https://github.com/openforcefield/2021-benchmarking-workshop
Materials for the 2021 OpenFF benchmarking workshop
https://github.com/openforcefield/2021-benchmarking-workshop
Last synced: 7 days ago
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Materials for the 2021 OpenFF benchmarking workshop
- Host: GitHub
- URL: https://github.com/openforcefield/2021-benchmarking-workshop
- Owner: openforcefield
- Created: 2021-08-27T16:40:51.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2021-08-31T22:28:24.000Z (over 4 years ago)
- Last Synced: 2023-08-21T16:21:05.590Z (almost 3 years ago)
- Language: Jupyter Notebook
- Size: 1.15 MB
- Stars: 0
- Watchers: 8
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# 2021-benchmarking-workshop
Materials for the 2021 OpenFF benchmarking workshop.
## Installation and getting started
#### 1. Clone the repository:
```
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.
#### 2. Install and activate the conda environment:
```
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.
#### 3. Start up the jupyter notebook with:
```
jupyter notebook workshop.ipynb
```
### Using a remote environment
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:/?token=
```
You will need this for the below instructions.
1. Open a terminal on your local host, and run the following, noting `` from the server output above:
```
ssh -N -L 8801:localhost:
```
2. In a web browser on your local host, enter the following in the URL bar
```
localhost:8801
```
3. Copy the token from the terminal running the server.
It should be among the output like that given above, where `` is shown.
Enter this into the prompt for the token to access the notebook.
### Alternative way to download workshop materials
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.
### Alternative way to install required software
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](https://github.com/openforcefield/2021-benchmarking-workshop/releases) 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
```