main_OGBMOL_graph_classification.py

"""
    IMPORTING LIBS
"""
import argparse
import glob
import json
import os
import random
import time

import matplotlib.pyplot as plt
import numpy as np
import torch
import torch.optim as optim
from tensorboardX import SummaryWriter
from torch.utils.data import DataLoader
from tqdm import tqdm

from data.data import LoadData  # import dataset
from nets.OGBMOL_graph_classification.load_net import gnn_model  # import GNNs


class DotDict(dict):
    def __init__(self, **kwds):
        self.update(kwds)
        self.__dict__ = self


"""
    GPU Setup
"""


def gpu_setup(use_gpu, gpu_id):
    os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"
    os.environ["CUDA_VISIBLE_DEVICES"] = str(gpu_id)

    if torch.cuda.is_available() and use_gpu:
        print("cuda available with GPU:", torch.cuda.get_device_name(0))
        device = torch.device("cuda")
    else:
        print("cuda not available")
        device = torch.device("cpu")
    return device


"""
    VIEWING MODEL CONFIG AND PARAMS
"""


def view_model_param(MODEL_NAME, net_params):
    model = gnn_model(MODEL_NAME, net_params)
    total_param = 0
    print("MODEL DETAILS:\n")
    # print(model)
    for param in model.parameters():
        # print(param.data.size())
        total_param += np.prod(list(param.data.size()))
    print("MODEL/Total parameters:", MODEL_NAME, total_param)
    return total_param


def train_val_pipeline(MODEL_NAME, dataset, params, net_params, dirs):
    t0 = time.time()
    per_epoch_time = []

    DATASET_NAME = dataset.name

    if net_params["pe_init"] == "lap_pe":
        tt = time.time()
        print("[!] -LapPE: Initializing graph positional encoding with Laplacian PE.")
        dataset._add_lap_positional_encodings(net_params["pos_enc_dim"])
        print("[!] Time taken: ", time.time() - tt)
    elif net_params["pe_init"] == "rand_walk":
        tt = time.time()
        print(
            "[!] -LSPE: Initializing graph positional encoding with rand walk features."
        )
        dataset._init_positional_encodings(
            net_params["pos_enc_dim"], net_params["pe_init"]
        )
        print("[!] Time taken: ", time.time() - tt)

        tt = time.time()
        print(
            "[!] -LSPE (For viz later): Adding lapeigvecs to key 'eigvec' for every graph."
        )
        dataset._add_eig_vecs(net_params["pos_enc_dim"])
        print("[!] Time taken: ", time.time() - tt)

    if MODEL_NAME in ["SAN", "GraphiT"]:
        if net_params["full_graph"]:
            st = time.time()
            print("[!] Adding full graph connectivity..")
            dataset._make_full_graph() if MODEL_NAME == "SAN" else dataset._make_full_graph(
                (net_params["p_steps"], net_params["gamma"])
            )
            print("Time taken to add full graph connectivity: ", time.time() - st)

    trainset, valset, testset = dataset.train, dataset.val, dataset.test

    evaluator = dataset.evaluator

    root_log_dir, root_ckpt_dir, write_file_name, write_config_file, viz_dir = dirs
    device = net_params["device"]

    # Write the network and optimization hyper-parameters in folder config/
    with open(write_config_file + ".txt", "w") as f:
        f.write(
            """Dataset: {},\nModel: {}\n\nparams={}\n\nnet_params={}\n\n\nTotal Parameters: {}\n\n""".format(
                DATASET_NAME, MODEL_NAME, params, net_params, net_params["total_param"]
            )
        )

    log_dir = os.path.join(root_log_dir, "RUN_" + str(0))
    writer = SummaryWriter(log_dir=log_dir)

