import argparse import glob import logging import os import ocpmodels """ This script provides users with an automated way to download, preprocess (where applicable), and organize data to readily be used by the existing config files. """ DOWNLOAD_LINKS = { "s2ef": { "200k": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_train_200K.tar", "2M": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_train_2M.tar", "20M": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_train_20M.tar", "all": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_train_all.tar", "val_id": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_val_id.tar", "val_ood_ads": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_val_ood_ads.tar", "val_ood_cat": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_val_ood_cat.tar", "val_ood_both": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_val_ood_both.tar", "test": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_test_lmdbs.tar.gz", "rattled": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_rattled.tar", "md": "https://dl.fbaipublicfiles.com/opencatalystproject/data/s2ef_md.tar", }, "is2re": "https://dl.fbaipublicfiles.com/opencatalystproject/data/is2res_train_val_test_lmdbs.tar.gz", } S2EF_COUNTS = { "s2ef": { "200k": 200000, "2M": 2000000, "20M": 20000000, "all": 133934018, "val_id": 999866, "val_ood_ads": 999838, "val_ood_cat": 999809, "val_ood_both": 999944, "rattled": 16677031, "md": 38315405, }, } def get_data(datadir, task, split, del_intmd_files): os.makedirs(datadir, exist_ok=True) if task == "s2ef" and split is None: raise NotImplementedError("S2EF requires a split to be defined.") if task == "s2ef": assert ( split in DOWNLOAD_LINKS[task] ), f'S2EF "{split}" split not defined, please specify one of the following: {list(DOWNLOAD_LINKS["s2ef"].keys())}' download_link = DOWNLOAD_LINKS[task][split] elif task == "is2re": download_link = DOWNLOAD_LINKS[task] os.system(f"wget {download_link} -P {datadir}") filename = os.path.join(datadir, os.path.basename(download_link)) logging.info("Extracting contents...") os.system(f"tar -xvf {filename} -C {datadir}") dirname = os.path.join( datadir, os.path.basename(filename).split(".")[0], ) if task == "s2ef" and split != "test": compressed_dir = os.path.join(dirname, os.path.basename(dirname)) if split in ["200k", "2M", "20M", "all", "rattled", "md"]: output_path = os.path.join(datadir, task, split, "train") else: output_path = os.path.join(datadir, task, "all", split) uncompressed_dir = uncompress_data(compressed_dir) preprocess_data(uncompressed_dir, output_path) verify_count(output_path, task, split) if task == "s2ef" and split == "test": os.system(f"mv {dirname}/test_data/s2ef/all/test_* {datadir}/s2ef/all") elif task == "is2re": os.system(f"mv {dirname}/data/is2re {datadir}") if del_intmd_files: cleanup(filename, dirname) def uncompress_data(compressed_dir): import uncompress parser = uncompress.get_parser() args, _ = parser.parse_known_args() args.ipdir = compressed_dir args.opdir = os.path.dirname(compressed_dir) + "_uncompressed" uncompress.main(args) return args.opdir def preprocess_data(uncompressed_dir, output_path): import preprocess_ef as preprocess parser = preprocess.get_parser() args, _ = parser.parse_known_args() args.data_path = uncompressed_dir args.out_path = output_path preprocess.main(args) def verify_count(output_path, task, split): paths = glob.glob(os.path.join(output_path, "*.txt")) count = 0 for path in paths: lines = open(path, "r").read().splitlines() count += len(lines) assert ( count == S2EF_COUNTS[task][split] ), f"S2EF {split} count incorrect, verify preprocessing has completed successfully." def cleanup(filename, dirname): import shutil if os.path.exists(filename): os.remove(filename) if os.path.exists(dirname): shutil.rmtree(dirname) if os.path.exists(dirname + "_uncompressed"): shutil.rmtree(dirname + "_uncompressed") if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument("--task", type=str, help="Task to download") parser.add_argument( "--split", type=str, help="Corresponding data split to download" ) parser.add_argument( "--keep", action="store_true", help="Keep intermediate directories and files upon data retrieval/processing", ) # Flags for S2EF train/val set preprocessing: parser.add_argument( "--get-edges", action="store_true", help="Store edge indices in LMDB, ~10x storage requirement. Default: compute edge indices on-the-fly.", ) parser.add_argument( "--num-workers", type=int, default=1, help="No. of feature-extracting processes or no. of dataset chunks", ) parser.add_argument( "--ref-energy", action="store_true", help="Subtract reference energies" ) parser.add_argument( "--data-path", type=str, default=os.path.join(os.path.dirname(ocpmodels.__path__[0]), "data"), help="Specify path to save dataset. Defaults to 'ocpmodels/data'", ) args, _ = parser.parse_known_args() get_data( datadir=args.data_path, task=args.task, split=args.split, del_intmd_files=not args.keep, )