All public logs

Combined display of all available logs of RCSWiki. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).

• 21:08, 1 October 2024 Dmitri talk contribs moved page Signalp to SignalP
• 20:57, 1 October 2024 Dmitri talk contribs created page Signalp (Created page with "= General = = Installation = = Links = ARC Software")
• 20:18, 30 April 2024 Dmitri talk contribs uploaded File:Cpmd-4.3-manual.pdf
• 20:18, 30 April 2024 Dmitri talk contribs created page File:Cpmd-4.3-manual.pdf
• 20:02, 30 April 2024 Dmitri talk contribs created page CPMD (Created page with "= General = = Links = ARC Software")
• 21:18, 23 April 2024 Dmitri talk contribs created page Quantum ESPRESSO (Created page with "= General = * QE Web site: http://www.quantum-espresso.org * EPW web site: http://epw.org.uk * User's Guide: https://www.quantum-espresso.org/Doc/user_guide/user_guide.html : Installation: https://www.quantum-espresso.org/Doc/user_guide/node7.html * Input keywords: https://www.quantum-espresso.org/Doc/INPUT_PW.html * CC Docs page: https://docs.computecanada.ca/wiki/Quantum_ESPRESSO '''Quantum Espresso''' is an integrated suite of Open-Source computer codes for ele...")
• 16:25, 21 March 2024 Dmitri talk contribs created page Bioconda (Created page with "= General = * Home page: https://bioconda.github.io/index.html * List of available packages: https://bioconda.github.io/conda-package_index.html = Links = ARC Software pages")
• 15:41, 19 October 2023 Dmitri talk contribs created page How to find detailed information about past jobs on ARC (Created page with "= Background = = Using Sampled Metrics = On the OOD portal, https://ood-arc.rcs.ucalgary.ca , login using your UofC credentials (it may require your full UofC email address instead of just user name). Once you log in, * Select '''Help --> View my job metrics''', : this will open an interface to your past jobs that are available in the database. * Find the job you want to check and there may be useful graphs of CPU, memory, and GPU (if applicabl...")
• 15:12, 19 October 2023 Dmitri talk contribs created page How to check states of ARC partitions and nodes (Created page with "= Background = = Node states = = Links = How-Tos")
• 19:29, 18 October 2023 Dmitri talk contribs created page FSL on ARC (Created page with "= Background = * Official Site: https://fsl.fmrib.ox.ac.uk * Downloads and Registration: : https://fsl.fmrib.ox.ac.uk/fsldownloads_registration '''FSL''' is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. It runs on macOS (Intel and M1/M2), Linux, and Windows via the Windows Subsystem for Linux, and is very easy to install. Most of the tools can be run both from the command line and as GUIs. To quote the relevant references...")
• 18:24, 16 October 2023 Dmitri talk contribs created page AFNI on ARC (Created page with "= AFNI Apptainer Containers = The more recent versions of AFNI installed on ARC have been built as Apptainer containers based off of the official public AFNI docker release: [https://hub.docker.com/u/afni]. See also the documentation section about the container: [https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/container.html] The full path to the directory with the container files is <code>/global/software/afni/containers</code>. To see what vers...")
• 21:27, 13 September 2023 Dmitri talk contribs created page ROOT (Created page with "= General = * https://root.cern.ch/ '''ROOT''' is a framework for data processing, born at CERN, at the heart of the research on high-energy physics. = Links = ARC Software pages")
• 17:11, 16 August 2023 Dmitri talk contribs created page How to run an interactive job on ARC (Created page with "= Background = Running jobs is the main and the only way to run computations on ARC. Normally, a user creates a '''job script''' and submit it to SLURM on ARC using the <code>sbatch</code> command to run a computation. The '''login node''', ARC's gateway, is only intended to do '''management work''', such as * data management, * software management, and * job management. The '''login node''' could also be used to '''software development''', if you write scripts, or i...")
• 20:29, 14 July 2023 Dmitri talk contribs created page How to find nodenames allocated by SLURM for a job (Created page with "= Background = When a distributed job that is planned to run on multiple nodes requests several compute nodes from SLURM the program that is going to perform the computations needs to know the names of the compute nodes which are allocated to the job by SLURM to use those nodes. If the program is based on the distributed MPI library then the distribution of the computational processed to the nodes is done by the MPI program launcher, <code>mpirun</code> or <code>mpiexe...")
