deeplearning/modulus/modulus-core-v030/_modules/modulus/datapipes/climate/era5_hdf5.html

Source code for modulus.datapipes.climate.era5_hdf5

# Copyright (c) 2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
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# Unless required by applicable law or agreed to in writing, software
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import h5py
import numpy as np
import torch

try:
    import nvidia.dali as dali
    import nvidia.dali.plugin.pytorch as dali_pth
except ImportError:
    raise ImportError(
        "DALI dataset requires NVIDIA DALI package to be installed. "
        + "The package can be installed at:\n"
        + "https://docs.nvidia.com/deeplearning/dali/user-guide/docs/installation.html"
    )

from dataclasses import dataclass
from typing import Iterable, List, Union, Tuple
from pathlib import Path
from torch.utils.data import Dataset
from ..datapipe import Datapipe
from ..meta import DatapipeMetaData

Tensor = torch.Tensor


[docs]@dataclass class MetaData(DatapipeMetaData): name: str = "ERA5HDF5" # Optimization auto_device: bool = True cuda_graphs: bool = True # Parallel ddp_sharding: bool = True
[docs]class ERA5HDF5Datapipe(Datapipe): """ERA5 DALI data pipeline for HDF5 files Parameters ---------- data_dir : str Directory where ERA5 data is stored stats_dir : Union[str, None], optional Directory to data statistic numpy files for normalization, if None, no normalization will be used, by default None channels : Union[List[int], None], optional Defines which ERA5 variables to load, if None will use all in HDF5 file, by default None batch_size : int, optional Batch size, by default 1 stride : int, optional Number of steps between input and output variables. For example, if the dataset contains data at every 6 hours, a stride 1 = 6 hour delta t and stride 2 = 12 hours delta t, by default 1 num_steps : int, optional Number of timesteps are included in the output variables, by default 1 patch_size : Union[Tuple[int, int], int, None], optional If specified, crops input and output variables so image dimensions are divisible by patch_size, by default None num_samples_per_year : int, optional Number of samples randomly taken from each year. If None, all will be use, by default None shuffle : bool, optional Shuffle dataset, by default True num_workers : int, optional Number of workers, by default 1 device: Union[str, torch.device], optional Device for DALI pipeline to run on, by default cuda process_rank : int, optional Rank ID of local process, by default 0 world_size : int, optional Number of training processes, by default 1 """ def __init__( self, data_dir: str, stats_dir: Union[str, None] = None, channels: Union[List[int], None] = None, batch_size: int = 1, num_steps: int = 1, stride: int = 1, patch_size: Union[Tuple[int, int], int, None] = None, num_samples_per_year: Union[int, None] = None, shuffle: bool = True, num_workers: int = 1, device: Union[str, torch.device] = "cuda", process_rank: int = 0, world_size: int = 1, ): super().__init__(meta=MetaData()) self.batch_size = batch_size self.num_workers = num_workers self.shuffle = shuffle self.data_dir = Path(data_dir) self.stats_dir = Path(stats_dir) if not stats_dir is None else None self.channels = channels self.stride = stride self.num_steps = num_steps self.num_samples_per_year = num_samples_per_year self.process_rank = process_rank self.world_size = world_size if isinstance(patch_size, int): patch_size = (patch_size, patch_size) self.patch_size = patch_size # Set up device, needed for pipeline if isinstance(device, str): device = torch.device(device) # Need a index id if cuda if device.type == "cuda" and device.index == None: device = torch.device("cuda:0") self.device = device # check root directory exists if not self.data_dir.is_dir(): raise IOError(f"Error, data directory {self.data_dir} does not exist") if not self.stats_dir is None and not self.stats_dir.is_dir(): raise IOError(f"Error, stats directory {self.stats_dir} does not exist") self.parse_dataset_files() self.load_statistics() self.pipe = self._create_pipeline()
[docs] def parse_dataset_files(self) -> None: """Parses the data directory for valid HDF5 files and determines training samples Raises ------ ValueError In channels specified or number of samples per year is not valid """ # get all input data files self.data_paths = sorted(self.data_dir.glob("????.h5")) for data_path in self.data_paths: self.logger.info(f"ERA5 file found: {data_path}") self.n_years = len(self.data_paths) self.logger.info(f"Number of years: {self.n_years}") # get total number of examples and image shape from the first file, # assuming other files have exactly the same format. self.logger.info(f"Getting file stats from {self.data_paths[0]}") with h5py.File(self.data_paths[0], "r") as f: # truncate the dataset to avoid out-of-range sampling data_samples_per_year = f["fields"].shape[0] - self.num_steps * self.stride self.img_shape = f["fields"].shape[2:] # If channels not provided, use all of them if self.channels is None: self.channels = [i for i in range(f["fields"].shape[1])] # If num_samples_per_year use all if self.num_samples_per_year is None: self.num_samples_per_year = data_samples_per_year # Adjust image shape if patch_size defined if self.patch_size is not None: self.img_shape = [ s - s % self.patch_size[i] for i, s in enumerate(self.img_shape) ] self.logger.info(f"Input image shape: {self.img_shape}") # Get total length self.total_length = self.n_years * self.num_samples_per_year self.length = self.total_length # Sanity checks if max(self.channels) >= f["fields"].shape[1]: raise ValueError( f"Provided channel has indexes greater than the number \ of fields {f['fields'].shape[1]}" ) if self.num_samples_per_year > data_samples_per_year: raise ValueError( f"num_samples_per_year ({self.num_samples_per_year}) > number of \ samples available ({data_samples_per_year})!" ) self.logger.info(f"Number of samples/year: {self.num_samples_per_year}") self.logger.info(f"Number of channels available: {f['fields'].shape[1]}")
[docs] def load_statistics(self) -> None: """Loads ERA5 statistics from pre-computed numpy files The statistic files should be of name global_means.npy and global_std.npy with a shape of [1, C, 1, 1] located in the stat_dir. Raises ------ IOError If mean or std numpy files are not found AssertionError If loaded numpy arrays are not of correct size """ # If no stats dir we just skip loading the stats if self.stats_dir is None: self.mu = None self.std = None return # load normalisation values mean_stat_file = self.stats_dir / Path("global_means.npy") std_stat_file = self.stats_dir / Path("global_stds.npy") if not mean_stat_file.exists(): raise IOError(f"Mean statistics file {mean_stat_file} not found") if not std_stat_file.exists(): raise IOError(f"Std statistics file {std_stat_file} not found") # has shape [1, C, 1, 1] self.mu = np.load(str(mean_stat_file))[:, self.channels] # has shape [1, C, 1, 1] self.sd = np.load(str(std_stat_file))[:, self.channels] if not self.mu.shape == self.sd.shape == (1, len(self.channels), 1, 1): raise AssertionError("Error, normalisation arrays have wrong shape")

