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Abaqus Abaqus is used for both the modeling and analysis of mechanical components and assemblies (pre processing) and visualizing the finite element analysis resu...

r7 - 04 Aug 2020 - 19:00 by AdminUser

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 ...

r3 - 03 Nov 2020 - 18:13 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...

r5 - 24 Jun 2020 - 19:39 by AdminUser

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:...

r8 - 06 Aug 2023 - 11:24 by UnknownUser

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...

NEW - 06 Aug 2023 - 11:24 by UnknownUser

AdminUserLeftBar

%ADDTOZONE{ "head" text=" #patternSideBarContents .foswikiUserName a:link, #patternSideBarContents .foswikiUserName a:visited { background:red; color:...

NEW - 06 Aug 2023 - 11:24 by UnknownUser

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...

NEW - 04 Aug 2020 - 20:11 by AdminUser

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...

r7 - 30 Jun 2021 - 14:49 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

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...

r9 - 14 Jul 2020 - 14:00 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

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

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...

NEW - 12 Jan 2017 - 19:41 by AdminUser

BrentLeague

BrentLeague

NEW - 16 Feb 2017 - 15:18 by RegistrationAgent

BrentTesting

BrentTesting

NEW - 01 Aug 2021 - 23:36 by RegistrationAgent

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...

r2 - 12 Jul 2020 - 22:12 by AdminUser

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...

r5 - 06 Aug 2020 - 02:01 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

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

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...

r3 - 14 Jan 2021 - 23:10 by AdminUser

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...

NEW - 08 Jul 2020 - 22:01 by AdminUser

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...

r2 - 13 Jul 2020 - 20:40 by AdminUser

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...

r2 - 14 Sep 2020 - 16:47 by AdminUser

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...

r2 - 17 Jan 2017 - 22:40 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

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...

r2 - 24 Jun 2020 - 21:21 by AdminUser

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...

r5 - 18 Jan 2021 - 04:18 by AdminUser

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...

r5 - 16 Oct 2020 - 21:21 by AdminUser

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...

NEW - 12 Jul 2020 - 16:40 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...

r4 - 14 Jul 2020 - 12:58 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

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

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

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...

NEW - 25 Aug 2016 - 16:29 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

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...

r7 - 30 Jul 2020 - 20:51 by AdminUser

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...

r3 - 21 Apr 2020 - 19:08 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 /apps/gamess/tests/standard/ex...

r2 - 10 Mar 2020 - 18:08 by AdminUser

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...

r6 - 24 Jun 2020 - 19:37 by AdminUser

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...

r16 - 24 Jun 2020 - 20:06 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

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

GroupTemplate

Edit this topic to add a description to the !

NEW - 06 Aug 2023 - 15:09 by UnknownUser

GroupViewTemplate

GroupViewTemplate %IF{ "'.GroupViewTemplate' allows 'change' AND 'GroupViewTemplate' = 'BaseGroup' AND 'GroupViewTemplate' = 'NobodyGroup' AND {AdminUser...

NEW - 06 Aug 2023 - 11:24 by UnknownUser

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

Hardware

Computing Resources Hardware

r8 - 23 May 2017 - 15:04 by 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...

NEW - 12 Jan 2017 - 19:28 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

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...

NEW - 06 Apr 2021 - 20:00 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

Number of topics: 50

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