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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...

NEW - 26 Aug 2016 - 16:15 by AdminUser

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...

r2 - 25 Mar 2021 - 19:53 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

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

MandoRodriguez

MandoRodriguez

NEW - 12 Apr 2023 - 15:34 by RegistrationAgent

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

Matlab

Using Matlab Interactively (GUI mode) You can run Matlab with the srun command: abc123@login01 ~ $ srun pty bash abc123@compute003 ~ $ module load matlab...

r7 - 24 Jun 2020 - 21:18 by AdminUser

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,...

r6 - 18 Dec 2020 - 16:15 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...

r3 - 24 Jul 2020 - 15:08 by AdminUser

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...

r4 - 14 Jul 2021 - 19:12 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

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

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

NobodyGroup

Used to prevent dangerous actions e.g. renaming put NobodyGroup as the only group allowed to rename a topic and it can't be renamed.

NEW - 06 Aug 2023 - 15:09 by UnknownUser

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

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

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

OpenSees

OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical systems subjected to earthquakes. We have ...

r2 - 04 Jan 2021 - 21:51 by AdminUser

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...

NEW - 12 Jul 2020 - 16:18 by AdminUser

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...

r2 - 11 Aug 2020 - 22:37 by AdminUser

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...

r4 - 14 May 2021 - 17:17 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

PatternSkinUserViewTemplate

NEW - 06 Aug 2023 - 14:01 by UnknownUser

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

ProjectContributor

Project Contributor Not an actual user of this site, but a person devoting some of his/her time to contribute to the Foswiki Open Source project. ProjectContribut...

NEW - 06 Aug 2023 - 11:24 by UnknownUser

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...

NEW - 09 Feb 2021 - 02:00 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...

r6 - 13 Aug 2020 - 19:27 by AdminUser

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...

r8 - 24 Jul 2020 - 13:58 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...

r18 - 02 Nov 2020 - 22:41 by AdminUser

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

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...

r2 - 25 Feb 2021 - 19:14 by AdminUser

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...

NEW - 14 Jan 2021 - 18:48 by AdminUser

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...

NEW - 02 Apr 2021 - 20:48 by AdminUser

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...

r3 - 02 Apr 2021 - 20:47 by AdminUser

RegistrationAgent

The RegistrationAgent User This is a user used by Foswiki when it registers new users. This user has special access to write to , and does not need an entry i...

NEW - 06 Aug 2023 - 15:09 by UnknownUser

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...

NEW - 14 Jul 2020 - 13:57 by AdminUser

RichardZanni

RichardZanni

NEW - 12 Apr 2023 - 15:24 by RegistrationAgent

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...

r3 - 20 Jan 2017 - 17:04 by AdminUser

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 ...

NEW - 18 Aug 2016 - 19:00 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 "srun" command. This will automatical...

r7 - 12 Jun 2020 - 16:36 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

SampleSlurmSubmitScripts

The page has been moved to UseSlurmOnShamu

r6 - 14 Jul 2020 - 21:49 by AdminUser

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...

r2 - 16 Sep 2021 - 23:25 by AdminUser

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...

NEW - 24 Jun 2020 - 22:28 by AdminUser

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...

r4 - 13 Jul 2020 - 15:13 by AdminUser

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...

r2 - 13 Jul 2020 - 04:32 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

SitePreferences

SitePreferences %MAKETEXT{ "Foswiki's default preferences are located in _1 , however settings defined here have override priority and should be used for lo...

r3 - 06 Aug 2023 - 11:24 by UnknownUser

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...

r4 - 14 Jul 2020 - 22:08 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...

r32 - 03 Jun 2021 - 20:48 by AdminUser

Number of topics: 50

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