Abaqus Abaqus is used for both the modeling and analysis of mechanical components and assemblies (pre processing) and visualizing the finite element analysis resu...
Main.AdminUser 02 Nov 2020 ABAQUS at UTSA Introduction ABAQUS is a software suite from Dassault Systems. It can be used for finite element analysis and computer ...
About Shamu cluster Shamu is UTSA's primary high performance (HPC) resource; heavily utilized by researchers, students, faculty and staff from a broad range of di...
%IF{"(NOT defined GROUP) OR $GROUP = ''" then=' How to add the first administrator If you haven\'t previously set up an administrator, follow these steps: (Note:...
Ansys Ansys is a graphical program so you will need to have X11 forwarded in order to use this program. To run the program, qlogin to grab a compute node, load th...
Blender How to use Blender on Shamu to render your scenes or animations. First you will need to upload your *.blend file to your home directory. If you need more ...
Bowtie Bowtie is an ultrafast, memory efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35 bp r...
Cell Ranger Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3’ RNA seq output to align reads, generate gene cell matrices and perfo...
Checkpointing is the action of saving the state of a running process to a checkpoint image file. Restart is the actions to resume the checkpointed application fro...
Common Languages and Compilers The Shamu research cluster contains many open source and licensed languages and compilers. Below is a list. Compilers Intel Parall...
Common Problems with Shamu This document will try to explain the most common issues and problems with Shamu. Why isn't my job running? Why can't I login? ...
Cuda Cuda is a GPU programming language developed by NVIDIA. Currently Shamu contains two (4) very high end GPU nodes consisting of eight (8) Telsa K80 GPU comput...
Parallelize Deep Learning Models Across Multiple GPU Devices Deep Learning models written in Tensorflow can automatically take advantage of a GPU device on a comp...
Frequently Asked Questions Who can use Shamu? The Shamu research cluster is available at no charge to all University of Texas at San Antonio students, faculty an...
VizLab and SiViRT The UTSA Advanced Visualization Laboratory (VizLab), managed by the Office of Information Technology, allows researchers from all disciplines of...
How to request an account on Shamu for Faculty Faculty members who wish to have an account on Shamu must submit their request via the form at https://utsa.az1.qua...
Fiji Fiji is an image processing package—a "batteries included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. In o...
Fluent When running Fluent v16 or above in parallel batch mode, additional parameters need to be added to the Fluent command line. Fluent supports integration wit...
Sample GPU submit script using the Caffe training network Using the Tesla K80 cards: #SBATCH partition="gpu" #SBATCH nodes=1 #SBATCH gres=gpu:k80:1 . /etc/prof...
Gamess How to run Gamess on Shamu Run test job from the command line$ cd ~$ mkdir gamess $ mkdir /local/ insert your abc123 $ cp p /apps/gamess/tests/standard/ex...
Getting Help Shamu Office Hours Shamu Office hours are held in the Tech Cafe Monday through Friday 8am to 5pm. No appointment necessary, just drop by. Email UTS...
Getting Started with Shamu Shamu is the Research Support Groups premier cluster consisting of many compute cores and GPU cores. Connecting from Windows environme...
Gizmo The simulation code GIZMO is a flexible, massively parallel, multi method multi physics code, with a wide range of different physics modules described in th...
Grid Engine Job Submission In order to use the Grid Engine commands you first need to load the "sge" module: abc123@login 0 0 abc123 $ module load sge You can su...
GroupViewTemplate %IF{ "'.GroupViewTemplate' allows 'change' AND 'GroupViewTemplate' = 'BaseGroup' AND 'GroupViewTemplate' = 'NobodyGroup' AND {AdminUser...
To install gubbins it's recommended that you install it into a python virtual environment. First follow the instruction to create a python VE here on this page (c...
Homer HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP Seq analysis. It is a collection of command line pr...
HOOMD blue is a general purpose particle simulation toolkit. It performs hard particle Monte Carlo simulations of a variety of shape classes, and molecular dynami...
LAMMPS LAMMPS is a classical molecular dynamics code, and an acronym for Large scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soli...
LS Dyna LS Dyna is a general purpose finite element program capable of simulating complex real world problems. It is used by the automobile, aerospace, constructi...
