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This page is intended to make searching and finding content contained in this Wiki easier to navigate. Each letter shows a number next to it. That number is the number of pages and headers that begin with that letter. Each content subject gives information on that particular subject or page .


Glossary

Space Index

0-9 ... 0 A ... 11 B ... 3 C ... 9 D ... 5 E ... 2
F ... 9 G ... 17 H ... 5 I ... 5 J ... 3 K ... 3
L ... 7 M ... 6 N ... 1 O ... 4 P ... 15 Q ... 2
R ... 11 S ... 23 T ... 6 U ... 14 V ... 3 W ... 3
X ... 0 Y ... 0 Z ... 0 !@#$ ... 0    

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A

Page: Account Policy
ARCC Policies for High Performance Computing - Account Policy Contents Glossary Frequently Asked Questions HPC/HPS Accounts Overview HPC/HPS accounts are available for all University faculty, staff, and students for the purpose of research. Account Sponso
Page: Acknowledgment Policy
The requirement to acknowledge ARCC and UWyo support for research. Contents Acknowledgment Policy Annual Reporting At the end of each academic year, ARCC requires an accomplishment report from each PI containing: The research results (in laymen terms supp
Page: Adding Files & Folders
Here we will talk about working with files and folders on your Shared Drive Contents Glossary Frequently Asked Questions Create Folders Create a new folder: https://storage.googleapis.com/support-kms-prod/d1C6vAbDiohX3TUNOadWi7e60XI0WyngDCNx On the left,
Page: ANGSD
This page details the use of ANGSD: Analysis of next generation Sequencing Data on teton. Contents Glossary Frequently Asked Questions Overview Homepage: ANGSD http://www.popgen.dk/angsd/index.php/ANGSD: ANGSD is a software for analyzing next generation s
Page: ANSYS Fluent
ANSYS Fluent software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from airflow over an aircraft wing to combustion in a furnace, from bubble columns t
Page: Applications
Explain what the page will be about. Contents Glossary Frequently Asked Questions If you require If you require a new application, or an update to an existing application, please following the guidelines on the Requesting Software https://arccwiki.atlassi
Page: ARCC Policies HPC
This page explains ARCC policies for high-performance computing. Contents These policies and procedures are intended to ensure that ARCC HPC facilities are fairly shared, effectively used, and support the University of Wyoming's research programs that rel
Page: ARCC Prerequisites
In order to use the high performance computing and research data storage that ARCC provides, users must first meet the prerequisites. The requirements are simple: users must be a UWyo faculty member or sponsored by one, possess an active UWyo account, be
Home page: ARCC Wiki
tetons_masthead.jpg Welcome to The Advanced Research Computing Center (ARCC) Wiki at the University of Wyoming! This wiki is intended to share information and best practices related to research computing among researchers and students. Visit Our Website
Page: Auxiliary Services
ARCC has gathered a list of auxiliary services to assist users in their research. Contents Glossary Frequently Asked Questions RStudio Connect https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/59310165/RStudio+Connect RStudio Connect is a publis
Page: Avizo (Loren)
The page details how to access/use Avizo on the Loren cluster. Contents Glossary Frequently Asked Questions Version 9.x.z - General Loren Cluster There are a number of versions of Avizo on the Loren cluster, and some specific to particular machines. Acros

B

Page: BarraCUDA
The aim of the BarraCUDA project is to develop a sequence mapping software that utilizes the massive parallelism of graphics processing units (GPUs) to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome
Page: BASH - Shell
The BASH (Bash, bash) or Bourne-Again SHell is the default shell on ARCC HPC resources. The bash shell is very robust, well documented, and full-featured. Bash can be a little uneasy for those unfamiliar with the shell. This page contains some external li
Page: BLAST
In bioinformatics, BLAST is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. Contents Glossary Frequently Asked Questions Overview

C

Page: C/C++
C++ is a general-purpose programming language created by Bjarne Stroustrup as an extension of the C programming language, or "C with Classes". This page contains links to the scientific libraries and software that utilizes the programming languages C and
Page: CGAL
The Computational Geometry Algorithms Library is an open-source software library of computational geometry algorithms. While primarily written in C++, Scilab bindings and bindings generated with SWIG are also available. Contents Glossary Overview CGAL is
Page: Client Connectivity
Users need to open a VPN connection to the UWyo Network in order to access the petaLibrary from off-campus. UWIT has set up Pulse Secure as the VPN client to the UWyo network. NOTE: These instructions may work for other Linux distributions, but we only su
Page: Command Line Interface (CLI)
The biggest change with using the new CLI is that the previous use of ssh has been replaced by a new command called "globus" (which is an application that must be installed). Contents Glossary Frequently Asked Questions Installation References The CLI app
Page: Compilers
Teton hosts several compiler collections. To utilize a compiler in any of these sets, one must utilize the module command to augment the environment to load the appropriate compiler set. To compile code that requires the utilization of the message passing
Page: COMSOL
COMSOL Multiphysics is a cross-platform finite element analysis, solver, and multiphysics simulation software. It allows conventional physics-based user interfaces and coupled systems of partial differential equations. Coming Soon Contents Glossary Overvi
Page: Contact
The Advanced Research Computing Center (ARCC) is the primary research computing facility for the University of Wyoming. It provides centralized scientific computing resources, including HPC and research storage, and is a gateway to other research institut
Page: Core Services
ARCC's goal is to support research in any way that we can. This includes providing access to our high performance computing environments, Teton and Loren; research data storage systems petaLibrary and Pathfinder; and various tools for facilitating the sto
Page: Cutadapt
Cutadapt https://arccwiki.atlassian.net/wiki/spaces/AIP/pages/542867467/Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. An older version can be here: modu