    # setting seeds
    random.seed(params["seed"])
    np.random.seed(params["seed"])
    torch.manual_seed(params["seed"])
    if device.type == "cuda":
        torch.cuda.manual_seed(params["seed"])
        torch.cuda.manual_seed_all(params["seed"])
        torch.backends.cudnn.deterministic = True
        torch.backends.cudnn.benchmark = False

    print("Training Graphs: ", len(trainset))
    print("Validation Graphs: ", len(valset))
    print("Test Graphs: ", len(testset))

    model = gnn_model(MODEL_NAME, net_params)
    model = model.to(device)

    optimizer = optim.Adam(
        model.parameters(), lr=params["init_lr"], weight_decay=params["weight_decay"]
    )
    scheduler = optim.lr_scheduler.ReduceLROnPlateau(
        optimizer,
        mode="min",
        factor=params["lr_reduce_factor"],
        patience=params["lr_schedule_patience"],
        verbose=True,
    )

    epoch_train_losses, epoch_val_losses = [], []
    epoch_train_accs, epoch_val_accs, epoch_test_accs = [], [], []

    # import train functions for all GNNs
    from train.train_OGBMOL_graph_classification import (
        evaluate_network_sparse as evaluate_network,
    )
    from train.train_OGBMOL_graph_classification import (
        train_epoch_sparse as train_epoch,
    )

    train_loader = DataLoader(
        trainset,
        num_workers=4,
        batch_size=params["batch_size"],
        shuffle=True,
        collate_fn=dataset.collate,
        pin_memory=True,
    )
    val_loader = DataLoader(
        valset,
        num_workers=4,
        batch_size=params["batch_size"],
        shuffle=False,
        collate_fn=dataset.collate,
        pin_memory=True,
    )
    test_loader = DataLoader(
        testset,
        num_workers=4,
        batch_size=params["batch_size"],
        shuffle=False,
        collate_fn=dataset.collate,
        pin_memory=True,
    )

    # At any point you can hit Ctrl + C to break out of training early.
    try:
        with tqdm(range(params["epochs"])) as t:
            for epoch in t:

                t.set_description("Epoch %d" % epoch)

                start = time.time()

                epoch_train_loss, epoch_train_acc, optimizer = train_epoch(
                    model, optimizer, device, train_loader, epoch, evaluator
                )

                epoch_val_loss, epoch_val_acc, __ = evaluate_network(
                    model, device, val_loader, epoch, evaluator
                )
                _, epoch_test_acc, __ = evaluate_network(
                    model, device, test_loader, epoch, evaluator
                )
                del __

                epoch_train_losses.append(epoch_train_loss)
                epoch_val_losses.append(epoch_val_loss)
                epoch_train_accs.append(epoch_train_acc)
                epoch_val_accs.append(epoch_val_acc)
                epoch_test_accs.append(epoch_test_acc)

                writer.add_scalar("train/_loss", epoch_train_loss, epoch)
                writer.add_scalar("val/_loss", epoch_val_loss, epoch)
                writer.add_scalar("train/_avg_prec", epoch_train_acc, epoch)
                writer.add_scalar("val/_avg_prec", epoch_val_acc, epoch)
                writer.add_scalar("test/_avg_prec", epoch_test_acc, epoch)
                writer.add_scalar(
                    "learning_rate", optimizer.param_groups[0]["lr"], epoch
                )

                if dataset.name == "ogbg-moltox21":
                    t.set_postfix(
                        time=time.time() - start,
                        lr=optimizer.param_groups[0]["lr"],
                        train_loss=epoch_train_loss,
                        val_loss=epoch_val_loss,
                        train_AUC=epoch_train_acc,
                        val_AUC=epoch_val_acc,
                        test_AUC=epoch_test_acc,
                    )
                elif dataset.name == "ogbg-molpcba":
                    t.set_postfix(
                        time=time.time() - start,
                        lr=optimizer.param_groups[0]["lr"],
                        train_loss=epoch_train_loss,
                        val_loss=epoch_val_loss,
                        train_AP=epoch_train_acc,
                        val_AP=epoch_val_acc,
                        test_AP=epoch_test_acc,
                    )

                per_epoch_time.append(time.time() - start)