MXnet Apache MXNet is a modern open source deep learning framework used to train, and deploy deep neural networks. It is scalable, allowing for fast model trainin...
Managing your Files Users on Shamu are automatically granted several locations to store their files. Most users will be storing their files in one of two location...
Sample submit script for non gui mode. You can copy/paste this script below to your Shamu directory, call it math.qsub. Submit the job on Shamu with qsub math.qsu...
Using Matlab Interactively (GUI mode) You can run Matlab with the srun command: abc123@login01 ~ $ srun pty bash abc123@compute003 ~ $ module load matlab...
Module Environments Each modulefile contains the information needed to configure the shell for an application. Once the Modules package is initialized, the enviro...
Monitoring your jobs Using the squeue Command Check the status of all jobs on Shamu using the squeue command (this is just an example compute names may be differ...
Mugsy Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear re...
Computing Resources Network The Shamu research cluster contains four (4) types of network configurations. * External network 10G public connection to the I...
Main.AdminUser 25 Sep 2019 You can make a free jupyter notebook on notebooks.azure.com by logging in to your microsoft account. After logging in if you go to 'My ...
Sun Grid Engine submit file for OpenFOAM #!/bin/bash # #$ S /bin/bash #$ N name_of_job #$ pe openmpi 16 . /etc/profile.d/modules.sh # Load program modules modu...
ParaView is an open source, multi platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data usin...
Main.AdminUser 26 Sep 2019 When you log into notebooks.azure.com go to your My Projects page. Click on Upload Github Repo and a form will come up. To upload the r...
Partition Definitions There are eight (8) Slurm partitions on Shamu that users are able to utilize. Below are their definitions. * defq This is the main queu...
Quick Start Guide The Research Computing Support Group at UTSA provides computing, storage and visualization resources to support research that has specialized or...
R How to add packages to your local repository Depending on the packages you want installed, you can do one of two things within R. First we load the R module an...
Running jobs on Shamu * Submitting your Batch Job Submit your code to run on the compute nodes. Create a submission script and specify options for better...
How to run Parallel Batch jobs On Shamu we have three (3) parallel Grid Engine environments but you only need to use one. First you need to load the "sge" module ...
How to run interactive jobs If you want to use a GUI or have a short program you want to test or debug, we suggest using the "srun" command. This will automatical...
To set up passwordless login you'll need to have set up an RSA key pair on your local machine for SSH. On linux and Mac OS. To generate an RSA keypair, just do t...
Windows Subsystem for Linux After the Windows 10 Fall Creators Update (FCU) released on October 17th 2017 Microsoft started to officially support on Windows OS th...
Shamu Fair Use Policy Effective July 13, 2020 Active Jobs Compute nodes will no longer be shared among multiple users. Instead, when a user grabs a compute nod...
Simple Single Threaded Job Script From the command line create a new file called myjob.sh using Nano or VIM. Below is a simple script which sets your SGE environm...
Main.AdminUser 01 Jul 2020 On July 13, 2020, the job scheduler Sun Grid Engine (SGE) on Shamu will be switched to Slurm, a new job scheduling system. Existing SGE...
Software Installed on Shamu Below is the list of software that is currently installed on Shamu. If you need additional software, please email your request to rcsg...
Computing Resources Storage The Shamu research cluster has approximately 150TB of shared storage utilizing a high speed 56GB/s Infiniband network. We use two re...
How to request an account on Shamu for Students Students who wish to have an account on Shamu must fill out the online account submission form located here: https...
How to submit your batch job Using the Slurm sample script located here, you will be able to submit your job with this command but first you need to load the "slu...
Torch Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first. It is easy to use and efficient, thanks to...
https://portal.tacc.utexas.edu/user guides To use TACC's Corral system you must request via TACC's User Portal for access: https://portal.tacc.utexas.edu/user gu...
The GPU resources on Shamu have been configured as a "consumable resource". This means you can request individual GPU cards, nodes, etc... We have two types of GP...
Shamu OnDemand Portal We recently introduced the OnDemand Portal which allows you as a user to connect to Shamu via a web browser instead of an SSH client. The On...
How to use your assigned job queue or compute nodes If you have purchased equipment and had it installed in Shamu you have the ability to dedicate individual comp...