D

Page: Data Transfer
There are many ways to transfer data with ARCC including Globus, Linux (scp, sftp, rsync), Samba (CIFS and SMB), and Science DMZ. Contents Glossary Training Introduction to Globus https://web.petalibrary.arcc.uwyo.edu/presentations/Globus_2017_cli.pdf Int
Page: Data Transfer and Access
The login nodes (i.e., teton.arcc.uwyo.edu http://teton.arcc.uwyo.edu) support the use of SCP, SFTP, and Rsync. One may be interested in doing SSH multiplexing if often, small transfers are required when working with current SSH connections. For large fil
Page: DENISE (Black Edition)
DENISE Black Edition is a 2D time-domain isotropic (visco) elastic FD modeling and full waveform inversion (FWI) code for P/SV-waves. Contents Glossary Overview 2D time-domain isotropic (visco)elastic finite-difference modeling and full waveform inversion
Page: DENISE - sh
DENISE-sh is a 2D time-domain isotropic (visco)elastic FD modeling and full waveform inversion (FWI) code for SH-waves. Contents Glossary Overview Homepage: 2D time-domain isotropic (visco)elastic FD modeling and full waveform inversion (FWI) code for SH-
Page: DFTB
This page details the DFTB+ application and how to call it via a module and through a bash script to run as a sbatch job. Contents Glossary Frequently Asked Questions Introduction DFTB https://dftbplus.org/ stands for Density Functional based Tight Bindin

E

Page: Ensembl VEP
The Ensembl Variant Effect Predictor (VEP) is a powerful toolset for the analysis, annotation, and prioritization of genomic variants, including in non-coding regions. The VEP accurately predicts the effects of sequence variants on transcripts, protein pr
Page: Events and Other Important Dates
Please check this page to see upcoming events and other important dates for planned outages, scheduled training and other special circumstances. Contents Glossary Frequently Asked Questions All Dates Important dates for ARCC by category. Maintenance There

F

Page: FastX - Software
FastX is a graphical user interface that provides a Linux GUI desktop to a remote client. With FastX, users are able to reliably connect to their Linux desktop from any device with a web browser. This page provides step by step instructions on using FastX
Page: FastX - Web Client
Objective of this tutorial is to describe FastX and demonstrate how it is used with the web client, and why would you want to use it. This is a comprehensive guide, feel free to use the Table of Contents below and jump to the sections that are relevant to
Page: FFTW
The Fastest Fourier Transform in the West is a software library for computing discrete Fourier transforms developed by Matteo Frigo and Steven G. Johnson at the Massachusetts Institute of Technology. FFTW is known as the fastest free software implementati
Page: File Editors
Several file editors are available to edit text-based source files and configuration files. The primary method of editing files is through the usage of console-based editors. The ones that have been proven to be most useful are: vim, emacs, pico, and nano
Page: First Steps
This page covers the first steps users should take after getting access to ARCC resources. Contents Glossary Frequently Asked Questions Know the General Policies There are a few Policies that apply to all ARCC resources that user need to keep in mind when
Page: Fortran
Fortran is a general-purpose, compiled imperative programming language that is especially suited to numeric computation and scientific computing. This page provides information about Fortran and a link to a page that explains how to use Fortran. Contents
Page: Frequently Asked Questions
This page contains frequently asked questions. If users have any trouble, questions, concerns, or suggestions, feel free to contact ARCC mailto:arcc-help@uwyo.edu. Contents Glossary General ARCC Troubleshooting Do I have to have a smartphone to use two-fa
Page: Futures/ Parallel etc.
Explain what the page will be about. Contents Glossary Heading Add Text Here Heading Add Text Here Heading Add Text Here Heading Add Text Here Heading Add Text Here
Page: FWT2D
FWT2D from Seiscope https://seiscope2.osug.fr/?lang=en is a massively parallel program for frequency-domain full-waveform tomography of wide-aperture seismic data. Contents Glossary Overview FWT2D 2D Full-Waveform Topography: is a massively parallel progr