                # Saving checkpoint
                ckpt_dir = os.path.join(root_ckpt_dir, "RUN_")
                if not os.path.exists(ckpt_dir):
                    os.makedirs(ckpt_dir)
                torch.save(
                    model.state_dict(),
                    "{}.pkl".format(ckpt_dir + "/epoch_" + str(epoch)),
                )

                files = glob.glob(ckpt_dir + "/*.pkl")
                for file in files:
                    epoch_nb = file.split("_")[-1]
                    epoch_nb = int(epoch_nb.split(".")[0])
                    if epoch_nb < epoch - 1:
                        os.remove(file)

                scheduler.step(epoch_val_loss)

                if optimizer.param_groups[0]["lr"] < params["min_lr"]:
                    print("\n!! LR EQUAL TO MIN LR SET.")
                    break

                # Stop training after params['max_time'] hours
                if time.time() - t0 > params["max_time"] * 3600:
                    print("-" * 89)
                    print(
                        "Max_time for training elapsed {:.2f} hours, so stopping".format(
                            params["max_time"]
                        )
                    )
                    break

    except KeyboardInterrupt:
        print("-" * 89)
        print("Exiting from training early because of KeyboardInterrupt")

    # ___, __, g_outs_train = evaluate_network(model, device, train_loader, epoch, evaluator)
    ___, __, g_outs_test = evaluate_network(
        model, device, test_loader, epoch, evaluator
    )
    del ___
    del __

    # OGB: Test scores at best val epoch
    epoch_best = epoch_val_accs.index(max(epoch_val_accs))

    test_acc = epoch_test_accs[epoch_best]
    train_acc = epoch_train_accs[epoch_best]
    val_acc = epoch_val_accs[epoch_best]

    if dataset.name == "ogbg-moltox21":
        print("Test AUC: {:.4f}".format(test_acc))
        print("Train AUC: {:.4f}".format(train_acc))
        print("Val AUC: {:.4f}".format(val_acc))
    elif dataset.name == "ogbg-molpcba":
        print("Test Avg Precision: {:.4f}".format(test_acc))
        print("Train Avg Precision: {:.4f}".format(train_acc))
    print("Convergence Time (Epochs): {:.4f}".format(epoch))
    print("TOTAL TIME TAKEN: {:.4f}s".format(time.time() - t0))
    print("AVG TIME PER EPOCH: {:.4f}s".format(np.mean(per_epoch_time)))

    if net_params["pe_init"] == "rand_walk" and g_outs_test is not None:
        # Visualize actual and predicted/learned eigenvecs
        from utils.plot_util import plot_graph_eigvec

        if not os.path.exists(viz_dir):
            os.makedirs(viz_dir)

        sample_graph_ids = [153, 103, 123]

        for f_idx, graph_id in enumerate(sample_graph_ids):

            # Test graphs
            g_dgl = g_outs_test[graph_id]

            f = plt.figure(f_idx, figsize=(12, 6))

            plt1 = f.add_subplot(121)
            plot_graph_eigvec(
                plt1, graph_id, g_dgl, feature_key="eigvec", actual_eigvecs=True
            )

            plt2 = f.add_subplot(122)
            plot_graph_eigvec(
                plt2, graph_id, g_dgl, feature_key="p", predicted_eigvecs=True
            )

            f.savefig(viz_dir + "/test" + str(graph_id) + ".jpg")

    writer.close()

