Wiki Directory_old
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.
Space Index
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0-91.1 Terms of Use PolicyPolicy directing terms for use of ARCC resources. Contents Glossary Frequently Asked Questions 1.1.1 UW Acceptable Use Policy ARCC clusters and UW resources are made available to the UW research community, and as such are covered by Unireg 8-1 https://www
1.2 Security and Privacy Policy
Privacy Policy for all ARCC resources. Contents Glossary Frequently Asked Questions 1.2.1 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
1.3 Acknowledgement Policy
1.3.1 Annual Reporting At the end of each academic year, ARCC requires an accomplishment report from each PI containing: The research results (in laymen terms supported by graphs, images, or videos produced) obtained using ARCC resources, A list of scient
2.1 ARCC HPC Policies
Glossary Frequently Asked Questions ARCC HPC 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 rely on computational facilities not a
2.1.2 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
2.1.3 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.
2.1.4 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
2.1.5 Storage Policy
ARCC High Performance Computing Policy - Storage Contents Glossary Frequently Asked Questions Overview ARCC provides several types of storage for researchers. Each is detailed below. Research Data Storage ARCC provides two options for research data storag
2.1.6 Default Service Quotas
ARCC High Performance Storage and HPC Compute Quotas Contents Glossary Frequently Asked Questions UW ARCC Default Service Quotas All services up to the listed quotas are provided to UW Researchers at no cost to them. Any services above standard service qu
2.1.7 Using ARCC Resources for Education
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 for clarification on any of them. Using HPC Servi
2.2 Cost of resources and services
This page details the actual cost of HPC at the University of Wyoming. Compute ARCC operates its HPC clusters via an investment model: a UW researcher may invest into compute nodes on the ARCC HPC clusters by funding their purchase. This gives them priori
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AAccounts: Access and SecurityOverview This page serves as a parent page for general information about obtaining an account to access HPC resources. HPC Account Requests Any HPC account may be requested using the Account Request Form https://arccwiki.atlassian.net/servicedesk/customer
Adios2
Overview Adios2 https://csmd.ornl.gov/software/adios2: ADIOS 2: The Adaptable Input Output (I/O) System version 2 is an open-source framework that addresses scientific data management challenges, e.g. scalable parallel I/O, as we approach the exascale era
Advanced Usage
Overview Pathfinder uses Ceph https://docs.ceph.com/en/pacific/rados/index.html internally to provide a generic S3 compliant storage endpoint. Ceph’s S3 implementation has many user configurable settings that can be tweaked from the CLI. This document aim
Alcova
Overview Alcova is a highly collaborative space geared toward project-oriented data storage for use by UWYO research groups and their collaborators. To provide users with a seamless computing experience, Alcova is connected to the UWyo network for blazin
Alphafold
Overview DeepMind: AlphaFold https://github.com/deepmind/alphafold: can accurately predict 3D models of protein structures and has the potential to accelerate research in every field of biology. Documentation AlphaFold Protein Structure Database https://a
ANGSD
Overview ANGSD http://www.popgen.dk/angsd/index.php/ANGSD: is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genoty
ANSYS Fluent
This software is not currently available. Overview ANSYS https://www.ansys.com/ Fluent software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from airfl
ant
Overview Ant https://ant.apache.org/: Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Ja
Applications
Below are various applications, compilers, and languages that we have documented. If you have difficulty using any of this software please see the Lmod page or fell free to get in touch with us at arcc-help@uwyo.edu mailto:arcc-help@uwyo.edu. If you requi
ARCC Commands
This page details the use of a variety of ARCC specific cluster related commands. Core Hour Usage for User: chu_user Usage: Calculate the total core usage hours for a user. Syntax: chu_user [-u|y|m|Y|h] options: u <user> : optional : username to look up -
ARCC Investment Program
rack.png Investing in compute nodes, storage, or specialty infrastructure in an HPC is often advantageous for many researchers. These advantages can become more apparent when comparing the time and capital a researcher and their cohorts can expend when se
ARCC Newsletter
ARCC_UW2.png Advanced Research Computing Center Spring 2023 Newsletter https://newsletter.pathfinder.arcc.uwyo.edu/index.html https://newsletter.pathfinder.arcc.uwyo.edu/index.html New Training Offerings training.png ARCC is proud to offer several new tra
ARCC Specialized Services
As research pulls innovation forward, these same innovations then lead the way for more groundbreaking research. Our specialized services, even if now commonplace or widely used can a byproduct of specific needs from a researcher. If we do not provide som
ARCC Wiki
notbrown.png UW ARCC: Primary Research Computing Facility at the University of Wyoming Welcome to The UW ARCC (Advanced Research Computing Center) Wiki This wiki is intended to share information and best practices related to research computing among rese
Astral
Overview Astral https://github.com/smirarab/ASTRAL: ASTRAL is a tool for estimating an unrooted species tree given a set of unrooted gene trees. Using Use the module name astral to discover versions available and to load the application. Multicore The ast
ATAT
Overview Alloy Theoretic Automated Toolkit https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/ (ATAT) is a generic name that refers to a collection of alloy theory tools developed by Axel van de Walle, in collaboration with various research grou
Augustus
Overview Augustus https://github.com/Gaius-Augustus/Augustus: AUGUSTUS is a program to find genes and their structures in one or more genomes. Using Use the module name augustus to discover versions available and to load the application. AUGUSTUS_CONFIG_P
Avizo
Overview Avizo https://www.thermofisher.com/us/en/home/electron-microscopy/products/software-em-3d-vis/avizo-software.html is an imaging data analysis tools designed by ThermoFischer Scientific to facilitate better understanding of your materials structur
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BBamtoolsOverview BamTools https://github.com/pezmaster31/bamtools: provides both a programmer's API and an end-user's toolkit for handling BAM files. Related wiki https://github.com/pezmaster31/bamtools/wiki Using Use the module name bamtools to discover versions
BarraCUDA
Overview 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 referen
BASH - Shell
Overview 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 ex
BayeScan
Overview BayeScan http://cmpg.unibe.ch/software/BayeScan/index.html aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet m
Bcftools
Overview BCFtools: is part of the Samtools https://www.htslib.org/ which is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: BCFtools (as with Samtools) use HTSlib internally, but these
Beartooth
Overview The Beartooth Compute Environment (AKA Beartooth) is a high performance computing (HPC) cluster that offers over 500 compute nodes and 1.2 PB of storage. ARCC works to maintain an expected uptime of 98%, allowing researchers to perform computatio
Beartooth DGX Node Changes
As part of the June 12-16 Beartooth maintenance, the two Beartooth DGX nodes listed in our Beartooth Hardware Summary table have been updated with Red Hat 8.8. Prior to our upgrade, the referenced nodes ran Ubuntu 18.04.2 LTS. Post upgrade they are runnin
Beartooth Filesystem
Overview: Beartooth uses the Teton Creek parallel filesystem configured with a 190 TB SSD tier for active data and 1.2 PB HDD capacity tier for less-used data. The system policy engine moves data automatically between pools (disks and tiers). The system w
Beartooth Hardware Summary Table
The table is based on July 26, 2023 data. Slurm Partition name Requestable features Node count Sockets/ Node Cores/ Socket Threads/ Core Total Cores/ Node RAM (GB) Processor (x86_64) Local Disks OS Use Case Key Attributes moran fdr, intel, sandy, ivy, com
Beartooth Software List
Overview Herein, find summaries of each package with links to a more detailed page for each package. Below is a list of software / applications that are available on Beartooth. Click the software title to learn more about a particular software package, in
Beartooth's "non-investor" partition
Beartooth has a special partition called “non-investor” that functions a little differently than other partitions. Rather than being based on a specific hardware set or level of investment, the non-investor partition lumps all community nodes into one par
Beast1
Overview Beast1 https://beast.community/: BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. Using Use the module name beast1 to discover versions available and to load the application. The application comes in two
Beast2
Overview BEAST2 https://www.beast2.org/ is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of rec
Bedops
Overview Bedops https://bedops.readthedocs.io/en/latest/index.html: BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other manag
Bedtools2
Overview bedtools2 https://github.com/arq5x/bedtools2: Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. Documentation https://bedtools.readthedocs.io/en/latest/ and tutorial http://quinlanla
BioPerl
Overview BioPerl https://bioperl.org/: BioPerl is the product of a community effort to produce Perl code which is useful in biology. Using Use the module name perl-bioperl to discover versions available and to load the application. Also note the version o
Biopython
Overview Biopython https://biopython.org/is a set of freely available tools for biological computation written in Python http://www.python.org/ by an international team of developers. The standard Biopython package and release supports the following forma
BLAST
Overview BLAST https://blast.ncbi.nlm.nih.gov/Blast.cgi: 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 sequence
Blender
Overview Blender https://www.blender.org/ is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline - modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creati
BlobTools2
Overview BlobTools2 https://blobtoolkit.genomehubs.org/blobtools2/is a reimplementation of BlobTools https://blobtools.readme.io/docs, written in Python 3 with a fully modular design to make creating new datasets and adding additional analysis types even
Bowtie2
Overview Bowtie2 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of chara
Brains
Overview Brains: Brains: BLR Reverberation-mapping Analysis In AGNs with Nested Sampling: A package for dynamically modeling broad-line regions, analyzing reverberation-mapping and spectro-astrometric data, and measuring the central black hole mass in act
Bridger
Overview Bridger https://sourceforge.net/projects/rnaseqassembly/: Bridger is a tool for de novo assembly of RNA-seq full-length transcriptome data. The Bridger algorithm adapts schemes used in Cufflink and Trinity. It can handle paired-end reads and mult
Busco
