200 recent changes in Main Web retrieved at 05:41 (GMT)

GettingHelp
Getting Help Shamu Office Hours Shamu Office hours are held in the MS building, MS 1.03.06N, Monday through Friday 8am to 5pm. No appointment necessary, just dro...
WebHome
Welcome to the Research Computing Support Group at UTSA! The Research Computing Support Group at UTSA provides computing, storage and visualization resources to s...
SubmittingYourBatchJob
How to submit your batch job Using the SGE sample script located here, you will be able to submit your job with this command but first you need to load the "sge" ...
QuickStartGuide
Quick Start Guide The Research Computing Support Group at UTSA provides computing, storage and visualization resources to support research that has specialized or...
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...
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...
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 "qlogin" command. This will automatic...
Mathematica
Sample submit script for non gui mode #!/bin/bash # # Your job name #$ N Mathematica # # Use current working directory #$ cwd # # Join stdout and stderr #$ j y...
SampleSlurmSubmitScripts
Single and Multithreaded Sample Script #!/bin/bash # #SBATCH job name=my_job #SBATCH output=my_output_file.txt # #SBATCH mail type=ALL #SBATCH mail user=my em...
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...
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...
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 ...
TensorFlow
We have the GPU version of TensorFlow installed on the GPU nodes with the Python 3.6.1 module install (native Python 2.7 version is currently not working). This d...
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...
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...
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/...
Paraview
ParaView is an open source, multi platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data usin...
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...
Slurm-NewJobSchedulingSystem
Main.AdminUser 01 Jul 2019 Starting from July 2019, SGE on Shamu will gradually be switched to Slurm, a new job scheduling system. In the transition period (about...
GettingStarted
Getting Started with Shamu Shamu is the Research Support Groups premier cluster consisting of many compute cores and GPU cores. Connect to Shamu using SSH You sh...
REvnironmentsInAnaconda
First load the anaconda3 module like this: module load anaconda3 You can create an R environment in conda via this command where 'my ve name' is the name you choo...
QueueDefinitions
Queue Definitions There are eight (8) queues on Shamu that users are able to utilize. Below are their definitions. * all.q This is the main queue and all use...
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...
UsingTheSystems
Using the System * Managing your Files Store, manage and how to transfer files to Shamu * Queue Definitions Queue definitions * Module Envi...
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...
ModuleEnvironments
Module Environments Each modulefile contains the information needed to configure the shell for an application. Once the Modules package is initialized, the enviro...
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...
Matlab
Using Matlab Interactively You can run Matlab with the qlogin command: abc123@login01 ~ $ qlogin abc123@compute003 ~ $ module load matlab/2015a abc123@...
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...
PythonVmsInAnaconda
If you need to install your own programs/modules in python you can do it via creating vms. Some programs may need specific versions of modules to work correctly a...
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...
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...
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...
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...
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...
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...
Fall2018TrainingSchedule
Fall 2018 Training Schedule 9/7/2018 Intro to High Performance Computing Location: NPB 1.412 9/21/2018 Intro to Parallel Programming ...
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...
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...
MonitoringYourJobs
Monitoring your jobs Using the qstat Command Check the status of all your jobs, or the jobs belonging to a specific user: qstat u username abc123@login01 ~ $ q...
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...
GPU
Sample GPU submit script using the Caffe training network #!/bin/bash # #$ cwd #$ j y #$ S /bin/bash #$ q gpu.q. /etc/profile.d/modules.shmodule load shared c...
SampleSGESubmitScripts
Sample SGE Submit Scripts * OpenMPI * Abaqus * Single Thread Job * R * GPU Main.AdminUser 17 May 2016
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...
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...
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...
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 ...
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...
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...
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...
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...
Facilities
VizLab and SiViRT The UTSA Advanced Visualization Laboratory (VizLab), managed by the Office of Information Technology, allows researchers from all disciplines of...
Network
Computing Resources Network The Shamu research cluster contains four (4) types of network configurations. * External network 10G public connection to the I...
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? ...
Hardware
Computing Resources Hardware
NWChem
Name : nwchemArch : x86_64Version : 6.6.27746Release : 22.el7Size : 7.1 kRepo : epel/x86_64Summary : Delivering High Performance Computational Chemistry to Scienc...
