Adding logging for metrics, model validation, processing on gpu, config updates

Author: shuyijia

.gitignore

@@ -162,5 +162,15 @@ dmypy.json
 # mac
 .DS_Store
 
-# self-defined
-questions.md
+# data
+./data/*
+
+# config
+./config/*
+
+server/
+
+main.py
+
+test*.py
+test*.ipynb

configs/config.yml

@@ -40,18 +40,17 @@ model:
   post_fc_count: 3
   pool: "global_mean_pool"
   pool_order: "early"
-
-
-optim:
   batch_norm: "True"
   batch_track_stats: "True"
   act: "relu"
   dropout_rate: 0.0
+
+optim:
   max_epochs: 250
   lr: 0.002
   #Loss functions (from pytorch) examples: l1_loss, mse_loss, binary_cross_entropy
   loss_fn: "l1_loss"
-  batch_size: 5
+  batch_size: 100
   optimizer:
     optimizer_type: "AdamW"
     optimizer_args: {}
@@ -64,9 +63,11 @@ dataset:
   # Whether to use "inmemory" or "large" format for pytorch-geometric dataset. Reccomend inmemory unless the dataset is too large
   # dataset_type: "inmemory"
   #Path to data files
-  src: "/Users/shuyijia/GitHub/Fung-Lab/MatDeepLearn_dev/data/bulk_data_500/"
+  src: "/global/cfs/projectdirs/m3641/Shared/Materials_datasets/MP_data_npj/raw/"
   #Path to target file within data_path
-  target_path: "/Users/shuyijia/GitHub/Fung-Lab/MatDeepLearn_dev/data/bulk_data_500/targets.csv"
+  target_path: "/global/cfs/projectdirs/m3641/Shared/Materials_datasets/MP_data_npj/targets.csv"
+  #Path to save processed data.pt file
+  pt_path: "/global/homes/s/shuyijia/datasets/MP_data_npj/"
   #Format of data files (limit to those supported by ASE)
   data_format: "json"
   #Method of obtaining atom idctionary: available:(onehot)