Overview Busco https://busco.ezlab.org/assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs. Using Use the module name busco to discover versions available and to load the application. Multicore The busco
BWA
Overview BWA https://github.com/lh3/bwa (Burrow-Wheeler Aligner) is a software package for mapping DNA sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. The first algo
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CC/C++Overview 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 languag
Canu
Overview Canu https://canu.readthedocs.io/en/latest/index.html: Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). Using Use the module name canu to discover versi
CDNest
Overview CDNest: CDNest: C version of diffusive nested sampling proposed by Brendon Brewer. GitHub https://github.com/LiyrAstroph/CDNest: Documentation https://cdnest.readthedocs.io/en/latest/ Using Use the module name cdnest to discover versions availabl
Cell Ranger ATAC
Overview Cell Ranger ATAC https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac is a set of analysis pipelines that process Chromium Single Cell ATAC data. Using Use the module name cell-ranger-atac to discove
CGAL
Overview CGAL https://www.cgal.org/index.html: is a software project that provides easy access to efficient and reliable geometric algorithms in the form of a C++ library. CGAL is used in various areas needing geometric computation, such as geographic inf
Circlator
Overview circlator https://sanger-pathogens.github.io/circlator/: (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Using Use the module name circlator to discover versions available and to load the app
Citing UW ARCC Resources
A requirement of all allocations and use of HPC resources managed by ARCC is to acknowledge ARCC support for your research. Our ability to identify supported scientific results helps ensure continued support from the State of Wyoming, federal agencies and
Clustal Omega
Overview Clustal Omega http://www.clustal.org/omega/: Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a f
cmake
Overview CMake https://cmake.org/: CMake is an open-source, cross-platform family of tools designed to build, test and package software. CMake is used to control the software compilation process using simple platform and compiler independent configuration
Cmdstan
Overview Stan https://mc-stan.org/: Stan is a state-of-the-art platform for statistical modeling and high-performance statistical computation. Stan Interfaces: The Stan modeling language and statistical algorithms are exposed through interfaces into many
Compilers
Overview Beartooth hosts a number of compilers with the GNU family collection currently being the primary with the majority of our software tree and libraries being built with it. Take a look at the child pages to see what other family of compilers are av
COMSOL
Overview Comsol http://comsol.com/: 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.
Configuring SSH Key on a Mac with Cyberduck
UW ARCC is changing the way you authenticate on our devices and ssh authentication is now available using a public/private ssh key combination. This makes it possible to authenticate your login on WildIris without a password. What this means for our users
Connecting to WildIris
Overview This document describes how to connect to WildIris. This is being developed. Install and Set up 2 Factor Authentication WildIris supports two factor login with a number of 2 factor authentication devices. UW ARCC has tested 2 factor authenticatio
Contact Information & Staff Listings
About ARCC 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 resear
Containers and Virtual Envs
Below are the containers and virtual environments currently available. Please see the child pages for details.
CUDA
Overview CUDA https://developer.nvidia.com/cuda-toolkit is a parallel computing platform and programming model developed by NVIDIA for general computing on graphical processing units (GPUs). With CUDA, developers are able to dramatically speed up computin
cuDNN
Overview cuDNN https://developer.nvidia.com/cudnn: The NVIDIA CUDA® Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks https://developer.nvidia.com/deep-learning. cuDNN provides highly tuned implementat
Cutadapt
Overview Cutadapt https://cutadapt.readthedocs.io/en/stable/ finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Using Use the module name cutadapt to discover version
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DData Storage ServicesOverview This page is a gateway to UW ARCC hosted storage, along with links to other storage related topics, resources and services. ARCC Hosted Research Data Storage ARCC offers research data storage as a core service. We currently offer two data storage
Datacenter Cooling Infrastructure Upgrade
Overview UW IT Datacenter has planned a critical infrastructure upgrade to increase overall power load available on Beartooth beginning Wednesday February 8th, 2023. This upgrade is necessary as we move forward to house new generations of equipment and s
DeepLabCut
Overview DeepLabCut http://www.mackenziemathislab.org/deeplabcut/: an efficient method for 2D and 3D markerless pose estimation based on transfer learning with deep neural networks. GitHub https://github.com/DeepLabCut/DeepLabCut Documentation https://dee
DENISE (Black Edition)
Overview DENISE Black Edition https://github.com/daniel-koehn/DENISE-Black-Edition: 2D time-domain isotropic (visco)elastic finite-difference modeling and full waveform inversion (FWI) code for P/SV-waves, which have been developed together with André Kur
DENISE - sh
Overview DENISE-sh: 2D time-domain isotropic (visco)elastic FD modeling and full waveform inversion (FWI) code for SH-waves Installed version from Fossa_Carolina_LBL_FWI_repro_pack Fossa_Carolina_LBL_FWI_repro_pack https://www.dropbox.com/s/5jgr389tbllmef
DFTB
Overview DFTB https://dftbplus.org/ stands for Density Functional based Tight Binding (and more). It is an implementation of the Density Functional based Tight Binding (DFTB) method, containing many extensions to the original method. The development is su
Documentation, Help and Policies
Overview This page is the jumping off point for ARCC help and broad spectrum service and utility documentation. Resource specific documentation can be found under each particular resource. Getting Help: Access to services can be requested by visiting the
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EEarlier This Year...A new way to request service and/or help (10 October 2022) Starting on 10 October, ARCC will be using a new portal for requesting services https://arccwiki.atlassian.net/servicedesk/customer/portals. UWIT’s ticketing system will no longer be used for ARCC
EddyPro Engine
Overview EddyPro https://github.com/LI-COR/eddypro-engine is a powerful open source software application for processing eddy covariance data. It computes fluxes of water vapor (evapotranspiration), carbon dioxide, methane, other trace gases, and energy wi
ELPA
Overview ELPA https://elpa.mpcdf.mpg.de/: The ELPA project has been started in 2008 with the aim to support the then up coming Petaflop HPC systems (hence the name Eigenvalue Solvers for Petaflop Applications). User Guide https://gitlab.mpcdf.mpg.de/elpa/
End User Support Services
Overview 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
EnergyPlus
Overview EnergyPlus https://energyplus.net/is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumption—for heating, cooling, ventilation, lighting, plug and process loads, and water use in
Ensembl-VEP
Overview Ensembl Variant Effect Predictor (VEP) https://uswest.ensembl.org/info/docs/tools/vep/index.htmlis a powerful toolset for the analysis, annotation, and prioritization of genomic variants, including in non-coding regions. The VEP accurately predic
Exonerate
Overview exonerate https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate: Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment model, either exhaustive dynamic programming or a
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FFastQCOverview FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which yo
FASTX-Toolkit
Overview FASTX-Toolkit http://hannonlab.cshl.edu/fastx_toolkit/: The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Using Use the module name fastx-toolkit to discover versions available and to load th
FFTW
Overview The Fastest Fourier Transform in the West (FFTW) is a software library https://en.wikipedia.org/wiki/Library_(computer_science) for computing discrete Fourier transforms https://en.wikipedia.org/wiki/Discrete_Fourier_transform (DFTs) developed by
File Editors
Overview 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,
File Management and Transfer through WebGUI
Overview Opens a new browser tab where you can navigate between your home, project and gscratch folders. Note: File upload is currently limited to a maximum size of 10G. image-20211018-203211.png image-20211018-203250.png Basic Web Interface Image 01: Bas
File Sharing over Globus
Globus allows users to share files and data with users at other institutions using a web browser or command line interface. Data is transferred between source and destination securely while maintaining high level performance and validates the data transfe
FileZilla
Overview FileZilla https://filezilla-project.org/: The free FTP solution. The FileZilla Client not only supports FTP, but also FTP over TLS (FTPS) and SFTP. It is open source software distributed free of charge under the terms of the GNU General Public Li
Fortran
Overview Fortran https://fortran-lang.org/en/ 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
FreeBayes
Overview FreeBayes https://github.com/freebayes/freebayes: a haplotype-based variant detector. Using Use the module name freebayes to discover versions available and to load the application. Module loading freebayes also loads the following applications:
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 For general issues please see our Known Issu
FunGAP
Overview FunGAP https://github.com/CompSynBioLab-KoreaUniv/FunGAP: Fungal Genome Annotation Pipeline. FunGAP performs gene prediction on given genome assembly and RNA-seq reads. Using The is no fungap module, instead we install this locally within a proje
FWT2D
Overview FWT2D http://seiscope.oca.eu/spip.php?rubrique7 from Seiscope https://seiscope2.osug.fr/?lang=en is a massively parallel program for frequency-domain full-waveform tomography of wide-aperture seismic data. FWT2D 2D Full-Waveform Topography: is a
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GGATKOverview GATK https://gatk.broadinstitute.org/hc/en-us: Genome Analysis Toolkit Variant Discovery in High-Throughput Sequencing Data. Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary
Gaussian and GaussView
Overview Gaussian https://gaussian.com/ 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 d
GDAL
Overview GDAL https://gdal.org/: GDAL is a translator library for raster and vector geospatial data formats that is released under an MIT style Open Source License https://gdal.org/license.html#license by the Open Source Geospatial Foundation http://www.o
GeneMark-ES Suite
Overview GeneMark http://exon.gatech.edu/index.html: A family of gene prediction programs developed at Georgia Institute of Technology , Atlanta, Georgia, USA. GeneMark-ES http://exon.gatech.edu/gmes_instructions.html: Unsupervised training is an importan
Gentools
Overview As part of a July 2022 workshop being delivered on the WildIris cluster, the following group of packages have been made available as a single module environment. Application / Package Version Notes: blobtools https://blobtools.readme.io/docs 1.1.