Atlas
Name : atlasArch : x86_64Version : 3.10.1Release : 10.el7Size : 21 MRepo : installedSummary : Automatically Tuned Linear Algebra SoftwareURL : http://math atlas.s...
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...
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 /cm/shared/apps/gamess/tests/s...
WikiUsers
List of UTSA Research Support Group users Below is a list of users with accounts. If you want to edit topics or see protected areas of the site then you can get a...
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...
Cuda
Cuda Cuda is a GPU programming language developed by NVIDIA. Currently Shamu contains two (2) very high end GPU nodes consisting of eight (8) Telsa K80 GPU comput...
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...
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...
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...
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...
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...
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...
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...
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 ...
SitePreferences
SitePreferences %MAKETEXT{ "Foswiki's default preferences are located in _1 , however settings defined here have override priority and should be used for local ...
WelcometoResearchComputingSupport
Welcome to Research Computing Support at UTSA! The Research Computing Support Group at UTSA provides computing, storage and visualization resources to support res...
GroupTemplate
Edit this topic to add a description to the !
NobodyGroup
Used to prevent dangerous actions e.g. renaming put NobodyGroup as the only group allowed to rename a topic and it can't be renamed.
RegistrationAgent
The RegistrationAgent User This is a user used by Foswiki when it registers new users. This user has special access to write to , and does not need an entry i...
UserHomepageHeader
Header of User Homepages Note: This is a maintenance topic, used by the Wiki administrator. The part between the horizontal rules gets included at the top of ever...
UserList
User List sorted by name %SEARCH{ "form.name~'*UserForm'" nosearch="on" type="query" header=" FirstName LastName Organization State Co...
UserListByDateJoined
User List sorted by date joined / updated %SEARCH{ "form.name~'*UserForm'" type="query" header=" Date joined Last updated FirstName...
UserListByLocation
User List sorted by location %SEARCH{ "form.name~'*UserForm'" type="query" header=" Country State FirstName LastName Organizat...
UserListHeader
Related topics: %SEARCH{ "name='WikiUsers' OR name='WikiGroups' OR name='UserList' OR name~'UserListBy*'" type="query" ...
WebLeftBarExample
" warn="off"}% * ** * * * * * * %IF{"istopic ''" then=" * $percntICON{\"statistics\"}$percnt $percntMAKETEXT{\"Statist...
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:...
AdminUser
Wiki Administrator User The AdminUser allows you to login without needing to register a user, or to temporarily login as AdminUser using the password set in confi...
AdminUserLeftBar
%ADDTOZONE{ "head" text=" #patternSideBarContents .foswikiUserName a:link, #patternSideBarContents .foswikiUserName a:visited { background:red; color:...
GroupViewTemplate
GroupViewTemplate %IF{ "'.GroupViewTemplate' allows 'change' AND 'GroupViewTemplate' = 'BaseGroup' AND 'GroupViewTemplate' = 'NobodyGroup' AND {AdminUser...
ProjectContributor
Project Contributor Not an actual user of this site, but a person devoting some of his/her time to contribute to the Foswiki Open Source project. ProjectContribut...
UnknownUser
The UnknownUser User UnknownUser is a reserved name. If the UnknownUser appears, it is probably because author information for a topic could not be recovered, per...
WebAtom
UTSA Research Support Group's Main web
WebNotify
* .WikiGuest
WebPreferences
Main Web Preferences Appearance * Set WEBBGCOLOR = #FFEFA6 * web specific background color, current color * Set SITEMAPLIST = on * Set WEBSUMMAR...
WebRss
" else="UTSA Research Support Group's Main web"}% /Main
WikiGroups
Wiki groups dashboard Showing all known groups that can be used to define access controls in UTSA Research Support Group. %TWISTY{ link=" " mode="div" }% ...
WikiGuest
The WikiGuest User A guest of this web, not unlike yourself. You can leave your trace behind you, just add your name in UserRegistration and create your own page....
Number of topics: 102

See also: rss-small RSS feed, recent changes with 50, 100, 200, 500, 1000 topics, all changes
Topic revision: r1 - 03 May 2016, UnknownUser
This site is powered by FoswikiCopyright © by the contributing authors. All material on this collaboration platform is the property of the contributing authors.
Ideas, requests, problems regarding UTSA Research Support Group? Send feedback