Merge pull request #24 from OpenBioML/fix-checkpointing

Fix checkpointing in fig 3 and 4

RED/agents/continuous_agents/rt3d.py

@@ -734,42 +734,63 @@ def Q_update(self, recurrent=True, monte_carlo=False, policy=True, verbose=False
             self.update_target_network(source=self.Q2_network, target=self.Q2_target, tau=self.polyak)
             self.update_target_network(source=self.policy_network, target=self.policy_target, tau=self.polyak)
 
-    def save_network(self, save_path):
-        '''
-        Saves networks to directory specified by save_path
-        :param save_path: directory to save networks to
-        '''
-
-        torch.save(self.policy_network, os.path.join(save_path, "policy_network.pth"))
-        torch.save(self.Q1_network, os.path.join(save_path, "Q1_network.pth"))
-        torch.save(self.Q2_network, os.path.join(save_path, "Q2_network.pth"))
-
-        torch.save(self.policy_target, os.path.join(save_path, "policy_target.pth"))
-        torch.save(self.Q1_target, os.path.join(save_path, "Q1_target.pth"))
-        torch.save(self.Q2_target, os.path.join(save_path, "Q2_target.pth"))
-
-    def load_network(self, load_path, load_target_networks=False):
-        '''
-        Loads netoworks from directory specified by load_path.
-        :param load_path: directory to load networks from
-        :param load_target_networks: whether to load target networks
-        '''
-
-        self.policy_network = torch.load(os.path.join(load_path, "policy_network.pth"))
-        self.policy_network_opt =  Adam(self.policy_network.parameters(), lr=self.pol_learning_rate)
-
-        self.Q1_network = torch.load(os.path.join(load_path, "Q1_network.pth"))
-        self.Q1_network_opt = Adam(self.Q1_network.parameters(), lr=self.val_learning_rate)
-
-        self.Q2_network = torch.load(os.path.join(load_path, "Q2_network.pth"))
-        self.Q2_etwork_opt = Adam(self.Q2_network.parameters(), lr=self.val_learning_rate)
-
+    def save_ckpt(self, save_path, additional_info=None):
+        '''
+        Creates a full checkpoint (networks, optimizers, memory buffers) and saves it to the specified path.
+        :param save_path: path to save the checkpoint to
+        :param additional_info: additional information to save (Python dictionary)
+        '''
+        ckpt = {
+            "policy_network": self.policy_network.state_dict(),
+            "Q1_network": self.Q1_network.state_dict(),
+            "Q2_network": self.Q2_network.state_dict(),
+            "policy_target": self.policy_target.state_dict(),
+            "Q1_target": self.Q1_target.state_dict(),
+            "Q2_target": self.Q2_target.state_dict(),
+            "policy_network_opt": self.policy_network_opt.state_dict(),
+            "Q1_network_opt": self.Q1_network_opt.state_dict(),
+            "Q2_network_opt": self.Q2_network_opt.state_dict(),
+            "additional_info": additional_info if additional_info is not None else {},
+        }
+
+        ### save buffers
+        for buffer in ("memory", "values", "states", "next_states", "actions", "rewards", "dones", 
+                       "sequences", "next_sequences", "all_returns"):
+            ckpt[buffer] = getattr(self, buffer)
+
+        ### save the checkpoint
+        torch.save(ckpt, save_path)
+
+    def load_ckpt(self, load_path, load_target_networks=True):
+        '''
+        Loads a full checkpoint (networks, optimizers, memory buffers) from the specified path.
+        :param load_path: path to load the checkpoint from
+        :param load_target_networks: whether to load the target networks as well
+        '''
+        ckpt = torch.load(load_path)
+
+        ### load networks
+        self.policy_network.load_state_dict(ckpt["policy_network"])
+        self.Q1_network.load_state_dict(ckpt["Q1_network"])
+        self.Q2_network.load_state_dict(ckpt["Q2_network"])
+
+        ### load target networks
         if load_target_networks:
-            self.policy_target = torch.load(os.path.join(load_path, "policy_target.pth"))
-            self.Q1_target = torch.load(os.path.join(load_path, "Q1_target.pth"))
-            self.Q2_target = torch.load(os.path.join(load_path, "Q2_target.pth"))
-        else:
-            print("[WARNING] Not loading target networks")
+            self.policy_target.load_state_dict(ckpt["policy_target"])
+            self.Q1_target.load_state_dict(ckpt["Q1_target"])
+            self.Q2_target.load_state_dict(ckpt["Q2_target"])
+
+        ### load optimizers
+        self.policy_network_opt.load_state_dict(ckpt["policy_network_opt"])
+        self.Q1_network_opt.load_state_dict(ckpt["Q1_network_opt"])
+        self.Q2_network_opt.load_state_dict(ckpt["Q2_network_opt"])
+
+        ### load buffers
+        for buffer in ("memory", "values", "states", "next_states", "actions", "rewards", "dones", 
+                       "sequences", "next_sequences", "all_returns"):
+            setattr(self, buffer, ckpt[buffer])
+
+        return ckpt
 