GEOS
Overview GEOS https://libgeos.org/: Is a C/C++ library for computational geometry with a focus on algorithms used in geographic information systems (GIS) software. It implements the OGC Simple Features geometry model and provides all the spatial functions
Getting Started with ARCC
Getting Started Get an HPC Account https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/1913684148/Accounts%3A+Access+and+Security#HPC-Account-Requests and be added to a project https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/1913684148
Getting Started with Southpass
SouthPass
gffcompare
Overview gffcompare http://ccb.jhu.edu/software/stringtie/gff.shtml#gffcompare: The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the "query" files), when compared with a reference annotation (a
Git
Overview Git https://git-scm.com/: Is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Using Use the module name git to discover versions available and to
GitLab
Overview https://gitlab.arcc.uwyo.edu https://gitlab.arcc.uwyo.edu is a collaborative code development service hosted on ARCC resources that runs the community edition of GitLab https://about.gitlab.com/. Requesting access to GitLab To request access, ple
Gitlab Maintenance Scheduled July 28-31, 2023
ARCC’s internal GitLab server will be undergoing scheduled maintenance from 8am Friday July 28th, through 8am Sunday July 30th, 2023 with additional maintenance July 31st from 9pm to 12am. During these times we will be upgrading our services and adding mo
Globus
Overview Globus is a cloud based SAAS (software-as-a-service) used to transfer, share, sync, and publish large amounts of data. It is supported and used extensively by most HPCs and major research facilities. Globus is designed to move very large data, ef
Globus Connect Personal Installation Guide
Before you begin working with Globus Connect Personal, you will need to have logged in to Globus and if you don’t have one already, set up your Globus account by logging into and configuring Globus Online. Additionally, you will need administrative access
Globus Online
Globus Online Globus manages file transfers between two computer systems. It is ideal for large files and available for many institutional clusters and networks. This document covers the basics of using Globus and provides external links to more detailed
Globus V5 Upgrade Announcement
New Globus endpoints make it easier to transfer large datasets to and from UW ARCC hosted resources UW ARCC has created new V5 endpoints which will improve data transfer capabilities between UW ARCC provided resources. Previously, both Beartooth and Alcov
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
GNU Compiler Collection
Overview We provide as part of the GCC: GNU Compiler Collection front ends for C, C++ and Fortran. Using Use the module name gcc to discover versions available and to load the application. Typically an application will have been been built with a particul
GNU OpenMP Example
Disclaimer: This is NOT a course on learning OpenMP. This is a very basic example on compiling an OpenMP example using the GNU compilers. What is OpenMP? OpenMP https://www.openmp.org/ is a “specification for a set of compiler directives, library routines
gnuplot
Overview gnuplot http://www.gnuplot.info/: A portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. Using Use the module name gnuplot to discover versions available and to load the application. Termi
Go
Overview: Go https://golang.org/: An open source programming language that makes it easy to build simple, reliable, and efficient software. Using Use the module name go to discover versions available and to load the application.
GPU - BLAST
Overview 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. Using a general-purpose graphics processing unit (GPU), we
Gromacs
Overview Gromacs https://www.gromacs.org/: A free and open-source software suite for high-performance molecular dynamics and output analysis. Forum https://gromacs.bioexcel.eu/: Welcome to the GROMACS community forum. GROMACS https://www.gromacs.org/ is a
GSL
Overview GSL https://www.gnu.org/software/gsl/: The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as
gsutil
Overview gsutil https://cloud.google.com/storage/docs/gsutil is a Python application that lets you access Cloud Storage from the command line. You can use gsutil to do a wide range of bucket and object management tasks, including: Creating and deleting bu
GUI Applications on SouthPass
This page will detail the current list of GUI related applications that have been tested on SouthPass and any related comments. GUI App Module Setup Minimum Desktop Configuration General Comments DeepLabCut []$ module load deeplabcut/2.2.0.2_gui []$ pytho
Guppy
Overview Guppy https://community.nanoporetech.com/downloads provides local accelerated basecalling for Nanopore. To use outside of the cluster you will need to register to directly access the software and documentation. Documentation: Here are some genera
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HHIFIASMOverview Hifiasm https://github.com/chhylp123/hifiasm is a fast haplotype-resolved de novo assembler initially designed for PacBio HiFi reads. Its latest release could support the telomere-to-telomere assembly by utilizing ultralong Oxford Nanopore reads.
High Performance Compute Services
Overview UW ARCC offers several HPC resources for different use cases. This core service is performed primarily over Beartooth, however ARCC maintains a number of specialty HPC resources for special use cases. UW ARCC maintained resources are listed below
HISAT2
Overview HISAT2 https://daehwankimlab.github.io/hisat2/ is a fast and sensitive alignment program for mapping next-generation sequencing reads (whole-genome, transcriptome, and exome sequencing data) against the general human population (as well as agains
How to make my videos on S3 stream instead of download
Overview You uploaded a .mp4 file to an S3 bucket on Pathfinder and generated a web URL. Now when you connect it simply downloads the file, but you’d rather have it stream. You need to change the http header and Content-Type associated with the file. How
HTSeq
Overview HTSeq https://htseq.readthedocs.io/en/master/: Analysing high-throughput sequencing data with Python. Using Use the module name htseq to discover versions available and to load the application. Loading the htseq module loads a conda environment w
HyDe
Overview HyDe https://hybridization-detection.readthedocs.io/index.html is a software package that detects hybridization in phylogenomic data sets using phylogenetic invariants. HyDe provides a number of python scripts that can be found under the Analyzin
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IIDEsIDEs: Integrated Development Environments is are software applications that provides comprehensive facilities for software development. An IDE normally consists of at least a source-code editor, build automation tools, and a debugger.
IGV
Overview IGV https://software.broadinstitute.org/software/igv/home: Integrative Genomics Viewer: is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data. It supports flexible integration of all the common types of g
ImageJ
Overview ImageJ https://imagej.net/: is open source software for processing and analyzing scientific images. Learn https://imagej.net/learn/ and User Guides https://imagej.net/learn/user-guides Using Use the module name imagejto discover versions availabl
ImageMagick
Overview ImageMagick https://imagemagick.org/index.php: is a free and open-source software suite for displaying, converting, and editing raster image and vector image files. It can read and write over 200 image file formats, and can support a wide range o
INBRE Investment Allocation List
Wy INBRE Data Science Core's ARCC Investment Nodes Name Cluster Make CPU Cores Memory wi001 WildIris Virtual (donated by ARCC) Intel VCPU 16 cores 64g wi002 WildIris Virtual (donated by ARCC) Intel VCPU 16 cores 64g wi003 WildIris Virtual (donated by ARCC
Infrastructure Issue - 4-25-2023
Overview Between 12 and 1pm, 4-25-23, ARCC became aware of an issue on a critical infrastructure switch. This has been corrected as of 1:20pm. Services impacted during this timeframe: Beartooth & Teton Creek (Beartooth Storage) SouthPass Alcova Storage Gl
Install Pulse Secure on Linux
Install on RHEL/Rocky Linux sudo yum update -y For RHEL 7: sudo wget -O /tmp/PulseSecureRHEL7.rpm https://www.uwyo.edu/infotech/services/software/pulsesecure/ps-pulse-linux-rhel7-22.2r1.0-b1295.rpm https://www.uwyo.edu/infotech/services/software/pulsesecu
Installing Software Yourself on an HPC Cluster
Overview 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, know
Intel oneAPI
Overview Intel oneAPI Toolkits: https://www.intel.com/content/www/us/en/developer/tools/oneapi/toolkits.html#gs.g0kl6m Build, analyze, and optimize high-performance, cross-architecture applications on CPUs and XPUs with best-in-class compilers, performanc
Interactive Desktop with GUI
Overview You’ll need to define your account and required wall time (as with salloc/sbatch) and then select a “Desktop Configuration” - we’ve initially setup three configurations, and as we understand general usage and listen to feedback, we can create mor
Interproscan
Overview InterPro http://www.ebi.ac.uk/interpro/ is a database which integrates together predictive information about proteins' function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and s
Introduction to Job Submission 01: Nodes, Tasks and Processors
Introduction The 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 that goes into a little more detail focusing on the
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
Investment Allocations
Overview Partition Total CPU Specific Nodes Mem Per CPU CPU Memory Total Node Total QoS Group CPU Limit ARCC 132 01-04 1000 132 575000M 5 6052 ATMO2GRID 768 461-480 1000 768 3500G 20 6688 CAMML 320 481-488 1000 320 6000G 8 6240 CHEMISTRY 96 279-284 1000 9
Investment FAQs
I would like to use special hardware that you don’t provide on the cluster currently. How would I get that added? This is where investments come in. Investing is the only way to get a specialty hardware we don’t currently have installed onto the cluster.
