/category/userinfo

  • Miniforge and UVA HPC

     Overview Miniforge provides the Conda and Mamba package managers, with the default channel being conda-forge.
    (Mamba is a reimplementation of the Conda package manager in C++ that uses a state-of-the-art library “libsolv” for much faster dependency solving.)
    We have transitioned from Anaconda to Miniforge on Oct 15, 2024. See here for details.
    Available Versions The current installation of Miniforge
    incorporates the most popular packages. To find the available versions and learn how to load them, run:
    module spider miniforge The output of the command shows the available Miniforge
    module versions.
    For detailed information about a particular Miniforge
    module, including how to load the module, run the module spider command with the module’s full version label.
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  • Slurm Script Generator
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  • Data Analytics Center

     The Data Analytics Center is the hub for assisting researchers across Grounds with the management and analysis of large datasets on Research Computing platforms.
    Quick Links How To Request
    DAC Support Include DAC Support
    in Your Grant Budget DAC Analytics
    Resource Awards Services We offer comprehensive computational solutions for your research projects including
    workflow development, software and computing platforms selection, new platform configuration, containerization, coding assistance, code optimization and parallelization, data collection and analysis, and machine learning and artificial intelligence support. Areas of Expertise Our staff have a variety of experience and expertise to assist with your next research project and many have been academic researchers.
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  • Digital Technology Core

     The Digital Technology Core (DTC) offers support for researchers who use or would like to use wearables, smartwatches, smartphones, or IoT devices.
    Services We offer comprehensive support for your research projects including
    device selection experimental design on-device software solutions always-on cloud infrastructures Areas of Expertise Our staff have a variety of experience and expertise:
    mobile app development machine learning signal processing noise filtering network protocols Past Collaborations We have years of experience with collaborations. A few of our past collaborations with UVA researchers are below.
    MindTrails Sensus How to Request Support We provide three tiers of support that can each be requested through a support request.
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  • Using UVA’s High-Performance Computing Systems

     Afton is the University of Virginia’s newest High-Performance Computing system. The Afton supercomputer is comprised of 300 compute node each with 96 compute cores based on the AMD EPYC 9454 architecture for a total of 28,800 cores. The increase in core count is augmented by a significant increase in memory per node compared to Rivanna. Each Afton node boasts a minimum of 750 Gigabytes of memory, with some supporting up to 1.5 Terabytes of RAM memory. The large amount of memory per node allows researchers to efficiently work with the ever-expanding datasets we are seeing across diverse research disciplines. The Afton and Rivanna systems provide access to 55 nodes with NVIDIA general purpose GPU accelerators (RTX2080, RTX3090, A6000, V100, A40, and A100), including an NVIDIA BasePOD.
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  • Apptainer and UVA HPC

     Introduction Apptainer is a continuation of the Singularity project (see here). On December 18, 2023 we migrated from Singularity to Apptainer.
    Containers created by Singularity and Apptainer are mutually compatible as of this writing, although divergence is to be expected.
    One advantage of Apptainer is that users can now build container images natively on the UVA HPC system.
    Apptainer and UVA HPC (after 12/18/2023) Apptainer is available as a module. The RC staff has also curated a library of pre-prepared Apptainer container images for popular applications as part of the shared software stack. Descriptions for these shared containers can be found via the module avail and module spider commands.
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  • Software Containers

     [Deprecated] On Dec 18, 2023 Singularity has been upgraded to Apptainer, a continuation of the Singularity project. Overview Singularity is a container application targeted to multi-user, high-performance computing systems. It interoperates well with Slurm and with the Lmod modules system. Singularity can be used to create and run its own containers, or it can import Docker containers.
    Creating Singularity Containers To create your own image from scratch, you must have root privileges on some computer running Linux (any version). Follow the instructions at the Singularity site. If you have only Mac or Windows, you can use the Vagrant environment. Vagrant is a pre-packed system that runs under several virtual-machine environments, including the free Virtualbox environment.
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  • Three Tiers For Support

     Tier 1: Training & Technical Support: Research computing provides training for the use of our systems. The training includes onboarding, introductory sessions, and computational workshops. Additionally, we provide technical support to researchers through our online support request form and virtual office hours. Through these formats, we are able to assist researchers with system access issues and troubleshooting computational problems on our systems. These are services that are provided at no-charge to researchers. Tier 2: Consultation: Initial project consultation and assessment are provided at no charge. If determined
    feasible, the DAC team member will advise the researcher of the specific support
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  • Allocations

     Time on Rivanna/Afton is allocated as Service Units (SUs). One SU corresponds to one core-hour. Multiple SUs make up what is called an allocation (e.g., a new allocation = 1M SUs). Allocations are managed through Grouper (requires VPN connection) groups that should be created by Principal Investigators (PIs) before they submit an allocation request. Eligibility and Account Creation All UVA faculty are eligible to serve as PI and request access to RC services (e.g. storage & HPC allocations, virtual machines, microservices) for their research group. Postdocs and staff are encouraged to use an allocation provided by a faculty sponsor, although they may request their own allocation pending departmental or RC approval.
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  • NVIDIA DGX BasePOD™

     Introducing the NVIDIA DGX BasePOD™ As artificial intelligence (AI) and machine learning (ML) continue to change how academic research is conducted, the NVIDIA DGX BasePOD, or BasePOD, brings new AI and ML functionality UVA’s High-Performance Computing (HPC) system. The BasePOD is a cluster of high-performance GPUs that allows large deep-learning models to be created and utilized at UVA.
    The NVIDIA DGX BasePOD™ on Rivanna and Afton, hereafter referred to as the POD, is comprised of:
    10 DGX A100 nodes with 2TB of RAM memory per node 80 GB GPU memory per GPU device Compared to the regular GPU nodes, the POD contains advanced features such as:
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  • Software Containers

     Overview Containers bundle an application, the libraries and other executables it may need, and even the data used with the application into portable, self-contained files called images. Containers simplify installation and management of software with complex dependencies and can also be used to package workflows.
    Please refer to the following pages for further information.
    Singularity (before Dec 18, 2023) Apptainer (after Dec 18, 2023) Short course: Software Containers for HPC Container Registries for UVA Research Computing Images built by Research Computing are hosted on Docker Hub (and previously Singularity Library).
    Singularity Library Due to storage limits we can no longer add Singularity images to Singularity Library.
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  • GPU-enabled Software and UVA HPC

     Please note that certain modules can only run on specific GPU types. This will be displayed in a message upon loading the module.
    Certain software applications may also able to take advantage of the advanced capabilities provided by the NVIDIA DGX BasePOD™.
    Learn More Module Category Description alphafold bio gpu Open source code for AlphaFold amber chem gpu Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. cellpose bio gpu a generalist algorithm for cellular segmentation clara-parabricks bio gpu NVIDIA Parabricks is the only GPU-accelerated computational genomics toolkit that delivers fast and accurate analysis for sequencing centers, clinical teams, genomics researchers, and next-generation sequencing instrument developers.
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  • Microservice Deployments

