#!/usr/bin/env python # coding: utf-8 # In[1]: # # Code to convert this notebook to .py if you want to run it via command line or with Slurm # from subprocess import call # command = "jupyter nbconvert Train.ipynb --to python" # call(command,shell=True) # # Import packages & functions # In[2]: import os import sys import json import argparse import numpy as np import time import random import h5py from tqdm import tqdm import webdataset as wds import gc import matplotlib.pyplot as plt import torch import torch.nn as nn from torchvision import transforms # tf32 data type is faster than standard float32 torch.backends.cuda.matmul.allow_tf32 = True # custom functions # import utils # In[ ]: local_rank = os.getenv('RANK') if local_rank is None: local_rank = 0 else: local_rank = int(local_rank) print("LOCAL RANK ", local_rank) ### Single-GPU config ### ## Feel free to uncomment the below 4 lines and comment out all the multi-gpu config code to simplify things for single-gpu # from accelerate import Accelerator # num_devices = torch.cuda.device_count() # if num_devices==0: num_devices = 1 # accelerator = Accelerator(split_batches=False) # global_batch_size = 128 ### Multi-GPU config ### from accelerate import Accelerator, DeepSpeedPlugin num_devices = torch.cuda.device_count() if num_devices==0: num_devices = 1 if num_devices <= 1 and utils.is_interactive(): # can emulate a distributed environment for deepspeed to work in jupyter notebook os.environ["MASTER_ADDR"] = "localhost" os.environ["MASTER_PORT"] = str(np.random.randint(10000)+9000) os.environ["RANK"] = "0" os.environ["LOCAL_RANK"] = "0" os.environ["WORLD_SIZE"] = "1" os.environ["GLOBAL_BATCH_SIZE"] = "128" # set this to your batch size! global_batch_size = os.environ["GLOBAL_BATCH_SIZE"] # alter the deepspeed config according to your global and local batch size if local_rank == 0: with open('deepspeed_config_stage2.json', 'r') as file: config = json.load(file) config['train_batch_size'] = int(os.environ["GLOBAL_BATCH_SIZE"]) config['train_micro_batch_size_per_gpu'] = int(os.environ["GLOBAL_BATCH_SIZE"]) // num_devices with open('deepspeed_config_stage2.json', 'w') as file: json.dump(config, file) else: # give some time for the local_rank=0 gpu to prep new deepspeed config file time.sleep(10) deepspeed_plugin = DeepSpeedPlugin("deepspeed_config_stage2.json") accelerator = Accelerator(split_batches=False, deepspeed_plugin=deepspeed_plugin) # In[ ]: print("PID of this process =",os.getpid()) device = accelerator.device print("device:",device) num_workers = num_devices print(accelerator.state) world_size = accelerator.state.num_processes distributed = not accelerator.state.distributed_type == 'NO' print("distributed =",distributed, "num_devices =", num_devices, "local rank =", local_rank, "world size =", world_size) print = accelerator.print # only print if local_rank=0 # # Configurations # In[3]: # if running this interactively, can specify jupyter_args here for argparser to use if utils.is_interactive(): # Example use jupyter_args = f"--data_path=/fsx/proj-fmri/shared/mindeyev2_dataset \ --model_name=test \ --subj=1 --batch_size={global_batch_size} --n_samples_save=0 \ --max_lr=3e-4 --mixup_pct=.66 --num_epochs=12 --ckpt_interval=999 --no-use_image_aug" jupyter_args = jupyter_args.split() print(jupyter_args) from IPython.display import clear_output # function to clear print outputs in cell get_ipython().run_line_magic('load_ext', 'autoreload') # this allows you to change functions in models.py or utils.py and have this notebook automatically update with your revisions get_ipython().run_line_magic('autoreload', '2') # In[4]: parser = argparse.ArgumentParser(description="Model Training Configuration") parser.add_argument( "--model_name", type=str, default="testing", help="name of model, used for ckpt saving and wandb logging (if enabled)", ) parser.add_argument( "--data_path", type=str, default="/fsx/proj-fmri/shared/natural-scenes-dataset", help="Path to where NSD data is stored / where to download it