What is Cheaha
Cheaha is currently the largest and fastest supercomputer in the state of Alabama.
Software Title | Description |
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UAB Research Computing System (RCS) | A collaborative data and computing framework used at the University of Alabama at Birmingham. Read more |
Cheaha Supercomputer system | The primary high-performance computing resource at the University of Alabama at Birmingham. Read more |
UAB Research Cloud | The UAB software platform for cloud computing, deployed as an infrastructure-as-a-service. Read more |
Cheaha Account Management system | Account creation and management tool for researchers and collaborators at UAB. Read more |
Duo Two-Factor Authentication (2FA) | A system that adds an extra layer of security by requiring two forms of authentication. Read more |
VPN software | Software that provides a secure connection over a less secure network by encrypting data. Read more |
SSH (Secure Shell) | A network protocol that provides a secure way to access remote systems and services. Read more |
OpenSSH | A suite of secure networking utilities based on the Secure Shell protocol. Read more |
Open OnDemand (OOD) | A web-based platform for access to high performance computing services. Read more |
Bash (UNIX Shell) | A Unix shell and command language used for scripting and command execution. Read more |
Lmod (Environment Modules system) | A tool to easily manage the environment variables of different software packages in a Unix shell. Read more |
SLURM (Simple Linux Utility for Resource Management) | A job scheduler system that allocates resources, manages queues, and schedules jobs to run on the supercomputer. Read more |
Git | A distributed version control system used to track changes in source code during software development. Read more |
UAB GitLab | A GitLab instance hosted on secure servers for use by researchers and collaborators at UAB. Read more |
Git Bash Terminal | A shell that provides a command-line interface to interact with Git on Windows. Read more |
GitHub | A web-based hosting service for version control using Git. Read more |
VSCode (Visual Studio Code) | A free source-code editor made by Microsoft for Windows, Linux and macOS with support for debugging, syntax highlighting, intelligent code completion, snippets, code refactoring, and embedded Git. Read more |
Globus | A software tool for managing data transfers between computers, storage systems, and cloud services. Read more |
RClone | A command-line program used to sync files and directories to and from multiple cloud storage providers. Read more |
FileZilla | A free, open-source FTP software used for transferring files over the Internet. Read more |
Cyberduck GUI | An open-source client for FTP and SFTP, WebDAV, and cloud storage, available for Mac OS X and Windows. Read more |
UAB Long-Term Storage (LTS) | A storage service offered by the University of Alabama at Birmingham for preserving research data. Read more |
AWS S3 (Amazon Web Services Simple Storage Service) | A scalable object storage service for storing and retrieving data in the cloud. Read more |
S3 Browser | A freeware Windows client for Amazon S3 and Amazon CloudFront. Read more |
Docker | An open-source platform used for developing, shipping, and running applications in isolated environments called containers. Read more |
Singularity | A container platform designed for use in high performance computing environments. Read more |
UAB Kubernetes | An open-source system for automating deployment, scaling, and management of containerized applications. Read more |
Anaconda | An open-source distribution of the Python and R programming languages, mainly aimed at scientific computing. Read more |
Jupyter Notebooks | An open-source web application that allows the creation and sharing of documents with live code, equations, visualizations, and narrative text. Read more |
Mamba (Python package manager) | A fast, robust, and scalable package manager for Python, designed to handle large dependencies in complex environments. Read more |
R (Programming Language) | A programming language and free software environment for statistical computing and graphics. Read more |
Matlab | A high-level language and interactive environment for numerical computation, visualization, and programming. Read more |
NVIDIA Clara Parabricks | A computational genomics software suite optimized for NVIDIA GPUs. Read more |
PyTorch | An open-source machine learning library for Python, used for applications such as natural language processing. Read more |
TensorFlow | An end-to-end open-source platform for machine learning, developed by Google Brain Team. Read more |
NVIDIA Drivers | Software modules that allow your operating system to effectively communicate with your NVIDIA graphics card. Read more |
NVIDIA CUDA | A parallel computing platform and application programming interface model created by NVIDIA, allowing developers to use CUDA-enabled graphics processing units for general purpose processing. Read more |
ServiceNow | Helpdesk software to allow users to create issues and connect with the Research Computing staff for assistance and guidance Read more |
Command | Description |
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du -sh | Use to check directory size. |
cd | Use to change the working directory. |
cp | Use to copy files and directories. |
mv | Use to move or rename files and directories. |
rm, rmdir | Use to delete files and directories. |
curl | Use to download files and webpages from the internet. |
mkdir | Use to create directories. |
touch | Use to create files. |
nano | Use to edit plain-text files. |
wc | Use to count lines, words, and characters in a file. |
cat, less | Use to display the contents of a file. |
head, tail | Use to display the start or end of a file. |
sort | Use to sort file contents. |
echo | Use to test a command. |
grep | Use to search for text within a file. |
exit | Use to close the session. |
clear | Use to clear the shell display. |
which | Use to find the location of a command. |
whatis, man | Use to learn about a command. |
ssh | Use for remote shell access. |
sftp | Use for remote file transfer. |
chmod | Use to manage file and directory permissions. |
chgrp | Use to change the group ownership of files and directories. |
getfacl, setfacl | Use to manage researcher access to files and directories. |
Git | Use as a version control system for software and document collaboration. |
Cheaha is currently the largest and fastest supercomputer in the state of Alabama.