     Kubernetes is a container orchestrator for both short-running (such as workflow/pipeline stages) jobs and long-running (such as web and database servers) services. Containerized applications running in the UVARC Kubernetes cluster are visible to UVA Research networks (and therefore from Rivanna, Afton, Skyline, etc.). Web applications can be made visible to the UVA campus or the public Internet. Kubernetes Research Computing runs microservices in a Kubernetes cluster that automates the deployment of many containers, making their
    management easy and scalable. This cluster will eventually consist of several dozen instances, >2000 cores and >2TB of memory allocated to
    running containerized services. It will also have over 300TB of cluster storage and can attach to both project and
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  • Container Services

     Container-based architecture, also known as “microservices,” is an approach to designing and running applications as a distributed set of components or layers. Such applications are typically run within containers, made popular in the last few years by Docker. Containers are portable, efficient, reusable, and contain code and any dependencies in a single package. Containerized services typically run a single process, rather than an entire stack within the same environment. This allows developers to replace, scale, or troubleshoot portions of their entire application at a time. General Availability (GA) of Kubernetes - Research Computing now manages microservice orchestration with Kubernetes, the open-source tool from Google.
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  • Preinstalled Strawberry Perl on Ivy Windows VM

     Perl Our VMs have Strawberry Perl 5.24 available as part of the Windows
    VM, as of the last writing. Licensed as open source under the GPL, it is most often used
    to develop mission critical software, and has excellent integration
    with markup languages such as HTML, XML, amongst others. Since it is both Object-Oriented and procedural, it could be used within a multitude
    of programming projects. It includes built in database integration via
    its DBI module. Other than DBI, it has thousands of modules, making it
    one of the most extensible languages. Due to its interpreted nature,
    Perl is similar to Python and would be easy to understand for those
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  • Ivy Secure Environment

     Ivy is a secure computing environment for researchers consisting of virtual machines (Linux and Windows). Researchers can use Ivy to process and store sensitive data with the confidence that the environment is secure and meets HIPAA, FERPA, CUI or ITAR requirements.
    Facilities Statement - Are you submitting a grant proposal and need standard information about UVA research computing environments? Get it here. Overview Ivy consists of both virtual computing environments and secure storage. In order to obtain access to either system, users must
    Submit an account request, Complete the Information Security Awareness Training, and Ensure their personal computer meets all High Security VPN requirements.
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  • Globus Data Transfer

     Globus is a simple, reliable, and fast way to access and move your research data between systems. Globus allows you to transfer data to and from systems such as:
    Laptops & personal workstations Rivanna/Afton HPC clusters High-Security Research Standard Storage Lab / departmental storage Tape archives Cloud storage Off-campus resources (ACCESS, National Labs) Globus can help you share research data with colleagues and co-investigators, or to move data back and forth between a lab workstation and Rivanna/Afton or your personal computer.
    Are your data stored at a different institution? At a supercomputing facility? All you need is your institution’s login credentials.
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  • `ssh` on UVA HPC

     The secure shell ssh is the primary application used to access the HPC system from the command line.
    Connecting to a Remote Host For Windows, MobaXterm is our recommended ssh client; this package also provides an SFTP client and an X11 server in one bundle.
    Mac OSX and Linux users access the cluster from a terminal through OpenSSH, which are preinstalled on these operating systems. Open a terminal (on OSX, the Terminal application) and type
    ssh -Y mst3k@login.hpc.virginia.edu where mst3k should be replaced by your user ID. You will generally need to use this format unless you set up your user account on your Mac or Linux system with your UVA ID.
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  • Commercial Data Sharing and Archiving Solutions

     Box® Non-sensitive cloud storage UVA Box is a cloud-based storage and collaboration service that gives eligible members of the University community the ability to access, store, and share up to 1 TB of public / internal use University files securely—anywhere, anytime, on any device. Read more DropBox®/Sookasa® Highly Sensitive Data (PHI/PII) storage If you plan on storing highly sensitive data such as PHI or PII, UVA Health System offers a secure encrypted storage for Health System affiliated researchers, students, and staff. “DropBox Sookasa” is a free cloud-based service hosted on Dropbox that can be accessed over the internet on any device.
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  • Rivanna Storage

     There are a variety of options for storing large-scale research data at UVa. Public and Internal Use data storage systems can be accessed from the Rivanna and Afton high performance computing systems.
    Storage Directories Name Quota Price Data Protection Accessible from Best Practices /home 200GB Free 1-week snapshots Rivanna/Afton /home is best used as a working directory when using Rivanna/Afton interactively. Slurm jobs run against /home will be slower than those run against /scratch. The /home directory is a personal storage space that is not shareable with other users. /scratch 10TB Free No backups, Data removed 90 days after last file access time Rivanna/Afton /scratch is a high performance parallel filesystem that is suitable for large scale computational work.
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  • Research Standard Storage

     Overview The Research Standard Storage file system provides users with a solution for research data storage and sharing. Public, internal use, and sensitive research data can be stored in Research Standard storage, and UVA Information Security provides details about data sensitivity classifications. Members in the same group have access to a shared directory created by the team lead or PI. Group membership can be defined and managed through Grouper (requires VPN connection). Research Standard storage is mounted on the HPC cluster and can also be accessed on a personal computer with an SMB mount, allowing for point-and-click file manipulation.
    As of July, 2024, Each PI with a Research Computing account will have up to 10 TB of Research Standard Storage at no charge.
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  • Cloud Storage Solutions

     Amazon Web Services Tiered object storage Amazon S3 and Glacier offer cloud-based, affordable, unlimited capacity for storage from anywhere. Advanced features include scalability, lifecycle management, encryption, and sharing. S3 is ideal for static files that need to be retrieved from any location (PDFs, images, video, etc.). Glacier is archival storage, perfect for grant compliance that requires data retention. How RC can help: Lower pricing - UVA has an Internet2 discount available for educational use. Contact us to create an account for you or your research project. Cost estimates - Cloud storage is not free. Consideration should be made to the size of your files and how often they will be retrieved.
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  • Command Line Data Transfer

     Standard Linux tools can efficiently transfer a small to moderate quantity of data to or from Rivanna/Afton.
    scp scp uses the secure shell (SSH) protocol to transfer files between your local machine and a remote host, or between two remote hosts.
    The following syntax enables copying from local to remote or vice versa. In both cases we are starting from the local system.
    By default, scp works from the level of the directory in which it is invoked.
    Copying from local to remote: scp source_file mst3k@hostaddress:target_file Copying from remote to local: scp mst3k@hostaddress:source_file target_file The following examples detail how to transfer data between your local computer and /project storage on Rivanna/Afton.
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  • Cyberduck