IOR
Overview IOR https://ior.readthedocs.io/en/latest/index.html is a parallel IO benchmark that can be used to test the performance of parallel storage systems using various interfaces and access patterns. The IOR repository also includes the mdtest benchmar
IPA
Overview Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies. IPA is an end-to-end solution, starting with
IQ-Tree
Overview IQ-Tree http://www.iqtree.org/: Efficient software for phylogenomic inference. Documentation http://www.iqtree.org/doc/. Using Use the module name iq-tree to discover versions available and to load the application. Multicore The iq-tree applicati
IT Datacenter Network Upgrade November 6, 2023 - All Day
UPDATE 10-18-23: B nodes are in a drain state in preparation for updates this week (October 18-20th 2023). The network infrastructure is scheduled for upgrade in the UW IT Datacenter November 6th. With this in mind, network switches feeding connections to
ITK
Overview 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 through extreme programming methodologies, ITK builds on a proven, spatially-oriented
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JJagsOverview Jags https://mcmc-jags.sourceforge.io/: Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. Using Use the module name jags to discover
Java
Overview Java https://www.java.com/en/ is a general-purpose programming language that is class-based and object-oriented and designed to have as few implementation dependencies as possible. The Java Development Kit is an implementation of either one of th
Job Management
Overview SouthPass allows you to view and manage your currently active jobs running on the cluster. Active Jobs image-20211018-203915.png image-20211018-203934.png image-20211018-203953.png You are able to view all or just your jobs. Your Jobs Under: My I
Julia
Overview Julia https://julialang.org/: The Julia Language: A fresh approach to technical computing. Using Use the module name julia to discover versions available and to load the language. Multicore Julia is developed to work within parallel computing htt
JupyterLab and Notebooks
image-20211018-193853.png image-20211018-193923.png image-20211018-193954.png JupyterLab Example Steps: Define account / walltime and other required core/memory and GPU resources. The maximum walltime allowed is 168 hours (seven days). We would ask you to
JupyterLab Kernels
Here is a list of available kernels that can be selected for a jupyter notebook: Note: You can not use the module system from the Beartooth cluster within a Jupyer Notebook - any environment you require needs to run within a specific kernel. Kernels Name
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KKallistoOverview Kallisto https://pachterlab.github.io/kallisto/: is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. manual http://pachterlab
KentUtils
Overview KentUtils is a suite of tools developed at the USCS Genome Browser https://genome.ucsc.edu/ lab. Using Use the module name kentutils to discover versions available and to load the application. Manual: To understand how an individual command works
Known Issues
Overview 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 emaili
Kraken
Overview KRAKEN2 https://ccb.jhu.edu/software/kraken2/index.shtml 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 h
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LLAMMPSOverview LAMMPS https://lammps.sandia.gov/index.html: Molecular Dynamics Simulator: LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has
Languages
This is the parent page, under which you’ll find child pages on a number of languages include C/C++, Fortran, Java, Python and R and associated scientific libraries and packages.
Launching the Matlab GUI:
When first logging into Southpass, you will be presented with a number of pinned options. Screenshot 2023-03-23 at 4.35.50 PM.png Matlab should be one of them. Select Matlab to start a VNC Session with Matlab. You will be presented with a number of option
LDhelmet
Overview LDhelmet https://github.com/popgenmethods/Ldhelmet: A software program for statistical inference of fine-scale crossover recombination rates from population genetic data. Using Use the module name ldmelmet to discover versions available and to lo
Libraries and Toolkits
These child pages are the most commonly used libraries we have installed, but there are many others that are not documented. Please use the module spider command to see what's available before contacting ARCC Support.
Linux - Logging Into HPC with ssh
The objective of this tutorial is to 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
LocalColabFold
Overview LocalColabFold https://github.com/YoshitakaMo/localcolabfold: LocalColabFold is an installer script designed to make ColabFold functionality available on users' local machines. An example on Using Use the module name localcolabfold to discover ve
Localizer
Overview Localizer https://localizer.csiro.au/software.html is a machine learning method for subcellular localization prediction in plant cells. LOCALIZER has been trained to predict either the localization of plant proteins or the localization of eukaryo
Logging Into HPC
Overview 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 throu
Loren
Overview Loren is a specialty GPU based HPC cluster used by Dr. Piri’s research group, the High Bay Research Group. Hardware Loren is a GPU-based Cluster with approximately 55 working compute nodes. Software Software on Loren varies see the subsections fo
Loren - Job Scheduler (Slurm)
The Loren cluster uses a job scheduler for managing and running job across the cluster. Slurm commands allow the user to submit job, query information about jobs and perform other functions. Here’s a link to a web page that describes how to use slurm, htt
Loren Hardware
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 to the cluster. Allows ssh access for users to interact with the Linux CLI. Storage Node Provi
Loren Software
Herein, find summaries of each package with links to a more detailed page for each package. Below is a list of software / applications that are available on Loren. Click the software title to learn more about a particular software package, including its a
Loren SSH Key Setup and Use
First, generate an SSH Key on your local client machine. On a PC Using command prompt (cmd): On your Local PC: Open a command prompt and run the following command: ssh-keygen On your Local PC: This should create a public/private rsa key pair. You will be
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MMac - Logging into HPC with sshThe objective of this tutorial is to 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
Macs
Overview With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis met
Maestro
Overview Maestro https://liulab-dfci.github.io/MAESTRO/: MAESTRO(Model-based AnalysEs of Single-cell Transcriptome and RegulOme) is a comprehensive single-cell RNA-seq and ATAC-seq analysis suit built using snakemake. Documentation https://baigal628.githu
Mafft
Overview MAFFT https://www.ebi.ac.uk/Tools/msa/mafft/: (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. Using Use the module name mafft to discover versions available and to load the application. Multi
MafTools
Overview This is a suite of the following three tools: mafTools https://github.com/dentearl/mafTools a collection of tools that operate on Multiple Alignment Format (maf) files. Which depends on: sonLib https://github.com/benedictpaten/sonLib is a compact
Maintenance Scheduled for August 4, 2023
ARCC Infrastructure Team will be performing maintenance this upcoming week on Friday, August 4, 2023. Maintenance is expected to last from 8:00am to 12:00pm MST. Several ARCC services will be impacted at the scheduled time including Beartooth, WildIris, O
Maintenance Scheduled for June 12-16, 2023
ARCC Infrastructure has scheduled Beartooth maintenance for June 12-16, 2023, starting at 07:00 on Monday. During this maintenance window ARCC will be updating system software to Redhat version 8.7, updating to the latest version of SLURM, and performing
Majic-Voila
Overview MAJIQ https://majiq.biociphers.org/ and Voila are two software packages that together detect, quantify, and visualize local splicing variations (LSV) from RNA-Seq data. MAJIQ: Documentation https://biociphers.bitbucket.io/majiq-docs-academic/ Usi
Major Changes to ARCC Services (Teton HPC Replacement) - 09/19/2022
Overview ARCC services will be undergoing substantial changes starting in the new year, with the goal of minimizing impacts on ongoing projects. Below you will find a list of the upcoming changes and how we can best ensure it is a smooth transition. If th
Maker
Overview Maker http://www.yandell-lab.org/software/maker.html: MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and t
MatLab
Overview MATLAB https://www.mathworks.com/products/matlab.html is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks. MATLAB allows matrix manipulations, plotting of functions and data, implementatio
Megan
Overview Megan https://software-ab.informatik.uni-tuebingen.de/download/megan/welcome.html: A tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project. Note: Megan is a GUI application and as such should
MetaShape
Overview Agisoft: Metashape https://www.agisoft.com/: Discover intelligent photogrammetry with Metashape. Process digital images and generate 3D spatial data. Fast and highly accurate. Manuals https://www.agisoft.com/downloads/user-manuals/ Forum https://
Metaxa2