def _create_pipeline(self) -> dali.Pipeline: """Create DALI pipeline Returns ------- dali.Pipeline HDF5 DALI pipeline """ pipe = dali.Pipeline( batch_size=self.batch_size, num_threads=2, prefetch_queue_depth=2, py_num_workers=self.num_workers, device_id=self.device.index, py_start_method="spawn", ) with pipe: source = ERA5DaliExternalSource( data_paths=self.data_paths, num_samples=self.total_length, channels=self.channels, stride=self.stride, num_steps=self.num_steps, num_samples_per_year=self.num_samples_per_year, batch_size=self.batch_size, shuffle=self.shuffle, process_rank=self.process_rank, world_size=self.world_size, ) # Update length of dataset self.length = len(source) // self.batch_size # Read current batch. invar, outvar = dali.fn.external_source( source, num_outputs=2, parallel=True, batch=False, ) if self.device.type == "cuda": # Move tensors to GPU as external_source won't do that. invar = invar.gpu() outvar = outvar.gpu() # Crop. h, w = self.img_shape invar = invar[:, :h, :w] outvar = outvar[:, :, :h, :w] # Standardize. if not self.stats_dir is None: invar = dali.fn.normalize(invar, mean=self.mu[0], stddev=self.sd[0]) outvar = dali.fn.normalize(outvar, mean=self.mu, stddev=self.sd) # Set outputs. pipe.set_outputs(invar, outvar) return pipe def __iter__(self): # Reset the pipeline before creating an iterator to enable epochs. self.pipe.reset() # Create DALI PyTorch iterator. return dali_pth.DALIGenericIterator([self.pipe], ["invar", "outvar"]) def __len__(self): return self.length