     Cyberduck is a transfer tool for Windows and Mac. It supports a large number of transfer targets and protocols. Only SFTP can be used with Rivanna/Afton. The free version will pop up donation requests.
    Download Download Cyberduck
    Connecting to the HPC System and File Transfer Launch Cyberduck. After launching Cyberduck, the user interface will open. To initiate a connection to UVA HPC, click the Open Connection button.
    Enter Your Credentials. From the drop-down menu, select SFTP (SSH File Transfer Protocol). Then enter the appropriate information in the following fields:
    Host: login.hpc.virginia.edu Username: your computing ID Password: your UVA HPC password Port: 22 When completed, click Connect.
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  • Filezilla

     Filezilla is a cross-platform data transfer tool. The free version supports FTP, FTPS, and SFTP. Only SFTP can be used with UVA HPC.
    Download Download Filezilla
    Connecting to the HPC System and File Transfer Launch FileZilla. After launching FileZilla, the user interface will open. In the left panel, you should see your local file system and files listed in the left side panels. You will enter your login credentials in the fields highlighted in the figure below.
    Enter Your Credentials. Fill in the Host, Username, Password, and Port fields.
    Host: login.hpc.virginia.edu Username: your computing ID Password: your Eservices password Port: 22 When completed, click Quickconnect.
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  • Perl

     Perl Our VMs have Perl 5.16.3 available as part of the base linux
    VM. Licensed as open source under the GPL, it is most often used
    to develop mission critical software, and has excellent integration
    with markup languages such as HTML, XML, amongst others. Since it is both Object-Oriented and procedural, it could be used within a multitude
    of programming projects. It includes built in database integration via
    its DBI module. Other than DBI, it has thousands of modules, making it
    one of the most extensible languages. Due to its interpreted nature,
    Perl is similar to Python and would be easy to understand for those
    Read more →
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  • Computing Systems

     UVA Research Computing can help you find the right system for your computational workloads. From supercomputers to HIPAA secure systems to cloud-based deployments with advanced infrastructure, various systems are available to researchers.
    Facilities Statement - Are you submitting a grant proposal and need standard information about UVA research computing environments? Get it here. High Performance Computing - Rivanna and Afton A traditional high performance cluster with a resource manager, a large file system, modules, and MPI processing. Get Started with UVA HPC Secure Computing for Highly Sensitive Data - Ivy A multi-platform, HIPAA-compliant system for secure data that includes dedicated virtual machines (Linux and Windows), JupyterLab Notebooks, and Apache Spark.
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  • UVA Anywhere VPN on Linux

     ITS does not support the UVA Anywhere VPN client on Linux. These instructions may work but they are provided for user information only. UVA RC does not support usage of the VPN on any platform.
    Setting up the VPN Install Software Prerequisites
    You must install some software using yum,dnf, or apt-get. Note the slight difference in naming convention between distributions.
    Rocy/Alma/RedHat/Fedora
    These distributions need the following packages:
    openssl openconnect NetworkManager-openconnect NetworkManager-openconnect-gnome Ubuntu
    The packages are the same but the names are different. Ubuntu 18.04 and up requires an additional package.
    openssl openconnect network-manager-openconnect network-manager-gnome network-manager-openconnect-gnome It will be necessary for Network Manager to be able to manage the connection.
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  • Pricing

     Below is a schedule of prices for Research Computing resources.
    High Performance Computing Allocations Type SU Limits Cost SU Expiration Standard None Free 12 months Purchased None $0.01 Never Instructional 100,000 Free 2 weeks after last training session A service unit (SU) resembles usage of a trackable hardware resource for a specified amount of time. In its simplest form 1 SU = 1 core hour, but the SU charge rate can vary based on the specific hardware used. Resources like GPUs and memory may incur additional SU charges. About Allocations
    Storage Name Security Cost Research Project Standard $70/TB per year Research Standard Standard $45/TB per year (Each PI with an RC account will be granted up to 10 TB of Research Standard Storage at no charge1) High-Security Research Standard High $45/TB/year Storage Details Request Storage
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  • ACCORD: Jupyter Lab

     Back to Overview
    Jupyter Lab allows for interactive, notebook-based analysis of data. A good choice for pulling quick results or refining your code in numerous languages including Python, R, Julia, bash, and others.
    Learn more about Jupyter Lab
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  • ACCORD: RStudio

     Back to Overview
    RStudio is the standard IDE for research using the R programming language.
    Learn more about RStudio
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  • ACCORD: Theia IDE

     Back to Overview
    Theia Python is a rich IDE that allows researchers to manage their files and data, write code with an intelligent editor, and execute code within a terminal session.
    Learn more about the Theia Python IDE
    Read more →
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  • R Updates: June 17, 2020

     During the June maintenance, we will make changes to R which will affect how your R programs run on Rivanna. Below is a list of the changes and how they will affect your code. 1. The gcc-built versions of R will be updated to goolf-built versions. Instead of loading gcc before loading R, you will need to load goolf or gcc openmpi. For example: module load goolf R/4.0.0.
    Remember to update any Slurm scripts that have module load gcc R or module load gcc R/3.x.x.
    2. The locations of the R libraries will be updated. We are changing the locations of the R libraries (i.
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  • Transitioning to New R Modules: June 17, 2020

     The recommended steps for transitioning your R programs after the June maintenance are as follows: Determine which version of R you will be using (e.g., R/3.6.3). Open a terminal window on the HPC system and load the version of R that you chose in step #1 (e.g., module load goolf R/3.6.3). (Optional) Run our script to rebuild your existing R library for the newer version of R. For example, if you had been using R/3.5.1 and are switching to R/3.6.3, type the following in the terminal window: updateRlib 3.5.1 . Make sure that you have loaded any other modules (e.
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  • UVA HPC Software

     Overview Research Computing at UVA offers a variety of standard software packages for all UVA HPC users. We also install requested software based on the needs of the high-performance computing (HPC) community as a whole. Software used by a single group should be installed by that group’s members, ideally on leased storage controlled by the group. Departments with a set of widely-used software packages may install them to the lsp_apps space. The Research Computing group also provides limited assistance for individual installations.
    For help installing research software on your PC, please contact Research Software Support at res-consult@virginia.edu.
    Software Modules and Containers Software on the HPC system is accessed via environment modules or containers.
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  • ACCESS: Advanced Cyberinfrastructure Coordination Ecosystem: Services and Support

     The NSF’s ACCESS (Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support) program builds upon the successes of the 11-year XSEDE project, while also expanding the ecosystem with capabilities for new modes of research and further democratizing participation. ACCESS Home: access-ci.org access-ci.org/about Allocations Allocations: allocations.access-ci.org Documentation Support: support.access-ci.org Community Engagement ACCESS: support.access-ci.org/affinity-groups Campus Champions: https://campuschampions.cyberinfrastructure.org UVa Research Computing has two Champions, Ed Hall and Katherine Holcomb For more help, please feel free to contact RC staff to set up a consultation or visit us during office hours.
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  • Data Transfer

     Efficient and reliable data transfer is a critical component of research computing. A variety of useful tools is available for rapid data transfer, whether you are transferring data from an external site or within different computing environments at UVA. Common Scenarios Transfer public or internal use data between local workstation/laptop and UVA storage Transfer sensitive or highly sensitive data to Ivy storage Transfer data between external institutions/supercomputing centers and UVA Transfer between UVA HPC and Cloud storage The data transfer method you choose heavily relies on the data sensitivity classification, where the data are currently located and to where you want to transfer the data.
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  • XSEDE: Extreme Science and Engineering Development Environment