     def reset_weights(self, policy=True):
         '''

RED/configs/example/Figure_3_RT3D_chemostat.yaml

@@ -9,6 +9,7 @@ explore_rate_mul: 1
 test_episode: False
 save_path: ${hydra:run.dir}
 ckpt_freq: 50
+load_ckpt_dir_path: null # directory containing agent's checkpoint to load ("agent.pt") + optionally "history.json" from which to resume training
 
 model:
   batch_size: ${eval:'${example.environment.N_control_intervals} * ${example.environment.n_parallel_experiments}'}

RED/configs/example/Figure_4_RT3D_chemostat.yaml

@@ -9,6 +9,7 @@ explore_rate_mul: 1
 test_episode: False
 save_path: ${hydra:run.dir}
 ckpt_freq: 50
+load_ckpt_dir_path: null # directory containing agent's checkpoint to load ("agent.pt") + optionally "history.json" from which to resume training
 
 model:
   batch_size: ${eval:'${example.environment.N_control_intervals} * ${example.environment.n_parallel_experiments}'}

examples/Figure_3_RT3D_chemostat/train_RT3D.py

@@ -1,4 +1,5 @@
 
+import json
 import math
 import os
 import sys
@@ -48,12 +49,35 @@ def train_RT3D(cfg : DictConfig):
     env, n_params = setup_env(cfg)
     total_episodes = cfg.environment.n_episodes // cfg.environment.n_parallel_experiments
     skip_first_n_episodes = cfg.environment.skip_first_n_experiments // cfg.environment.n_parallel_experiments
-
-    history = {k: [] for k in ["returns", "actions", "rewards", "us", "explore_rate"]}
-    update_count = 0
+    starting_episode = 0
+
+    history = {k: [] for k in ["returns", "actions", "rewards", "us", "explore_rate", "update_count"]}
+
+    ### load ckpt
+    if cfg.load_ckpt_dir_path is not None:
+        print(f"Loading checkpoint from: {cfg.load_ckpt_dir_path}")
+        # load the agent
+        agent_path = os.path.join(cfg.load_ckpt_dir_path, "agent.pt")
+        print(f"Loading agent from: {agent_path}")
+        additional_info = agent.load_ckpt(
+            load_path=agent_path,
+            load_target_networks=True,
+        )["additional_info"]
+        # load history
+        history_path = os.path.join(cfg.load_ckpt_dir_path, "history.json")
+        if os.path.exists(history_path):
+            print(f"Loading history from: {history_path}")
+            with open(history_path, "r") as f:
+                history = json.load(f)
+        # load explore rate
+        if "explore_rate" in history and len(history["explore_rate"]) > 0:
+            explore_rate = history["explore_rate"][-1]
+        # load starting episode
+        if "episode" in additional_info:
+            starting_episode = additional_info["episode"] + 1
 
     ### training loop
-    for episode in range(total_episodes):
+    for episode in range(starting_episode, total_episodes):
         actual_params = np.random.uniform(
             low=cfg.environment.actual_params,
             high=cfg.environment.actual_params,
@@ -108,11 +132,10 @@ def train_RT3D(cfg : DictConfig):
                 sequences[i].append(np.concatenate((state, action)))
 