These instructions are intended to guide researchers on creating new accounts and managing existing accounts.
Cheaha supports most research software, including RStudio, Jupyter, and MATLAB.
This segment of the docs has instructions for creating accounts for external collaborators
To make the most of Cheaha, become familiar with Linux commands related to job submission and queuing.
For assistance with Cheaha, visit the UAB IT Research Computing support portal
UAB IT Security is available to help review your data and figure out its data classification. All research data is at least Sensitive.
Visit the Research Computing Marketplace to choose from the available resources.
Not seeing what you need? Click the link to request approval for a new resource.
Please use our self-service account registration by visiting the rc.uab.edu. Login using Single Sign-on (SSO) with your UAB Campus (BlazerID) credentials and fill in the form to create your account automatically. For more details please visit our documentation.
Cheaha is a campus resource dedicated to enhancing research computing productivity at UAB. Cheaha is managed by UAB Information Technology's Research Computing group (UAB ITRC) and is available to members of the UAB community in need of increased computational capacity. Cheaha supports high-performance computing (HPC) and high throughput computing (HTC) paradigms.
Yes, please follow these instructions to get an account for your external collaborator.
Go to rc.uab.edu in your web browser (Chrome works best) and login.
Every user gets 3 storage locations:
Please visit our Cheaha documentation for more information about using Cheaha.
Check out the Grants & Publications section on the research computing resources page. Here you can find both a short and long description of HPC resources at UAB for grant and article submissions. If you need a letter of support, contact UAB IT Research Computing at
UAB IT Research Computing provides comprehensive support for researchers that use Cheaha, develop and maintain the cluster, and provide advanced software and consulting support if needed by researchers. Research Computing staff also maintain proposal support documentation, such as letters of commitment and facilities descriptions, to allow researchers a tighter focus on their projects.
New data transfer option between Cheaha high-performance computing
New software tools will help Research Computing identify and resolve service issues more quickly.
Globus data transfer service is now certified for transfer of protected health information (PHI).
Updated documentation for Research Computing resources and services.
Research Computing moves to new, state-of-the-art datacenter.
New cloud computing platform for research workflows.
New long-term storage option for research data.
New data transfer option for Box users.
New datacenter provides more reliable and scalable infrastructure.
Research Computing demonstrates commitment to data security.
New educational offering for the UAB research community.
New talent joins the Research Computing team.
New web interface for accessing Research Computing resources.
New data transfer software added to service portfolio.
As UAB’s first assistant vice president for research computing, Dr. Zottola is a pioneer at UAB and a partner to researchers across campus. Under his leadership, research computing has helped increase the competitive advantage for grants and speeding discoveries that can change the world.
UAB IT added 72 graphics processing units, which will boost the Cheaha supercomputer’s power to 450 teraflops. A teraflop is a unit of computing speed equal to 1 trillion floating-point operations per second. This latest expansion makes Cheaha far and away the fastest supercomputer in Alabama and one of the five fastest at academic institutions in the Southeast — and knocking on the door of the Top 500, a list of the fastest supercomputers in the world.
UAB IT launched a 100Gbps network, one of the fastest in the state, and implemented a grant-funded Science DMZ to separate research network traffic from the rest of campus. The Science DMZ provides high-speed network to access national and international data repositories and share large research data sets in the era of Big Data.
UAB IT received additional funding from the deans of the College of Arts and Sciences and schools of Engineering and Public Health to grow the compute capacity provided by the prior year's seed funding, growing computing speed from 10 teraflops within the last year to 110 teraflops. The expansion added compute nodes, and the 6-petabyte file system came online.
This file system provided each user 5 TB of personal space, additional space for shared projects and a greatly expanded scratch storage all in a single file system. The 2015 and 2016 investments combined to provide a completely new core for the Cheaha cluster, allowing the retirement of earlier compute generations.