G

Page: GATK
GATK https://gatk.broadinstitute.org/hc/en-us: Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data Contents Glossary Overview GATK https://gatk.broadinstitute.org/hc/en-us: Developed in the Data Sciences Platform at the Broad Inst
Page: Gaussian & GaussView
Gaussian is a computer program used by chemists, chemical engineers, biochemists, physicists, and other scientists. It utilizes fundamental laws of quantum mechanics to predict energies, molecular structures, spectroscopic data (NMR, IR, UV, etc) and much
Page: Getting Connected to the petaLibrary
This page will direct you on how to request access to the petaLibrary and how to connect to the library. Users can connect to the petaLibrary whether they are on campus via SMB or off-campus using Globus, access to the petaLibrary is also available from t
Page: Getting Started
This page will help users get started using ARCC resources. Contents Glossary Frequently Asked Questions ARCC Prerequisites ARCC requires you to have the following to be in place before you can use ARCC High-Performance Computing or Research Data Storage
Page: Globus - Data Transfer
Globus manages file transfers between two machines (two servers, a server, and a personal machine, or two personal machines). It is ideal for large files and available for many institutional clusters and networks. Files can be transferred between Teton, t
Page: Globus Personal Endpoint
A personal endpoint can be created on a computer to transfer files between it and other endpoints. The software application Globus Connect Personal must be installed on a computer to create an endpoint on it and must be running to use the endpoint for a t
Page: Globus Plus
This page contains information about Globus Plus and how to use it. Contents Glossary Frequently Asked Questions Check Whether Your Account Has Globus Plus Access and Upgrade if Necessary Login at globus.org https://www.globus.org/ and go to the Account p
Page: Glossary
This page contains a quick reference guide of common research computing terms. Contents Research Computing: Quick Reference ACL An access-control list, with respect to a computer file system, is a list of permissions attached to an object. An ACL specifie
Page: GPU - BLAST
The Basic Local Alignment Search Tool (BLAST) is one of the most widely used bioinformatics tools. GPU-BLAST can align query sequences against those present in a selected target database. Contents Glossary Overview Using a general-purpose graphics process
Page: GSL
The library provides a wide range of mathematical routines such as random number generators, special functions, and least-squares fitting. There are over 1000 functions in total with an extensive test suite. Contents Glossary Coming Soon Add Text Here Hea
Page: GSuite Cloud Storage for Research
While not an ARCC service, we provide support to UWyo researchers who wish to use GSuite Cloud storage for their research projects. Please keep in mind that this storage is now limited and requests for G Suite storage will be thoroughly vetted. Contents G
Page: GSuite Desktop Integration
On this page we will discuss how to integrate Google Drive into your desktop environment to work seamlessly between the two platforms. The way to do this involves installing some software onto your desktop/laptop and you must have permission to do so, or
Page: GSuite on Linux
Page: GSuite on MacOS
With Drive File Stream, you stream your Drive files directly from the cloud to your Mac, freeing up disk space and network bandwidth. Because Drive files are stored in the cloud, any changes you or your collaborators make are automatically updated everywh
Page: GSuite on Windows
With Drive File Stream, you stream your Drive files directly from the cloud to your PC, freeing up disk space and network bandwidth. Because Drive files are stored in the cloud, any changes you or your collaborators make are automatically updated everywhe
Page: GSuite Quotas
Explain what the page will be about. Contents Glossary Frequently Asked Questions Heading Add Text Here Heading Add Text Here Heading Add Text Here Heading Add Text Here Heading Add Text Here
Page: GSuite Shared Drive Roles
On this page we will discuss how to manage users and mange their roles on your GSuite Shared Drive. Contents Glossary Frequently Asked Questions Membership Roles When you add new members, they’re given Content manager access. You can change a member's acc

H

Page: Hardware - Loren
This page contains information about the nodes and networks used with Loren. Contents Glossary Nodes Node Name Description Management Node The management node is the node that runs the Slurm controller and manages the cluster. Login Node User access node
Page: Hardware - Teton
This Wiki section contains information about the hardware used for research and/or run on the high performance computing system https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/295179/High-Performance+Computing+HPC+Teton at UWyo. Contents Gloss
Page: High Performance Computing
In today's compute-intensive research environment, it is important to have resources that are able to perform particular tasks. ARCC provides users with The Teton Compute Environment, which is a high-performance computing (HPC) cluster with over 500 compu
Page: HPC Installed Software - Loren
Explain what the page will be about. Contents Glossary Heading Add Text Here Heading Add Text Here Heading Add Text Here Heading Add Text Here Heading Add Text Here
Page: HTSeq
HTSeq https://htseq.readthedocs.io/en/master/: Analysing high-throughput sequencing data with Python Contents Glossary Frequently Asked Questions Module Latest: [salexan5@tlog2 ~]$ module spider htseq ------------------------------------------------------

