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Abaqus
Abaqus Abaqus is used for both the modeling and analysis of mechanical components and assemblies (pre processing) and visualizing the finite element analysis resu...
r7 - 04 Aug 2020 - 19:00 by AdminUser
AbaqusUsageOnSHAMU
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 ...
r3 - 03 Nov 2020 - 18:13 by AdminUser
AboutShamuCluster
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...
r5 - 24 Jun 2020 - 19:39 by AdminUser
AdminGroup
%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:...
r8 - 06 Aug 2023 - 11:24 by UnknownUser
AdminUserLeftBar
%ADDTOZONE{ "head" text=" #patternSideBarContents .foswikiUserName a:link, #patternSideBarContents .foswikiUserName a:visited { background:red; color:...
NEW - 06 Aug 2023 - 11:24 by UnknownUser
Ansysv171
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...
r3 - 19 Mar 2019 - 19:39 by AdminUser
Atlas
Name : atlasArch : x86_64Version : 3.10.1Release : 10.el7Size : 21 MRepo : installedSummary : Automatically Tuned Linear Algebra SoftwareURL : http://math atlas.s...
NEW - 03 Apr 2017 - 20:19 by AdminUser
Blender
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 ...
r2 - 11 Apr 2018 - 18:45 by AdminUser
Bowtie
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...
NEW - 12 Jan 2017 - 19:41 by AdminUser
Caffe
Caffe Interactive Usage on the GPU nodes Grab a GPU node with qlogin: abc123@login ~ $ qlogin q gpu.q abc123@login ~ $ module load caffe Copy the caffe exampl...
r2 - 10 Apr 2018 - 14:04 by AdminUser
CellRanger
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...
r4 - 04 Feb 2020 - 20:51 by AdminUser
CheckpointAndRestart
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...
NEW - 08 Jul 2020 - 22:01 by AdminUser
CommonLanguagesAndCompilers
Common Languages and Compilers The Shamu research cluster contains many open source and licensed languages and compilers. Below is a list. Compilers Intel Parall...
r2 - 17 Jan 2017 - 22:40 by AdminUser
CommonProblems
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? ...
NEW - 16 Jun 2017 - 20:07 by AdminUser
Cuda
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...
r2 - 24 Jun 2020 - 21:21 by AdminUser
DeepLearningModelParallelization
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...
r5 - 16 Oct 2020 - 21:21 by AdminUser
FAQ
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...
r4 - 14 Jul 2020 - 12:58 by AdminUser
Facilities
VizLab and SiViRT The UTSA Advanced Visualization Laboratory (VizLab), managed by the Office of Information Technology, allows researchers from all disciplines of...
r3 - 17 Aug 2017 - 15:44 by BrentLeague
Faculty
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...
r3 - 17 Aug 2017 - 16:02 by AdminUser
Fall2018TrainingSchedule
Fall 2018 Training Schedule 9/7/2018 Intro to High Performance Computing Location: NPB 1.412 9/21/2018 Intro to Parallel Programming ...
NEW - 29 Aug 2018 - 20:40 by AdminUser
Fiji
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...
NEW - 25 Aug 2016 - 16:29 by AdminUser
Fluent
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...
r5 - 23 Jul 2019 - 20:13 by AdminUser
GPU
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...
r3 - 21 Apr 2020 - 19:08 by AdminUser
Gamess
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...
r2 - 10 Mar 2020 - 18:08 by AdminUser
GettingHelp
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...
r6 - 24 Jun 2020 - 19:37 by AdminUser
GettingStarted
Getting Started with Shamu Shamu is the Research Support Groups premier cluster consisting of many compute cores and GPU cores. Connecting from Windows environme...
r16 - 24 Jun 2020 - 20:06 by AdminUser
Gizmo
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...
NEW - 31 May 2018 - 14:34 by AdminUser
GridEngineJobSubmission
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...
r11 - 31 Oct 2019 - 15:57 by AdminUser
GroupViewTemplate
GroupViewTemplate %IF{ "'.GroupViewTemplate' allows 'change' AND 'GroupViewTemplate' = 'BaseGroup' AND 'GroupViewTemplate' = 'NobodyGroup' AND {AdminUser...
NEW - 06 Aug 2023 - 11:24 by UnknownUser
Gubbins
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...
r2 - 06 Dec 2018 - 20:16 by AdminUser
Homer
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...
NEW - 12 Jan 2017 - 19:28 by AdminUser
Hoomd
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...
r2 - 04 Feb 2020 - 14:40 by AdminUser
LAMMPS
LAMMPS LAMMPS is a classical molecular dynamics code, and an acronym for Large scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soli...
r3 - 04 Sep 2019 - 14:29 by AdminUser
LS-Dyna
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...
NEW - 26 Aug 2016 - 16:15 by AdminUser
MXnet
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...
r3 - 10 Jul 2018 - 17:49 by AdminUser
ManagingYourFiles
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...
r5 - 18 Jun 2019 - 13:59 by AdminUser
Mathematica
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...
r2 - 05 Feb 2020 - 13:56 by AdminUser
Matlab
Using Matlab Interactively (GUI mode) You can run Matlab with the srun command: abc123@login01 ~ $ srun pty bash abc123@compute003 ~ $ module load matlab...
r7 - 24 Jun 2020 - 21:18 by AdminUser
ModuleEnvironments
Module Environments Each modulefile contains the information needed to configure the shell for an application. Once the Modules package is initialized, the enviro...
r3 - 24 Jul 2020 - 15:08 by AdminUser
MonitoringYourJobs
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...
r4 - 14 Jul 2021 - 19:12 by AdminUser
Mugsy
Mugsy Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear re...
