSM [500px] * Add new array manually - specify management IP addresses of each controller (default = 192.168.129.101 & 192.128.129.102). Give the array a name (eg: NFS01) [500px] * Once added, connect to array * Do not automatically configure array when prompted (select No) text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:quantum_espresso?rev=1639060966&do=diff General Info Quantum ESPRESSO is a software suite for ab initio quantum chemistry methods of electronic-structure calculation and materials modeling, distributed for free under the GNU General Public License. It is based on Density Functional Theory, plane wave basis sets, and pseudopotentials (both norm-conserving and ultrasoft). ESPRESSO is an acronym for opEn-Source Package for Research in Electronic Structure, Simulation, and Optimization. text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:start?rev=1639060966&do=diff ACELab * OpenNebula KVM SR-IOV Driver text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:test?rev=1639060966&do=diff Testing Discussion This is a test of the discussion plugin to enable comments on selected pages. Comments are available to non-registered readers and uses the captcha plugin to foil spambots. When editing pages: Don't Panic. The 'Preview' button does not show the comments; but they text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:usage_guide?rev=1639060966&do=diff CMC User guide This guide is intended for CHPC stuff and special users. Overview The CMC cluster is built using Dell servers. The system consist of a Power Edge M1000e Chassis with 16 M6220 compute nodes. Each of the compute nodes have 12 cores and 36 text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:user_guide?rev=1639060966&do=diff CMC User guide This guide is intended for CHPC stuff and special users. Overview The CMC cluster is built using Dell servers. The system consist of a Power Edge M1000e Chassis with 16 M6220 compute nodes. Each of the compute nodes have 12 cores and 36 text/html 2021-12-09T16:42:46+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.chpc.ac.za/acelab:wrf?rev=1639060966&do=diff General Info Weather Research and Forecasting (WRF) is a numerical weather prediction (NWP) system designed to serve both atmospheric research and operational forecasting needs. source Useful Links HPCAC Best Practices <http://www.hpcadvisorycouncil.com/pdf/WRF_Best_Practices.pdf> WRF Compile Guide <http://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php> Installation Guide