With the arrival of a new chief information technology officer at UAB, UAB IT ramped up attention to its research computing infrastructure. New CIO Dr. Curt Carver secured a $500,000 grant from the Alabama Innovation Fund for a 3-petabyte research storage array. With an immediate impact, the institution stabilized research compute funding and provided the necessary funding so that research computing was not funded from reserves.
UAB IT received $500,000 from the university’s Mission Support Fund for a compute cluster seed expansion of 48 teraflops. This investment recognized the crucial role computation plays in supporting and advancing research.
In 2013, UAB IT Research Computing acquired an OpenStack cloud and Ceph storage software fabric through a partnership between Dell and Inktank in order to extend cloud computing solutions to the researchers at UAB and enhance the interfacing capabilities for HPC.
UAB IT invested in the foundation hardware to expand long-term storage and virtual machine capabilities with acquisition of 12 Dell 720xd system, each containing 16 cores, 96GB RAM, and 36TB of storage, creating a 192 core and 432TB virtual compute and storage fabric. Additionally, hardware investment by the School of Public Health's Section on Statistical Genetics added three 384GB large memory nodes and an additional 48 cores to the QDR Infiniband fabric.
UAB was awarded a National Institutes of Health Small Instrumentation Grant to further increase analytical and storage capacity. The grant funds were combined with the annual investment funds, adding 576 cores (48 nodes) based on the Intel Westmere 2.66 GHz CPU, a quad data rate Infiniband fabric with 32 uplinks, an additional 120 TB of storage for the DDN fabric, and additional hardware to improve reliability.
Additional improvements to the research compute platform involved extending the UAB Research Network to link the Business and Engineering Center and RUST data centers, adding 20TB of user and ancillary services storage.
In 2009, annual investment funds were directed toward establishing a fully connected dual data rate Infiniband network between the compute nodes added in 2008 and laying the foundation for a research storage system with a 60TB DDN storage system accessed via the Lustre distributed file system. The Infiniband and storage fabrics were designed to support significant increases in research data sets and their associated analytical demand.
Money was allocated by UAB IT for hardware upgrades, which led to the acquisition of an additional 192 cores and migrated Cheaha's core infrastructure to the Dell blade clustering solution. The expansion provided a three-fold increase in processor density over the original hardware and enabled more computing power to be located in the same physical space with room for expansion, an important consideration in light of the continued growth in processing demand. This hardware represented a major technology upgrade that included space for additional expansion to address over-all capacity demand and enable resource reservation.
The 2008 upgrade began a continuous resource improvement plan that included a phased development approach for Cheaha with ongoing increases in capacity and feature enhancements being brought into production via an open community process, leveraging a federated systems model developed through NSF Award #0330543. Software improvements rolled into the 2008 upgrade included grid computing services to access distributed compute resources and orchestrate jobs using the GridWay meta-scheduler. An initial 10Gigabit Ethernet link establishing the UABgrid Research Network was designed to support high-speed data transfers between clusters connected to this network.
Using a 2001 infrastructure development grant from the National Science Foundation (NSF EPS-0091853), UAB created the Cheaha high-performance computing cluster with the acquisition of a 64-node computer cluster with 128 total cores. Cheaha — named after Alabama’s highest peak — expanded the compute capacity available at UAB and was the first general-access resource for the community.
It led to expanded roles for UAB IT in research computing support through the development of the UAB Shared HPC Facility in the Business and Engineering Complex and provided further engagement in Globus-based grid computing resource development on campus via UABgrid and regionally via SURAgrid.
While most of the world has done its best to stay as far as possible from SARS-CoV–2, the coronavirus that causes COVID–19, a select group of researchers moved closer. For some dedicated scientists at UAB, that means spending workdays and nights a few inches away from the planet’s Public Enemy No. 1. To find a way to stop a killer like SARS-CoV–2 you must look it in the face — culturing the virus in a lab and keeping stocks on hand to test new treatments and perform crucial experiments.
“Essentials of Modern Neuroscience” was created by Franklin R. Amthor, Ph.D., professor of psychology in the College of Arts and Sciences; Anne B. Theibert, Ph.D., professor of neurobiology; David G. Standaert, M.D., Ph.D., John N. Whitaker Endowed Chair of the Department of Neurology; and Erik D. Roberson, M.D., Ph.D., Rebecca Gale Endowed Professor of Neurology and Neurobiology. Theibert and Amthor led the basic science section, while Roberson and Standaert led the clinical section. About 30 additional authors, mostly UAB faculty, wrote individual chapters. The book is published by McGraw-Hill Education.
