Open Ondemand

Body

What is Open OnDemand?

Open OnDemand is a browser-based web interface that provides access to SDSU's HPC clusters without needing an SSH client or command line knowledge. It is the recommended option for users who prefer a graphical interface.

Using Open OnDemand you can:

Access a web-based terminal (shell) directly in your browser
Browse, upload, download, and manage your files
Submit and monitor Slurm jobs
Launch interactive applications such as Jupyter Notebook, JupyterLab, and RStudio
View and manage your active interactive sessions

Both Innovator and Discovery have their own separate OnDemand portals with different URLs and different available applications.

Innovator Open OnDemand

Accessing Innovator OnDemand

Open your browser and navigate to:

https://hpcportal.sdstate.edu

Innovator OnDemand Menu Overview

Files

Home Directory — browse and manage files in your home directory (/home/jacks.local/username)
Scratch Directory — browse and manage files in your scratch directory (/mmfs1/scratch/jacks.local/username)

Jobs

Active Jobs — view all currently running and queued jobs on Innovator
Job Composer — create and submit Slurm job scripts through a graphical interface

Clusters

Innovator Shell Access — opens a web-based terminal for full command line access to Innovator in your browser

Common Configuration Fields for All Innovator Interactive Apps

When launching any interactive app on Innovator, you will see these configuration fields:

Node Type — select the partition to run on. Options vary per app but include Compute, Big Memory, GPU, and Quickq
Number of cores — how many CPUs to request. Maximum is 48 for all node types
Memory Allocation (in GB) — how much RAM to request. Maximum: 250 GB for compute/quickq, 2014 GB for bigmem, 502 GB for GPU
Number of hours — how long your session will run before automatically closing
Email address for Slurm notifications (optional but recommended) — you will receive an email when your session starts and ends
Additional modules (optional) — space-separated list of extra modules to load, for example mpich/3.2.1

Available node types on Innovator:

Compute — 46 nodes, 1-48 cores, 256 GB RAM, 14-day walltime
Big Memory — 4 nodes, 1-48 cores, 2 TB RAM, 14-day walltime
GPU — 14 nodes, 1-48 cores, 512 GB RAM, 2x NVIDIA A100 80GB per node, 14-day walltime
Quickq — 46 nodes, 1-48 cores, 256 GB RAM, 12-hour walltime. Best for short jobs that do not need GPU or large memory

Innovator Interactive Desktop

Launches a full graphical desktop environment running on an Innovator node directly in your browser. Useful for applications that require a graphical user interface.

Cellpose

Cellpose is a deep learning-based software tool designed for the segmentation of cells in microscopy images.

Available node types: GPU (recommended), Quickq
Number of cores: 1-48, maximum 48 for both queues
Memory Allocation: maximum 250 GB for quickq, 502 GB for GPU
Maximum hours: 4 hours
GPUs: request 1x NVIDIA A100 80GB. Cellpose GUI does not support multi-GPU processing so only 1 GPU is available per session
Launch Flags: optional flags to customize how Cellpose launches, for example --Zstack launches with the Zstack flag
Note: Quickq does not offer GPU acceleration. Use the GPU partition for faster image processing and segmentation

ChimeraX

ChimeraX is a molecular visualization tool for structural biology used to visualize and analyze molecular structures.

Available node types: Compute, Big Memory, GPU, Quickq
Number of cores: 1-48
Memory Allocation: maximum 250 GB for quickq/compute, 2014 GB for bigmem, 502 GB for GPU
Maximum hours: 24 hours
Additional modules: optional

Code Server (VS Code)

Code Server allows you to run Visual Studio Code (VS Code) on an Innovator node and access it from your browser. You can write and run code directly on the cluster using a familiar VS Code interface without needing to install VS Code locally.

Available node types: Compute, Big Memory, GPU, Quickq
Number of cores: 1-48
Memory: maximum 250 GB for quickq/compute, 2014 GB for bigmem, 502 GB for GPU
Maximum hours: 24 hours
CUDA Version: select a CUDA version if using a GPU node. A GPU node is required to use CUDA
Code Server Version: Code Server 4.92.2
Number of GPUs: enter none for no GPU, 1 for one GPU, or 2 for both GPUs on the node. If not using a GPU node enter none

Deepchem

DeepChem is an open-source Python library that applies deep learning to chemistry, biology, and drug discovery. It provides tools for molecular featurization, predictive modeling, and access to benchmark datasets. Ideal for building models to predict molecular properties or perform virtual screening.

Available node types: Compute, Big Memory, GPU, Quickq
Number of cores: 1-48
Memory Allocation: maximum 250 GB for quickq/compute, 2014 GB for bigmem, 502 GB for GPU
Maximum hours: 24 hours for compute/bigmem/GPU, 12 hours for quickq

HEC-HMS

HEC-HMS (Hydrologic Engineering Center — Hydrologic Modeling System) is software for hydrological modeling and simulation.

Available node types: Compute only
Number of cores: 1-48
Memory Allocation: maximum 250 GB
Maximum hours: 168 hours (7 days)
Additional modules: optional

Haploview

Haploview is a tool for the analysis and visualization of linkage disequilibrium and haplotype data in genetic studies.

Available node types: Compute, Quickq
Number of cores: 1-48
Memory Allocation: maximum 250 GB for both queues
Maximum hours: 4 hours
Additional modules: optional

Jupyter Notebook

Jupyter Notebook launches an interactive Python notebook server on an Innovator node. Useful for data analysis, machine learning, and scientific computing.

