The anaconda environment and datasets are already available in a shared folder
- Clone this repo
git clone https://github.com/MKorablyov/LambdaZero
- Setup Config
cd LamdaZero
cp ./misc/external_dirs_cfg external_dirs.cfg
vi external_dirs.cfg # change the name of your Summaries folder
# LambdaZero needs the following folders:
# (1) Programs: Third-party softwares. These are already installed on beluga to /lustre03/project/6004852/mkkr/Programs
# (2) Datasets: Datasets not included in this repo. These are already installed on beluga to /lustre03/project/6004852/mkkr/Datasets
# (3) Summaries: where the program will write output. Please, indicate your own location for this- Test if the setup is working on one of the most basic scripts, on an interactive session on Beluga
cd LambdaZero/examples/mpnn
salloc --time=1:0:0 --cpus-per-task=4 --gres=gpu:1 --mem=32G --account=rrg-bengioy-ad
# Load environment variables (this would load the python environment modules with gcc/cuda modules)
source LambdaZero/misc/beluga_load_env.sh
# add current working repo to python path to allow global imports IE: import LambdaZero.some_module
export PYTHONPATH="${PYTHONPATH}:/path-to-where-you-have-current-work-repo/LambdaZero"
# run mpnn training script
python train_mpnn.py
# for batch submisisons check LambdaZero/misc
# and for the beluga documentation refer to docs.mila.quebecInstallation is complicated in practice - better default option is to use shared env on Beluga Install anaconda
Create the conda environment, based on your os:
conda env create -f ( environment-linux.yml |environment-mac.yml ) [-n env_name]
This will create an environment named lz by default. Activate this environment
conda activate [env_name]
LambdaZero depends on external programs (such as Dock6 and UCSF Chimera) and datasets (brutal dock and fragdb etc. ) that are not provided in this repo. These can be installed by running:
bash install-prog-datasets.sh [-d dataset_path] [-p programs_path] [-s summaries_path]
this script would create a locator file called external_dirs.cfg that is machine specific and is used by the LambdaZero core to be able to call external dependencies.
Note that the install-prog-data.sh script should be executed from within the conda environment as some python
dependencies are required to download the external programs.
Finally, install LambdaZero with the following command:
pip install -e .
For running RL experiments, it is recommended to use 4 GPUs, 12 CPUs and 64GB memory. You can start an interactive session as follows:
salloc --time=3:0:0 --account=rrg-bengioy-ad --gres=gpu:4 -c 12 --mem=64GWithin the interactive session, you can load the environment with the following commands:
source /lustre03/project/6004852/mkkr/LambdaZero/misc/beluga_load_env.sh
export PYTHONPATH="${PYTHONPATH}:/path-to-where-you-have-current-work-repo/LambdaZero" Run PPO
cd ~/LambdaZero/LambdaZero/examples/PPO
# To change the number of workers, GPUs used by the algorithm, refer to the config in `train_ppo.py`
python train_ppo.py ppo_graph_001
# you should see something like this
#+----------------------------------+----------+--------------------+-----------+------------------+------+--------+
#| Trial name | status | loc | reward | total time (s) | ts | iter |
#|----------------------------------+----------+--------------------+-----------+------------------+------+--------|
#| PPO_BlockMolGraphEnv_v3_4e681962 | RUNNING | 192.168.2.216:4735 | -0.582411 | 27.1576 | 4000 | 1 |
#+----------------------------------+----------+--------------------+-----------+------------------+------+--------+
... Run AlphaZero
cd ~/LambdaZero/LambdaZero/examples/AlphaZero
# To change the number of workers, GPUs used by the algorithm, refer to the config in `train_az.py`
python train_az.py az001... Run LambdaBO (RL+BO)
cd ~/LambdaZero/LambdaZero/examples/bayesian_models/rl
# To change the number of workers, GPUs used by the algorithm, refer to the config in `train_bayesian_reward.py`
python train_bayesian_reward.pyTrain vanilla MPNN on biophysics simulation data
cd ~/LambdaZero/LambdaZero/datasets/brutal_dock
python split_random.py
cd ~/LambdaZero/LambdaZero/examples/mpnn
python train_mpnn.py
Use environment, make random walks, call oracles:
cd ~/LambdaZero/LambdaZero/examples/oracles
python oracle_examples.py
A sample script for batch jobs is available in misc\sample_job.sh. Please set the appropriate path to your scripts as well as the resources you need.
The job can be launched as follows:
sbatch sample_job.shMILA cluster docs. MILA Compute Canada Docs Compute Canada Docs
