Merge pull request #55 from Liwb5/develop

update mol task for ogb

ogb_examples/graphproppred/mol/README.md

@@ -18,11 +18,16 @@ python setup.py install
 ### How to run
 For example, use GPU to train model on ogbg-molhiv dataset and ogb-molpcba dataset.
 ```
-export CUDA_VISIBLE_DEVICES=1
-python -u main.py --config hiv_config.yaml
+CUDA_VISIBLE_DEVICES=1 python -u main.py --config hiv_config.yaml --use_cuda
 
-export CUDA_VISIBLE_DEVICES=2
-python -u main.py --config pcba_config.yaml
+CUDA_VISIBLE_DEVICES=2 python -u main.py --config pcba_config.yaml --use_cuda
+```
+
+If you want to use CPU to train model, environment variables `CPU_NUM` should be specified and should be in the range of 1 to N, where N is the total CPU number on your machine.
+```
+CPU_NUM=1 python -u main.py --config hiv_config.yaml
+
+CPU_NUM=1 python -u main.py --config pcba_config.yaml
 ```
 
 ### Experiment results

ogb_examples/graphproppred/mol/args.py

@@ -25,6 +25,7 @@ from utils.args import ArgumentGroup
 
 # yapf: disable
 parser = argparse.ArgumentParser(__doc__)
+parser.add_argument('--use_cuda', action='store_true')
 model_g = ArgumentGroup(parser, "model", "model configuration and paths.")
 model_g.add_arg("init_checkpoint",          str,  None,           "Init checkpoint to resume training from.")
 model_g.add_arg("init_pretraining_params",  str,  None,
@@ -80,7 +81,6 @@ data_g.add_arg("random_seed",         int,  None,     "Random seed.")
 data_g.add_arg("buf_size",         int,  1000,     "Random seed.")
 
 run_type_g = ArgumentGroup(parser, "run_type", "running type options.")
-run_type_g.add_arg("use_cuda",                     bool,   False,  "If set, use GPU for training.")
 run_type_g.add_arg("num_iteration_per_drop_scope", int,    10,    "Iteration intervals to drop scope.")
 run_type_g.add_arg("do_train",                     bool,   True,  "Whether to perform training.")
 run_type_g.add_arg("do_val",                       bool,   True,  "Whether to perform evaluation on dev data set.")

ogb_examples/graphproppred/mol/hiv_config.yaml

 task_name: hiv
-use_cuda: True
 seed: 15391
 dataset_name: ogbg-molhiv
 eval_metrics: null 

ogb_examples/graphproppred/mol/main.py

@@ -171,8 +171,10 @@ def main(args):
 if __name__ == "__main__":
     args = parser.parse_args()
     if args.config is not None:
-        args = Config(args.config, isCreate=True, isSave=True)
+        config = Config(args.config, isCreate=True, isSave=True)
 
-    log.info(args)
+    config['use_cuda'] = args.use_cuda
 
-    main(args)
+    log.info(config)
+
+    main(config)

ogb_examples/graphproppred/mol/pcba_config.yaml

 task_name: pcba
-use_cuda: True
 seed: 28994
 dataset_name: ogbg-molpcba
 eval_metrics: null