From 13f265a51c1c551cb7d128627650c93bf6a84cb8 Mon Sep 17 00:00:00 2001 From: leilayesufu Date: Tue, 12 Dec 2023 09:24:44 +0100 Subject: [PATCH 1/8] clean out unneeded dependencies --- Dockerfile | 2 -- 1 file changed, 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 658647e..5672030 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,12 +3,10 @@ MAINTAINER ersilia RUN pip install rdkit RUN pip install git+https://github.com/bp-kelley/descriptastorus -RUN pip install tqdm>=4.62.2 RUN pip install typed-argument-parser==1.6.1 RUN pip install scikit-learn RUN pip install torch RUN pip install pandas -RUN pip install tensorboardX==2.0 RUN pip install scipy>=1.4.1 RUN pip install hyperopt RUN pip install protobuf==3.18.3 From 3a6dbe76e0049601140474eba5ecd10486f1227e Mon Sep 17 00:00:00 2001 From: leilayesufu Date: Tue, 12 Dec 2023 09:35:48 +0100 Subject: [PATCH 2/8] clean up --- Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/Dockerfile b/Dockerfile index 5672030..c1ef19f 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,6 +7,7 @@ RUN pip install typed-argument-parser==1.6.1 RUN pip install scikit-learn RUN pip install torch RUN pip install pandas +RUN pip install tensorboardX==2.0 RUN pip install scipy>=1.4.1 RUN pip install hyperopt RUN pip install protobuf==3.18.3 From 5ed4cdbd7473e311477e24e847bee19c023d6eef Mon Sep 17 00:00:00 2001 From: leilayesufu Date: Tue, 12 Dec 2023 10:01:03 +0100 Subject: [PATCH 3/8] remove TensorboardX --- model/framework/code/chemprop/train/run_training.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/framework/code/chemprop/train/run_training.py b/model/framework/code/chemprop/train/run_training.py index 214b622..93686fd 100644 --- a/model/framework/code/chemprop/train/run_training.py +++ b/model/framework/code/chemprop/train/run_training.py @@ -7,7 +7,7 @@ import warnings warnings.filterwarnings("ignore", category=np.VisibleDeprecationWarning) import pandas as pd -from tensorboardX import SummaryWriter +#from tensorboardX import SummaryWriter import torch from tqdm import trange from torch.optim.lr_scheduler import ExponentialLR From 9c48bcae737a78d7bd1f5479f583ac3fbf356ebd Mon Sep 17 00:00:00 2001 From: leilayesufu Date: Tue, 12 Dec 2023 10:08:47 +0100 Subject: [PATCH 4/8] remove tensorboard --- Dockerfile | 1 - 1 file changed, 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index c1ef19f..5672030 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,7 +7,6 @@ RUN pip install typed-argument-parser==1.6.1 RUN pip install scikit-learn RUN pip install torch RUN pip install pandas -RUN pip install tensorboardX==2.0 RUN pip install scipy>=1.4.1 RUN pip install hyperopt RUN pip install protobuf==3.18.3 From 3b1a790cda0a8d076d32348634d3d417cbe2e4cb Mon Sep 17 00:00:00 2001 From: leilayesufu Date: Tue, 12 Dec 2023 10:15:17 +0100 Subject: [PATCH 5/8] remove tensorboard --- model/framework/code/chemprop/train/train.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/framework/code/chemprop/train/train.py b/model/framework/code/chemprop/train/train.py index 8901a6e..e779cb8 100644 --- a/model/framework/code/chemprop/train/train.py +++ b/model/framework/code/chemprop/train/train.py @@ -2,7 +2,7 @@ from typing import Callable import numpy as np -from tensorboardX import SummaryWriter +#from tensorboardX import SummaryWriter import torch import torch.nn as nn from torch.optim import Optimizer From dd1af4f8252c972c8c4624c8af61858a420419ac Mon Sep 17 00:00:00 2001 From: leilayesufu Date: Tue, 12 Dec 2023 10:26:11 +0100 Subject: [PATCH 