    """
        Write the results in out_dir/results folder
    """
    if dataset.name == "ogbg-moltox21":
        with open(write_file_name + ".txt", "w") as f:
            f.write(
                """Dataset: {},\nModel: {}\n\nparams={}\n\nnet_params={}\n\n{}\n\nTotal Parameters: {}\n\n
        FINAL RESULTS\nTEST AUC: {:.4f}\nTRAIN AUC: {:.4f}\nVAL AUC: {:.4f}\n\n
        Convergence Time (Epochs): {:.4f}\nTotal Time Taken: {:.4f} hrs\nAverage Time Per Epoch: {:.4f} s\n\n\n""".format(
                    DATASET_NAME,
                    MODEL_NAME,
                    params,
                    net_params,
                    model,
                    net_params["total_param"],
                    test_acc,
                    train_acc,
                    val_acc,
                    epoch,
                    (time.time() - t0) / 3600,
                    np.mean(per_epoch_time),
                )
            )
    elif dataset.name == "ogbg-molpcba":
        with open(write_file_name + ".txt", "w") as f:
            f.write(
                """Dataset: {},\nModel: {}\n\nparams={}\n\nnet_params={}\n\n{}\n\nTotal Parameters: {}\n\n
        FINAL RESULTS\nTEST AVG PRECISION: {:.4f}\nTRAIN AVG PRECISION: {:.4f}\nVAL AVG PRECISION: {:.4f}\n\n
        Convergence Time (Epochs): {:.4f}\nTotal Time Taken: {:.4f} hrs\nAverage Time Per Epoch: {:.4f} s\n\n\n""".format(
                    DATASET_NAME,
                    MODEL_NAME,
                    params,
                    net_params,
                    model,
                    net_params["total_param"],
                    test_acc,
                    train_acc,
                    val_acc,
                    epoch,
                    (time.time() - t0) / 3600,
                    np.mean(per_epoch_time),
                )
            )


def main():
    """
    USER CONTROLS
    """

