2021-01-14 Benchmarking Testing Party Meeting notes

Owned by Jeffrey Wagner, created
Last updated: Apr 29, 2021
1 min read

Date

Jan 14, 2021

Participants

  • @Jeffrey Wagner

  • @David Dotson

  • @David Hahn

  • @Joshua Horton

Discussion topics

Item

Notes

Item

Notes

Planning

  • Goal is to find inputs that make software do something wrong, DON’T try to diagnose, just report on the issue tracker.

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Generic workflow

Step 1: Get a linux computer

  • Option A: Have a linux computer

  • Option B: Set up a docker container like this:

# (if starting from docker) docker pull continuumio/miniconda docker run -it continuumio/miniconda # Inside the docker container groupadd -r app useradd -r -g app -d /home/app -s /bin/bash -c "Docker image user" app mkdir /home/app chown app /home/app su app cd wget "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" bash Miniconda3-latest-Linux-x86_64.sh -b -p miniconda3 . miniconda3/etc/profile.d/conda.sh conda activate base

Step 2: Install the software

Option A: Make a development build from master

conda install -y anaconda-client -n base conda env create openforcefield/openff-benchmark-optimization conda activate openff-benchmark-optimization conda remove --force openff-benchmark git clone https://github.com/openforcefield/openff-benchmark.git cd openff-benchmark pip install -e .

Option B: Make a production/stable build

conda install -y anaconda-client -n base conda env create openforcefield/openff-benchmark-optimization conda activate openff-benchmark-optimization

Option C: Using a single file installer

 

Step 3: Get some molecules

Option A: Make one from SMILES

Step 4: Run the workflow

Action items

Decisions