2021-01-14 Benchmarking Testing Party Meeting notes

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.

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

# If using docker, either wget the installer, or move it in using docker cp
bash openff-benchmark-2021.01.21.2-py37-Linux-x86_64.sh -b -p miniconda3
. miniconda3/etc/profile.d/conda.sh
conda activate

Step 3: Get some molecules

Option A: Make one from SMILES

# To make a simple single-conf molecule from SMILES
python
from openforcefield.topology import Molecule
mol = Molecule.from_smiles('COCOCOCOCO')
mol.generate_conformers()
mol.to_file('input.sdf', file_format='sdf')

Step 4: Run the workflow

# preprocess
openff-benchmark preprocess validate -g BBB input.sdf
openff-benchmark preprocess generate-conformers 1-validate_and_assign/
openff-benchmark preprocess coverage-report 2-generate_conformers -f openff_unconstrained-1.3.0.offxml

# optimize
## qm calculations
openff-benchmark optimize execute --season "1:1" -o 3-export-compute-qm 2-generate_conformers/
## mm calculations
openff-benchmark optimize execute --season "1:2" -o 3-export-compute-mm 3-export-compute-qm/b3lyp-d3bj/dzvp/

# analysis 
openff-benchmark report compare-forcefields --input-path 3-export-compute-mm/ --input-path 3-export-compute-qm/b3lyp-d3bj/dzvp/  --ref-method b3lyp-d3bj
# plots
openff-benchmark report plots --input-path 4-compare_conformers --ref-method b3lyp-d3bj

Meetings