    parser = argparse.ArgumentParser()
    parser.add_argument(
        "--config",
        help="Please give a config.json file with training/model/data/param details",
    )
    parser.add_argument("--gpu_id", help="Please give a value for gpu id")
    parser.add_argument("--model", help="Please give a value for model name")
    parser.add_argument("--dataset", help="Please give a value for dataset name")
    parser.add_argument("--out_dir", help="Please give a value for out_dir")
    parser.add_argument("--seed", help="Please give a value for seed")
    parser.add_argument("--epochs", help="Please give a value for epochs")
    parser.add_argument("--batch_size", help="Please give a value for batch_size")
    parser.add_argument("--init_lr", help="Please give a value for init_lr")
    parser.add_argument(
        "--lr_reduce_factor", help="Please give a value for lr_reduce_factor"
    )
    parser.add_argument(
        "--lr_schedule_patience", help="Please give a value for lr_schedule_patience"
    )
    parser.add_argument("--min_lr", help="Please give a value for min_lr")
    parser.add_argument("--weight_decay", help="Please give a value for weight_decay")
    parser.add_argument(
        "--print_epoch_interval", help="Please give a value for print_epoch_interval"
    )
    parser.add_argument("--L", help="Please give a value for L")
    parser.add_argument("--hidden_dim", help="Please give a value for hidden_dim")
    parser.add_argument("--out_dim", help="Please give a value for out_dim")
    parser.add_argument("--residual", help="Please give a value for residual")
    parser.add_argument("--edge_feat", help="Please give a value for edge_feat")
    parser.add_argument("--readout", help="Please give a value for readout")
    parser.add_argument("--kernel", help="Please give a value for kernel")
    parser.add_argument("--n_heads", help="Please give a value for n_heads")
    parser.add_argument("--gated", help="Please give a value for gated")
    parser.add_argument(
        "--in_feat_dropout", help="Please give a value for in_feat_dropout"
    )
    parser.add_argument("--dropout", help="Please give a value for dropout")
    parser.add_argument("--layer_norm", help="Please give a value for layer_norm")
    parser.add_argument("--batch_norm", help="Please give a value for batch_norm")
    parser.add_argument(
        "--sage_aggregator", help="Please give a value for sage_aggregator"
    )
    parser.add_argument("--data_mode", help="Please give a value for data_mode")
    parser.add_argument("--num_pool", help="Please give a value for num_pool")
    parser.add_argument("--gnn_per_block", help="Please give a value for gnn_per_block")
    parser.add_argument("--embedding_dim", help="Please give a value for embedding_dim")
    parser.add_argument("--pool_ratio", help="Please give a value for pool_ratio")
    parser.add_argument("--linkpred", help="Please give a value for linkpred")
    parser.add_argument("--cat", help="Please give a value for cat")
    parser.add_argument("--self_loop", help="Please give a value for self_loop")
    parser.add_argument("--max_time", help="Please give a value for max_time")
    parser.add_argument("--pos_enc_dim", help="Please give a value for pos_enc_dim")
    parser.add_argument("--alpha_loss", help="Please give a value for alpha_loss")
    parser.add_argument("--lambda_loss", help="Please give a value for lambda_loss")
    parser.add_argument("--pe_init", help="Please give a value for pe_init")
    args = parser.parse_args()
    with open(args.config) as f:
        config = json.load(f)
    # device
    if args.gpu_id is not None:
        config["gpu"]["id"] = int(args.gpu_id)
        config["gpu"]["use"] = True
    device = gpu_setup(config["gpu"]["use"], config["gpu"]["id"])
    # model, dataset, out_dir
    if args.model is not None:
        MODEL_NAME = args.model
    else:
        MODEL_NAME = config["model"]
    if args.dataset is not None:
        DATASET_NAME = args.dataset
    else:
        DATASET_NAME = config["dataset"]
    dataset = LoadData(DATASET_NAME)
    if args.out_dir is not None:
        out_dir = args.out_dir
    else:
        out_dir = config["out_dir"]
    # parameters
    params = config["params"]
    if args.seed is not None:
        params["seed"] = int(args.seed)
    if args.epochs is not None:
        params["epochs"] = int(args.epochs)
    if args.batch_size is not None:
        params["batch_size"] = int(args.batch_size)
    if args.init_lr is not None:
        params["init_lr"] = float(args.init_lr)
    if args.lr_reduce_factor is not None:
        params["lr_reduce_factor"] = float(args.lr_reduce_factor)
    if args.lr_schedule_patience is not None:
        params["lr_schedule_patience"] = int(args.lr_schedule_patience)
    if args.min_lr is not None:
        params["min_lr"] = float(args.min_lr)
    if args.weight_decay is not None:
        params["weight_decay"] = float(args.weight_decay)
    if args.print_epoch_interval is not None:
        params["print_epoch_interval"] = int(args.print_epoch_interval)
    if args.max_time is not None:
        params["max_time"] = float(args.max_time)
    # network parameters
    net_params = config["net_params"]
    net_params["device"] = device
    net_params["gpu_id"] = config["gpu"]["id"]
    net_params["batch_size"] = params["batch_size"]
    if args.L is not None:
        net_params["L"] = int(args.L)
    if args.hidden_dim is not None:
        net_params["hidden_dim"] = int(args.hidden_dim)
    if args.out_dim is not None:
        net_params["out_dim"] = int(args.out_dim)
    if args.residual is not None:
        net_params["residual"] = True if args.residual == "True" else False
    if args.edge_feat is not None:
        net_params["edge_feat"] = True if args.edge_feat == "True" else False
    if args.readout is not None:
        net_params["readout"] = args.readout
    if args.kernel is not None:
        net_params["kernel"] = int(args.kernel)
    if args.n_heads is not None:
        net_params["n_heads"] = int(args.n_heads)
    if args.gated is not None:
        net_params["gated"] = True if args.gated == "True" else False
    if args.in_feat_dropout is not None:
        net_params["in_feat_dropout"] = float(args.in_feat_dropout)
    if args.dropout is not None:
        net_params["dropout"] = float(args.dropout)
    if args.layer_norm is not None:
        net_params["layer_norm"] = True if args.layer_norm == "True" else False
    if args.batch_norm is not None:
        net_params["batch_norm"] = True if args.batch_norm == "True" else False
    if args.sage_aggregator is not None:
        net_params["sage_aggregator"] = args.sage_aggregator
    if args.data_mode is not None:
        net_params["data_mode"] = args.data_mode
    if args.num_pool is not None:
        net_params["num_pool"] = int(args.num_pool)
    if args.gnn_per_block is not None:
        net_params["gnn_per_block"] = int(args.gnn_per_block)
    if args.embedding_dim is not None:
        net_params["embedding_dim"] = int(args.embedding_dim)
    if args.pool_ratio is not None:
        net_params["pool_ratio"] = float(args.pool_ratio)
    if args.linkpred is not None:
        net_params["linkpred"] = True if args.linkpred == "True" else False
    if args.cat is not None:
        net_params["cat"] = True if args.cat == "True" else False
    if args.self_loop is not None:
        net_params["self_loop"] = True if args.self_loop == "True" else False
    if args.pos_enc_dim is not None:
        net_params["pos_enc_dim"] = int(args.pos_enc_dim)
    if args.alpha_loss is not None:
        net_params["alpha_loss"] = float(args.alpha_loss)
    if args.lambda_loss is not None:
        net_params["lambda_loss"] = float(args.lambda_loss)
    if args.pe_init is not None:
        net_params["pe_init"] = args.pe_init

