Initial commit: RoseTTAFold-All-Atom configured for Wes with Harbor images and s3:// paths

rf2aa/SE3Transformer/se3_transformer/runtime/arguments.py

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+# Copyright (c) 2021, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+#
+# Permission is hereby granted, free of charge, to any person obtaining a
+# copy of this software and associated documentation files (the "Software"),
+# to deal in the Software without restriction, including without limitation
+# the rights to use, copy, modify, merge, publish, distribute, sublicense,
+# and/or sell copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
+#
+# SPDX-FileCopyrightText: Copyright (c) 2021 NVIDIA CORPORATION & AFFILIATES
+# SPDX-License-Identifier: MIT
+
+import argparse
+import pathlib
+
+from rf2aa.SE3Transformer.se3_transformer.data_loading import QM9DataModule
+from rf2aa.SE3Transformer.se3_transformer.model import SE3TransformerPooled
+from rf2aa.SE3Transformer.se3_transformer.runtime.utils import str2bool
+
+PARSER = argparse.ArgumentParser(description='SE(3)-Transformer')
+
+paths = PARSER.add_argument_group('Paths')
+paths.add_argument('--data_dir', type=pathlib.Path, default=pathlib.Path('./data'),
+                   help='Directory where the data is located or should be downloaded')
+paths.add_argument('--log_dir', type=pathlib.Path, default=pathlib.Path('/results'),
+                   help='Directory where the results logs should be saved')
+paths.add_argument('--dllogger_name', type=str, default='dllogger_results.json',
+                   help='Name for the resulting DLLogger JSON file')
+paths.add_argument('--save_ckpt_path', type=pathlib.Path, default=None,
+                   help='File where the checkpoint should be saved')
+paths.add_argument('--load_ckpt_path', type=pathlib.Path, default=None,
+                   help='File of the checkpoint to be loaded')
+
+optimizer = PARSER.add_argument_group('Optimizer')
+optimizer.add_argument('--optimizer', choices=['adam', 'sgd', 'lamb'], default='adam')
+optimizer.add_argument('--learning_rate', '--lr', dest='learning_rate', type=float, default=0.002)
+optimizer.add_argument('--min_learning_rate', '--min_lr', dest='min_learning_rate', type=float, default=None)
+optimizer.add_argument('--momentum', type=float, default=0.9)
+optimizer.add_argument('--weight_decay', type=float, default=0.1)
+
+PARSER.add_argument('--epochs', type=int, default=100, help='Number of training epochs')
+PARSER.add_argument('--batch_size', type=int, default=240, help='Batch size')
+PARSER.add_argument('--seed', type=int, default=None, help='Set a seed globally')
+PARSER.add_argument('--num_workers', type=int, default=8, help='Number of dataloading workers')
+
+PARSER.add_argument('--amp', type=str2bool, nargs='?', const=True, default=False, help='Use Automatic Mixed Precision')
+PARSER.add_argument('--gradient_clip', type=float, default=None, help='Clipping of the gradient norms')
+PARSER.add_argument('--accumulate_grad_batches', type=int, default=1, help='Gradient accumulation')
+PARSER.add_argument('--ckpt_interval', type=int, default=-1, help='Save a checkpoint every N epochs')
+PARSER.add_argument('--eval_interval', dest='eval_interval', type=int, default=1,
+                    help='Do an evaluation round every N epochs')
+PARSER.add_argument('--silent', type=str2bool, nargs='?', const=True, default=False,
+                    help='Minimize stdout output')
+
+PARSER.add_argument('--benchmark', type=str2bool, nargs='?', const=True, default=False,
+                    help='Benchmark mode')
+
+QM9DataModule.add_argparse_args(PARSER)
+SE3TransformerPooled.add_argparse_args(PARSER)