I

Page: Installing Software Yourself on HPC Cluster
There are different ways that software modules can be installed on the Teton cluster, including modules that are available to everyone and modules that are available to a specific project or user. When new software installation is requested, knowing wheth
Page: Introduction to Job Submission 01: Nodes, Tasks and Processors
Introduction The Slurm https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/3113024/Slurm+Workload+Manager page introduces the basics of creating a batch script that is used on the command line with the sbatch command to submit and request a job on
Page: Introduction to Job Submission: 02: Memory and GPUs
Introduction The Slurm https://arccwiki.uwyo.edu/index.php/Software:_Slurm page introduces the basics of creating a batch script that is used on the command line with the sbatch command to submit and request a job on the cluster. This page is an extension
Page: Introductory Tutorials
A list of pages that include step-by-step tutorials to get a basic foundation of each of our research computing services. Contents Glossary Frequently Asked Questions General Using Two-Factor Authentication This tutorial is a comprehensive overview of how
Page: ITK (Loren)
Explain what the page will be about. Contents Glossary Frequently Asked Questions About: ITK https://itk.org/ is an open-source, cross-platform library that provides developers with an extensive suite of software tools for image analysis. Developed throu

J

Page: Java
Java is a general-purpose programming language that is class-based and object-oriented and designed to have as few implementation dependencies as possible. This page contains links to software that utilizes the programming language Java. Contents Glossary
Page: JDK
Java Development Kit (JDK) is a development environment for building applications and components using the Java programming language. Contents Glossary Overview The Java Development Kit is an implementation of either one of the Java Platform, Standard Edi
Page: Job Scheduling Policy
ARCC Policies for High Performance Computing - Job Scheduling Policy Contents Glossary Frequently Asked Questions Job Scheduling on ARCC HPC Systems This section reflects the general ARCC policy for scheduling jobs on all HPC systems administered by ARCC.

K

Page: KentUtils
KentUtils is a suite of tools developed at the USCS Genome Browser https://genome.ucsc.edu/ lab. Contents Glossary Frequently Asked Questions Module: Latest: []$ module spider kentutils ---------------------------------------------------------------------
Page: Known Issues
The purpose of this page is to inform users of ongoing issues known to ARCC. Here we detail what each problem is and what we are doing to remedy it. Any issues that users come across that are not detailed on this page should inform ARCC by emailing us at
Page: Kraken
Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techn

L

Page: LAMMPS
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. LAMMPS makes use of Message Passing Interface for parallel communication and is free and open-source software, distribute
Page: Languages
This page contains a list of links the languages and libraries used on Teton. Contents Glossary C/C++ https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/177504330/C+C+ Scientific Libraries https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pag
Page: Linux - Data Transfer
This page goes over the methods used to transfer data including scp, sftp, and rsync in Linux. In the following examples, the remote system is always teton.arcc.uwyo.edu http://teton.arcc.uwyo.edu. While the local host is always a computer system hosted o
Page: Linux - Logging Into HPC with ssh
The objective of this tutorial is show how to login to the HPC services that ARCC provides. Generally speaking all of our HPC services support login via ssh protocol and the focus of this page. We also provide links to other pages that are specific to dif
Page: Lmod - Software
Lmod is a powerful piece of software that the ARCC leverages for managing dynamic user environments and access to complicated software stacks. The software was developed at the Texas Advanced Computing Center (TACC) to enhance the concepts and functionali
Page: Logging Into HPC
We support several methods to login to our HPC services. On this page you will find links to several tutorials on how to login to our HPC systems including Teton and Loren. Please find the tutorial that best describes your use case and read through it for
Page: Loren
Loren is a GPU based HPC cluster. Contents Glossary Frequently Asked Questions Overview Loren is a specialty HPC cluster used by Dr. Piri’s research group, the High Bay Research Group. Hardware https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/1

M

Page: Mac - Logging into HPC with ssh
The objective of this tutorial is show how to login to the HPC services that ARCC provides. Generally speaking all of our HPC services support login via ssh protocol and the focus of this page. We also provide links to other pages that are specific to dif
Page: MLST
Multilocus sequence typing is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial species using the DNA sequences of internal fragments of multiple housekeeping genes Contents Glossary Overvi
Page: ModelTest
ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces. Contents Glossary Overview ModelTest Ho
Page: MOOSE
Homepage: MOOSE https://www.mooseframework.org/ Multiphysics Object-Oriented Simulation Environment provides a plug-in infrastructure that simplifies definitions of physics, material properties, and postprocessing. includes an ever-expanding set of physic
Page: MSP360 Explorer (Cloudberry)
MSP360™ Explorer provides a user interface allowing you to access, move and manage files across your local storage and the cloud storage of your choice. Instructions for using Pathfinder with MSP360 Explorer are below. Contents Glossary Frequently Asked Q
Page: MUMmer
MUMmer is a system for rapidly aligning large DNA sequences to one another, it is very fast and easy to run. The current version, release 4.x, can find all 20-bp maximal exact matches between two bacterial genomes in just a few seconds on a typical deskto

