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Role and Support Scope
Our Systems & Research Computing IT team ensures that the infrastructure, platforms, and services...
Classroom Use of the HPC
Classroom use of the HPC is permitted, however there are a few things to consider with respect to...
Jupyter Hub Open OnDemand Application
We now have Jupyter Lab available through Open OnDemand. It is accessed similarly to other intera...
HPC Cluster Description
App State HPC AppState HPC is an educational and research cluster with 2 compute nodes for a tot...
RStudio Open OnDemand Application
We now have RStudio available through Open OnDemand. It is accessed similarly to other interactiv...
Storage
Quota Our HPC cluster has 18TB of storage available to all users. By default we enforce a quota ...
Running Juicer on the HPC
Setting up your juiceDir To get started with Juicer, you will need to have a directory where your...
HPC Tutorials
This is a youtube playlist that contains videos for beginners on how to use the HPC and some best...
Jupyter Notebooks in Python Virtual Environments
Jupyter Notebook is a popular data science and analysis application written in Python. It is prob...
Virtual Desktops in Open OnDemand
Open OnDemand makes available two different virtual desktop options. These are accessible via the...
Accessing the HPC via Open OnDemand
Our HPC cluster has a web interface available at ondemand.appstate.edu to anyone with an account ...
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 i...
TEST DELETE
Building Conda environments in Apptainer
Apptainer is a containerization technology forked from Singularity. It's free, open source and co...
Patching and Pausing Jobs
On HPC1 use squeue to determine what jobs are running on what nodes: squeue --long Tue May 27 13:...
Issues Connecting to the HPC
Connection troubleshooting If you are trying to connect to the HPC (ssh <your_username>@hpc1.its....
Running Juicebox
ssh with X11 enabled In order to use Juicebox on the HPC, you have to ssh with X11 enabled, which...
Data transfer onto the HPC
At some point, you will inevitably need to get data from the HPC back onto your local machine, or...
Nextflow.config file with Slurm compatibility
process { executor = 'slurm' time = < number of hours ('h') days ('d') to let job run eg....
Example SLURM Script (from video)
(Link to original video) fastqc.sh and multiqc.sh scripts at bottom of page (slurm script) #!/bin...