Overview Metaxa2 https://microbiology.se/software/metaxa2/: Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data. Manual https://microbiology.se/publ/metaxa2_users_guide_2.2.pdf Using Use the module name
MFiX
Overview MFiX https://mfix.netl.doe.gov/ is an open-source multiphase flow solver, providing a Two-Fluid Model (TFM), a Discrete Element Model (DEM), a Particle In Cell (PIC) model, and a Hybrid model. General documentation https://mfix.netl.doe.gov/produ
Micromamba
Overview Mamba https://mamba.readthedocs.io/en/latest/: Mamba is a fast, robust, and cross-platform package manager. Micromamba https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html: is a tiny version of the mamba package manager. It is a stat
Miniconda
Overview Miniconda https://docs.conda.io/en/latest/miniconda.html is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages, including pip, zlib and a few others. I
Miniforge - Mamba
Overview Miniforge https://github.com/conda-forge/miniforge: This repository holds the minimal installers for Conda https://conda.io/ and Mamba https://github.com/mamba-org/mamba specific to conda-forge https://conda-forge.org/, with the following feature
MLST
Overview Multilocus Sequence Typing (MLST) https://bitbucket.org/genomicepidemiology/mlst/src/master/: Multilocus sequence typing is a technique in molecular biology for the typing of multiple loci. The procedure characterizes isolates of microbial specie
ModelTest
Overview ModelTest-NG https://github.com/ddarriba/modeltest 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 inte
MOOSE
Overview 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
Moran Node Retirement
Overview: ARCC Infrastructure tentatively plans to retire the following Moran compute nodes beginning October 16th, 2023. This is being done to vacate space for the installation of newer hardware on ARCC’s next HPC cluster. Beginning Monday October 16th
Moving Your Data
Overview In the world of HPC there is frequent need to move and copy your files and folders between locations. This page covers various methods of performing these basic file operations. SMB/CIFS Data Transfer over GUI - (AKA: “just copy-paste”) With so m
MPI
Disclaimer: This is NOT a course on learning MPI. This is a very basic introduction on what MPI is and how to use across our clusters. What is MPI? The Message Passing Interface: MPI is standardized and portable message-passing standard designed to functi
MSMC2
Overview MSMC2 https://github.com/stschiff/msmc2: This program implements MSMC2, a method to infer population size history and population separation history from whole genome sequencing data. MSMC: Tutorial https://github.com/stschiff/msmc-tools/blob/mast
MSP360 Explorer (Cloudberry)
Overview MSP360™ Explorer provides a graphical user interface allowing you to access, move and manage files across your local storage and the cloud storage of your choice (no third-party servers in between). Instructions for using Pathfinder with MSP360 E
MultiQC
Overview MultiQC https://multiqc.info/is a tool to aggregate bioinformatics results across many samples into a single report. It is written in Python and contains modules for a large number of common bioinformatics tools. Using Use the module name multiqc
MUMmer4
Overview MUMmer https://mummer4.github.io/ 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 ju
Muscle
Overview Muscle https://www.drive5.com/muscle/: Muscle v5 is a major re-write of MUSCLE based on new algorithms. Alignment ensembles : Muscle v5 can generate ensembles of high-accuracy alternative alignments. All replicates have equal average accuracy on
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NNCBI-Datasets-CLIOverview NCBI-Datasets https://www.ncbi.nlm.nih.gov/datasets/: A one-stop shop for finding, browsing, and downloading genomic data. GitHub https://github.com/ncbi/datasets: Command line tools https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-inst
NCBI-RMBlast
Overview RMBlast https://www.repeatmasker.org/RMBlast.html: RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmbl
NCO
Overview NCO https://sourceforge.net/projects/nco/ netCDF Operators: Command-line operators for netCDF and HDF files GitHub https://github.com/nco/nco: User Guide https://nco.sourceforge.net/nco.html Using Use the module name nco to discover versions avai
NetCDF
Overview NetCDF https://downloads.unidata.ucar.edu/netcdf/: Network Common Data Form: is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Using We currently
Network Issues 7-24-23
Overview At approximately 3:30pm ARCC Infrastructure became aware of a networking issue resulting in latency when accessing blog1 and blog2. This has been corrected as of 5:30pm. Services impacted during this timeframe: Login to Beartooth on blog1 and bl
Newick Utils
Overview Shell Tools for Processing Phylogenetic Trees Link to documentation: https://github.com/tjunier/newick_utils/blob/master/doc/nwutils_tutorial.pdf https://github.com/tjunier/newick_utils/blob/master/doc/nwutils_tutorial.pdf Using Use the module na
News and Announcements
Overview Please check this page to see upcoming events and other important dates for planned outages, scheduled training and other special circumstances. Current or Upcoming News and Notifications: We need your feedback: April 12,2024 ARCC is planning a w
Nextflow
Overview Nextflow https://www.nextflow.io/index.html: Data-driven computational pipelines Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting
Node Purchase Estimates
Overview Below are the price estimates to be used for planning possible node investments within Beartooth. This type of purchase is only available to UWyo faculty PIs. See https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/1627815937/Cost+of+reso
NVidia HPC SDK
Overview NVidia’s HPC SDK https://developer.nvidia.com/hpc-sdk. is a comprehensive suite of compilers, libraries and tools for HPC, including the proven compilers, libraries and software tools essential to maximizing developer productivity and the perform
NWSC Transitions
Overview This page details the role of NWSC, what they do, links to their service portal/support and who to contact when transitioning from Beartooth to NWSC’s Cluster. What is NWSC NWSC stands for the NCAR Wyoming Super Computing Center. They are a high
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OOnDemand Maintenance Scheduled This WeekARCC Infrastructure Team will be performing maintenance to OnDemand resources this week. WildIris OnDemand resources will be offline maintenance Tuesday October 3rd, 2023. Beartooth OnDemand resources through https://southpass.arcc.uwyo.edu https://southp
oneAPI: AI Analytics Toolkit:
Overview AI Kit https://www.intel.com/content/www/us/en/developer/tools/oneapi/ai-analytics-toolkit.html: The AI Kit gives data scientists, AI developers, and researchers familiar Python tools and frameworks to accelerate end-to-end data science and analy
oneAPI: Compiling
Overview The Intel oneAPI ecosystm provides a number of compilers and libraries. This page contains contains information about what compilers are provided on Beartooth including some basic examples and command-line instructions on how to compile. Compiler
oneAPI: Python
Overview Intel Distribution for Python https://www.intel.com/content/www/us/en/developer/tools/oneapi/distribution-for-python.html: provides: Near-native performance through acceleration of core numerical and machine learning packages with libraries like
OpenBLAS
Overview BLAS https://netlib.org/blas/ (Basic Linear Algebra Subprograms) is a specification that prescribes a set of low-level routines for performing common linear algebra operations such as vector addition, scalar multiplication, dot products, linear c
OpenFOAM
Note: There are two flavors of OpenFOAM: OpenFOAM.org https://openfoam.org/ variant released by the OpenFOAM Foundation Ltd. OpenFOAM.com https://www.openfoam.com/ variant by OpenCFD Ltd an affiliate of ESI Group. When using OpenFOAM and contacting ARCC,
Opening Dashboard
Once connected to SouthPass, you’ll see the opening dashboard, which is your central point of navigating around the services. image-20211018-185030.png What we have are a set of Interactive Apps that provide a means for users to launch and connect to inte
OpenMPI
Overview OpenMPI https://www.open-mpi.org/: The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Using Use the module name openmpi to
OpenMPI/IntelMPI
Overview 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. OpenMPI Open MPI is a Message Passi
OpenSMOKE
Overview OpenSMOKE++ https://www.opensmokepp.polimi.it/ Suite is a general framework for numerical simulations of reacting systems with very detailed kinetic mechanisms, including thousands of chemical species and reactions. OpenSMOKE++ can handle simulat
ORCA
Overview MPI CEC https://www.cec.mpg.de/en/home: Max Planck Institute for Chemical Energy Conversion An ab initio, DFT and semiempirical SCF-MO package. Please read the “End User License Agreement (EULA) for the ORCA software” before using the software: U
OrthoFinder
Overview OrthoFinder https://github.com/davidemms/OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers rooted gene trees for all orthogroups and infers a rooted species tree
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PP7zipOverview P7zip (sourceforge) http://p7zip.sourceforge.net/ 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
Packmol
Overview PACKMOL http://leandro.iqm.unicamp.br/m3g/packmol/home.shtml: Initial configurations for Molecular Dynamics Simulations by packing optimization. Examples on using packmol can be found here http://leandro.iqm.unicamp.br/m3g/packmol/examples.shtml.