to", ) parser.add_argument( "--subj",type=int, default=1, choices=[1,2,5,7], ) parser.add_argument( "--batch_size", type=int, default=32, help="Batch size can be increased by 10x if only training v2c and not diffusion prior", ) parser.add_argument( "--wandb_log",action=argparse.BooleanOptionalAction,default=False, help="whether to log to wandb", ) parser.add_argument( "--resume_from_ckpt",action=argparse.BooleanOptionalAction,default=False, help="if not using wandb and want to resume from a ckpt", ) parser.add_argument( "--wandb_project",type=str,default="stability", help="wandb project name", ) parser.add_argument( "--mixup_pct",type=float,default=.33, help="proportion of way through training when to switch from BiMixCo to SoftCLIP", ) parser.add_argument( "--use_image_aug",action=argparse.BooleanOptionalAction,default=True, help="whether to use image augmentation", ) parser.add_argument( "--num_epochs",type=int,default=240, help="number of epochs of training", ) parser.add_argument( "--lr_scheduler_type",type=str,default='cycle',choices=['cycle','linear'], ) parser.add_argument( "--ckpt_saving",action=argparse.BooleanOptionalAction,default=True, ) parser.add_argument( "--ckpt_interval",type=int,default=5, help="save backup ckpt and reconstruct every x epochs", ) parser.add_argument( "--seed",type=int,default=42, ) parser.add_argument( "--max_lr",type=float,default=3e-4, ) parser.add_argument( "--n_samples_save",type=int,default=0,choices=[0,1], help="Number of reconstructions for monitoring progress, 0 will speed up training", ) if utils.is_interactive(): args = parser.parse_args(jupyter_args) else: args = parser.parse_args() # create global variables without the args prefix for attribute_name in vars(args).keys(): globals()[attribute_name] = getattr(args, attribute_name) print("global batch_size", batch_size) batch_size = int(batch_size / num_devices) print("batch_size", batch_size) # In[5]: outdir = os.path.abspath(f'../train_logs/{model_name}') if not os.path.exists(outdir): os.makedirs(outdir,exist_ok=True) if use_image_aug: import kornia from kornia.augmentation.container import AugmentationSequential img_augment = AugmentationSequential( kornia.augmentation.RandomResizedCrop((224,224), (0.6,1), p=0.3), kornia.augmentation.Resize((224, 224)), kornia.augmentation.RandomHorizontalFlip(p=0.3), kornia.augmentation.ColorJitter(brightness=0.4, contrast=0.4, saturation=0.2, hue=0.1, p=0.3), kornia.augmentation.RandomGrayscale(p=0.3), same_on_batch=False, data_keys=["input"], ) # # Prep data, models, and dataloaders # ## Dataloader # In[6]: if subj==1: num_train = 24958 num_test = 2770 test_batch_size = num_test def my_split_by_node(urls): return urls train_url = f"{data_path}/wds/subj0{subj}/train/" + "{0..36}.tar" print(train_url) train_data = wds.WebDataset(train_url,resampled=False,nodesplitter=my_split_by_node)\ .shuffle(750, initial=1500, rng=random.Random(42))\ .decode("torch")\ .rename(behav="behav.npy", past_behav="past_behav.npy", future_behav="future_behav.npy", olds_behav="olds_behav.npy")\ .to_tuple(*["behav", "past_behav", "future_behav", "olds_behav"]) train_dl = torch.utils.data.DataLoader(train_data, batch_size=batch_size, shuffle=False, drop_last=False, pin_memory=True) test_url = f"{data_path}/wds/subj0{subj}/test/" + "0.tar" print(test_url) test_data = wds.WebDataset(test_url,resampled=False,nodesplitter=my_split_by_node)\ .shuffle(750, initial=1500, rng=random.Random(42))\ .decode("torch")\ .rename(behav="behav.npy", past_behav="past_behav.npy", future_behav="future_behav.npy", olds_behav="olds_behav.npy")\ .to_tuple(*["behav", "past_behav", "future_behav", "olds_behav"]) test_dl = torch.utils.data.DataLoader(test_data, batch_size=test_batch_size, shuffle=False, drop_last=False, pin_memory=True) # ### check dataloaders are working # In[7]: # test_indices = [] # test_images = [] # for test_i, (behav, past_behav, future_behav, old_behav) in enumerate(test_dl): # test_indices = np.append(test_indices, behav[:,0,5].numpy()) # test_images = np.append(test_images, behav[:,0,0].numpy()) # test_indices = test_indices.astype(np.int16) # print(test_i, (test_i+1) * test_batch_size, len(test_indices)) # print("---\n") # train_indices = [] # train_images = [] # for train_i, (behav, past_behav, future_behav, old_behav) in enumerate(train_dl): # train_indices = np.append(train_indices, behav[:,0,5].long().numpy()) # train_images = np.append(train_images, behav[:,0,0].numpy()) # train_indices = train_indices.astype(np.int16) # print(train_i, (train_i+1) * batch_size, len(train_indices)) # ## Load voxel betas, K-means clustering model, and images # In[8]: # load betas f = h5py.File(f'{data_path}/betas_all_subj0{subj}.hdf5', 'r') voxels = f['betas'][:] print(f"subj0{subj} betas loaded into memory") voxels = torch.Tensor(voxels).to("cpu").half() if subj==1: voxels = torch.hstack((voxels, torch.zeros((len(voxels), 5)))) print("voxels", voxels.shape) num_voxels = voxels.shape[-1] # load orig images f = h5py.File(f'{data_path}/coco_images_224_float16.hdf5', 'r') images = f['images'][:] images = torch.Tensor(images).to("cpu").half() print("images", images.shape) # In[9]: from models import Clipper eva02_model = Clipper("ViT-L/14", device=torch.device(f"cuda:{local_rank}"), hidden_state=True, norm_embs=True) clip_seq_dim = 257 clip_emb_dim = 768 hidden_dim = 4096 # In[10]: class MindEyeModule(nn.Module): def __init__(self): super(MindEyeModule, self).__init__() def forward(self, x): return x model = MindEyeModule() model # In[11]: class RidgeRegression(torch.nn.Module): # make sure to add weight_decay when initializing optimizer def __init__(self, input_size, out_features): super(RidgeRegression, self).__init__() self.linear = torch.nn.Linear(input_size, out_features) def forward(self, x): return self.linear(x) model.ridge = RidgeRegression(voxels.shape[1], out_features=hidden_dim) utils.count_params(model.ridge) utils.count_params(model) b = torch.randn((2,voxels.shape[1])) print(b.shape, model.ridge(b).shape) # In[12]: from functools import partial class BrainNetwork(nn.Module): def __init__(self, out_dim=768, in_dim=15724, clip_size=768, h=4096, n_blocks=4, norm_type='ln', act_first=False, use_projector=True, drop1=.5, drop2=.15): super().__init__() norm_func = partial(nn.BatchNorm1d, num_features=h) if norm_type == 'bn' else partial(nn.LayerNorm, normalized_shape=h) act_fn = partial(nn.ReLU, inplace=True) if norm_type == 'bn' else nn.GELU act_and_norm = (act_fn, norm_func) if act_first else (norm_func, act_fn) self.mlp = nn.ModuleList([ nn.Sequential( nn.Linear(h, h), *[item() for item in act_and_norm], nn.Dropout(drop2) ) for _ in range(n_blocks) ]) self.lin1 = nn.Linear(h, out_dim, bias=True) self.n_blocks = n_blocks self.clip_size = clip_size self.use_projector = use_projector if use_projector: self.projector = nn.Sequential( nn.LayerNorm(clip_size), nn.GELU(), nn.Linear(clip_size, 2048), nn.LayerNorm(2048), nn.GELU(), nn.Linear(2048, 2048), nn.LayerNorm(2048), nn.GELU(), nn.Linear(2048, clip_size) ) def forward(self, x): residual = x for res_block in range(self.n_blocks): x = self.mlp[res_block](x) x += residual residual = x x = x.reshape(len(x), -1) x = self.lin1(x) if self.use_projector: return self.projector(x.reshape(len(x), -1, self.clip_size)) return x model.backbone = BrainNetwork(in_dim=hidden_dim, clip_size=clip_emb_dim, out_dim=clip_seq_dim*clip_emb_dim, use_projector=True) utils.count_params(model.backbone) utils.count_params(model) b = torch.randn((2,hidden_dim)) print(b.shape, model.backbone(b).shape) # In[13]: no_decay = ['bias', 'LayerNorm.bias', 'LayerNorm.weight'] opt_grouped_parameters = [ {'params': [p for n, p in model.ridge.named_parameters()], 'weight_decay': 1e-2}, {'params': [p for n, p in model.backbone.named_parameters() if not any(nd in n for nd in no_decay)], 'weight_decay': 1e-2}, {'params': [p for n, p in model.backbone.named_parameters() if any(nd in n for nd in no_decay)], 'weight_decay': 0.0}, ] optimizer = torch.optim.AdamW(opt_grouped_parameters, lr=max_lr) if lr_scheduler_type == 'linear': lr_scheduler = torch.optim.lr_scheduler.LinearLR( optimizer, total_iters=int(num_epochs*(num_train*num_devices//batch_size)), last_epoch=-1 ) elif lr_scheduler_type == 'cycle': total_steps=int(num_epochs*(num_train*num_devices//batch_size)) lr_scheduler = torch.optim.lr_scheduler.OneCycleLR( optimizer, max_lr=max_lr, total_steps=total_steps, final_div_factor=1000, last_epoch=-1, pct_start=2/num_epochs ) def save_ckpt(tag): ckpt_path = outdir+f'/{tag}.pth' print(f'saving {ckpt_path}',flush=True) unwrapped_model = accelerator.unwrap_model(model) try: torch.save({ 'epoch': epoch, 'model_state_dict': unwrapped_model.state_dict(), 'optimizer_state_dict': optimizer.state_dict(), 'lr_scheduler': lr_scheduler.state_dict(), 'train_losses': losses, 'test_losses': test_losses, 'lrs': lrs, }, ckpt_path) except: print("Couldn't save... moving on to prevent crashing.") del unwrapped_model print("\nDone with model preparations!") # # Weights and Biases # In[14]: # params for wandb if local_rank==0 and wandb_log: # only use main process for wandb logging import wandb wandb_project = 'stability' wandb_run = model_name wandb_notes = '' print(f"wandb {wandb_project} run {wandb_run}") wandb.login(host='https://stability.wandb.io')#, relogin=True) wandb_config = { "model_name": model_name, "clip_variant": clip_variant, "batch_size": batch_size, "num_epochs": num_epochs, "use_image_aug": use_image_aug, "max_lr": max_lr, "lr_scheduler_type": lr_scheduler_type, "mixup_pct": mixup_pct, "num_train": num_train, "num_test": num_test, "seed": seed, "distributed": distributed, "num_devices": num_devices, "world_size": world_size, } print("wandb_config:\n",wandb_config) if True: # wandb_auto_resume print("wandb_id:",model_name) wandb.init( id = model_name, project=wandb_project, name=wandb_run, config=wandb_config, notes=wandb_notes, resume="allow", ) else: wandb.init( project=wandb_project, name=wandb_run, config=wandb_config, notes=wandb_notes, ) else: wandb_log = False # # Main # In[15]: epoch = 0 losses, test_losses, lrs = [], [], [] best_test_loss = 1e9 soft_loss_temps = utils.cosine_anneal(0.004, 0.0075, num_epochs - int(mixup_pct * num_epochs)) # Optionally resume from checkpoint # if resume_from_ckpt: print("\n---resuming from last.pth ckpt---\n") try: checkpoint = torch.load(outdir+'/last.pth', map_location='cpu') except: print('last.pth failed... trying last_backup.pth') checkpoint = torch.load(outdir+'/last_backup.pth', map_location='cpu') epoch = checkpoint['epoch'] print("Epoch",epoch) optimizer.load_state_dict(checkpoint['optimizer_state_dict']) lr_scheduler.load_state_dict(checkpoint['lr_scheduler']) diffusion_prior.load_state_dict(checkpoint['model_state_dict']) del checkpoint elif wandb_log: if wandb.run.resumed: print("\n---resuming from last.pth ckpt---\n") try: checkpoint = torch.load(outdir+'/last.pth', map_location='cpu') except: print('last.pth failed... trying last_backup.pth') checkpoint = torch.load(outdir+'/last_backup.pth', map_location='cpu') epoch = checkpoint['epoch'] print("Epoch",epoch) optimizer.load_state_dict(checkpoint['optimizer_state_dict']) lr_scheduler.load_state_dict(checkpoint['lr_scheduler']) diffusion_prior.load_state_dict(checkpoint['model_state_dict']) del checkpoint torch.cuda.empty_cache() # In[16]: model, optimizer, train_dl, test_dl, lr_scheduler = accelerator.prepare( model, optimizer, train_dl, test_dl, lr_scheduler ) # In[17]: print(f"{model_name} starting with epoch {epoch} / {num_epochs}") progress_bar = tqdm(range(epoch,num_epochs), ncols=1200, disable=(local_rank!