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Page: NVidia HPC SDK
This page is focused on NVidia’s HPC SDK https://developer.nvidia.com/hpc-sdk. This SDK currently under exploration by the ARCC team so please appreciate that support is limited but feel free to use and send any feedback to arcc-info@uwyo.edu mailto:arcc-

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Page: Open-Source Tools
This section of the wiki contains several code and other tools that ARCC has found useful. These tools are free to use to the larger research community. Contents Glossary Heading Add Text Here Heading Add Text Here Heading Add Text Here Heading Add Text H
Page: OpenBLAST
In scientific computing https://en.wikipedia.org/wiki/Computational_science, OpenBLAS is an open-source https://en.wikipedia.org/wiki/Open-source_software implementation of the BLAS https://en.wikipedia.org/wiki/BLAS (Basic Linear Algebra Subprograms) API
Page: OpenMPI/ IntelMPI
Message Passing Interface is a standardized and portable message-passing standard designed by a group of researchers from academia and industry to function on a wide variety of parallel computing architectures. Contents Glossary OpenMPI Open MPI is a Mess
Page: OpenSMOKE
This page details how to load the OpenSMOKE++ module. Contents Glossary Frequently Asked Questions OpenSMOKE++ https://www.opensmokepp.polimi.it/ Suite is a general framework for numerical simulations of reacting systems with very detailed kinetic mechani

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Page: P7zip
P7zip is a port of 7za.exe for POSIX systems like Unix (Linux, Solaris, OpenBSD, FreeBSD, Cygwin, AIX, ...), MacOS X and also for BeOS and Amiga. 7za.exe is the command-line version of 7-zip, see Z-zip http://www.7-zip.org/ 7-Zip is a file archiver with t
Page: Packages/ Libraries
Explain what the page will be about. Contents Glossary RStan https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/123011082/RStan RStan is the R interface to Stan. It is distributed on CRAN as the RStan package and its source code is hosted on GitH
Page: ParaView
This page details how to access ParaView on the Teton cluster. Although ParaView is installed as a module on the Teton cluster, to be able to use it in its GUI form you will need to FastX onto Teton and start it up from a terminal. ´╗┐Contents Versions: Use
Page: ParaView (Loren)
This page details how to access ParaView on the Loren cluster. Although ParaView is installed as a module on the Loren cluster, to be able to use it in its GUI form you will need to FastX onto the specific loren101 node and start it up from a terminal. ´╗┐C
Page: Partitions
The Slurm configuration on Teton is quite complicated to help with the layout of hardware, investors, and runtime limits. The following tables represent the partition on Teton. Some require a QoS which will be auto-assigned during job submission. The tabl
Page: Pathfinder
Named after one of Wyoming’s reservoirs on the North Platte River, Pathfinder is a low-cost storage solution that enables a Cloud-like presence for research data hosted by ARCC. The system is built to be expandable and provides data protection. Its core f
Page: PerGEOS (Loren)
The page details how to access/use PerGEOS on the Loren cluster. Contents Glossary Frequently Asked Questions Version 1.x.z - General Loren Cluster There are a number of versions of PerGEOS on the Loren cluster, and some specific to particular machines. A
Page: petaLibrary
For convenience and organization, the petaLibrary is split into two distinct areas. The first area, Data Commons https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/82247742/petaLibrary#Data-Commons, is for data being utilized in active research p
Page: petaLibrary Policies
This page goes over the ARCC petaLibrary policies. Contents petaLibrary Policies Data Protection Backups Data Protection/Backups Policy: Data residing in Commons, Homes, or Restricted file shares are protected each night with a read-only snapshot. 20 snap
Page: PETSc
PETSc https://www.mcs.anl.gov/petsc/index.html, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. Contents Glossary F
Page: Policies
The following is a list of general computer use policies, procedures, and security rules that apply to individual end-users of the Advanced Research Computing Center (ARCC) resources. These policies and procedures are intended to ensure that UW Research C
Page: Privacy Policy
Privacy Policy for all ARCC resources. Contents Data Collection The information collected through this site, and other UW pages/sites linked from it (e.g. a help ticket system), includes the necessary information to provide and manage ARCC products and se
Page: PSMC
The Pairwise Sequentially Markovian Coalescent (PSMC) method uses the genome sequence of a single individual to estimate demographic history covering a time span of thousands of generations. Contents Glossary Overview Pairwise Sequentially Markovian Coale
Page: Python
Python is an interpreted, high-level, general-purpose programming language. Created by Guido van Rossum and first released in 1991, Python's design philosophy emphasizes code readability with its notable use of significant whitespace. Contents Glossary Us
Page: Python Libraries Available
Current Python libraries available are listed below. Contents Glossary Using PyTorch https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/177209438/Using+PyTorch PyTorch is an open source machine learning library based on the Torch library. Using T