NEW - 30 Mar 2017 - 14:49 by AdminUser
NWChem
Name : nwchemArch : x86_64Version : 6.6.27746Release : 22.el7Size : 7.1 kRepo : epel/x86_64Summary : Delivering High Performance Computational Chemistry to Scienc...
NEW - 04 Apr 2017 - 14:21 by AdminUser
Network
Computing Resources Network The Shamu research cluster contains four (4) types of network configurations. * External network 10G public connection to the I...
r2 - 26 Jul 2017 - 15:43 by AdminUser
NotebooksOnAzureCloud
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 ...
r2 - 26 Sep 2019 - 19:44 by AdminUser
OpenFOAM
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...
NEW - 23 Jul 2019 - 14:46 by AdminUser
OpenMPI
OpenMPI Submit Script #!/bin/bash # #$ S /bin/bash export MYAPP=./test_openmpi export MYAPP_FLAGS='' #$ N TEST_OPENMPI #$ pe openmpi 4 . /etc/profile.d/...
r6 - 23 Jul 2019 - 15:16 by AdminUser
Paraview
ParaView is an open source, multi platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data usin...
NEW - 23 Jul 2019 - 14:57 by AdminUser
PerilNotebookExample
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...
NEW - 26 Sep 2019 - 20:37 by AdminUser
QueueDefinitions
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...
r8 - 24 Jul 2020 - 13:58 by AdminUser
QuickStartGuide
Quick Start Guide The Research Computing Support Group at UTSA provides computing, storage and visualization resources to support research that has specialized or...
r18 - 02 Nov 2020 - 22:41 by AdminUser
R
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...
r12 - 23 Jan 2020 - 16:46 by AdminUser
RunningJobs
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...
r3 - 20 Jan 2017 - 17:04 by AdminUser
RunningParallelBatchJobs
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 ...
NEW - 18 Aug 2016 - 19:00 by AdminUser
RunningYourInteractiveJobsThroughBatch
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...
r7 - 12 Jun 2020 - 16:36 by AdminUser
SampleSGESubmitScripts
Sample SGE Submit Scripts * OpenMPI * Abaqus * Single Thread Job * R * GPU Main.AdminUser 17 May 2016
r4 - 14 Jun 2018 - 13:38 by AdminUser
SettingUpPasswordlessLogin
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...
r2 - 16 Sep 2021 - 23:25 by AdminUser
SetupWindowsSubsystemForLinux(Advanced)
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...
NEW - 24 Jun 2020 - 22:28 by AdminUser
ShamuFairUsePolicy
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...
r4 - 13 Jul 2020 - 15:13 by AdminUser
SingleThreadJob
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...
r4 - 28 Aug 2018 - 18:20 by AdminUser
Slurm-NewJobSchedulingSystem
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...
r4 - 14 Jul 2020 - 22:08 by AdminUser
SoftwareAndApplications
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...
r32 - 03 Jun 2021 - 20:48 by AdminUser
Storage
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...
r4 - 27 Jun 2018 - 13:52 by AdminUser
Students
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...
r3 - 18 Aug 2017 - 15:51 by AdminUser
SubmittingYourBatchJob
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...
r5 - 12 Jun 2020 - 16:39 by AdminUser
Torch
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...
NEW - 04 May 2018 - 16:35 by AdminUser
Trainings
Explore, register for, and review the trainings offered by the Research Computing group. 1 Linux * Slides: Express Linux Tutorial * Video Recording...
r2 - 14 Jan 2022 - 21:27 by AdminUser
UsingTACCSResources
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...
r8 - 04 Aug 2020 - 14:57 by AdminUser
UsingTheGPUResources
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...
r4 - 20 Jul 2020 - 20:02 by AdminUser
UsingTheOnDemandPortal
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...
r3 - 29 Oct 2020 - 22:04 by AdminUser
UsingTheSystems
Using the System * Managing your Files Store, manage and how to transfer files to Shamu * Queue Definitions Queue definitions * Module Envi...
r5 - 18 Jun 2019 - 12:54 by AdminUser
UsingYourAssignedJobQueueOrComputeNodes
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...
r2 - 18 Aug 2016 - 19:02 by AdminUser
VMD
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...
NEW - 14 Oct 2016 - 20:24 by AdminUser
VisualFM
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...
NEW - 08 Nov 2018 - 19:07 by AdminUser
WelcometoResearchComputingSupport
Welcome to Research Computing Support at UTSA! The Research Computing Support Group at UTSA provides computing, storage and visualization resources to support res...
NEW - 16 May 2016 - 14:46 by AdminUser
WhyCanTILogin
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...
r2 - 09 May 2018 - 13:39 by AdminUser
WhyIsnTMyJobRunning
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...
r2 - 13 Oct 2017 - 14:42 by AdminUser
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