     XSEDE’s Mission was to substantially enhance the productivity of a growing community of scholars, researchers, and engineers through access to advanced digital services that support open research; and coordinate and add significant value to the leading cyberinfrastructure resources funded by the NSF and other agencies. — The XSEDE project ended on August 31, 2022 and was succeeded by the ACCESS project.
    XSEDE Home: www.xsede.org
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  • Storage FAQs

     Accidental File Deletions Why Lease Storage Leased Storage Options File Transfer with Globus Permission Denied Error with Globus Help! I deleted my files accidentally! What can I do? For your home storage, the directory is /home/.snapshots . Snapshots are created once per day. Find the date you wish to find the snapshot for and navigate to your computing id. For GPFS Research Project (leased) storage, the directory is /gpfs/gpfs0/project/.snapshots. Neither Research Standard (leased) nor scratch storage is backed up in any way. Why should I lease storage? Leasing storage from Research Computing means that you do not have to run your own data server or backup system.
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  • Frequently Asked Questions

     General Do you have a general computing question?
    Read our FAQ› Rivanna and Afton High Performance Computing Platforms
    Read our FAQ › Ivy Secure Data Computing Platform
    Read our FAQ › Storage Research Data Storage & Transfer
    Read our FAQ ›
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  • Rivanna and Afton FAQs

     General Usage Allocations Research Software Job Management Storage Management Data Transfer Downloading Files Other Questions General Usage How do I gain access to Rivanna/Afton? A faculty member must first request an allocation on the HPC system. Full details can be found here.
    How do I log on to Rivanna/Afton? Use an SSH client from a campus-connected machine and connect to login.hpc.virginia.edu. Instructions for using ssh and other login tools, as well as recommended clients for different operating systems, are here. You can also access the HPC system through our Web-based interface Open OnDemand or FastX.
    Off Campus? Connecting to Rivanna and Afton HPC systems from off Grounds via Secure Shell Access (SSH) or FastX requires a VPN connection.
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  • Research Data Storage

     There are a variety of options for storing research data at UVA. Public and internal use data storage systems can be accessed from the Rivanna and Afton high performance computing systems. Sensitive and highly sensitive data can be stored and accessed within the Ivy secure computing environment. University Information Security provides an overview of the data sensitivity classifications.
    All UVA faculty are eligible to serve as PI and request access to RC services (e.g. storage & HPC allocations, virtual machines, microservices) for their research group. Postdocs and staff are encouraged to use an allocation provided by a faculty sponsor, although they may request their own allocation pending departmental or RC approval.
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  • Graphical SFTP/SCP Transfer Tools

     Several options are available to transfer data files between a local computer and the HPC system through user-friendly, graphical methods.
    Off Campus? Connecting to Rivanna and Afton HPC systems from off Grounds via Secure Shell Access (SSH) or FastX requires a VPN connection. We recommend using the UVA More Secure Network if available. The UVA Anywhere VPN can be used if the UVA More Secure Network is not available. Only Windows and Mac OSX operating systems are supported by the Cisco client provided by ITS. Linux users should refer to these unsupported instructions to install and configure a VPN. The More Secure Network requires authentication through Duo; users should follow the instructions on the dialog box to enter "
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  • Software on Ivy Linux Virtual Machines

     Each Linux Virtual Machine (VM) comes with a set of preinstalled software applications. Each VM can further be customized via installation of optional software packages.
    An overview of available software packages for Windows VMs is provided here.
    Preinstalled Software Software Versions Description Anaconda2023.07-py3.11 The open-source Anaconda Distribution is the easiest way to perform Python/R data science and machine learning on Linux, Windows, and Mac OS X. R4.3.1 R is a free software environment for statistical computing and graphics. RStudio Server2023.06.2 RStudio Server enables you to provide a browser based interface to a version of R running on a remote Linux server.
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  • Software on Ivy Windows Virtual Machines

     Each Windows Virtual Machine (VM) comes with a set of preinstalled software applications. Each VM can further be customized via installation of optional software packages.
    An overview of available software packages for Linux VMs is provided here.
    Preinstalled Software Software Versions Description Miniconda4.11.0 (Python 3.9.7) The open-source Anaconda Distribution is the easiest way to perform Python/R data science and machine learning on Linux, Windows, and Mac OS X. R4.3.1 R is a free software environment for statistical computing and graphics. RStudio1.4.1106 RStudio is an integrated development environment for R, with a console, syntax-highlighting editor that supports direct code execution, and tools for plotting, history, debugging and workspace management.
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  • Data Transfer

     Data transfer Public & Moderately Sensitive Data Transfer Secure Copy (scp) scp uses secure shell (SSH) protocol to transfer files between your local machine and a remote host. scp can be used with the following syntax:
    scp [source] [destination]
    scp SourceFile mst3k@login.hpc.virginia.edu:/scratch/mst3k
    scp SourceFile mst3k@login.hpc.virginia.edu:/project/Grouper_group_name
    Detailed instructions and examples for using scp are listed here.
    Secure File Transfer Protocol (sftp) sftp is a network protocol for secure file management. Instructions and examples for using sftp are located here.
    Graphical File-Transfer Applications Filezilla and Cyberduck, and MobaXterm are examples of open source SFTP client software for file management through an interactive graphical user interface.
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  • Research Project Storage

     Overview The Research Project Storage file system provides users with a collaborative space for data storage and sharing. Public, internal use, and sensitive research data can be stored in Research Project storage, and UVA Information Security provides details about data sensitivity classifications. Members in the same group have access to a shared directory created by the team lead or PI. Group membership can be defined and managed through Grouper (requires VPN connection). /project storage is mounted on the HPC cluster and runs on a new scale-out NAS file system.
    If you are not a researcher, UVA ITS offers Value storage for long-term storage of large scale data.
    Read more →
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  • FastX Web Portal

     Overview FastX is a commercial solution that enables users to start an X11 desktop environment on a remote system. It is available on the UVA HPC frontends. Using it is equivalent to logging in at the console of the frontend.
    Using FastX for the Web We recommend that most users access FastX through its Web interface. To connect, point a browser to:
    https://fastx.hpc.virginia.edu
    Off Campus? Connecting to Rivanna and Afton HPC systems from off Grounds via Secure Shell Access (SSH) or FastX requires a VPN connection. We recommend using the UVA More Secure Network if available. The UVA Anywhere VPN can be used if the UVA More Secure Network is not available.
    Read more →
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  • Open OnDemand

