Available Container Images
JupyerHub makes use of a container image to execute your code/commands. You must use a container image that contains the software you wish to use. We use provide official Jupyter Docker Stacks notebook images. However, additional images can be created for specific needs.
All images include GPU Nvidia and CUDA support, and will provide access to GPU resources if selected during container launch.
Some container images have been discontinued, see discontinued container images for alternatives.
General Container Images
The following general purpose containers are available for use.
| Name | Image | Software | JupyterHub Instance |
|---|---|---|---|
| Jupyter Stack Minimal Notebook | minimal-notebook | Ubuntu 22.04.4 JupyterLab 4.2.4 Python 3.11.9 Git 2.34.1 vi nano wget unzip tzdata |
CSU TIDE, SDSU |
| Jupyter Stack R Notebook | r-notebook | (Everything in jupyter/minimal-notebook) The R interpreter and base environment IRKernel to support R code in Jupyter notebooks tidyverse packages from conda-forge caret, crayon, devtools, forecast, hexbin, htmltools, htmlwidgets, nycflights13, randomforest, rcurl, rmarkdown, rodbc, rsqlite, shiny, tidymodels, unixodbc packages from conda-forge |
CSU TIDE, SDSU |
| Jupyter Stack SciPy Notebook | scipy-notebook | (Everything in jupyter/minimal-notebook) altair, beautifulsoup4, bokeh, bottleneck, cloudpickle, conda-forge::blas=*=openblas, cython, dask, dill, h5py, matplotlib-base, numba, numexpr, openpyxl, pandas, patsy, protobuf, pytables, scikit-image, scikit-learn, scipy, seaborn, sqlalchemy, statsmodel, sympy, widgetsnbextension, xlrd packages ipympl and ipywidgets for interactive visualizations and plots in Python notebooks Facets for visualizing machine learning datasets |
CSU TIDE, SDSU |
| Jupyter Stack Tensorflow Notebook | tensorflow-notebook | (Everything in jupyter/scipy-notebook and its ancestor images) tensorflow machine learning library Jupyter Server Proxy to support TensorBoard |
CSU TIDE, SDSU |
| Jupyter Stack PyTorch Notebook | pytorch-notebook | (Everything in jupyter/scipy-notebook and its ancestor images) pytorch machine learning library (torch, torchaudio, torchvision) |
CSU TIDE, SDSU |
| Jupyter Stack Julia Notebook | julia-notebook | (Everything in jupyter/minimal-notebook) The Julia compiler and base environment IJulia to support Julia code in Jupyter notebook Pluto.jl reactive Julia notebook interface, made accessible with jupyter-pluto-proxy HDF5 package |
TIDE, SDSU |
| Jupyter Stack Datascience Notebook | datascience-notebook | (Everything in the jupyter/scipy-notebook, jupyter/r-notebook, and jupyter/julia-notebook images and their ancestor images) rpy2 package |
CSU TIDE, SDSU |
The following diagram shows the relationship of the above container images.
graph LR;
A[minimum-notebook]-->B[r-notebook];
A-->H[scipy-notebook];
A-->G[julia-notebook];
A-->C[scipy-notebook]-->D[tensorflow-notebook];
C-->E[datascience-notebook];
Custom Container Images
| Name | Image | Software | JupyterHub Instance |
|---|---|---|---|
| NRP R Studio Notebook | r-studio | (Everything in jupyter/r-notebook and its ancestors) R Studio |
CSU TIDE, SDSU |
| Eclipse C/C++ Desktop | eclipse-notebook | (Everything in jupyter/minimal-notebook) Eclipse IDE for C/C++ Developers 2024-06 release for Linux x86_64 build-essential Jupyter Desktop xfce4 desktop |
CSU TIDE, SDSU |
| Kube Notebook | kube-notebook | (Everything in jupyter/minimal-notebook) rclone kubectl Jupyter Desktop Code Server (VS Code) Globus Connect Personal NB Conda Kernels |
CSU TIDE, SDSU |
| SageMath Notebook | sagemath-notebook | (Everything in jupyter/scipy-notebook and its ancestors) SageMath Kernel |
CSU TIDE, SDSU |
| GIS Notebook | gis-notebook | (Everything in jupyter/pytorch-notebook and its ancestors) beautifulsoup4 boto3 eo-learn geopandas geoplot laspy lightgbm natsort netcdf4 networkx psycopg2 pysal rasterio rclone selenium sentinelhub xeus-python |
CSU TIDE, SDSU |
| Health-Informatics-Notebook | health-informatics-notebook | (Everything in jupyter/scipy-notebook and its ancestors) bcftools biopython bwa ensembl-vep fastp goalign gotree mafft modeltest-ng mummer pytest raxml-ng samtools spades varscan |
CSU TIDE, SDSU |
