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Training
Explore, register for, and review the trainings offered by the Research Computing group. NEC Code Vectorization and Vector Engine Training Recording Link Part 1...
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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...
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User List sorted by name %SEARCH{ "form.name~'*UserForm'" nosearch="on" type="query" header=" FirstName LastName Organization State Co...
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User List sorted by date joined / updated %SEARCH{ "form.name~'*UserForm'" type="query" header=" Date joined Last updated FirstName...
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%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:...
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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...
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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....
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FirstName LastName Email WikiName Mando Rodriguez Armando.Rodriguez #64;utsa.edu MandoRodriguez Thomas Freeman Thomas.Freeman #64;utsa.edu ...
Trainings
Explore, register for, and review the trainings offered by the Research Computing group. 1 Linux * Slides: Express Linux Tutorial * Video Recording...
SettingUpPasswordlessLogin
To set up passwordless login you'll need to have set up an RSA key pair on your local machine for SSH. On linux and Mac OS. To generate an RSA keypair, just do t...
MonitoringYourJobs
Monitoring your jobs Using the squeue Command Check the status of all jobs on Shamu using the squeue command (this is just an example compute names may be differ...
AnsysLumerical
Use Lumerical You can skip steps 1 10 on Shamu and ARC. You can skip steps 1 10 on Stampede2 if Lumerical executable path is provided. Please follow the instructi...
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...
ParallelProgrammingInR
R parallelization with mclapply mclapply is a parallelized version of lapply if provided mc.cores 1. For mc.cores == 1, it simply calls lapply​. By default, the m...
IntelOneAPI
Intel oneAPI is an open, unified programming model built on standards to simplify the development and deployment of data centric workloads across CPUs, GPUs, FPGA...
REnvironments
Create local R library Repo As Python packages, we suggest that users maintain their R library repoes in the home directory. Install R libraries using 'install.p...
REvnironmentsInAnaconda
Create local R library Repo As Python packages, we suggest that users maintain an R library repo in the home directory. Install R libraries using 'install.packag...
MFIX
MFiX is an open source multiphase flow solve. The detailed information can be found at https://mfix.netl.doe.gov/. The software is installed as a global shared Py...
UseSlurmOnShamu
Slurm (Simple Linux Utility for Resource Management) is a highly configurable workload manager and job scheduler for an HPC cluster. It is an open source software...
R-CorruptedRLibrariesWhenUsingBioconductor
If the user uses bioconductor for biology projects in R and their R library becomes corrupted you can do this command in the R prompt. BiocManager::valid() At t...
PythonEnvs-SavingAndImportingInAPackageList
It's handy to make a package list from your conda virtual environment in case you install something that breaks it or you want to replicate the packages exactly o...
DeepLearningModel
TensorFlow CPU Version First, grab a compute node with srun and start a Python Virtualenv environment: abc123@login 0 0 ~ $ srun n 80 N 1 time=48:00:00 pty b...
Checkpoint-and-RestartForDeepLearningModelsWithTensorflow
By using the checkpoint feature, model progress can be saved during training. The model can resume training where it left off and avoid starting from scratch if s...
R-ERRORC++14StandardRequestedButCXX14IsNotDefined
If you get the error: C 14 standard requested but CXX14 is not defined You need to create some environment variables that R can use to compile the code. If it do...
OpenSees
OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes. We have ...
MessagePassingInterface(MPI)
MPI Basics MPI is standardized and portable standard which defines the syntax and semantics of library routines for users writing portable parallel programs in C,...
AbaqusUsageOnSHAMU
Main.AdminUser 02 Nov 2020 ABAQUS at UTSA Introduction ABAQUS is a software suite from Dassault Systems. It can be used for finite element analysis and computer ...
QuickStartGuide
Quick Start Guide The Research Computing Support Group at UTSA provides computing, storage and visualization resources to support research that has specialized or...
UsingTheOnDemandPortal
Shamu OnDemand Portal We recently introduced the OnDemand Portal which allows you as a user to connect to Shamu via a web browser instead of an SSH client. The On...
UsingJetstream
Jetstream is a level 1 service provider of XSEDE (Extreme Science and Engineering Discovery Environment). It is a user friendly cloud computing environment for re...
DeepLearningModelParallelization
Parallelize Deep Learning Models Across Multiple GPU Devices Deep Learning models written in Tensorflow can automatically take advantage of a GPU device on a comp...
CheckpointAndRestartSequentialAndMulti-threadingBatchJobs
Here is a Slurm job script for submit a job with checkpoint feature: #!/bin/bash# Put your SLURM options here#SBATCH partition=defq # change to proper par...
UsingSingularity
Singularity is available on Shamu for users to run container based applications. Users can access the software via the module system, as shown below: abc123@shamu...
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...