     Overview Open OnDemand is a graphical user interface that allows access to UVA HPC via a web browser. Within the Open OnDemand environment users have access to a file explorer; interactive applications like JupyterLab, RStudio Server & FastX Web; a command line interface; and a job composer and job monitor.
    Logging in to UVA HPC The HPC system is accessible through the Open OnDemand web client at https://ood.hpc.virginia.edu. Your login is your UVA computing ID and your password is your Netbadge password. Some services, such as FastX Web, require the Eservices password. If you do not know your Eservices password you must change it through ITS by changing your Netbadge password (see instructions).
    Read more →
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  • Open OnDemand: File Explorer

     Open OnDemand provides an integrated file explorer to browse and manage small files. Rivanna and Afton have multiple locations to store your files with different limits and policies. Specifically, each user has a relatively small amount of permanent storage in his/her home directory and a large amount of temporary storage (/scratch) where large data sets can be staged for job processing. Researchers can also lease storage that is accessible on Rivanna. Contact Research Computing or visit the storage website for more information.
    The file explorer provides these basic functions:
    Renaming of files Viewing of text and small image files Editing text files Downloading & uploading small files To see the storage locations that you have access to from within Open OnDemand, click on the Files menu.
    Read more →
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  • Open OnDemand: Job Composer

     Open OnDemand allows you to submit Slurm jobs to the cluster without using shell commands.
    The job composer simplifies the process of:
    Creating a script Submitting a job Downloading results Submitting Jobs We will describe creating a job from a template provided by the system.
    Open the Job Composer tab from the Open OnDemand Dashboard.
    Go to the New Job tab and from the dropdown, select From Template. You can choose the default template or you can select from the list.
    Click on Create New Job. You will need to edit the file that pops up, so click the light blue Open Editor button at the bottom.
    Read more →
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  • Logging in to the UVA HPC systems

     The UVA HPC systems (Rivanna and Afton) are accessible through a web portal, secure shell terminals, or a remote desktop environment. For of all of these access points, your login is your UVA computing ID and your password is your Eservices password. If you do not know your Eservices password you must change it through ITS.
    Off Campus? Connecting to Rivanna and Afton HPC systems from off Grounds via Secure Shell Access (SSH) or FastX requires a VPN connection. We recommend using the UVA More Secure Network if available. The UVA Anywhere VPN can be used if the UVA More Secure Network is not available.
    Read more →
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  • MobaXterm

     MobaXterm is the recommended login tool for Windows users. It bundles a tabbed ssh client, a graphical drag-and-drop sftp client, and an X11 window server for Windows, all in one easy-to-use package. Some other tools included are a simple text editor with syntax coloring and several useful Unix utilities such as cd, ls, grep, and others, so that you can run a lightweight Linux environment on your local machine as well as use it to log in to a remote system.
    Download To download MobaXterm, click the link below. Select the “Home” version, “Installer” edition,
    Download MobaXterm
    Run the installer as directed.
    Read more →
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  • Slurm Job Manager

     SLURM Would you like to take an interactive SLURM quiz? y/N |
    Overview UVA HPC is a multi-user, managed environment. It is divided into login nodes (also called frontends), which are directly accessible by users, and compute nodes, which must be accessed through the resource manager. Users prepare their computational workloads, called jobs, on the login nodes and submit them to the job controller, a component of the resource manager that runs on login nodes and is responsible for scheduling jobs and monitoring the status of the compute nodes.
    We use Slurm, an open-source tool that manages jobs for Linux clusters.
    Read more →
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  • Software Modules

     The lmod modules system on the HPC system enables users to easily set their environments for selected software and to choose versions if appropriate.
    The lmod system is hierarchical; not every module is available in every environment. We provide a core environment which contains most of the software installed by Research Computing staff, but software that requires a compiler or MPI is not in that environment and a compiler must first be loaded.
    View All Modules   Basic Commands List all available software
    module avail Use key to list all modules in a particular category. The current choices are
    base, bio, cae, chem, compiler, data, debugger, devel, geo, ide, lang, lib, math, mpi, numlib, perf, phys, system, toolchain, tools, vis, licensed Example:
    Read more →
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  • UVA HPC Software List

     Module Category Description R lang R is a free software environment for statistical computing and graphics. abinit chem ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. abseil lib Abseil is an open-source collection of C++ library code designed to augment the C++ standard library. The Abseil library code is collected from Google's own C++ code base, has been extensively tested and used in production, and is the same code we depend on in our daily coding lives.
    Read more →
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  • Acknowledgement in Publications

     Recognition and documentation of the contribution that Research Computing’s systems and support play in breakthrough research is essential to ensuring continued support for and availability of cutting-edge computing resources at The University of Virginia. Please cite UVA Research Computing in any research report, journal article, or other publication that requires citation of an author’s contributions.
    Suggested format:
    The authors acknowledge Research Computing at The University of Virginia for providing computational resources and technical support that have contributed to the results reported within this publication. URL: https://rc.virginia.edu
    Read more →
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  • Tools for Research

     Tools and software projects that UVA Research Computing has collaborated on:
    LOLAweb LOLAweb is a web server and interactive results viewer for enrichment of overlap between a user-provided query region set (a bed file) and a database of region sets. It provides an interactive result explorer to visualize the highest ranked enrichments from the database. LOLAweb is a web interface to the LOLA R package. Launch LOLAweb BARTweb There are a number of commercially licensed tools available to UVa researchers for free. These products, including UVa Box, Dropbox (Health System) and CrashPlan, are most suitable for small-scale storage needs.
    Learn more
    Read more →
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  • Highly Sensitive Data Storage - Ivy

     Overview Residing within the High Security Zone (HSZ), the Ivy secure computing environment is designed to fit your highly sensitive research computing needs and meets HIPAA, FERPA, CUI and ITAR compliance standards. Within the HSZ, researchers can store their highly sensitive research data in High-Security Research Standard Storage.
    Ivy Central Storage Ivy Central Storage (ICS) was an HSD parking zone and central storage pool with a capacity greater than 1PB. This storage space was available for researchers with highly sensitive data and could be mounted on an Ivy Virtual Machine.
    As of 10/15/24, ICS will be upgraded to High-Security Research Standard Storage.
    Read more →
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  • Bioinformatics Packages on Ivy Linux VM

    Available Packages The following bioinformatics packages are available on the Ivy Linux Virtual Machines
    Bowtie2 Bowtie2 is a memory-efficient tool for aligning short sequences to long reference genomes.
    For bowtie2 usage information, please click [here] (/userinfo/ivy/ivy-linux-sw/bioinformatics/bowtie2)
    HISAT2 HISAT2 is a fast and sensitive tool for aligning short reads against the general human population
    (as well as single reference genome)

    • Requires approval before installation
      For HISAT2 usage information, please click here
    Read more →
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  • Bioinformatics Packages on Windows VM

     Available Packages The following bioinformatics packages are available on the Windows Virtual Machines
    Bowtie2 For more information on bowtie2, please click [here] (/userinfo/ivy/ivy-windows-sw/bioinformatics/bowtie2) –>
    HISAT2 Requires approval before installation. For more information on HISAT2, please click here
    Read more →
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  • Bowtie2 on Ivy Linux VM