| Astro Notebook | astro-notebook | (Everything in jupyter/scipy-notebook and its ancestors) astropy astroquery photutils emcee corner fsps lxml reportlab SKIRT PTS |
CSU TIDE, SDSU |
| LLM Notebook | llm-notebook | (Everything in jupyter/pytorch-notebook and its ancestors) rclone FastChat Ollama Code Server (VS Code) Jupyter AI bitsandbytes transformers peft accelerate trl ollama-python openai pyaudio portaudio cuda-nvcc deepspeed langchain huggingface_hub auto_gptq autoawq xformers dask-kubernetes chromadb |
CSU TIDE, SDSU |
| George Lab Notebook | georgelab-notebook | (Everything in jupyter/scipy-notebook and its ancestors) rclone VS Code Server opencv gudhi tabulate ripser persim nb_conda_kernels tissue-forge (CPU and GPU) |
SDSU |
| MATLAB + Pulmonary Toolkit | Image is available upon request | (Everything in jupyter/scipy-notebook and its ancestors) MATLAB r2024b MATLAB pulmonarytoolkit rclone NBIA Data Retriever Jupyter Desktop |
SDSU |
| MATLAB + Bertini | Image is available upon request | (Everything in jupyter/datascience-notebook) Bertini LikelihoodProfiler MATLAB r2024b PyTorch StructuralIdentifiability |
SDSU |
| Kaya Lab Notebook | kaya-notebook | (Everything in jupyter/minimal-notebook) Code Server (VS Code) torch_amr environment |
SDSU |
| MESA Notebook | mesa-notebook | (Everything in jupyter/minimal-notebook) binutils libx11-6 libx11-dev make mesa-r24.03.1 tcsh unzip zlib1g zlib1g-dev |
SDSU |
| PyTorch Geometric Notebook | torch-geometric-notebook | (Everything in jupyter/pytorch-notebook and its ancestors) Code Server (VS Code) PyTorch Geometric rclone |
SDSU |
| FST3 Notebook | fst3-notebook | (Everything in jupyter/minimal-notebook) fst3 conda environment |
SDSU |
| ClimaAtmos Notebook | ClimaAtmos-Notebook | (Everything in jupyter/julia-notebook and its ancestors) ClimaAtmos ClimaCore ClimaCoupler cuda-runtime openmpi |
SDSU |
| RStudio Desktop Notebook | rstudio-desktop-notebook | (Everything in NRP R Studio Notebook) RStudio Jupyter Desktop |
SDSU |
| Molecular Dynamics Notebook | molecular-dynamics-notebook | (Everything in jupyter/scipy-notebook and its ancestors) LAMMPS Jupyter Desktop Quantum Espresso cmake gcc g++ openmpi-bin ovito vim |
SDSU |
| TEND Lab Notebook | tend-lab-notebook | (Everything in jupyter/r-notebook) AFNI Code Server (VS Code) Jupyter Desktop rclone SUMA TEND Lab conda environment |
SDSU |
| BART Notebook | bart-notebook | (Everything in jupyter/scipy-notebook) BART Code Server (VS Code) Custom environment Globus Connect Personal Jupyter Desktop NB Conda Kernels rclone |
SDSU |
The following diagram shows the relationship between the general and custom container images.
graph LR;
%% Base images
A[minimal-notebook]
B[r-notebook]
C[scipy-notebook]
D[pytorch-notebook]
E[julia-notebook]
F[datascience-notebook]
%% Derived notebooks
A --> eclipse-notebook
A --> kube-notebook
A --> kaya-notebook
A --> mesa-notebook
A --> fst3-notebook
B --> r-studio
B --> tend-lab-notebook
r-studio --> rstudio-desktop-notebook
C --> sagemath-notebook
C --> health-informatics-notebook
C --> astro-notebook
C --> georgelab-notebook
C --> molecular-dynamics-notebook
C --> bart-notebook
C --> matlab-pulmonary
F --> matlab-bertini
D --> gis-notebook
D --> llm-notebook
D --> torch-geometric-notebook
E --> climaatmos-notebook
%% Aliases for MATLAB custom images
matlab-pulmonary[MATLAB + Pulmonary Toolkit]
matlab-bertini[MATLAB + Bertini]
%% Aliases for names with hyphens not ideal as node IDs
r-studio[NRP R Studio Notebook]
rstudio-desktop-notebook[RStudio Desktop Notebook]
eclipse-notebook[Eclipse C/C++ Desktop]
kube-notebook[Kube Notebook]
sagemath-notebook[SageMath Notebook]
gis-notebook[GIS Notebook]
health-informatics-notebook[Health-Informatics-Notebook]
astro-notebook[Astro Notebook]
llm-notebook[LLM Notebook]
georgelab-notebook[George Lab Notebook]
kaya-notebook[Kaya Lab Notebook]
mesa-notebook[MESA Notebook]
torch-geometric-notebook[PyTorch Geometric Notebook]
fst3-notebook[FST3 Notebook]
climaatmos-notebook[ClimaAtmos Notebook]
molecular-dynamics-notebook[Molecular Dynamics Notebook]
tend-lab-notebook[TEND Lab Notebook]
bart-notebook[BART Notebook]
Discontinued Container Images
| Name | Alternative |
|---|---|
| Stack PRP | Jupyter Stack PyTorch Notebook in general container images |