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Running Juicer on the HPC
Setting up your juiceDir To get started with Juicer, you will need to have a directory where your input files exist. The juiceDir should contain a folder called fastq, a folder called references, and a folder called restriction_sites. The names should be exact...
Running Juicebox
ssh with X11 enabled In order to use Juicebox on the HPC, you have to ssh with X11 enabled, which allows for GUI apps to use your local computer graphics even while the software is installed on the hpc. To do this simply execute: ssh -X <your_username>@hpc1.it...
Issues Connecting to the HPC
Connection troubleshooting If you are trying to connect to the HPC (ssh <your_username>@hpc1.its.appstate.edu) but are finding that the SSH client is hanging or getting a message that the 'login has timed out', there are a few troubleshooting steps you can go ...
Patching and Pausing Jobs
On HPC1 use squeue to determine what jobs are running on what nodes: squeue --long Tue May 27 13:16:59 2025 JOBID PARTITION NAME USER STATE TIME TIME_LIMI NODES NODELIST(REASON) 8957 compute a1748355 azeezoe PEN...
Accessing the HPC via Open OnDemand
Our HPC cluster has a web interface available at ondemand.appstate.edu to anyone with an account on the cluster. This provides a more user friendly experience for people who are perhaps not comfortable with a Linux command line environment. Open OnDemand also...
Managing your files and using the web Bash Shell in OpenOnDemand
Our Research Computing HPC cluster now has file management and a bash shell available for users in a web browser via Open OnDemand. Under the Files menu there's a link to your Home Directory: This will allow you to manage, edit, upload and download data...
Virtual Desktops in Open OnDemand
Open OnDemand makes available two different virtual desktop options. These are accessible via the Interactive Apps menu: The ASU Cluster Desktop is available for all HPC users, the Computer Science Desktop is a reserved instance for users in the Department ...
Jupyter Notebooks in Python Virtual Environments
Jupyter Notebook is a popular data science and analysis application written in Python. It is probably one of our most requested resources here at AppState Research Computing. We now have some self-service ways to run it on our compute nodes. Probably the quick...
Building Conda environments in Apptainer
Apptainer is a containerization technology forked from Singularity. It's free, open source and compatible with Docker and Singularity images. This has the advantage of keeping all of your Conda environment programs in one convienent file and avoiding conflicts...
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Policies Pages
Storage
Quota Our HPC cluster has 18TB of storage available to all users. By default we enforce a quota of 400GB per user. If you require more please submit a ticket and request an increase. Please also provide a timeline for how long you require the additional stora...
Policies
Policies regarding storage and access to the on-prem HPC cluster.
IT Support
Role and Support Scope
Our Systems & Research Computing IT team ensures that the infrastructure, platforms, and services you rely on are available, functional, and performant. We focus on diagnosing and resolving system-level issues so you can focus on your research and development ...
RStudio Open OnDemand Application
We now have RStudio available through Open OnDemand. It is accessed similarly to other interactive applications, first login to OnDemand and from the home screen select Rstudio from under Interactive Apps and Servers: Next, fill out the information requeste...