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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...
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:...
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 do the following: ssh X abc123 #64;log...
Atlas
Name : atlasArch : x86_64Version : 3.10.1Release : 10.el7Size : 21 MRepo : installedSummary : Automatically Tuned Linear Algebra SoftwareURL : http://math atlas.s...
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...
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...
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...
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? ...
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...
Facilities
VizLab and SiViRT The UTSA Advanced Visualization Laboratory (VizLab), managed by the Office of Information Technology, allows researchers from all disciplines of...
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...
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...
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...
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 ...
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...
GroupTemplate
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GroupViewTemplate
GroupViewTemplate %IF{ "'.GroupViewTemplate' allows 'change' AND 'GroupViewTemplate' = 'BaseGroup' AND 'GroupViewTemplate' = 'NobodyGroup' AND {AdminUser...
Hardware
Computing Resources Hardware
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...
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...
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...
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...
Matlab
Using Matlab Interactively You can run Matlab with the qlogin command: abc123@login 0 0 ~ $ qlogin abc123@compute 0 3 ~ $ module load matlab/2015a abc1...
ModuleEnvironments
Module Environments Each modulefile contains the information needed to configure the shell for an application. Once the Modules package is initialized, the enviro...
MonitoringYourJobs
Monitoring your jobs Content coming soon! Main.AdminUser 16 Jun 2017
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...
NWChem
Name : nwchemArch : x86_64Version : 6.6.27746Release : 22.el7Size : 7.1 kRepo : epel/x86_64Summary : Delivering High Performance Computational Chemistry to Scienc...
Network
Computing Resources Network The Shamu research cluster contains four (4) types of network configurations. * External network 10G public connection to the I...
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.
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/...
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...
QueueDefinitions
Queue Definitions There are five (5) queues on Shamu that users are able to utilize. Below are their definitions. * all.q This is the main queue and all user...
QuickStartGuide
Quick Start Guide The Research Computing Support Group at UTSA provides computing, storage and visualization resources to support research that has specialized or...
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...
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...
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...
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 ...
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...
SampleSGESubmitScripts
Sample SGE Submit Scripts * OpenMPI * Abaqus * Single Thread Job * R Main.AdminUser 17 May 2016
SingleThreadJob
Simple Single Threaded Job Script #!/bin/bash # #$ cwd #$ j y #$ S /bin/bash #. /etc/profile.d/modules.sh date sleep 10 date Main.AdminUser 27 Jun 2016
SitePreferences
SitePreferences %MAKETEXT{ "Foswiki's default preferences are located in _1 , however settings defined here have override priority and should be used for local ...
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 rcis...
Storage
Computing Resources Storage The Shamu research cluster has approximately 64TB of shared storage utilizing a high speed 56GB/s Infiniband network. We use two Del...
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...
SubmittingYourBatchJob
How to submit your batch job Using the SGE sample script located in this wiki, you will be able to submit your job with this command but first you need to load th...
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...
Number of topics: 50
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Topic revision: r1 - 03 May 2016, UnknownUser
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