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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...
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...
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:...
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...
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 ...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
GroupViewTemplate
GroupViewTemplate %IF{ "'.GroupViewTemplate' allows 'change' AND 'GroupViewTemplate' = 'BaseGroup' AND 'GroupViewTemplate' = 'NobodyGroup' AND {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...
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...
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...
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 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...
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...
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/...
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...
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...
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 * GPU 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
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 150TB of shared storage utilizing a high speed 56GB/s Infiniband network. We use two re...
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 here, you will be able to submit your job with this command but first you need to load the "sge" ...
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...
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...
UsingTheSystems
Using the System * Managing your Files Store and manage your files on Shamu and other research clusters * Queue Definitions Queue definitions ...
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...
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...
WelcometoResearchComputingSupport
Welcome to Research Computing Support at UTSA! The Research Computing Support Group at UTSA provides computing, storage and visualization resources to support res...
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...
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...
Number of topics: 57
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