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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 23:51 (GMT)
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
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...
r42 - 20 Feb 2020 - 19:08 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...
r5 - 13 Feb 2020 - 19:54 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...
r6 - 06 Feb 2020 - 14:29 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
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
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
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
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" ...
r4 - 14 Jan 2020 - 15:13 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...
r16 - 02 Dec 2019 - 22:23 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...
r28 - 27 Nov 2019 - 16:27 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 "qlogin" command. This will automatic...
r6 - 20 Nov 2019 - 16:37 by AdminUser
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...
NEW - 05 Nov 2019 - 19:11 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
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
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
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...
r8 - 04 Sep 2019 - 14:46 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
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
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
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
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...
r2 - 02 Jul 2019 - 20:44 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...
r15 - 26 Jun 2019 - 15:23 by AdminUser
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...
r2 - 21 Jun 2019 - 13:21 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
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
ModuleEnvironments
Module Environments Each modulefile contains the information needed to configure the shell for an application. Once the Modules package is initialized, the enviro...
r2 - 03 Jun 2019 - 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...
r2 - 03 Jun 2019 - 14:02 by AdminUser
Matlab
Using Matlab Interactively You can run Matlab with the qlogin command: abc123@login01 ~ $ qlogin abc123@compute003 ~ $ module load matlab/2015a abc123@...
r5 - 15 May 2019 - 20:53 by AdminUser
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
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
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
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
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
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
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
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
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
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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