                 ### log episode data
-                e_us[i].append(u)
+                e_us[i].append(u.tolist())
                 next_states.append(next_state)
-                if reward != -1: # dont include the unstable trajectories as they override the true return
-                    e_rewards[i].append(reward)
-                    e_returns[i] += reward
+                e_rewards[i].append(reward)
+                e_returns[i] += reward
             states = next_states
 
         ### do not memorize the test trajectory (the last one)
@@ -129,9 +152,11 @@ def train_RT3D(cfg : DictConfig):
         ### train agent
         if episode > skip_first_n_episodes:
             for _ in range(cfg.environment.n_parallel_experiments):
-                update_count += 1
-                update_policy = update_count % cfg.policy_delay == 0
+                history["update_count"].append(history["update_count"][-1] + 1 if len(history["update_count"]) > 0 else 1)
+                update_policy = history["update_count"][-1] % cfg.policy_delay == 0
                 agent.Q_update(policy=update_policy, recurrent=True)
+        else:
+            history["update_count"].append(history["update_count"][-1] if len(history["update_count"]) > 0 else 0)
 
         ### update explore rate
         explore_rate = cfg.explore_rate_mul * agent.get_rate(
@@ -143,7 +168,7 @@ def train_RT3D(cfg : DictConfig):
 
         ### log results
         history["returns"].extend(e_returns)
-        history["actions"].extend(np.array(e_actions).transpose(1, 0, 2))
+        history["actions"].extend(np.array(e_actions).transpose(1, 0, 2).tolist())
         history["rewards"].extend(e_rewards)
         history["us"].extend(e_us)
         history["explore_rate"].append(explore_rate)
@@ -164,17 +189,20 @@ def train_RT3D(cfg : DictConfig):
             )
 
         ### checkpoint
-        if cfg.ckpt_freq is not None and episode % cfg.ckpt_freq == 0:
+        if (cfg.ckpt_freq is not None and episode % cfg.ckpt_freq == 0) \
+            or episode == total_episodes - 1:
             ckpt_dir = os.path.join(cfg.save_path, f"ckpt_{episode}")
             os.makedirs(ckpt_dir, exist_ok=True)
-            agent.save_network(ckpt_dir)
-            for k in history.keys():
-                np.save(os.path.join(ckpt_dir, f"{k}.npy"), np.array(history[k]))
-
-    ### save results and plot
-    agent.save_network(cfg.save_path)
-    for k in history.keys():
-        np.save(os.path.join(cfg.save_path, f"{k}.npy"), np.array(history[k]))
+            agent.save_ckpt(
+                save_path=os.path.join(ckpt_dir, "agent.pt"),
+                additional_info={
+                    "episode": episode,
+                }
+            )
+            with open(os.path.join(ckpt_dir, "history.json"), "w") as f:
+                json.dump(history, f)
+
+    ### plot
     plot_returns(
         returns=history["returns"],
         explore_rates=history["explore_rate"],

examples/Figure_4_RT3D_chemostat/train_RT3D.py

@@ -1,4 +1,5 @@
 
+import json
 import math
 import os
 import sys
@@ -47,12 +48,35 @@ def train_RT3D(cfg : DictConfig):
     env, n_params = setup_env(cfg)
     total_episodes = cfg.environment.n_episodes // cfg.environment.n_parallel_experiments
     skip_first_n_episodes = cfg.environment.skip_first_n_experiments // cfg.environment.n_parallel_experiments
-
-    history = {k: [] for k in ["returns", "actions", "rewards", "us", "explore_rate"]}
-    update_count = 0
+    starting_episode = 0
+
+    history = {k: [] for k in ["returns", "actions", "rewards", "us", "explore_rate", "update_count"]}
+
+    ### load ckpt
+    if cfg.load_ckpt_dir_path is not None:
+        print(f"Loading checkpoint from: {cfg.load_ckpt_dir_path}")
+        # load the agent
+        agent_path = os.path.join(cfg.load_ckpt_dir_path, "agent.pt")
+        print(f"Loading agent from: {agent_path}")
+        additional_info = agent.load_ckpt(
+            load_path=agent_path,
+            load_target_networks=True,
+        )["additional_info"]
+        # load history
+        history_path = os.path.join(cfg.load_ckpt_dir_path, "history.json")
+        if os.path.exists(history_path):
+            print(f"Loading history from: {history_path}")
+            with open(history_path, "r") as f:
+                history = json.load(f)
+        # load explore rate
+        if "explore_rate" in history and len(history["explore_rate"]) > 0:
+            explore_rate = history["explore_rate"][-1]
+        # load starting episode
+        if "episode" in additional_info:
+            starting_episode = additional_info["episode"] + 1
 