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Page: QIIME
Quantitative Insights Into Microbial Ecology (QIIME) is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other pla
Page: Quantum Espresso
This page details how to load the Quantum Espresso module and provides a basic template on how to run via the slurm sbatch command. Contents Glossary Frequently Asked Questions Check and Load Versions Use the module spider command to check the current ver

R

Page: R
R is a programming language and free software environment for statistical computing and graphics supported by the R Foundation for Statistical Computing. The R language is widely used among statisticians and data miners for developing statistical software
Page: R Shiny Server
The content on this page describes the R Shiny Server specialty service that we offer. Contents Glossary Frequently Asked Questions About Shiny Server RStudio lets you put Shiny web applications and interactive documents online in the way that works best
Page: Ray
Ray is a parallel software that computes de novo genome assemblies with next-generation sequencing data. The software is written in C++ and can run in parallel on numerous interconnected computers using the message-passing interface (MPI) standard. Conten
Page: rclone
Rclone is a command line program to manage files on cloud storage. It is a feature rich alternative to cloud vendors' web storage interfaces. Over 40 cloud storage products https://rclone.org/#providers support rclone including S3 object stores, business
Page: Requesting Software
This page details the list of questions that you need to consider and provide details on when requesting new or an update to software. This will assist us in understanding your needs and assessing and prioritizing the installation. Contents Glossary Frequ
Page: Research Data Storage
The UW Libraries and UW/IT have collaborated on a shared digital data repository designed to provide two main functions: 1) a storage service for UW researchers who need to reliably and safely store and securely exchange data with students, and collaborat
Page: Research Projects
This section of the wiki is for projects using ARCC resources to give information on their project, related science, and use of ARCC resources, that they would like to share with the research community. Contents Glossary Research Projects Project Page Dep
Page: Research: Publications and Reports
This page contains details about publications produced using ARCC resources. Contents Publications Produced Using ARCC Resources Project: EvolvingAI Clune J, Mouret J-B, Lipson H (2013) The evolutionary origins of modularity. Proceedings of the Royal Soci
Page: ROHan
ROHan is a Bayesian framework to estimate local rates of heterozygosity, infer runs of homozygosity (ROH) and compute global rates of heterozygosity outside of ROHs. ROHan can work on modern and ancient samples with signs of ancient DNA damage. Contents G
Page: RStan
RStan is the R interface to Stan. It is distributed on CRAN as the RStan package and its source code is hosted on GitHub. Contents Glossary Frequently Asked Questions Overview RStan https://mc-stan.org/rstan/: The R interface to Stan CRAN: RStan https://c
Page: RStudio Connect
RStudio Connect is a publishing platform for the work your teams create in R and Python. Use push-button publishing from the RStudio IDE, scheduled execution of reports, and flexible security policies to bring the power of data science to your entire ente