• 17:53, 1 May 2023 Dmitri talk contribs created page How to change locale settings (Created page with "= General = = Links = How-Tos")
• 16:55, 19 April 2023 Dmitri talk contribs created page How to use ARC scratch space (Created page with "= Background = = Links = How Tos")
• 20:53, 12 April 2023 Dmitri talk contribs created page Nektar++ (Created page with "= General = * Web site: https://www.nektar.info/ * Speed Comparison among Nektar++ Solvers : https://www.nektar.info/speed-comparison-among-nektar-solvers/ '''Nektar++''' is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers. The framework comes with a number of solvers and als...")
• 21:05, 7 March 2023 Dmitri talk contribs created page How to understand absolute and relative paths in Linux (Created page with "= General = = Links = How-Tos")
• 18:20, 1 March 2023 Dmitri talk contribs created page ORCA (Created page with "= General = ORCA is a flexible, efficient and easy-to-use general-purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. == Licensing == If you wish to use prebuilt ORCA executables: # You ha...")
• 17:49, 1 March 2023 Dmitri talk contribs created page How to request GPUs for batch jobs on ARC (Created page with "= GPUs on ARC = Currently, there are three partitions on ARC that have usable CUDA GPUs, '''gpu-v100''', '''gpu-a100''', and '''bigmem'''. ARC's configuration keeps changing depending on addition of new hardware and retiring of the old hardware, so you have to check available hardware on ARC before starting a new set of computations. * First, check the available partitions with GPUs on ARC following this article: : How to find available partitions on ARC. * Then,...")
• 21:30, 13 February 2023 Dmitri talk contribs created page How to convert a Docker container to an Apptainer container (Created page with "= General = = Links = More How-Tos")
• 22:39, 19 January 2023 Dmitri talk contribs created page How to find available partitions on ARC (Created page with "ARC is a relatively large and very heterogeneous cluster. It has lots of compute nodes and some of these nodes are very different in their hardware specifications and performance capabilities. On ARC, nodes with similar specifications are grouped into SLURM partitions. To use ARC effectively and to its full potential it is important that the researchers who use ARC can find available partitions and see important features of the nodes in those partitions. For this pur...")
• 22:15, 21 December 2022 Dmitri talk contribs created page How to find current limits on ARC (Created page with " Checking the current limits on ARC is recommended before planning a new series of computations, especially if GPUs are required for the computations. The current limits can...")
• 21:31, 17 November 2022 Dmitri talk contribs created page Data ownership (Created page with "= General = * '''Request to Access a Network Account without Consent''' Form: : https://www.ucalgary.ca/legal-services/sites/default/files/teams/1/Forms-Privacy-Request-to-Ac...")
• 22:24, 6 October 2022 Dmitri talk contribs created page UofC Services (Created page with "* Official '''Research Computing Services''' (RCS) page: : https://it.ucalgary.ca/research-computing-services : Research Computing Services (RCS) is a consulting and support g...")
• 15:34, 22 August 2022 Dmitri talk contribs moved page How to check the GPU utilization to How to check GPU utilization without leaving a redirect
• 15:23, 22 August 2022 Dmitri talk contribs created page How to check the GPU utilization (Created page with "= General = = Links = How-Tos")
• 20:11, 19 August 2022 Dmitri talk contribs created page How to generate a usage report from SLURM (Created page with "= General = SLURM provides the <code>sreport</code> command to generate reports. = Use cases = == Getting usage report for specific users == The default usage is given in...")
• 22:23, 10 August 2022 Dmitri talk contribs created page How to organize a shared storage space (Created page with "Access to the shared space is controlled by a Unix group. This is one of the level of Unix permissions controls. Please read our Wiki article on Linux permissions (same a...")
• 20:31, 5 August 2022 Dmitri talk contribs created page CESM (Created page with "= General = * National Center for Atmospheric Research (NCAR): : https://ncar.ucar.edu/ * Project site: https://ncar.ucar.edu/what-we-offer/models/community-earth-system-mo...")