6/8] minor changes --- model/framework/code/chemprop/train/run_training.py | 3 ++- model/framework/code/chemprop/train/train.py | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/model/framework/code/chemprop/train/run_training.py b/model/framework/code/chemprop/train/run_training.py index 93686fd..8977066 100644 --- a/model/framework/code/chemprop/train/run_training.py +++ b/model/framework/code/chemprop/train/run_training.py @@ -7,7 +7,8 @@ import warnings warnings.filterwarnings("ignore", category=np.VisibleDeprecationWarning) import pandas as pd -#from tensorboardX import SummaryWriter +#from tensorboardX +import SummaryWriter import torch from tqdm import trange from torch.optim.lr_scheduler import ExponentialLR diff --git a/model/framework/code/chemprop/train/train.py b/model/framework/code/chemprop/train/train.py index e779cb8..e3beefb 100644 --- a/model/framework/code/chemprop/train/train.py +++ b/model/framework/code/chemprop/train/train.py @@ -2,7 +2,8 @@ from typing import Callable import numpy as np -#from tensorboardX import SummaryWriter +#from tensorboardX +import SummaryWriter import torch import torch.nn as nn from torch.optim import Optimizer From e263fccbc5a5b3aa7efd9c1367c3044b3361e6ce Mon Sep 17 00:00:00 2001 From: leilayesufu Date: Tue, 12 Dec 2023 10:35:24 +0100 Subject: [PATCH 7/8] Tensorboardx --- .../code/chemprop/train/run_training.py | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/model/framework/code/chemprop/train/run_training.py b/model/framework/code/chemprop/train/run_training.py index 8977066..e578be7 100644 --- a/model/framework/code/chemprop/train/run_training.py +++ b/model/framework/code/chemprop/train/run_training.py @@ -7,8 +7,7 @@ import warnings warnings.filterwarnings("ignore", category=np.VisibleDeprecationWarning) import pandas as pd -#from tensorboardX -import SummaryWriter +#from tensorboardX import SummaryWriter import torch from tqdm import trange from torch.optim.lr_scheduler import ExponentialLR @@ -244,13 +243,13 @@ def run_training(args: TrainArgs, # Train ensemble of models for model_idx in range(args.ensemble_size): - # Tensorboard writer - save_dir = os.path.join(args.save_dir, f'model_{model_idx}') - makedirs(save_dir) - try: - writer = SummaryWriter(log_dir=save_dir) - except: - writer = SummaryWriter(logdir=save_dir) + # # Tensorboard writer + # save_dir = os.path.join(args.save_dir, f'model_{model_idx}') + # makedirs(save_dir) + # try: + # writer = SummaryWriter(log_dir=save_dir) + # except: + # writer = SummaryWriter(logdir=save_dir) # Load/build model if args.checkpoint_paths is not None: From 4574c5806c13f92ceab8428490da577dc57ab9ef Mon Sep 17 00:00:00 2001 From: leilayesufu Date: Tue, 12 Dec 2023 10:41:27 +0100 Subject: [PATCH 8/8] minor changes --- model/framework/code/chemprop/train/train.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/model/framework/code/chemprop/train/train.py b/model/framework/code/chemprop/train/train.py index e3beefb..549c296 100644 --- a/model/framework/code/chemprop/train/train.py +++ b/model/framework/code/chemprop/train/train.py @@ -2,8 +2,7 @@ from typing import Callable import numpy as np -#from tensorboardX -import SummaryWriter +#from tensorboardX import SummaryWriter import torch import torch.nn as nn from torch.optim import Optimizer @@ -26,7 +25,7 @@ def train( n_iter: int = 0, atom_bond_scaler: AtomBondScaler = None, logger: logging.Logger = None, - writer: SummaryWriter = None, + #writer: SummaryWriter = None, ) -> int: """ Trains a model for an epoch.