     ### training loop
-    for episode in range(total_episodes):
+    for episode in range(starting_episode, total_episodes):
         # sample params from uniform distribution
         actual_params = np.random.uniform(
             low=cfg.environment.lb,
@@ -108,11 +132,10 @@ def train_RT3D(cfg : DictConfig):
                 sequences[i].append(np.concatenate((state, action)))
 
                 ### log episode data
-                e_us[i].append(u)
+                e_us[i].append(u.tolist())
                 next_states.append(next_state)
-                if reward != -1: # dont include the unstable trajectories as they override the true return
-                    e_rewards[i].append(reward)
-                    e_returns[i] += reward
+                e_rewards[i].append(reward)
+                e_returns[i] += reward
             states = next_states
 
         ### do not memorize the test trajectory (the last one)
@@ -129,9 +152,11 @@ def train_RT3D(cfg : DictConfig):
         ### train agent
         if episode > skip_first_n_episodes:
             for _ in range(cfg.environment.n_parallel_experiments):
-                update_count += 1
-                update_policy = update_count % cfg.policy_delay == 0
+                history["update_count"].append(history["update_count"][-1] + 1 if len(history["update_count"]) > 0 else 1)
+                update_policy = history["update_count"][-1] % cfg.policy_delay == 0
                 agent.Q_update(policy=update_policy, recurrent=True)
+        else:
+            history["update_count"].append(history["update_count"][-1] if len(history["update_count"]) > 0 else 0)
 
         ### update explore rate
         explore_rate = cfg.explore_rate_mul * agent.get_rate(
@@ -143,7 +168,7 @@ def train_RT3D(cfg : DictConfig):
 
         ### log results
         history["returns"].extend(e_returns)
-        history["actions"].extend(np.array(e_actions).transpose(1, 0, 2))
+        history["actions"].extend(np.array(e_actions).transpose(1, 0, 2).tolist())
         history["rewards"].extend(e_rewards)
         history["us"].extend(e_us)
         history["explore_rate"].append(explore_rate)
@@ -164,17 +189,20 @@ def train_RT3D(cfg : DictConfig):
             )
 
         ### checkpoint
-        if cfg.ckpt_freq is not None and episode % cfg.ckpt_freq == 0:
+        if (cfg.ckpt_freq is not None and episode % cfg.ckpt_freq == 0) \
+            or episode == total_episodes - 1:
             ckpt_dir = os.path.join(cfg.save_path, f"ckpt_{episode}")
             os.makedirs(ckpt_dir, exist_ok=True)
-            agent.save_network(ckpt_dir)
-            for k in history.keys():
-                np.save(os.path.join(ckpt_dir, f"{k}.npy"), np.array(history[k]))
-
-    ### save results and plot
-    agent.save_network(cfg.save_path)
-    for k in history.keys():
-        np.save(os.path.join(cfg.save_path, f"{k}.npy"), np.array(history[k]))
+            agent.save_ckpt(
+                save_path=os.path.join(ckpt_dir, "agent.pt"),
+                additional_info={
+                    "episode": episode,
+                }
+            )
+            with open(os.path.join(ckpt_dir, "history.json"), "w") as f:
+                json.dump(history, f)
+
+    ### plot
     plot_returns(
         returns=history["returns"],
         explore_rates=history["explore_rate"],