StochSS-Compute

StochSS-Compute is a compute delegation server for the StochSS family of stochastic simulation software. StochSS-Compute allows for one to run StochSS or GillesPy2 simulations on distributed cloud compute resources.

PLEASE REGISTER AS A USER, so that we can prove StochSS-Compute has many users when we seek funding to support development. StochSS-Compute is part of the StochSS project.

Example Quick Start

1. Installing dependencies & stochss_compute

Using a python virtual environment (documentation):

git clone https://github.com/StochSS/stochss-compute.git
cd stochss-compute
python3 -m venv venv 
source venv/bin/activate
pip3 install -r requirements.txt

OR

Global install of dependencies:

git clone https://github.com/StochSS/stochss-compute.git
cd stochss-compute
pip3 install -r requirements.txt

PyPI:

pip3 install stochss_compute

2. Start up the server and compute backend

Using the startup script dialogue:

python3 startup.py

3. An example is contained in ./examples/StartHere.ipynb:

# source venv/bin/activate # Uncomment if using a virtual environment
jupyter notebook --port 9999 examples/StartHere.ipynb

• Jupyter should launch automatically. If not, copy and paste the following URL into your web browser:
  http://localhost:9999/notebooks/examples/StartHere.ipynb

Docker

• As an alternative to the above steps, you can use Docker.

docker run -it --rm --network host stochss/stochss-compute:latest

• Stochss-compute is now running on localhost:29681.
• The cache defaults to the current working directory under sd-cache. To set a new path for the cache, you can pass one to docker run:

docker run -it --rm --network host -v $PWD/MyCache:/usr/src/app/sd-cache stochss/stochss-compute

License

StochSS-Compute is licensed under the GNU General Public License version 3. Please see the file LICENSE for more information.

Acknowledgments

This work has been funded by National Institutes of Health (NIH) NIBIB Award No. 2R01EB014877-04A1.

StochSS-Compute uses numerous open-source packages, without which it would have been effectively impossible to develop this software with the resources we had. We want to acknowledge this debt. In alphabetical order, the packages are:

• Jupyter – web application for creating documents containing code, visualizations and narrative text
• Dask.Distributed – a library for distributed computation

Finally, we are grateful for institutional resources made available by the University of North Carolina at Asheville, the University of California at Santa Barbara, and Uppsala University.