• 19:36, 28 July 2022 Dmitri talk contribs created page How to work with large number of small files (Created page with "= Background = = From Python = == Working with files inside a TAR file == * <code>tarfile</code> module: : https://www.askpython.com/python-modules/tarfile-module")
• 18:12, 22 July 2022 Dmitri talk contribs created page How to use array jobs in SLURM (Created page with " <syntaxhighlight lang=bash> #!/bin/bash #SBATCH --account=def-someuser #SBATCH --time=0-0:5 #SBATCH --array=1-10 ./myapplication $SLURM_ARRAY_TASK_ID </syntaxhighlight>")
• 14:28, 4 July 2022 Dmitri talk contribs created page How to compress data for archival (Created page with "= Using '''tar''' command = == One file == == One directory == == Several files ==")
• 18:30, 30 June 2022 Dmitri talk contribs created page Fmriprep on ARC (Created page with "= General = = Using on ARC = <pre> $ singularity run /global/software/fmriprep/containers/fmriprep-20.2.3.simg --help You are using fMRIPrep-20.2.3, and a newer version of...")
• 17:47, 3 June 2022 Dmitri talk contribs created page How to request an interactive GPU on ARC (Created page with "Currently, there are two partitions on ARC that have usable CUDA GPUs, '''gpu-v100''', and '''bigmem'''. The <code>arc.hardware</code> tool can be used to see that. <pre> $ a...")
• 17:41, 3 June 2022 Dmitri talk contribs created page How-Tos (Created page with " * How to transfer data")
• 16:38, 21 April 2022 Dmitri talk contribs created page HDF5 (Created page with "= General =")
• 19:29, 31 January 2022 Dmitri talk contribs created page Conda on ARC (Created page with "= Background = '''Conda''' is a tool for managing and deploying applications, environments and packages. == Usage message == <pre> $ conda --help usage: conda [-h] [-V] comm...")
• 16:52, 7 December 2021 Dmitri talk contribs created page How to get an account (Created page with "= General = = Application form = * What is your status with UofC? * What research group do you work for? Who is your supervisor? (If you are a Principal Investigator your...")
• 15:08, 1 September 2021 Dmitri talk contribs created page External collaborators (Created page with " * This reference guide provides instructions on how to initiate a template-based hire for a '''General Associate Relationship''' :https://www.ucalgary.ca/hr/sites/default/fi...")
• 19:40, 2 June 2021 Dmitri talk contribs moved page On-line resources for new Linux users to On-line resources for new Linux and ARC users without leaving a redirect
• 18:20, 30 April 2021 Dmitri talk contribs created page On-line resources for new Linux users (Created page with "= General = = Linux command line = * If you are new to Linux, there is an easy to use reference for the Linux command line. : It is available for free download: http://linu...")
• 22:37, 29 March 2021 Dmitri talk contribs created page RCS Software Management Group (Created page with "= RCS Software Management Group = = Minutes = == Meeting: March 18th 2021 == Participants: * David Schulz * Dmitri Rozmanov * Ian Percel * Tannistha Nandi Minutes of the...")
• 18:12, 21 December 2020 Dmitri talk contribs created page Acknowledging Research Computing Services Group (Created page with "If the resources and help provided by the RCS group have been instrumental to your research, researchers are encouraged to acknowledge the Research Computing Services at UofC...")
• 19:34, 5 October 2020 Dmitri talk contribs created page Security and privacy (Created page with "= General = = Teleconferencing = * Microsoft Teams vs Zoom: : https://ucalgary.service-now.com/it?id=kb_article&sys_id=bd5c14f1dbc454d4f710777a8c9619ee")
• 16:03, 4 August 2020 Dmitri talk contribs created page Perl (Created page with "= General = = Installing your own copy of Perl = <pre> $ mkdir -p ~/src/perl $ cd ~/src/perl $ wget $ tar xvf perl-5.32.0.tar.gz $ cd perl-5.32.0/ $ unset PERL5LIB $ u...")
• 19:49, 21 July 2020 Dmitri talk contribs created page General Cluster Guidelines and Policies (Created page with "= General Rules = * Never run anything related to your research on the '''Login Node'''. : The '''login node''' is for ** Data management, that is file management, compressio...")
• 18:10, 30 June 2020 Dmitri talk contribs created page Python (Created page with "= General = = Installing your own Python = = Running Python scripts on ARC =")
• 21:42, 19 May 2020 Dmitri talk contribs created page GROMACS (Created page with "= General = = How to use =")
• 19:45, 29 April 2020 Dmitri talk contribs created page Jupyter Notebooks (Created page with "= General = = Jupyter Hub on ARC = Connect on http://jupyter.ucalgary.ca.")