The University of Alabama System Board of Trustees appointed Mona Fouad, M.D., the inaugural holder of the Edward E. Partridge, M.D., Endowed Chair for Cancer Disparity Research during its June 4 meeting. Matthew Macaluso, D.O., was appointed the first holder of the Bee McWane Reid Endowed Chair in Psychiatry and Neurobiology in the Department of Psychiatry and Behavioral Neurobiology.
During the past 15 years, Limdi and colleagues have identified clinical and genetic factors that account for response to anticoagulant and antiplatelet therapies. These blood-thinning drugs, including warfarin (Coumadin) and clopidogrel (Plavix), are widely used to prevent clotting in patients at risk for stroke, atrial fibrillation and other conditions. Among other findings, the investigators have demonstrated that race influences the dose requirements for warfarin, and a simple genetic test to determine a patient’s response to clopidogrel can significantly reduce the risk of cardiovascular events in patients receiving a heart stent.
No one wants to get coronavirus. Unfortunately, most everybody already has. Not THE coronavirus, as in SARS-CoV-2, the novel coronavirus that causes COVID-19, but OC43 and HKU1, two other members of the same beta-coronavirus family. "Twenty percent of what we call colds are caused by these two coronaviruses that circulate widely in humans," said Troy Randall, Ph.D., professor in the School of Medicine departments of Medicine and Microbiology. "Most of us have been infected at least once or twice in our lifetimes by these two."
In some ways Elizabeth Worthey, Ph.D., is a typical nerd. She likes having lots of computer screens and solving puzzles and nothing so much as coming up with novel ways to use software to solve complex problems. Unlike most geeks, though, Worthey is intimately familiar with her own source code. A chunk of her laptop hard drive is dedicated to a complete copy of her DNA, which she had sequenced nearly a decade ago.
A new study by Sharafeldin at UAB is pointing to a better method of identifying patients at highest risk of cognitive problems after BMT, and her work was highlighted at the American Society for Clinical Oncology’s annual meeting in June. Now she is testing an innovative therapy to bring brains back from the fog — computer games.
Patel, a senior from Gulf Shores, and Moore, a junior from Birmingham, were the first two undergraduates hired into UAB IT Research Computing’s new paid internship program when it launched in January.
Monroe and colleague Ravi Tripathi, a software developer, found a way to scale up their training efforts. In April, they launched the Data Science Club. This isn’t a traditional lab journal club — it’s more like the Dollar Shave Club for machine-learning and biostats. For free.
Frank Skidmore, M.D., assistant professor of neurology, is studying brain images for his research on Parkinson’s disease. For Skidmore, the intricacies in size, shape and surface folds of every brain image must be mapped to a template to allow comparisons. The computational power of the UAB supercomputer allows him to “see” in five dimensions for certaintypes of brain images —the computer is able to work in those higher-dimensional spaces that humans cannot. His research can lead to faster diagnoses for his patients —and better treatment.
Kristina Visscher, Ph.D., assistant professor of neurobiology, is studying visual processing, analyzing huge amounts of data per subject. Her work studies how the brain adapts after long-term changes in visual input, such as macular degeneration.
Ryoichi Kawai, Ph.D., associate professor of physics, uses the supercomputer for what may be the largest calculation on campus —determining the electronic structure for a cube made up of just 216 atoms of zinc sulfide doped with chromium or iron. His research is laying the groundwork for a better infrared laser, which could be used for a variety of treatments from shrinking tumors to removing kidney stones.
Dr. Adrienne Lahti, director of the Division of Behavioral Neurobiology at UAB, is a new user to the research computing cluster. When she submitted a grant to the National Institutes of Health in 2017, she received the NIH’s highest possible impact score — placing her application in the first percentile.
David Crossman, Ph.D., bioinformatics director in UAB’s Heflin Center for Genomic Science, deciphers the sequences of human genomes for patients seeking a diagnosis in UAB’s Undiagnosed Diseases Program. The expanded computer cluster allows him to get answers in hours as opposedto weeks. Speeding the processing time to crunch genome sequencing data means faster diagnoses — and faster treatment and better health outcomes — for his patients.
Dr. Hassan Fathallah-Shaykh, a professor of neurology, works to detect cancer in MRI images using new mathematical models and techniques. Using the new technology implemented by this project, Hassan working with an engineering student, won the 2016 Worldwide Multimodal Brain Tumor Image Segmentation Challengeby analyzing 118,000 MRI images to detect cancer in less than 12 hours. “The supercomputer worked like magic, without any glitches. It is evident that I would not have been able to compete without the supercomputer resource,” he said.