PAPI
Overview Performance Application Programming Interface (PAPI) https://icl.utk.edu/papi/provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major micropro
Parallel (gnu)
Overview GNU Parallel https://www.gnu.org/software/parallel/: GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. T
ParaView
Overview ParaView https://www.paraview.org/: ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The d
Parflow
Overview Homepage https://parflow.org/: ParFlow hydrologic model: Modelling surface and subsurface flow on high-performance computers GitHub https://github.com/parflow/parflow and Releases https://github.com/parflow/parflow/releases Using ParFlow is curre
Partner Organizations
ARCC partners with a number of regional and national education and computational research organizations. Shell 3D Visualization Center http://www.uwyo.edu/ser/visualization-center/index.html The Shell 3D Visualization Center's mission is to create and mai
Password Resets and Account Lock Outs
Login Methods: If you are unable to log into ARCC related resources, the first thing to identify would be what account you’re using for login. Most of our users access our services using their UWYO domain accounts with UWYO secured 2 factor authentication
Past Announcements
Overview A parent page for navigating all posted ARCC Announcements and Release Dates. Beartooth HPC Performance Issues: April 12, 2024 ARCC became aware of an issue affecting use and performance on the Beartooth HPC cluster. To prevent further issues, jo
Pathfinder
Overview Named after one of Wyoming’s reservoirs on the North Platte River, Pathfinder is a low-cost, expandable storage solution that enables a cloud-like presence for research data hosted by ARCC. Its core functionality is hosting onsite backups as well
PathoFact
Overview PathoFact https://git-r3lab.uni.lu/laura.denies/PathoFact: PathoFact is an easy-to-use modular pipeline for the metagenomic analyses of toxins, virulence factors and antimicrobial resistance. Additionally, PathoFact combines the prediction of the
Paup
Overview Paup https://paup.phylosolutions.com/: Phylogenetic Analysis Using PAUP: This appears to be an alpha version application, with the FAQ last updated in Feb 2007 and the manual dated 2017. This is the command-line version, not the GUI version. Usin
PerGEOS
Overview ThermoFisher: PerGEOS https://www.thermofisher.com/us/en/home/electron-microscopy/products/software-em-3d-vis/pergeos-software.html: Fast and repeatable imaging-based digital rock analysis. Improved petroleum reservoir evaluation with meaningful
Perl
Overview: Perl 5 https://www.perl.org/ is a highly capable, feature-rich programming language with over 27 years of development. Using Use the module name perl to discover versions available and to load the application.
petaLibrary Policies
This page goes over the ARCC petaLibrary policies. Contents Glossary Frequently Asked Questions Alcova petaLibrary Policies Data Protection Backups Data Protection/Backups Policy: Data residing in Project or Restricted file shares are protected each night
PETSc
Overview 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. Using Use
PGDSpider
Overview PGDSpider http://www.cmpg.unibe.ch/software/PGDSpider/: PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. Manual: 2.1.1.5.pdf http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider%20manual_vers%2
Picard
Overview Picard https://broadinstitute.github.io/picard/: Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. Using Use the module name picard to discover versions availabl
PLINK
Overview PLINK https://www.cog-genomics.org/plink/: is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Using Use the module name plink to disc
Policies
Our department’s mission is to provide the best possible high performance computing services and resources to facilitate and optimize research activities at the University of Wyoming. This page serves as an index for ARCC Policies applicable to all end-us
Prodigal
Overview Prodigal https://github.com/hyattpd/Prodigal: Fast, reliable protein-coding gene prediction for prokaryotic genomes. Using Use the module name prodigal to discover versions available and to load the application.
Prokka
Overview Prokka https://github.com/tseemann/prokka used for rapid prokaryotic genome annotation. Whole genome annotation is the process of identifying features of interest in a set of genomic DNA sequences, and labelling them with useful information. Prok
Proovread
Overview Homepage: GitHub: proovread https://github.com/BioInf-Wuerzburg/proovread: PacBio hybrid error correction through iterative short read consensus. Using Use the module name proovread to discover versions available and to load the application. The
PSMC
Overview The Pairwise Sequentially Markovian Coalescent (PSMC https://github.com/lh3/psmc) method uses the genome sequence of a single individual to estimate demographic history covering a time span of thousands of generations. Using Use the module name p
Publications and Reports
The following are publications made possible by ARCC resources. Any UW faculty that would like to highlight the research that has benefited from ARCC resources are invited to contact us https://arccwiki.atlassian.net/wiki/spaces/DOCUMENTAT/pages/155058180
PyCharm
Overview PyCharm https://www.jetbrains.com/pycharm/: A Python IDE for developers. We have installed the Community Edition. Using Use the module name pycharm to discover versions available and to load the application. No particular version of Python is set
Python
Overview Python https://www.python.org/ 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
Python - Miniconda - Conda - Pip
This page highlights the interplay between using Python and Miniconda on the Beartooth cluster, and how pip/conda install work alongside each other. This page assumes: You already know how to program using Python and have used pip install to install packa
Python Libraries Available
These child pages are the few libraries that we have documented. Python has hundreds/thousands of available libraries, which can be acquired through tools such as pip or conda.
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QQiime2Overview Quantitative Insights Into Microbial Ecology (QIIME https://qiime2.org/) 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
Quantum Espresso
Overview Quantum ESPRESSO https://www.quantum-espresso.org/: Is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pse
QUAST
Overview QUAST https://cab.spbu.ru/software/quast/is a genome assembly evaluation tool. QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitabl
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RROverview R https://www.r-project.org/: 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 miner
R Package Issues
XML Issue When installing the R XML package either explicitly, or as part of a dependency to a parent package, XML package fails to install: * installing *source* package ‘XML’ ... ** package ‘XML’ successfully unpacked and MD5 sums checked ** using stage
R Packages/Libraries
Overview This page details some of the common issues to be aware of when transitioning from using R on a desktop, to using R on the HPC cluster. The child pages here are the only packages/libraries we have documented, but many more exist. Installing Packa
R Workshop Environments
R4 and Seurat Workshop: Date: 10/23/2023 Title: Created for the Tools for Single-Cell Genomics Analysis Workshops. Part 1: Single-Cell RNA Sequencing Data Analysis Presenter: Dr Qian-Quan Sun Environment: Conda environment build with R v4.3.1 and Seurat h
R4.0.5 + Packages
This page related to an older Teton cluster, but the process of identifying available packages still holds for other clusters. Overview ARCC is currently exploring ways to best support R users across the clusters and disciplines and the 100s of libraries
Ranger
Overview Ranger https://ranger.github.io/: is a console file manager with VI key bindings. It provides a minimalistic and nice curses interface with a view on the directory hierarchy. User Guide https://github.com/ranger/ranger/wiki/Official-user-guide an
RAxML
Overview RAxML https://cme.h-its.org/exelixis/web/software/raxml/(Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. Hands-on session https://cme.h-its.org/exe
Ray
Overview Ray http://denovoassembler.sourceforge.net/index.htmlis 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
rclone
Contents Overview Rclone is a command line program to manage files on a wide variety of storage. It is a feature rich alternative to cloud vendors' web storage interfaces. Over 40 cloud storage products https://rclone.org/#providers support rclone includi
RClone Util
Overview RClone https://rclone.org/: 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 support rclone including S3 object stores, bu
Re-creating Globus Shared Collections and Bookmarks in V5
UW ARCC has upgraded to v5 and created new v5 endpoints to improve data transfer capabilities from our HPC resources. The upgrade from Globus 4 to Globus 5 means all users who have created bookmarks or shared collections to v4 endpoints will need to recre
Removing a user from your Globus Share
Upon project completion or project changes, you may find you need to revoke file sharing permissions. This can be done in two ways: You may delete the shared endpoint (usually to be done when data transfer or project has reached completion and you no long
RepeatMasker
Overview RepeatMasker https://www.repeatmasker.org/: RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. Using Use the module name repeatmasker to discover versions available and to load the appl
Request a Workshop or Training
Overview Users may request the use of ARCC’s HPC resources to host short courses, trainings or workshops. Often these requests may include several pieces outlined below. ARCC Users may request a workshop or training by e-mailing arcc-help@uwyo.edu mailto:
Requesting Software
Request Details When requesting software please consider the questions below and try to provide, where possible, as much related detail. We do appreciate that depending on your expertise with the software you might not be able to answer all of the followi
Resources and Services
Overview This is the gateway to technical information and documentation that is specific to each of ARCC’s computational hardware resources/services. High Performance Computing Services This core service is primarily being performed by Beartooth. Beartoot
RevBayes
Overview RevBayes https://revbayes.github.io/: Provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics.