    # OGBMOL*
    num_classes = dataset.dataset.num_tasks  # provided by OGB dataset class
    net_params["n_classes"] = num_classes

    if MODEL_NAME == "PNA":
        D = torch.cat(
            [
                torch.sparse.sum(g.adjacency_matrix(transpose=True), dim=-1).to_dense()
                for g, label in dataset.train
            ]
        )
        net_params["avg_d"] = dict(
            lin=torch.mean(D),
            exp=torch.mean(torch.exp(torch.div(1, D)) - 1),
            log=torch.mean(torch.log(D + 1)),
        )

    root_log_dir = (
        out_dir
        + "logs/"
        + MODEL_NAME
        + "_"
        + DATASET_NAME
        + "_GPU"
        + str(config["gpu"]["id"])
        + "_"
        + time.strftime("%Hh%Mm%Ss_on_%b_%d_%Y")
    )
    root_ckpt_dir = (
        out_dir
        + "checkpoints/"
        + MODEL_NAME
        + "_"
        + DATASET_NAME
        + "_GPU"
        + str(config["gpu"]["id"])
        + "_"
        + time.strftime("%Hh%Mm%Ss_on_%b_%d_%Y")
    )
    write_file_name = (
        out_dir
        + "results/result_"
        + MODEL_NAME
        + "_"
        + DATASET_NAME
        + "_GPU"
        + str(config["gpu"]["id"])
        + "_"
        + time.strftime("%Hh%Mm%Ss_on_%b_%d_%Y")
    )
    write_config_file = (
        out_dir
        + "configs/config_"
        + MODEL_NAME
        + "_"
        + DATASET_NAME
        + "_GPU"
        + str(config["gpu"]["id"])
        + "_"
        + time.strftime("%Hh%Mm%Ss_on_%b_%d_%Y")
    )
    viz_dir = (
        out_dir
        + "viz/"
        + MODEL_NAME
        + "_"
        + DATASET_NAME
        + "_GPU"
        + str(config["gpu"]["id"])
        + "_"
        + time.strftime("%Hh%Mm%Ss_on_%b_%d_%Y")
    )
    dirs = root_log_dir, root_ckpt_dir, write_file_name, write_config_file, viz_dir

    if not os.path.exists(out_dir + "results"):
        os.makedirs(out_dir + "results")

    if not os.path.exists(out_dir + "configs"):
        os.makedirs(out_dir + "configs")

    net_params["total_param"] = view_model_param(MODEL_NAME, net_params)
    train_val_pipeline(MODEL_NAME, dataset, params, net_params, dirs)


main()