     Bowtie2 is a memory-efficient tool for aligning short sequences to long reference genomes.
    It indexes the genome using FM Index, which is based on Burrows-Wheeler Transform algorithm,
    to keep its memory footprint small. Bowtie2 supports gapped, local and paired-end alignment modes.
    Alignment to a known reference using Bowtie2 is often an essential first step in a myriad of NGS analyses workflows.
    Bowtie2 Usage Alignment using bowtie2 is a 2-step process - indexing the reference genome, followed by aligning the sequence data.
    Create indexes of your reference genome of interest stored in reference.fasta file:
    bowtie2-build [option(s)] <reference.fasta> <bt2-index-basename> This will create new files with the provided basename and extensions .
    Read more →
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  • Bowtie2 on Ivy Windows VM

     Bowtie2 is a memory-efficient tool for aligning short sequences to long reference genomes.
    It indexes the genome using FM Index, which is based on Burrows-Wheeler Transform algorithm,
    to keep its memory footprint small. Bowtie2 supports gapped, local and paired-end alignment modes.
    Alignment to a known reference using Bowtie2 is often an essential first step in a myriad of NGS analyses workflows.
    Bowtie2 Usage Alignment using bowtie2 is a 2-step process - indexing the reference genome, followed by aligning the sequence data.
    Create indexes of your reference genome of interest stored in reference.fasta file:
    bowtie2-build [option(s)] <reference.fasta> <bt2-index-basename> This will create new files with the provided basename and extensions .
    Read more →
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  • Data Analysis Packages on Ivy Linux VM

    Available Packages The following Data Analysis packages are available on the Ivy Linux Virtual Machines
    MATLAB MATrix LABoratory (MATLAB for short) is a software designed for quick scientific calculations, such as matrix manipulation, plotting, and others.
    It has hundreds of built-in functions for a wide variety of computations and several tools designed for specific
    research disciplines, including statistics and partial differential equations.

    • Limited licenses available, for more information on MATLAB and licensing, please click [here] (/userinfo/ivy/ivy-linux-sw/data-analysis/matlab)
      SAS SAS is large platform independent software with multiple components, and is used for statistical analysis, data ETL operations, as well as several other
    Read more →
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  • Data Analysis Packages on Ivy Windows VM

    Available Packages The following Data Analysis packages are available on the Ivy Windows Virtual Machines
    MATLAB MATrix LABoratory (MATLAB for short) is a software designed for quick scientific calculations, such as matrix manipulation, plotting, and others.
    It has hundreds of built-in functions for a wide variety of computations and several tools designed for specific
    research disciplines, including statistics and partial differential equations.

    • Limited licenses available, for more information on MATLAB and licensing, please click [here] (/userinfo/ivy/ivy-windows-sw/data-analysis/matlab)
      SAS SAS is large platform independent software with multiple components, and is used for statistical analysis, data ETL operations, as well as several other
    Read more →
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  • Database Software on Ivy Linux VM

     The following database software are available on the Ivy Linux Virtual Machines
    MySQL Is the most popular open-source relational database, used in academia and industry worldwide. It has been
    in use for over 20 years and is backed by a large developer community. It is available in both free and
    proprietary versions.
    MariaDB MariaDB is a community developed version of MySQL, and is highly compatible with MySQL and other relational databases. Existing databases can be easily migrated between MySQL and MariaDB, and vice versa.
    PostgreSQL Unlike MariaDB and MySQL, PostgreSQL is an object relational database, and can be used in a manner similar to other relational databases.
    Read more →
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  • HISAT2 on Ivy Linux VM
    • Please note that HISAT2 requires approval prior to installation on the VM
      HISAT2 is a fast and sensitive tool for aligning short reads against the general human population
      (as well as single reference genome). It indexes the genome using a Hierarchical Graph FM Index
      (HGFM) strategy, i.e. a large set of small indexes that collectively cover the whole genome
      (each index representing a genomic region of 56 Kbp).
      HISAT2 Usage: Alignment using HISAT2 is a 2-step process - indexing the reference genome, followed by aligning the sequence data.
      Create indexes of your reference genome of interest stored in reference.fasta file:
    Read more →
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  • HISAT2 on Ivy Windows VM
    • Please note that HISAT2 requires approval prior to installation on the VM
      HISAT2 is a fast and sensitive tool for aligning short reads against the general human population
      (as well as single reference genome). It indexes the genome using a Hierarchical Graph FM Index
      (HGFM) strategy, i.e. a large set of small indexes that collectively cover the whole genome
      (each index representing a genomic region of 56 Kbp).
      HISAT2 Usage: Alignment using HISAT2 is a 2-step process - indexing the reference genome, followed by aligning the sequence data.
      Create indexes of your reference genome of interest stored in reference.fasta file:
    Read more →
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  • UVa Licensed SPSS on Ivy Windows VM

     SPSS Overview SPSS (or Statistical Package for Social Sciences), was initially developed as a social survey project but later on has grown to encompass statistical
    applications in almost all disciplines. Different industries use SPSS for their data analysis work. Its features include database management, reporting,
    graphing, among many others.
    SPSS Usage SPSS is available only on the Windows VM at the moment. To run SPSS go to:
    Start Menu > All Programs > IBM SPSS Statistics Licensing We have a limited number of SPSS licenses available, which are provided on a first-come-first-serve basis.
    As a consequence, availability of SPSS on your VM is not always guaranteed once a VM request is submitted.
    Read more →
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  • cTAKES on Ivy Linux VMs

     cTAKES Overview cTAKES or The clinical Text Analysis and Knowledge Extraction System, is a Mayo Clinic developed Natural Language Processing (NLP) tool used to
    extract information out of clinical records. It is open-source, and built on the Apache Unstructured Information Management Architecture. cTAKES
    is modular, expandable, for a number of generic use cases, and contains excellent best practice notes.
    cTAKES Usage cTAKES components Some of cTAKES components are listed below:
    Sentence boundary detection (OpenNLP technology)
    *Tokenization (rule-based) Morphologic normalization (NLM’s LVG) POS tagging (OpenNLP technology) Shallow parsing (OpenNLP technology) Named Entity Recognition Negation and context identification (both based on NegEx) cTAKES Named Entities cTAKES contains the following Named Entities:
    Read more →
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  • cTAKES on Ivy Windows VMs

     cTAKES Overview cTAKES or The clinical Text Analysis and Knowledge Extraction System, is a Mayo Clinic developed Natural Language Processing (NLP) tool used to
    extract information out of clinical records. It is open-source, and built on the Apache Unstructured Information Management Architecture. cTAKES
    is modular, expandable, for a number of generic use cases, and contains excellent best practice notes.
    cTAKES Usage cTAKES components Some of cTAKES components are listed below:
    Sentence boundary detection (OpenNLP technology)
    *Tokenization (rule-based) Morphologic normalization (NLM’s LVG) POS tagging (OpenNLP technology) Shallow parsing (OpenNLP technology) Named Entity Recognition Negation and context identification (both based on NegEx) cTAKES Named Entities cTAKES contains the following Named Entities:
    Read more →
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  • User Licensed Stata on Ivy Linux VMs