Rmpi
Overview Rmpi https://cran.r-project.org/web/packages/Rmpi/index.html: An interface (wrapper) to MPI. It also provides interactive R manager and worker environment. Using This usage relates to using this library on Beartooth. note We currently only have v
ROHan
Overview ROHan http://grenaud.github.io/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 wit
RoseTTAFold
Overview RoseTTAFold: This package contains deep learning models and related scripts to run RoseTTAFold. This repository is the official implementation of RoseTTAFold: Accurate prediction of protein structures and interactions using a 3-track network. Git
RStan
These instructions were for an older Teton cluster, in principle the process should work for Beartooth and other clusters - but with updated module loads. Overview RStan https://mc-stan.org/rstan/: The R interface to Stan. It is distributed on CRAN as the
RStudio on the Cluster
Overview: Using RStudio on the Cluster RStudio https://posit.co/products/open-source/rstudio/ is available on the cluster, and thus in principle can be loaded and used anywhere. To use it effectively: Do not load and use on the login nodes. This will affe
Ruby
Overview: Ruby: A dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. Using Use the module name ruby to discover versions available and to load the appl
Rust
Overview Rust https://www.rust-lang.org/: A language empowering everyone to build reliable and efficient software. Using Use the module name rust to discover versions available and to load the application.
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SSalmonOverview Salmon https://salmon.readthedocs.io/en/latest/index.html: Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Using Use the module name salmon to discover versions available
Samtools
Overview Samtools https://www.htslib.org/ is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format BCFtools: Reading/wri
SAVA
Overview SAVA https://github.com/daniel-koehn/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/triclini
Science DMZ - Data Transfer
Overview 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.
Screen and Tmux Commands
Overview The Linux tmux and GNU screen commands are terminal multiplexers – in brief, these commands let a user launch and use multiple shell sessions from a single ssh session. The screen or tmux commands also allow a user to start a process in a termina
SeqKit
Overview SeqKit https://bioinf.shenwei.me/seqkit/: A cross-platform and ultrafast toolkit for FASTA/Q file manipulation. Using Use the module name seqkit to discover versions available and to load the application. Multicore: The seqkitcommand can be ran w
Sequence Hub CLI
Overview The BaseSpace Sequence Hub CLI https://developer.basespace.illumina.com/docs/content/documentation/getting-started/overview tool suite is a set of command-line tools available for interacting with BaseSpace, Illumina's cloud-based sequencing info
Sharing data from Pathfinder via expiring URLs
Overview Objects stored on Pathfinder can be shared over the web with an expiring URL. Below are methods for creating an expiring URL for an object stored on Pathfinder. MSP360 Explorer (Cloudberry) Once the item that is to be shared has been uploaded to
Shells
Below are the only available documented shells on the cluster.
Shovill
Overview Shovill https://github.com/tseemann/shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velve
SignalP
Overview SignalP 6.0 https://services.healthtech.dtu.dk/services/SignalP-6.0/ predicts the presence of signal peptides and the location of their cleavage sites in proteins from Archaea, Gram-positive Bacteria, Gram-negative Bacteria and Eukarya. In Bacter
Singularity
Overview Singularity is a free, cross-platform and open-source computer program that performs operating-system-level virtualization also known as containerization. One of the main uses of Singularity is to bring containers and reproducibility to scientifi
SLiM
Overview SLiM https://messerlab.org/slim/ is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Using Using Use the module nam
Slurm and Preemption
What is Preemption? Our clusters, with Slurm, currently have what is called preemption enabled which is the act of stopping one or more low-priority jobs to let a high-priority job run. If you have submitted a job that has been allocated to a compute node
Slurm Job Arrays
Why Use a Job Array? If you have the same job that you want to run 10s, 100s, 1000s of times, with maybe only the initial inputs and/or setup being different across the jobs, then a Job Array allows you to submit a single job rather than submitting each o
Slurm Job Performance
Overview: What is Performance In it’s simplest form there are three performance metrics any user can consider: How much the core(s) were utilized? How much memory was used? How long the job took? How much read/write was performed? This isn’t currently cov
Slurm Queue Messages
Overview This page details some of the common Slurm messages a user will see after a job has been submitted and is in the queue waiting to run: Messages QOSGrpCpuLimit “The job's QOS has reached its aggregate CPU limit.” This message stems from the policy
Slurm Workload Manager
Overview 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 can be used to schedule jobs, control resource access,
Slurm: Getting Started-Jobs and Nodes
Overview 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%3A+Getting+Started-Jobs+and+Nodes#Batch-Jobs and interactive https://arccwiki.atlassian.net/w
Slurm: Jobs within a Job
Overview Typically when a user submits a job, then this job is a self-contained single job. Its starts, it runs, it finishes. But, depending on your use-case you can run other child jobs, in parallel, within this parent job. There are a number of ways thi
Snakemake
Overview Snakemake https://snakemake.readthedocs.io/en/stable/: The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamless
Snap-korf
Overview snap http://korflab.ucdavis.edu/software.html: (Semi-HMM-based Nucleic Acid Parser) gene prediction tool Using Use the module name snap-korf to discover versions available and to load the application. The snap-korf GitHub repo does not have tagge
SNOPT
Overview 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 program
Software
Overview 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+Tetonsystems at UWyo. It pr
Software Migration: Beartooth
Software Related Changes from Teton to Beartooth: We are not performing an exact copy of what is currently available on Teton, but using this opportunity to clean up and update the cluster related software. Click here for a current list of software availa
Software, FASTX, and Old GPUs being Decommissioned
Email to arcc-announce@uwyo.edu mailto:arcc-announce@uwyo.edu on 11/11/22 There will be three changes to the HPC services offered by ARCC when we transition to Beartooth. First, the software base that exists today on Teton will be upgraded to new version
SourceTracker2
Overview SourceTracker2 https://github.com/biota/sourcetracker2: Contamination is a critical issue in high-throughput metagenomic studies, yet progress toward a comprehensive solution has been limited. We present SourceTracker, a Bayesian approach to esti
SouthPass
this page is being reviewed for content (completeness, accuracy, usability, etc) Overview SouthPass is ARCC’s implementation of OnDemand https://openondemand.org/. It is a publicly accessible site for access to ARCC’s High Performance Computing resources.
SPades
Overview SPades https://cab.spbu.ru/software/spades/: It’s all about the viruses: new coronaSPAdes, rnaviralSPAdes and metaviralSPAdes pipelines. Using Use the module name spades to discover versions available and to load the application. Multicore: Some
SRA-Toolkit
Overview The NCBI SRA Toolkit https://hpc.nih.gov/apps/sratoolkit.html enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format. Using Use the module name sratoolkitto discover versions avail
Stacks
Overview Stacks https://catchenlab.life.illinois.edu/stacks/: Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, suc
Star
Overview Star https://github.com/alexdobin/STAR: Spliced Transcripts Alignment to a Reference. There is a comment on this page detailing “this release was tested with the default parameters for human and mouse genomes. Mammal genomes require at least 16GB
Start Processing
Start Processing ARCC uses the Slurm Workload Manager https://slurm.schedmd.com/ to regulate user submitted tasks on our HPC systems. Unless otherwise noted, if you’re running a job, Slurm is managing the resources. There are two primary ways of doing wor
StringTie
Overview StringTie http://ccb.jhu.edu/software/stringtie/ is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quanti
Structure
Overview Structure https://web.stanford.edu/group/pritchardlab/structure.html: The program structure is a free software package for using multi-locus genotype data to investigate population structure. Manual https://web.stanford.edu/group/pritchardlab/str
Subversion
Overview Subversion https://subversion.apache.org/: Subversion exists to be universally recognized and adopted as an open-source, centralized version control system characterized by its reliability as a safe haven for valuable data; the simplicity of its
Support for External HPC Resources
Overview This page details external HPC resources supported by UW ARCC and support policy. This page will be updated whenever necessary, and as additional resources become available. If you plan to use NWSC for HPC resources, please be aware that UW ARCC’
Support for NWSC
Overview NWSC has several supercomputing resources available to UW Researchers. These include: Casper https://arc.ucar.edu/knowledge_base/70549550, Cheyenne https://arc.ucar.edu/knowledge_base/70549542, and their newest supercomputing resource, Derecho ht
System Querying - Beartooth
Overview: Compute Job Information 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 th
System Querying - Loren
Overview: Compute Job Information 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
System Status
Beartooth Cluster Status 311 of 351 Nodes Active (38 Node(s) Free, 2 Node(s) Offline) |████████████████████████████████████████████------| 88.60% 4588 of 14636 Processors Active (10000 Processor(s) Free, 48 Processor(s) Offline) |███████████████----------
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TTesseractOverview Tesseract https://tesseract-ocr.github.io/ is an open source text recognition (OCR) Engine, available under the Apache 2.0 license. GitHub https://github.com/tesseract-ocr/tesseract Documentation for version 4.x.y https://tesseract-ocr.github.io/
Teton