VMD What is VMD? See also http://www.ks.uiuc.edu/Research/vmd/ VMD is designed for the visualization and analysis of biological systems such as protei...
http://ccwu.me/vsfm/ VisualSFM is a GUI application for 3D reconstruction using structure from motion (SFM). The reconstruction system integrates several of my pr...
Welcome to Research Computing Support at UTSA! The Research Computing Support Group at UTSA provides computing, storage and visualization resources to support res...
Why can't I log into Shamu? * You don't have an account on Shamu. All logins to Shamu are based on your campus myUTSA ID. * There could be a network issue f...
Why isn't my job running on Shamu? * System load is high on the compute nodes * A system downtime has been scheduled and jobs are being held. Check the mess...
RUNNING C, C , FORTRAN, PYTHON, AND R CODE BOTH SERIAL AND PARALLEL MODES ARE COVERED WHERE APPLICABLE This section covers the steps to run sample serial and ...
Getting Help ARC Office Hours Shamu Office hours are held in the Tech Cafe Monday through Friday 8am to 5pm. No appointment necessary, just drop by. Email UTS T...
Foswiki Upgrade Guide This guide covers upgrading from a previous version of Foswiki to Foswiki 2.x. This upgrade procedure is used to upgrade a to a new major v...
About Arc Cluster Arc is UTSA's primary high performance (HPC) resource; utilized by researchers, students, faculty and staff from a broad range of disciplines. C...
Arc Fair Use Policy Active Jobs Compute nodes are not shared among multiple users. Instead, when a user grabs a compute node, they will be the only user allowed ...
Frequently Asked Questions Who can use Arc? The Arc research cluster is available at no charge to all University of Texas at San Antonio students, faculty and st...
Table of Contents LOGGING INTO ARC. 1 ACCESSING COMPUTE NODES ON ARC. 1 RUNNING JOBS INTERACTIVELY WITH THE SRUN COMMAND.. 3 SUBMITTING BATCH JOBS WITH THE SBATCH...
How to request an account on Arc for Faculty Faculty members who wish to have an account on Arc must submit their request via the form at https://utsa.az1.qualtri...
Sample GPU submit script using the Caffe training network Using the Tesla K80 cards: #SBATCH partition="gpu" #SBATCH nodes=1 #SBATCH gres=gpu:k80:1 . /etc/pr...
Getting Help Submit a Service Request Follow this link to access your ServiceNow portal. At the homepage, select the Research tile and select the category for ...
Table of Contents LOGGING INTO ARC. 1 ACCESSING COMPUTE NODES ON ARC. 1 RUNNING JOBS INTERACTIVELY WITH THE SRUN COMMAND.. 3 SUBMITTING BATCH JOBS WITH THE SBATCH...
Table of Contents LOGGING INTO ARC. 1 ACCESSING COMPUTE NODES ON ARC. 1 RUNNING JOBS INTERACTIVELY WITH THE SRUN COMMAND.. 3 SUBMITTING BATCH JOBS WITH THE SBATCH...
Monitoring your jobs Using the squeue Command Check the status of all jobs on Arc using the squeue command (this is just an example compute names may be differe...
Running jobs on Arc * Submitting your Batch Job Submit your code to run on the compute nodes. Create a submission script and specify options for better j...
Arc Fair Use Policy Active Jobs Compute nodes will no longer be shared among multiple users. Instead, when a user grabs a compute node, they will be the only use...
Slurm (Simple Linux Utility for Resource Management) is a highly configurable workload manager and job scheduler for an HPC cluster. It is open source software ba...
https://portal.tacc.utexas.edu/user guides To use TACC's Corral system you must request via TACC's User Portal for access: https://portal.tacc.utexas.edu/user g...
The GPU resources on Arc have been configured as a "consumable resource". This means you can request individual GPU cards, nodes, etc... We have two types of GPU ...
***The OnDemand Portal is Currently not in Production on Arc We will notify users when it has become production ready*** We recently introduced the OnDemand Por...
Using NEC SX Aurora Vector Engines On Arc This guide provides an overview of the NEC SX Aurora TSUBASA Vector Engines (VE) nodes available on the Arc HPC Cluster....
Arc is UTSA's primary high performance computing (HPC) resource; heavily utilized by researchers, students, faculty and staff from a broad range of disciplines. A...