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Page: Samba - Data Transfer
ARCC supports accessing the Teton filesystem via SMB/CIFS from Windows, macOS, and Linux when needing to access the data from outside the cluster, but still on the UW campus. One can use SMB to connect to the Teton storage using the UW credentials provide
Page: SAVA
SAVA: 3D seismic finite-difference modeling, Full Waveform Inversion (FWI) and Reverse Time Migration (RTM) code for wave propagation in isotropic (visco)-acoustic/elastic and anisotropic orthorhombic/triclinic elastic media, which I developed together wi
Page: Science DMZ - Data Transfer
A Science DMZ ("science demilitarized zone") is a portion of a larger network that has been configured and optimized for high-volume bulk data transfer, remote experiment control, and data visualization for high-performance science applications Contents G
Page: Scientific Computing Libraries
Explain what the page will be about. Contents Glossary CGLA https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/107479246/CGAL Computational Geometry Algorithms Library FFTW https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/177602571/FFT
Page: Share & Collaborate in Shared Drives
Any files you put in a shared drive are automatically shared with members of the shared drive. Any member can also share files with people who aren’t members unless you restrict sharing. Do not Share the entire Shared Drive with Multiple Roles. Especially
Page: Sharing an Endpoint
This page explains how to share an endpoint using Globus. Contents Glossary Frequently Asked Questions Transferring Data Using the Globus Web Interface Logging In Login to the Globus website: Go to globus.org https://www.globus.org/ and click the Login bu
Page: Singularity
Coming Soon Contents Glossary Coming Soon Add Text Here Heading Add Text Here Heading Add Text Here Heading Add Text Here Heading Add Text Here
Page: Slurm - Jobs and Nodes
Slurm is the basis of which all jobs are to be submitted, this includes batch https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/91193649/Slurm+Jobs+and+Nodes#Batch-Jobs and interactive https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/
Page: Slurm Job Arrays
This page will introduction the details to using Slurm Job Arrays: More details can be found on the Slurm Job Array Support https://slurm.schedmd.com/job_array.html page. Contents Glossary Frequently Asked Questions Why Use a Job Array? If you have the sa
Page: Slurm Job Performance
This page will detail how to use the slurm commands to view various performance values for a job, such as CPU and memory usage. Contents Glossary Frequently Asked Questions Note: On some clusters and other articles they will talk about ssh-ing on to speci
Page: Slurm Workload Manager
The Slurm Workload Manager https://slurm.schedmd.com is a powerful and flexible workload manager used to schedule jobs on high performance computing (HPV) clusters. The Slurm Workload Manager is can be used to schedule jobs, control resource access, provi
Page: SNOPT
SNOPT is a general-purpose system for constrained optimization. It minimizes a linear or nonlinear function subject to bounds on the variables and sparse linear or nonlinear constraints. It is suitable for large-scale linear and quadratic programming and
Page: Software - Loren
This page contains information about the software specific to Loren. Contents Glossary Code A large number of locally written codes are also used and developed on the cluster using C, C++, Fortran, and other languages. GUI On the specialty GUI nodes, user
Page: Software - Teton
This Wiki section contains information about the software used for research and/or run on the high performance computing https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/295179/High-Performance+Computing+HPC+Tetonsystem at UWyo. It provides sho
Page: Software Policy
ARCC Policies for High Performance Computing - Software Policy Contents Glossary Frequently Asked Questions Software Acquisition, Installation, and Support (AIS) Policy Overview This document defines the ARCC's software policy regarding software acquisiti
Page: Software Update Log
This page shows when the software was installed or last updated, the current version, and what was added during the update. When loading a module we recommend always defining the version you require, and not relying on what you think the default version m
Page: Software Update Log: Loren
This page shows when the software was installed or last updated, the current version, and what was added during the update. When loading a module we recommend always defining the version you require, and not relying on what you think the default version m
Page: SourceTracker2
This page details the use of the SourceTracker2 application. Contents Glossary Frequently Asked Questions Overview Homepage: SourceTracker2 https://github.com/biota/sourcetracker2: Contamination is a critical issue in high-throughput metagenomic studies,
Page: Spades
This page details how to load the Spades module. Contents Glossary Frequently Asked Questions SPades https://cab.spbu.ru/software/spades/: It’s all about the viruses: new coronaSPAdes, rnaviralSPAdes and metaviralSPAdes pipelines. V3.15.2: Manual https://
Page: Storage Policy
ARCC Policies for High Performance Computing - Storage Policy Contents Glossary Frequently Asked Questions Overview Code-named Teton, the ARCC high-performance storage system (HPS) is a high speed, tiered storage system designed to maximize performance wh
Page: System Querying - Loren
Loren uses the Slurm Job Scheduler for managing and running jobs within the cluster. The job scheduler makes sure that the cluster resources are efficiently scheduled and used by user jobs. Jobs are submitted to a single partition and slurm runs them on
Page: System Querying - Teton
System querying is helpful to understand what is happening with the system. Meaning, what compute jobs are running, storage quotas, past compute job history, etc. This page contains commands and examples of how to find that information. Contents Glossary
Page: System Status
This page shows the statuses of petaLibrary, Teton Storage Compute, and Teton Storage NES/SMB. System Statuses Globus Endpoint Status To see the latest available status, reload this page. The status shown here is updated every two hours. ARCC Managed Lice

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Page: Terms of Use Policy
General policies on the use of ARCC resources. Contents Applicable Policies and Acceptance Acceptance The process of requesting an allocation on an ARCC resource includes acceptance of any policies specific to that resource, and of this Terms of Use which
Page: Teton
The Teton Compute Environment, or Teton for short, is a high performance computing (HPC) cluster with over 500 compute nodes that allow researchers to perform computation-intensive analysis on large datasets. Teton contains high performance data storage s
Page: Teton Filesystem
This page details information on the filesystems on Teton. Contents Glossary Frequently Asked Questions Global Filesystems The Teton global parallel filesystem configured with a 160 TB SSD tier for active data and 1.2 PB HDD capacity tier for less-used da
Page: The Web Interface
Explain what the page will be about. Contents Glossary Frequently Asked Questions Transferring Data Using the Globus Web Interface Logging in Login to the Globus website: Go to globus.org https://www.globus.org/ and click the Login button. In the drop-dow
Page: Training & Other Resources
ARCC provides training on using ARCC resources and other research computing topics through various scheduled courses, online courses, and other methods. Contents Glossary ARCC Provided Training ARCC Courses on WyoLearn ARCC Courses can be found on the Wyo
Page: TREES
TREES: The Terrestrial Regional Ecosystem Exchange Simulator (TREES) is a dynamic biophysical process based simulation model. Contents Glossary Frequently Asked Questions Overview: The current module was built from the TREES Workshop 2020 https://github.c

