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You are here: UTSA Research Support Group>Main Web>WebChanges (03 May 2016, UnknownUser)Edit Attach
50 recent changes in Main Web retrieved at 19:03 (GMT)
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...
r5 - 18 Jan 2019 - 17:24 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...
r2 - 04 Jan 2019 - 15:05 by AdminUser
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...
r5 - 19 Dec 2018 - 18:23 by AdminUser
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
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...
r7 - 03 Dec 2018 - 16:39 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
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...
r24 - 08 Nov 2018 - 19:06 by AdminUser
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...
r30 - 07 Nov 2018 - 19:06 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...
r7 - 23 Oct 2018 - 19:09 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...
r3 - 03 Oct 2018 - 14:28 by AdminUser
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...
r7 - 01 Oct 2018 - 15:34 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...
r2 - 20 Sep 2018 - 14:29 by AdminUser
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...
r3 - 12 Sep 2018 - 16:18 by AdminUser
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...
r5 - 07 Sep 2018 - 14:51 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/...
r5 - 07 Sep 2018 - 14:51 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
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...
r10 - 29 Aug 2018 - 19:44 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
QuickStartGuide
Quick Start Guide The Research Computing Support Group at UTSA provides computing, storage and visualization resources to support research that has specialized or...
r14 - 17 Jul 2018 - 22:04 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
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...
r13 - 27 Jun 2018 - 14:14 by AdminUser
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...
r2 - 27 Jun 2018 - 14:12 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...
NEW - 27 Jun 2018 - 14:02 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
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...
NEW - 14 Jun 2018 - 13:42 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
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
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
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
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
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
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...
r3 - 10 Apr 2018 - 13:18 by AdminUser
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" ...
r3 - 14 Mar 2018 - 19:49 by AdminUser
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...
r4 - 14 Mar 2018 - 19:18 by AdminUser
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...
r3 - 28 Feb 2018 - 17:04 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
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
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
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
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
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
Hardware
Computing Resources Hardware
r8 - 23 May 2017 - 15:04 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
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
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
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...
NEW - 22 Mar 2017 - 15:31 by AdminUser
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...
r2 - 16 Feb 2017 - 15:19 by AdminUser
ZhiweiWang
ZhiweiWang
NEW - 16 Feb 2017 - 15:19 by RegistrationAgent
BrentLeague
BrentLeague
NEW - 16 Feb 2017 - 15:18 by RegistrationAgent
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...
r4 - 31 Jan 2017 - 19:18 by AdminUser
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