     Stata Overview Stata is a graphical data analysis tool developed by StataCorp, and is short for Statistics and Data. It
    is used in various disciplines, including biomedicine, economics, epidemiology, among others. It is capable
    of performing statistical analysis, simulations, regression, and data management. Besides the standard version
    Stata also ships with the MP version (multi=processing), and SE for large databases.
    Users requesting an installation of Stata are required to provide their own license. Please consult with us before
    requesting an installation.
    You may also request a Stata license from the UVa Software Gateway
    Installing programs from SSC Please first run the following commands to use the proxy:
    Read more →
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  • User Licensed Stata on Ivy Windows VMs

     Stata Overview Stata is a graphical data analysis tool developed by StataCorp, and is short for Statistics and Data. It
    is used in various disciplines, including biomedicine, economics, epidemiology, among others. It is capable
    of performing statistical analysis, simulations, regression, and data management. Besides the standard version
    Stata also ships with the MP version (multi=processing), and SE for large databases.
    Users requesting an installation of Stata are required to provide their own license. Please consult with us before
    requesting an installation.
    You may also request a Stata license from the UVa Software Gateway
    Installing programs from SSC Please first run the following commands to use the proxy:
    Read more →
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  • UVa Licensed IDL on Ivy Linux VMs

     IDL Overview IDL, short for Interactive Data Language, is an interactive shell based data analysis programming language. Used vastly in medical imaging, it can quickly create visualizations and graphs
    of large data sets in a few easy steps due to its vector nature. FORTRAN users would be familiar with the IDL syntax. IDL is not to be confused with
    Java IDL or Microsoft IDL.
    Basic IDL Usage To start IDL, open a terminal window and type idl. This will start the interactive shell.
    Variables in IDL To initialize variables in IDL, type:
    <variable_name> = <variable_value> e.g.
    x = 3 and hit Enter/Return
    Read more →
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  • UVa Licensed IDL on Ivy Windows VMs

     IDL Overview IDL, short for Interactive Data Language, is an interactive shell based data analysis programming language. Used vastly in medical imaging, it can quickly create visualizations and graphs
    of large data sets in a few easy steps due to its vector nature. FORTRAN users would be familiar with the IDL syntax. IDL is not to be confused with
    Java IDL or Microsoft IDL.
    Licensing We have a limited number of IDL Licenses available, which are provided on a first-come-first-serve basis.
    As a consequence, availability of IDL on your VM is not always guaranteed once a VM request is submitted.
    Read more →
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  • UVa Licensed MATLAB on Ivy Linux Virtual Machines

     MATLAB Overview MATLAB is a high-performance language for technical computing. It integrates
    computation, visualization, and programming environment. MATLAB stands for MATrix LABoratory. MATLAB was made
    to provide easy access to matrix software developed by the LINPACK (linear system package)
    and EISPACK (Eigen system package) projects. MATLAB includes a programming language
    environment with built-in editing and debugging tools, and supports object-oriented programming.
    Programming in MATLAB MATLAB has many advantages compared to conventional computer languages (e.g.,
    C, FORTRAN) for solving technical problems. MATLAB is an interactive system whose
    basic data element is an array, and almost all problems can be solved in MATLAB using that
    Read more →
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  • UVa Licensed MATLAB on Ivy Windows Virtual Machines

     MATLAB Overview MATLAB is a high-performance language for technical computing. It integrates
    computation, visualization, and programming environment. MATLAB stands for MATrix LABoratory. MATLAB was made
    to provide easy access to matrix software developed by the LINPACK (linear system package)
    and EISPACK (Eigen system package) projects. MATLAB includes a programming language
    environment with built-in editing and debugging tools, and supports object-oriented programming.
    Programming in MATLAB MATLAB has many advantages compared to conventional computer languages (e.g.,
    C, FORTRAN) for solving technical problems. MATLAB is an interactive system whose
    basic data element is an array, and almost all problems can be solved in MATLAB using that
    Read more →
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  • UVa Licensed SAS on the Ivy Linux VM

     SAS Overview SAS is a command-driven software package used for statistical analysis
    and data visualization. It is available in .
    It is one of the most widely used statistical software packages in both industry and academia.
    You may use it if you have a large number of statistical algorithms. It is not limited to an industry,
    and could be used in both scientific and non-scientific contexts. We only offer the Teaching & Research version
    at the moment.
    Common Usage For this example we will use a common scenario from SAS Clinical Standards Toolkit, which is used for supporting clinical
    research activities.
    Read more →
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  • UVa Licensed SAS on the Ivy Windows VM

     SAS Overview SAS is a command-driven software package used for statistical analysis
    and data visualization. It is available in .
    It is one of the most widely used statistical software packages in both industry and academia.
    You may use it if you have a large number of statistical algorithms. It is not limited to an industry,
    and could be used in both scientific and non-scientific contexts. We only offer the Teaching & Research version
    at the moment.
    Common Usage For this example we will use a common scenario from SAS Clinical Standards Toolkit, which is used for supporting clinical
    research activities.
    Read more →
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  • Image Processing Software on Ivy Linux VM

     Pre-approved packages The following software packages are pre-approved for image processing on an Ivy Linux VM
    KNIME KNIME is open source analytics platform for data mining and pipelining.
    KNIME’s Image Processing Plugin allows users to perform common image processing
    techniques such as registration, segmentation, and feature extraction. KNIME is compatible with over 120 image file types and can be
    used alongside ImageJ.
    ImageJ ImageJ is a Java-based image processing program developed at the NIH.
    ImageJ can be used interactively through a graphical user interface or automatically with Java.
    OpenCV OpenCV is an open source library for computer vision applications.
    OpenCV includes modules for image processing, video analysis, machine learning, and much more.
    Read more →
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  • Image Processing Software on Ivy Windows VM

     Pre-approved packages The following software packages are pre-approved for image processing on an Ivy Windows VM
    Axiovision Axiovision is software for microscopy image processing and analysis.
    Axiovision is highly configurableto meet the needs of your individual workflows.
    KNIME KNIME is open source analytics platform for data mining and pipelining.
    KNIME’s Image Processing Plugin allows users to perform common image
    processing techniques such as registration, segmentation, and feature extraction. KNIME is compatible with over 120 image file types and can be used alongside ImageJ.
    ImageJ ImageJ is a Java-based image processing program developed at the NIH.
    ImageJ can be used interactively through a graphical user interface or automatically with Java.
    Read more →
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  • LibreOffice On Ivy Linux VM

     LibreOffice Overview Our Linux VMs come prepackaged with the open source alternative to Microsoft Office(R), called LibreOffice.
    As of last writing, version 5 is installed, including the specific software suites mentioned below.
    LibreOffice is compatible with all Microsoft Office formats, and can be connected to services like
    Google Drive or DropBox. It is available under the Mozilla Public License. LibreOffice is full GUI
    software and would require you to RDP into your VM or use a graphical tool such as FastX in order to
    render it.
    LibreOffice Writer LibreOffice Writer is the word processor component of LibreOffice. It can save documents in .
    Read more →
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  • Preinstalled Java SDK on Ivy Linux VM