[docs]class ERA5DaliExternalSource: """DALI Source for lazy-loading the HDF5 ERA5 files Parameters ---------- data_paths : Iterable[str] Directory where ERA5 data is stored num_samples : int Total number of training samples channels : Iterable[int] List representing which ERA5 variables to load stride : int Number of steps between input and output variables num_steps : int Number of timesteps are included in the output variables num_samples_per_year : int Number of samples randomly taken from each year batch_size : int, optional Batch size, by default 1 shuffle : bool, optional Shuffle dataset, by default True process_rank : int, optional Rank ID of local process, by default 0 world_size : int, optional Number of training processes, by default 1 Note ---- For more information about DALI external source operator: https://docs.nvidia.com/deeplearning/dali/archives/dali_1_13_0/user-guide/docs/examples/general/data_loading/parallel_external_source.html """ def __init__( self, data_paths: Iterable[str], num_samples: int, channels: Iterable[int], num_steps: int, stride: int, num_samples_per_year: int, batch_size: int = 1, shuffle: bool = True, process_rank: int = 0, world_size: int = 1, ): self.data_paths = list(data_paths) # Will be populated later once each worker starts running in its own process. self.data_files = None self.num_samples = num_samples self.chans = list(channels) self.num_steps = num_steps self.stride = stride self.num_samples_per_year = num_samples_per_year self.batch_size = batch_size self.shuffle = shuffle self.last_epoch = None self.indices = np.arange(num_samples) # Shard from indices if running in parallel self.indices = np.array_split(self.indices, world_size)[process_rank] # Get number of full batches, ignore possible last incomplete batch for now. # Also, DALI external source does not support incomplete batches in parallel mode. self.num_batches = len(self.indices) // self.batch_size def __call__(self, sample_info: dali.types.SampleInfo) -> Tuple[Tensor, Tensor]: if sample_info.iteration >= self.num_batches: raise StopIteration() if self.data_files is None: # This will be called once per worker. Workers are persistent, # so there is no need to explicitly close the files - this will be done # when corresponding pipeline/dataset is destroyed. self.data_files = [h5py.File(path, "r") for path in self.data_paths] # Shuffle before the next epoch starts. if self.shuffle and sample_info.epoch_idx != self.last_epoch: # All workers use the same rng seed so the resulting # indices are the same across workers. np.random.default_rng(seed=sample_info.epoch_idx).shuffle(self.indices) self.last_epoch = sample_info.epoch_idx # Get local indices from global index. idx = self.indices[sample_info.idx_in_epoch] year_idx = idx // self.num_samples_per_year in_idx = idx % self.num_samples_per_year data = self.data_files[year_idx]["fields"] # Has [C,H,W] shape. invar = data[in_idx, self.chans] # Has [T,C,H,W] shape. outvar = np.empty((self.num_steps,) + invar.shape, dtype=invar.dtype) for i in range(self.num_steps): out_idx = in_idx + (i + 1) * self.stride outvar[i] = data[out_idx, self.chans] return invar, outvar def __len__(self): return len(self.indices)
© Copyright 2023, NVIDIA Modulus Team. Last updated on Jan 25, 2024.