Overview The Teton Compute Environment (Teton) is a high performance computing (HPC) cluster that offers over 500 compute nodes and 1.2 PB of storage, with an expected uptime of 98%, allowing researchers to perform computation-intensive analyses on datase
Teton Filesystem
Overview: 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 data. The system policy engine moves data automatically between pools (disks and tiers). The sys
Teton Hardware Summary Table
Slurm Partition name Requestable features Node count Sockets/ Node Cores/ Socket Threads/ Core Total Cores/ Node RAM (GB) Processor (x86_64) Local Disks OS Moran Regular moran fdr, intel, sandy, ivy, community 280 2 8 1 16 64 or 128 Intel Ivybridge/ Sandy
Teton Software List
Overview Herein, find summaries of each package with links to a more detailed page for each package. Below is a list of software / applications that are available on Teton. Click the software title to learn more about a particular software package, includ
Teton's "non-investor" partition
Teton has a special partition called “non-investor” that functions a little differently than other partitions. Rather than being based on a specific hardware set or level of investment, the non-investor partition lumps all community nodes into one partiti
The Command Line Interface
This page discusses finding and using the Command Line Interface (CLI) in the three OS families: Linux, OSX, and Windows. A CLI is a text based interface in which the user can manually type commands to do various things, as opposed to a Graphical User Int
The Module System: LMOD
Overview Lmod is a powerful piece of software that ARCC leverages for managing dynamic user environments and access to complicated software stacks. Our configuration of Lmod uses a hierarchy for the organization of software that starts with compilers. Com
Tips for Writing a Successful NWSC Proposal
General submission format Five-page request typically Project information (title, lead, etc.) Project overview and strategic linkages Science objectives Computational experiments and resource requirements (HPC, DAV, and storage) Supporting information Mul
Tmux Cheat Sheet
Sessions Start a new session Show all sessions tmux tmux ls tmux new tmux list-sessions tmux new-session Ctrl + b s :new Attach to last session Start a new session with the name mysession tmux a tmux new -s mysession tmux at :new -s mysession tmux attach
Training & Other Resources
Overview ARCC provides training on using ARCC resources and other research computing topics through various scheduled courses, online courses, and other methods. ARCC Provided Training ARCC Courses on WyoLearn ARCC Courses can be found on the WyoLearn Cat
Training Accounts for Short Courses/Training
Overview ARCC maintains twenty-five training accounts that educators can use for various computation related short courses that require temporary access to ARCC’s HPC resources by students who are external to UWyo. Check-out Please fill out the https://ar
Training/Workshop Checklist
For every Workshop or Training Request, ARCC requires specific information in order to fulfill the request and plan for required resources and environmental requirements. Please review the list of required information and provide any information required
Training/Workshop Responsibilities
ARCC training hosts providing a workshop or course over our resources are subject to responsibilities described below. Additional information on how to host a training or workshop is available here. Assistance is available by e-mailing arcc-help@uwyo.edu
TransDecoder
Overview TransDecoder https://github.com/TransDecoder/TransDecoder/wiki (Find Coding Regions Within Transcripts): identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity
TREES
Overview TREES: The Terrestrial Regional Ecosystem Exchange Simulator (TREES) is a dynamic biophysical process based simulation model. The current module was built from the TREES Workshop 2020 https://github.com/dscottmackay/TREES-Workshop-2020. This site
Trimmomatic
Overview Trimmomatic http://www.usadellab.org/cms/?page=trimmomatic is a flexible read trimming tool for Illumina NGS data. Using Use the module name trimmomatic to discover versions available and to load the application. ARCC has created a wrapper script
Trinity
Overview Trinity https://github.com/trinityrnaseq/trinityrnaseq/wiki: Trinity assembles transcript sequences from Illumina RNA-Seq data. Using Use the module name trinity to discover versions available and to load the application. Trinity has been built a
Troubleshooting the Matlab GUI on SouthPass
Overview: This page goes over the most common problems when running an Interactive Matlab VNC Session “I minimized Matlab and can’t get back to the window” To get back to Matlab, you’ll just be using your mouse for a minute. Ignore the keyboard temporaril
Two-factor Authentication
Overview Also known as 2FA, two factor authentication is a type of multi-factor authentication (MFA). MFA confirms a user's claimed identity by using multiple separate components that fall into the following general categories: Something you know (e.g. yo
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UUSearchOverview USearch https://www.drive5.com/usearch/: A unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST. We have installed the 32-bit https:
Using Dadi
ARCC is aware that the exact details and versions presented here are out-of-date, but the general process is still valid. We will endeavor to update this page as soon as we can. Overview Dadi https://dadi.readthedocs.io/en/latest/ is a powerful software t
Using PyTorch
ARCC is aware that the exact details and versions presented here are out-of-date, but the general process is still valid. We will endeavor to update this page as soon as we can. Overview PyTorch is an open source machine learning library based on the Torc
Using TensorFlow
Overview TensorFlow https://www.tensorflow.org/ is an end-to-end open source platform for machine learning. It has a comprehensive, flexible ecosystem of tools, libraries and community resources that lets researchers push the state-of-the-art in ML and de
Using Your Investment Partition
How slurm allocates nodes to your jobs if your project has an investment, and/or if you explicitly define a partition can be a little confusing. The following provides a high-level overview. Explicitly Define a Partition If you explicitly define a partiti
Utilities
ARCC has put together a list of utilities for users to utilize. Note: Some utilities will come as part of the system (i.e. do not have a module): For example: bzip2 Some utilities will come as part of the system but might have a module with a newer versio
UW ARCC Aims to Widen Student Exposure to HPC
Overview: Many UW students aren’t provided with an obvious avenue in which to explore High Performance Computing during their time as a student. In order to make HPC more accessible, UW ARCC has created a new project on Beartooth. This project is intended
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VVASPOverview 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. VASP Homepage https
VASPKIT
Overview VASPKIT https://vaspkit.com/index.html#: Aims at providing a powerful and user-friendly interface to perform high throughput analysis of various material properties from the raw calculated data using the widely-used VASP code. The program can be
Vcf2gwas
Overview vcf2gwas https://github.com/frankvogt/vcf2gwas is a Python-built API for GEMMA, PLINK and bcftools performing GWAS directly from a VCF file as well as multiple post-analysis operations. Manual https://github.com/frankvogt/vcf2gwas/blob/main/MANUA
VCFtools
Overview VCFtools https://vcftools.github.io/ is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic varia
VS-Code
Overview Visual Studio Code https://code.visualstudio.com/: Visual Studio Code is a lightweight but powerful source code editor which runs on your desktop and is available for Windows, macOS and Linux. It comes with built-in support for JavaScript, TypeSc
VSEARCH
Overview VSEARCH https://github.com/torognes/vsearch: The aim of this project is to create an alternative to the USEARCH tool developed by Robert C. Edgar (2010). … We have implemented a tool called VSEARCH which supports de novo and reference based chime
VTK
Overview 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 rendering, a suite of widgets for 3D interaction, and extensive 2D plotting capa
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WWannier90Overview Wannier90 http://www.wannier.org/ is an open-source code (released under GPLv2 http://www.gnu.org/licenses/old-licenses/gpl-2.0.html) for generating maximally-localized Wannier functions and using them to compute advanced electronic properties of
WildIris
Overview WildIris is a speciality cluster to enable outreach for INBRE researchers and Wyoming community college students. It can be securely accessed anywhere, anytime using SSH connectivity with two-factor authentication. It is made up of hybrid machine
WildIris Authentication Changes
UW ARCC is changing the way you authenticate on our devices and ssh authentication is now available using a public/private ssh key combination. This makes it possible to authenticate your login on WildIris without a password. What this means for our users
WildIris Globus
Globus Online Globus manages file transfers between two endpoints which may be at different Institutions, on Campus or your workstation. It is ideal for large files and available for many institutional clusters and networks. This document covers the basic
WildIris OnDemand
Overview WildIris OnDemand is an implementation of OnDemand https://openondemand.org/. It is a publicly accessible site for access to BioInfomatic’s WildIris High Performance Computing resource. With OnDemand, you can upload and download files; create, ed
WildIris Software
Overview Herein, find summaries of each package with links to a more detailed page for each package. Below is a list of software / applications that are available on WildIris. Click the software title to learn more about a particular software package, inc
Windows - Logging into HPC with ssh
Overview 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. By the end of
Windows - MobaXterm Login
Overview This tutorial is describes and demonstrates how to use the ssh client MobaXTerm on a Windows computer to log into an HPC system. By the end of this Tutorial you should be able to know how to find, download and install MobaXTerm on Windows as well
Workshop Hosting FAQs
You request a lot of information in your checklist. Is this all really necessary? Workshops frequently entail multiple users accessing the cluster at once. Since all of these users perform the same or similar activities at the same time, they often requir
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