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Page: User Services
ARCC provides consultation and training services as a core ARCC service. This service is for all researchers at UWyo whether they use the HPC system, the Research Data Storage System, or if they have any other Research Computing topics they want to be cov
Page: Using a GSuite Shared Drive at UWyo
This page will discuss how to use a GSuite Shared Drive with your research team. Contents Glossary Frequently Asked Questions Setting Up a Shared Drive In order to set up a Shared Drive you must contact the UWIT Application Security Office at accounts-it@
Page: Using ARCC Resources for Education Policies
We offer the use of our HPC and Storage core services in UWYO courses for educational purposes. Before requesting ARCC resources for a class please read the following policies and make sure to contact ARCC https://arccwiki.atlassian.net/wiki/spaces/DOCUME
Page: Using Dadi
Dadi https://dadi.readthedocs.io/en/latest/ is a powerful software tool for simulating the joint frequency spectrum (FS) of genetic variation among multiple populations and employing the FS for population-genetic inference. Contents Glossary Frequently As
Page: Using Fortran
Fortran is a general-purpose, compiled imperative programming language that is especially suited to numeric computation and scientific computing, this page details how to use Fortran. Contents Glossary How to Use Fortran Fortran Basics The Fortran languag
Page: Using Globus with the petaLibrary
Globus can be used with the petaLibrary. Contents Glossary Overview System Name Globus Endpoint Name ARCC petaLibrary ARCC petaLibrary Add Text Here Heading Add Text Here Heading Add Text Here Heading Add Text Here Heading Add Text Here
Page: Using Miniconda to Install Software
Miniconda version of Anaconda is a free minimal installer for conda that is available as modules on Teton. It includes only conda, Python, the packages they depend on, and a small number of other useful packages, including pip, zlib, and a few others. It
Page: Using MS Office Files in Google Drive
Explain what the page will be about. Contents Glossary Frequently Asked Questions Heading Add Text Here Heading Add Text Here Heading Add Text Here Heading Add Text Here Heading Add Text Here
Page: Using PyTorch
PyTorch https://pytorch.org/ is a Python package that provides two high-level features: Tensor computation (like NumPy) with strong GPU acceleration Deep neural networks built on a tape-based autograd system Contents Glossary Frequently Asked Questions Ov
Page: Using TensorFlow
TensorFlow https://www.tensorflow.org/ is a free and open-source software library for dataflow and differentiable programming across a range of tasks. Contents Glossary Frequently Asked Questions Overview TensorFlow is an end-to-end open source platform f
Page: Using the DGX Nodes
The page details using the DGX nodes, specifically running the Python TensorFlow package from within a Conda environment, with examples on the type of submission templates and output. Introduction: DGX nodes: These are on a special partition that requires
Page: Using the Wiki
This page is a how-to for using and for navigating this Wiki site. Information on navigation resources and directions are provided, along with resources that will be helpful to users. In addition to these helpful tools, this page contains information rela
Page: Using Two-Factor Authentication
Objective of this tutorial is to describe what two-factor authentication is, why we use it at ARCC, and demonstrate how it gets used. We use the same methods that UWIT uses for second factor tokens and instructions on how to enroll can be found on their k
Page: Utilities
ARCC has put together a list of utilities for users to utilize. Contents Glossary Frequently Asked Questions P7zip https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/107479452/P7zip A Unix port of the 7z file archiver.

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Page: VASP
The Vienna Ab initio Simulation Package (VASP), is a package for performing ab initio quantum mechanical calculations using either Vanderbilt pseudopotentials, or the projector augmented wave method and a plane wave basis set. NOTE: VASP is NOT publicly a
Page: VSEARCH
This page details how to load and basic use of VSEARCH. Contents Glossary Frequently Asked Questions Overview The main support page for VSEARCH can be found here https://github.com/torognes/vsearch, where you can find additional documentation and the curr
Page: VTK (Loren)
Explain what the page will be about. Contents Glossary Frequently Asked Questions About: The Visualization Toolkit https://vtk.org/ (VTK) is open source software for manipulating and displaying scientific data. It comes with state-of-the-art tools for 3D

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Page: Wiki Directory
This page is intended to make searching and finding content contained in this Wiki easier to navigate. Each letter shows a number next to it. That number is the number of pages and headers that begin with that letter. Each content subject gives informatio
Page: Windows - Logging into HPC with ssh
Objective of this tutorial is to describe and demonstrate the various methods for logging into an HPC system from a computer running the Windows Operating System (OS). This one covers the use of the native Command Prompt to use ssh. This is a comprehensiv
Page: Windows - MobaXterm Login
Objective of this tutorial is describe and demonstrate how to use the ssh client MobaXTerm on a Windows computer to log into an HPC system. This is a comprehensive guide, feel free to use the Table of Contents below and jump to the sections that are relev

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