=0)) test_image, test_voxel = None, None mse = nn.MSELoss() for epoch in progress_bar: model.train() fwd_percent_correct = 0. bwd_percent_correct = 0. test_fwd_percent_correct = 0. test_bwd_percent_correct = 0. for train_i, (behav, past_behav, future_behav, old_behav) in enumerate(train_dl): with torch.cuda.amp.autocast(): optimizer.zero_grad() voxel = voxels[behav[:,0,5].cpu().long()].to(device) image = images[behav[:,0,0].cpu().long()].to(device) if use_image_aug: image = img_augment(image) clip_target = eva02_model.embed_image(image.float()) assert not torch.any(torch.isnan(clip_target)) if epoch < int(mixup_pct * num_epochs): voxel, perm, betas, select = utils.mixco(voxel) voxel_ridge = model.ridge(voxel) clip_voxels = model.backbone(voxel_ridge) clip_voxels_norm = nn.functional.normalize(clip_voxels.flatten(1), dim=-1) clip_target_norm = nn.functional.normalize(clip_target.flatten(1), dim=-1) if epoch < int(mixup_pct * num_epochs): loss_clip = utils.mixco_nce( clip_voxels_norm, clip_target_norm, temp=.006, perm=perm, betas=betas, select=select) else: epoch_temp = soft_loss_temps[epoch-int(mixup_pct*num_epochs)] loss_clip = utils.soft_clip_loss( clip_voxels_norm, clip_target_norm, temp=epoch_temp) loss = loss_clip utils.check_loss(loss) accelerator.backward(loss) optimizer.step() losses.append(loss.item()) lrs.append(optimizer.param_groups[0]['lr']) # forward and backward top 1 accuracy labels = torch.arange(len(clip_target_norm)).to(clip_voxels_norm.device) fwd_percent_correct += utils.topk(utils.batchwise_cosine_similarity(clip_voxels_norm, clip_target_norm), labels, k=1) bwd_percent_correct += utils.topk(utils.batchwise_cosine_similarity(clip_target_norm, clip_voxels_norm), labels, k=1) if lr_scheduler_type is not None: lr_scheduler.step() model.eval() for test_i, (behav, past_behav, future_behav, old_behav) in enumerate(test_dl): with torch.no_grad(): with torch.cuda.amp.autocast(): # all test samples should be loaded per batch such that test_i should never exceed 0 if len(behav) != num_test: print("!",len(behav),num_test) ## Average same-image repeats ## if test_image is None: voxel = voxels[behav[:,0,5].cpu().long()] image = behav[:,0,0].cpu().long() unique_image, sort_indices = torch.unique(image, return_inverse=True) for im in unique_image: locs = torch.where(im == image)[0] if test_image is None: test_image = images[im][None] test_voxel = torch.mean(voxel[locs],axis=0)[None] else: test_image = torch.vstack((test_image, images[im][None])) test_voxel = torch.vstack((test_voxel, torch.mean(voxel[locs],axis=0)[None])) # random sample of 300 random_indices = torch.randperm(len(test_voxel))[:300] voxel = test_voxel[random_indices].to(device) image = test_image[random_indices].to(device) assert len(image) == 300 clip_target = eva02_model.embed_image(image.float()) voxel_ridge = model.ridge(voxel) clip_voxels = model.backbone(voxel_ridge) clip_voxels_norm = nn.functional.normalize(clip_voxels.flatten(1), dim=-1) clip_target_norm = nn.functional.normalize(clip_target.flatten(1), dim=-1) loss_clip = utils.soft_clip_loss( clip_voxels_norm, clip_target_norm, temp=.006) loss = loss_clip utils.check_loss(loss) test_losses.append(loss.item()) # forward and backward top 1 accuracy labels = torch.arange(len(clip_target_norm)).to(clip_voxels_norm.device) test_fwd_percent_correct += utils.topk(utils.batchwise_cosine_similarity(clip_voxels_norm, clip_target_norm), labels, k=1) test_bwd_percent_correct += utils.topk(utils.batchwise_cosine_similarity(clip_target_norm, clip_voxels_norm), labels, k=1) if local_rank==0: if utils.is_interactive(): # clear_output(wait=True) print("---") assert (test_i+1) == 1 logs = {"train/loss": np.mean(losses[-(train_i+1):]), "test/loss": np.mean(test_losses[-(test_i+1):]), "train/lr": lrs[-1], "train/num_steps": len(losses), "test/num_steps": len(test_losses), "train/fwd_pct_correct": fwd_percent_correct.item() / (train_i + 1), "train/bwd_pct_correct": bwd_percent_correct.item() / (train_i + 1), "test/test_fwd_pct_correct": test_fwd_percent_correct.item() / (test_i + 1), "test/test_bwd_pct_correct": test_bwd_percent_correct.item() / (test_i + 1), } progress_bar.set_postfix(**logs) # Save model checkpoint and reconstruct if epoch % ckpt_interval == 0: if not utils.is_interactive(): save_ckpt(f'last') if wandb_log: wandb.log(logs) # wait for other GPUs to catch up if needed accelerator.wait_for_everyone() torch.cuda.empty_cache() gc.collect() print("\n===Finished!===\n") if ckpt_saving: save_ckpt(f'last') if not utils.is_interactive(): sys.exit(0)