git clone https://github.com/dashabalashova/boltz-benchmark.git
run predictions
git clone https://github.com/jwohlwend/boltz/
cd boltz
python3 -m venv .venvs/boltz
source .venvs/boltz/bin/activate
pip install -e .[cuda]
screen -S screen1
source .venvs/boltz/bin/activate
mkdir -p runs/casp16/
cp ../boltz-benchmark/runs/casp16/run.sh runs/casp16/run.sh
cp -r ../boltz-benchmark/data/processed/examples/msa examples
cp -r ../boltz-benchmark/data/processed/examples/yamls_L1000 examples
cp -r ../boltz-benchmark/data/processed/examples/yamls_L3000 examples
chmod +x runs/casp16/run.sh
runs/casp16/run.sh
# Ctrl+a+d
deactivate
cd ..
run predictions
git clone https://github.com/dashabalashova/boltz-screen.git
mv boltz-screen boltz2-b
cd boltz2-b
python3 -m venv .venvs/boltz2-b
source .venvs/boltz2-b/bin/activate
pip install -e .[cuda]
screen -S screen2
source .venvs/boltz2-b/bin/activate
mkdir -p runs/casp16_b/
cp ../boltz-benchmark/runs/casp16_b/run.sh runs/casp16_b/run.sh
cp -r ../boltz-benchmark/data/processed/examples/msa examples
cp -r ../boltz-benchmark/data/processed/examples/yamls_L1000 examples
cp -r ../boltz-benchmark/data/processed/examples/yamls_L3000 examples
chmod +x runs/casp16_b/run.sh
runs/casp16_b/run.sh
# Ctrl+a+d
deactivate
cd ..
run predictions
mkdir boltz2-nim
cd boltz2-nim
docker login nvcr.io
export NGC_API_KEY=<nvapi-...>
export LOCAL_NIM_CACHE=~/.cache/nim
mkdir -p $LOCAL_NIM_CACHE
chmod -R 777 $LOCAL_NIM_CACHE
docker pull nvcr.io/nim/mit/boltz2:latest
docker run -it \
--gpus all \
-p 8000:8000 \
-e NGC_API_KEY \
-v "$HOME/.cache/nim":/opt/nim/.cache \
--name boltz2nim \
nvcr.io/nim/mit/boltz2:latest
# new terminal
cd boltz2-nim
screen -S screen3
mkdir -p runs/casp16_nim/
cp ../boltz-benchmark/runs/casp16_nim/run.sh runs/casp16_nim/run.sh
cp ../boltz-benchmark/runs/casp16_nim/casp16.py runs/casp16_nim/casp16.py
cp -r ../boltz-benchmark/data/processed/examples/msa examples
cp -r ../boltz-benchmark/data/processed/examples/yamls_L1000 examples
cp -r ../boltz-benchmark/data/processed/examples/yamls_L3000 examples
chmod +x runs/casp16_nim/run.sh
runs/casp16_nim/run.sh
# Ctrl+a+d
cd ..
collect affinities
cd boltz-benchmark
chmod +x scripts/collect_affinities.sh
scripts/collect_affinities.sh
copy logs
mkdir -p results/logs
cp -a ../boltz/logs/. results/logs/
mkdir -p results/logs_b4
cp -a ../boltz2-b/logs/. results/logs_b4/
mkdir -p results/logs_nim
cp -a ../boltz2-nim/logs/. results/logs_nim/
run notebooks:
- notebooks/logs_b0.ipynb
- notebooks/logs_b4.ipynb
- notebooks/logs_nim.ipynb
- notebooks/casp16_samp_steps.ipynb
- notebooks/casp16_nbatch-batch-nim.ipynb