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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...
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 ...
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:...
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:...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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...
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 (4) very high end GPU nodes consisting of eight (8) Telsa K80 GPU comput...
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...
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...
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...
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...
Fall2018TrainingSchedule
Fall 2018 Training Schedule 9/7/2018 Intro to High Performance Computing Location: NPB 1.412 9/21/2018 Intro to Parallel Programming ...
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...
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...
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...
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...
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...
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...
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...
GroupTemplate
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GroupViewTemplate
GroupViewTemplate %IF{ "'.GroupViewTemplate' allows 'change' AND 'GroupViewTemplate' = 'BaseGroup' AND 'GroupViewTemplate' = 'NobodyGroup' AND {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...
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...
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...
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...
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Topic revision: r1 - 03 May 2016, UnknownUser
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