     Java SDK Overview Ivy Linux VMs are installed with Java SDK 1.8. Java is a popular Object-Oriented programming
    language and is used in a multitude of scenarios. It is available under the GNU General Public
    License for all users. The SDK consists of a large number of tools such as javac that
    help in application development.
    Running Java commands from the Command Line Open a Command Line Terminal and enter java followed by the desired command. E.g. to find
    the version of the SDK
    java -version Running your code To compile java code, first cd to the location of your .
    Read more →
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  • Preinstalled Java SDK on Ivy Windows VM

     Java SDK Overview Ivy Windows VMs are installed with Java SDK 1.8. Java is a popular Object-Oriented programming
    language and is used in a multitude of scenarios. It is available under the GNU General Public
    License for all users. The SDK consists of a large number of tools such as javac that
    help in application development.
    Running Java commands from the Command Prompt Open a Windows Command Prompt and enter java followed by the desired command. E.g. to find
    the version of the SDK
    java -version Running your code To compile java code, first cd to the location of your .
    Read more →
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  • Preinstalled Perl on Ivy Linux VMs

     Perl Our VMs have Perl 5.16.3 available as part of the base linux
    VM. Licensed as open source under the GPL, it is most often used
    to develop mission critical software, and has excellent integration
    with markup languages such as HTML, XML, amongst others. Since it is both Object-Oriented and procedural, it could be used within a multitude
    of programming projects. It includes built in database integration via
    its DBI module. Other than DBI, it has thousands of modules, making it
    one of the most extensible languages. Due to its interpreted nature,
    Perl is similar to Python and would be easy to understand for those
    Read more →
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  • Preinstalled Rodeo on Ivy Linux VM

     Rodeo Overview Our Linux VMs are installed with Rodeo version 2.5, as of the last update. Rodeo is a lightweight, Python based, IDE for data science.
    It has a very streamlined code-to-plot workflow, with easily extensible packages that make it simple to
    analyze difficult patterns in data. It includes many data analysis features under one roof, and adopts features from
    iPython Notebook (it actually runs atop the iPython kernel). Like most Python projects,
    it is open source and available for free.
    Launching Rodeo You can launch Rodeo from the Applications menu. It is a self-contained IDE that would not require any knowledge of the command line.
    Read more →
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  • Preinstalled Rodeo On Ivy Windows VM

     Rodeo Overview Our Windows VMs are installed with Rodeo version 1.3, as of the last update. Rodeo is a lightweight, Python based, IDE for data science.
    It has a very streamlined code-to-plot workflow, with easily extensible packages that make it simple to
    analyze difficult patterns in data. It includes many data analysis features under one roof, and adopts features from
    iPython Notebook (it actually runs atop the iPython kernel). Like most Python projects,
    it is open source and available for free.
    Launching Rodeo You can launch Rodeo from the Start menu. It is a self-contained IDE that would not require any knowledge of the command line.
    Read more →
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  • Sumatra PDF on Ivy Windows VM

     Sumatra PDF Overview Sumatra PDF is an open source software to view PDF files in Windows. It could be used to view PDF documents stored within the Ivy VM.
    As of the latest version, Sumatra supports multiple formats including PDF, EPUB, MOBI, and XPS.
    Running Sumatra PDF From the Start menu, go to All Programs and search for Sumatra PDF. Click on the icon to run it.
    More Information For more information, visit the Sumatra PDF official website.
    Read more →
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  • Preinstalled Python 2 and Python 3 with Anaconda on Ivy Linux VM

     Anaconda Our VMs have Python 2 and 3 available as part of the Anaconda distribution. Please refer to this page for more information.
    Read more →
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  • Preinstalled R on Ivy Linux VM

     R Overview R is an open source programming language, used by Data Miners, Scientists, Data Analysts,
    and Statisticians. It is available under the GNU GPL V2 license from the Comprehensive R
    Archive Network
    R can be used for many statistical, modeling, and graphical solutions. It is very Object-Oriented in nature and is
    easily extensible.
    Running the command line R console Type R at the terminal to launch the R console.
    Installing packages Our Linux VMs come equipped with R preinstalled. Most major R packages are also installed
    and further could be installed from CRAN using (from within the R console)
    Read more →
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  • Preinstalled R on Ivy Windows VM

     R Overview R is an open source programming language, used by Data Miners, Scientists, Data Analysts,
    and Statisticians. It is available under the GNU GPL V2 license from the Comprehensive R
    Archive Network
    R can be used for many statistical, modeling, and graphical solutions. It is very Object-Oriented in nature and is
    easily extensible.
    Running Rstudio from the desktop You can start R in a Graphical interface using the RStudio application from the desktop
    Running the command line R console Type R at the command prompt to launch the R console.
    Installing packages Our Windows VMs come equipped with R preinstalled.
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  • Preinstalled Python 2 and Python 3 with Anaconda on Ivy Windows VM

     Anaconda Our VMs have python 2 and 3 available as part of the Anaconda
    distribution. Anaconda comes installed with many packages best suited
    for scientific computing, data processing, and data analysis, while making deployment
    very simple. Its package manager conda installs and updates python packages and
    dependencies, keeping different package versions isolated on a project-by-project basis.
    Anaconda is available as open source under the New BSD license. It also ships
    with pip, the common python package manager.
    Installing packages Packages could be installed via pip or conda package managers
    Installing packages on a Windows VM
    A) Using conda
    From the Start menu, open a new Command Prompt (or Anaconda prompt) window, and type:
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  • Preinstalled Office 2016 on Ivy Windows VM

     Microsoft Office Overview The Ivy Windows VMs are installed with Microsoft Office 2016. Features such as OneDrive are not available
    since Ivy is not connected to the public internet. Therefore in order to load documents in and out of the
    VM, you would have to use the Globus DTN.
    Available Software The following software packages are available for use on the Ivy Windows VM:
    Word 2016 Excel 2016 PowerPoint 2016 Access 2016 OneNote 2016 Outlook 2016 Publisher 2016 Running Office All Office software could be accessed from the Start menu using Start > All Programs
    More Information For more Information about Microsoft Office, please visit its official website.
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  • User Guides

     High Performance Computing Standard and high security HPC to run your code, generally written in R, Python or shell scripts.
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  • Computing Environments at UVA

     Research Computing (UVA-RC) serves as the principal center for computational resources and associated expertise at the University of Virginia (UVA). Each year UVA-RC provides services to over 433 active PIs that sponsor more than 2463 unique users from 14 different schools/organizations at the University, maintaining a breadth of systems to support the computational and data intensive research of UVA’s researchers.
    High Performance Computing UVA-RC’s High Performance Computing (HPC) systems are designed with high-speed networks, high performance storage, GPUs, and large amounts of memory in order to support modern compute and memory intensive programs. UVA-RC operates two HPC systems, Rivanna and Afton.
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