Materials for the 2021 OpenFF benchmarking workshop.
git clone git@github.com:openforcefield/2021-benchmarking-workshop.git
cd 2021-benchmarking-workshop
If this step fails, an alternative is provided at the bottom of this README.
conda env create -f env.yml
conda activate 2021-benchmarking-workshop
If this step fails, an alternative is provided at the bottom of this README.
jupyter notebook workshop.ipynb
If you performed the installation instructions above on a remote host accessible via SSH, you can connect to the Jupyter notebook server through an SSH tunnel.
Among the notebook server output from the instructions above, you should see a line like:
[I 17:17:45.169 NotebookApp] http://localhost:<port>/?token=<token-content>
You will need this for the below instructions.
- Open a terminal on your local host, and run the following, noting
<port>from the server output above:
ssh -N -L 8801:localhost:<port> <remote-host>
- In a web browser on your local host, enter the following in the URL bar
localhost:8801
- Copy the token from the terminal running the server.
It should be among the output like that given above, where
<token-content>is shown. Enter this into the prompt for the token to access the notebook.
If you are unable to run git clone on your machine, you can instead click on the green Code button on the front page of this repository and download its contents as a zip file.
If you are unable to run the conda env create command above, you can download a "single-file installer" that will deploy a conda installation with all the workshop software into your userspace. The single file installers are in the "Assets" section of the latest release of this repository. This single file installer is installed as follows (this is shown for Bash on Mac, the filenames/source commands will be slightly different on csh/Linux)
bash openff-benchmark-2021.08.04.0-py37-MacOSX-x86_64.sh -b -p ./miniconda3
source miniconda3/etc/profile.d/conda.sh
conda activate