ParallelProgrammingInPython
Single Node Parallelization A program in Python programming language can utilize the power of the multiple CPU/Core on a computer to significantly improve the per...
CUDA
CUDA is a parallel computing platform and programming model developed by NVIDIA for general purpose computing on GPU devices. CUDA application can dramatically sp...
Anaconda-EnvironmentReportsCorruptedMetadataWhenYouTryToInstallPackages
If a conda environment reports errors like a "corrupted manifest" file or "package manifest can't be found" then you can perform this command to scrub all package...
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...
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...
GNUParallel
GNU Parallel is a shell tool for executing many sequential tasks at the same time on one or more nodes. It is useful for running a large number of sequential task...
ModuleEnvironments
Module Environments Each modulefile contains the information needed to configure the shell for an application. Once the Modules package is initialized, the enviro...
QueueDefinitions
Partition Definitions There are eight (8) Slurm partitions on Shamu that users are able to utilize. Below are their definitions. * defq This is the main queu...
UsingTheGPUResources
The GPU resources on Shamu have been configured as a "consumable resource". This means you can request individual GPU cards, nodes, etc... We have two types of GP...
Slurm-NewJobSchedulingSystem
Main.AdminUser 01 Jul 2020 On July 13, 2020, the job scheduler Sun Grid Engine (SGE) on Shamu will be switched to Slurm, a new job scheduling system. Existing SGE...
SampleSlurmSubmitScripts
The page has been moved to UseSlurmOnShamu
ApplicationCheckpointAndRestart
Checkpoint and Restart Checkpointing is the action of saving the state of a running process to a checkpoint image file. Restart is the actions to resume the check...
RestartScriptGenerationExample
Here's a simple example of a checkpointing program being run with a slurm job script that will automatically generate a restart script for when you need to restar...
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...
CheckpointAndRestartSequentialAndMulti-threadingApplicationsInteractively(nonBatch)
To checkpoint and restart an interactive job, follow the steps below: log onto a compute node from the login node. srun pty bash Load the dmtcp module module...
ShamuFairUsePolicy
Shamu Fair Use Policy Effective July 13, 2020 Active Jobs Compute nodes will no longer be shared among multiple users. Instead, when a user grabs a compute nod...
SimpleCheckpoingAndRestartForPythonUsingAClass
This is a simple example of a program that checkpoints using python and the pickle class. It will run for 15 minutes. The script checks for a file called "countin...
CProgrammingWithSelf-DefinedCheckpoint-and-Restart
Checkpoint and restart with DMTCP can create large disk images, and the checkpoint details are controlled by the third party system. To avoid the problems, the pr...
EmbedDMTCPCheckpointAndRestartInCCode
In the previous examples, the checkpoint action is controlled by the coordinator, either by i number_of_second option or by manually type in 'c' in the coordinat...
OtherTools
Checkpoint and Restart Checkpointing is the action of saving the state of a running process to a checkpoint image file. Restart is the actions to resume the check...
CheckpointAndRestart
Checkpointing is the action of saving the state of a running process to a checkpoint image file. Restart is the actions to resume the checkpointed application fro...
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...
SetupWindowsSubsystemForLinux(Advanced)
Windows Subsystem for Linux After the Windows 10 Fall Creators Update (FCU) released on October 17th 2017 Microsoft started to officially support on Windows OS th...
Cuda
Cuda Cuda is a GPU programming language developed by NVIDIA. Currently Shamu contains two (4) very high end GPU nodes consisting of eight (8) Telsa K80 GPU comput...
Matlab
Using Matlab Interactively (GUI mode) You can run Matlab with the srun command: abc123@login01 ~ $ srun pty bash abc123@compute003 ~ $ module load matlab...
GettingStarted
Getting Started with Shamu Shamu is the Research Support Groups premier cluster consisting of many compute cores and GPU cores. Connecting from Windows environme...
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...
GettingHelp
Getting Help Shamu Office Hours Shamu Office hours are held in the Tech Cafe Monday through Friday 8am to 5pm. No appointment necessary, just drop by. Email UTS...
SubmittingYourBatchJob
How to submit your batch job Using the Slurm sample script located here, you will be able to submit your job with this command but first you need to load the "slu...
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 "srun" command. This will automatical...
GPU
Sample GPU submit script using the Caffe training network Using the Tesla K80 cards: #SBATCH partition="gpu" #SBATCH nodes=1 #SBATCH gres=gpu:k80:1 . /etc/prof...
TransferringFilesWithFilezilla
How to connect to shamu with filezilla to transfer files. This was done with filezilla 3.47.2.1 The quickconnect button When you open the program, there is a 'qu...
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...
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...
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...
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...
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...
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 ...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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 ...
WelcometoResearchComputingSupport
Welcome to Research Computing Support at UTSA! The Research Computing Support Group at UTSA provides computing, storage and visualization resources to support res...
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