Available node types: Compute, Big Memory, GPU, Quickq
Number of cores: 1-48
Memory Allocation: maximum 250 GB for quickq/compute, 2014 GB for bigmem, 502 GB for GPU
Maximum hours: 24 hours for compute/bigmem/GPU, 12 hours for quickq
GPUs (GPU node only): request 1 or 2 NVIDIA A100 80GB GPUs
Additional modules: optional
Important: Only one Jupyter Notebook session is allowed at a time. Use Jupyter primarily for debugging and testing. Once scripts are ready, submit them via sbatch for efficient processing
Conda environments: Personal Conda environments in your /home can be accessed. Ensure the package ipykernel is installed in your Conda environment

JupyterLab

JupyterLab is the next-generation Jupyter interface providing a file browser, multiple notebooks, terminals, and text editors in a single interface.

Available node types: Compute, Big Memory, GPU, Quickq
Number of cores: 1-48 (default is 10)
Memory Allocation: maximum 250 GB for quickq/compute, 2014 GB for bigmem, 502 GB for GPU
Maximum hours: 24 hours for compute/bigmem/GPU, 12 hours for quickq
GPUs (GPU node only): request 1 or 2 NVIDIA A100 80GB GPUs
Additional modules: optional
Important: Only one Jupyter session is allowed at a time. Additional sessions will not start until your first session completes
Conda environments: Personal Conda environments in your /home can be used. Ensure ipykernel is installed

Napari

Napari is a multi-dimensional image viewer for scientific data, launched on Innovator for use with MicroSam.

Available node types: Compute, Big Memory, GPU, Quickq
Number of cores: 1-48
Memory Allocation: maximum 250 GB for quickq/compute, 2014 GB for bigmem, 502 GB for GPU
Maximum hours: 24 hours
Additional modules: optional

ParaView

ParaView is a powerful open-source software package for the visualization of scientific, engineering, and analytical data.

Available node types: GPU (recommended), Quickq
Number of cores: 1-48, maximum 48 for both queues
Memory Allocation: maximum 250 GB for quickq, 502 GB for GPU
Maximum hours: 4 hours
GPUs: request 1 NVIDIA A100 80GB GPU
Note: Quickq does not offer GPU acceleration but can be used for small or infrequent tasks, or when the GPU queue is full

RStudio Server

RStudio Server launches an RStudio IDE session on an Innovator node for statistical computing and graphics using R.

Available node types: Compute, Big Memory, GPU, Quickq
Number of cores: 1-48
Memory Allocation: maximum 250 GB for quickq/compute, 2014 GB for bigmem, 502 GB for GPU
Maximum hours: 24 hours for compute/bigmem/GPU, 12 hours for quickq
R Version: R 4.3.2 mkl

TASSEL

TASSEL is software for evaluating trait associations, evolutionary patterns, and linkage disequilibrium in genetic data.

Available node types: Compute, Quickq
Number of cores: 1-48
Memory Allocation: maximum 250 GB for quickq/compute, 2014 GB for bigmem, 502 GB for GPU

TensorBoard

TensorBoard is a visualization toolkit to help you understand and monitor the performance of your machine learning models. It provides insights to help refine models, troubleshoot issues, and improve your machine learning projects.

Available node types: Compute, Quickq
Number of cores: 1-48
Memory: maximum 250 GB for both queues
Maximum hours: 24 hours
TensorBoard Log Directory: enter the path on Innovator that contains your data to visualize. For example: /home/jacks.local/username

VisIt

VisIt is an open source, interactive, scalable visualization, animation, and analysis tool. Users can quickly generate visualizations, animate them through time, manipulate them with a variety of operators and mathematical expressions, and save the resulting images and animations for presentations.

Available node types: GPU (recommended), Quickq
Number of cores: 1-48, maximum 48 for both queues
Memory Allocation: maximum 250 GB for quickq, 502 GB for GPU
Maximum hours: 4 hours
GPUs: request 1 NVIDIA A100 80GB GPU
Note: Quickq does not offer GPU acceleration but can be used for small or infrequent tasks, or when the GPU queue is full

Discovery Open OnDemand

Accessing Discovery OnDemand

Open your browser and navigate to:

https://mydiscovery.sdstate.edu

Discovery OnDemand Menu Overview

Files

Home Directory — browse and manage files in your home directory (/home/jacks.local/username)

Jobs

Active Jobs — view all currently running and queued jobs on Discovery
Job Composer — create and submit Slurm job scripts through a graphical interface

Clusters

Discovery Shell Access — opens a web-based terminal for full command line access to Discovery in your browser

Common Configuration Fields for All Discovery Interactive Apps

When launching any interactive app on Discovery, you will see these configuration fields:

Node Type — Compute or GPU depending on the app
Number of cores — maximum is 48 for all queues
Memory Allocation (in GB) — maximum 502 GB for GPU. For compute, memory requests over 250 GB will be automatically routed to a high-memory node. There are only 2 high-memory nodes on Discovery so please request only the memory you need as requesting more than necessary may increase your wait time. For jobs requiring 250 GB or less, 10 standard compute nodes are available
Number of hours — maximum 24 hours for all apps
Email address for Slurm notifications (optional but recommended) — you will receive an email when your session starts and ends
Additional modules (optional) — space-separated list of extra modules to load

Available node types on Discovery interactive apps:

Compute — general compute nodes. Memory requests over 250 GB are automatically routed to high-memory nodes (2 TB RAM). 10 standard compute nodes available for jobs requiring 250 GB or less
GPU — Discovery GPU nodes with up to 2x NVIDIA H100 GPU cards per node, 512 GB RAM

Haploview (Discovery)