A compute delegation package for the StochSS family of stochastic simulators
Project description
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.
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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 todocker 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.
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