bionemo-webdatamodule

To install, execute the following:

pip install -e .

To run unit tests, execute:

pytest -v .

WebDataModule

class WebDataModule(L.LightningDataModule)

A LightningDataModule for using webdataset tar files.

WebDataModule is a LightningDataModule for using webdataset tar files to setup PyTorch datasets and dataloaders. This data module takes as input a dictionary: Split -> tar file directory and vaiours webdataset config settings. In its setup() function, it creates the webdataset object chaining up the input pipeline_wds workflow. In its train/val/test_dataloader(), it creates the WebLoader object chaining up the pipeline_prebatch_wld workflow.

Examples:

---

1. create the data module with input directory to webdataset tar files. Depending on which of the downstream Lightning.Trainer methods are called, e.g., Trainer.fit(), Trainer.validate(), Trainer.test() or Trainer.predict(), only a subset of the train, val and test splits need to be specified in the various input options to the data module:

• Trainer.fit() requires the train and val splits
• Trainer.validate() requires the val split
• Trainer.test() requires the test splits
• Trainer.predict() requires the test splits

Here is an example of constructing the data module for Trainer.fit():

>>> from bionemo.webdatamodule.datamodule import Split, WebDataModule
>>>
>>> tar_file_prefix = "shards"
>>>
>>> dirs_of_tar_files = {
>>>     Split.train: "/path/to/train/split/tars",
>>>     Split.val: "/path/to/val/split/tars",
>>> }
>>>
>>> n_samples {
>>>     Split.train: 1000,
>>>     Split.val: 100,
>>> }
>>>
>>> # this is the string to retrieve the corresponding data object from the
>>> # webdataset file (see
>>> # https://github.com/webdataset/webdataset?tab=readme-ov-file#the-webdataset-format
>>> # for details)
>>> suffix_keys_wds = "tensor.pyd"
>>>
>>> seed = 27193781
>>>
>>> # Specify the routines to process the samples in the WebDataset object.
>>> # The routine is a generator of an Iterable of generators that are chained
>>> # together by nested function calling. The following is equivalent of
>>> # defining a overall generator of `shuffle(untuple(...))` which
>>> # untuples the samples and shuffles them. See webdataset's Documentation
>>> # for details.
>>> # NOTE: the `untuple` is almost always necessary due to the webdataset's
>>> # file parsing rule.
>>>
>>> untuple = lambda source : (sample for (sample,) in source)
>>>
>>> from webdatast import shuffle
>>> pipeline_wds = {
>>>     Split.train : [untuple, shuffle(n_samples[Split.train],
>>>                                     rng=random.Random(seed_rng_shfl))],
>>>     Split.val: untuple
>>> }
>>>
>>> # Similarly the user can optionally define the processing routine on the
>>> # WebLoader (the dataloader of webdataset).
>>> # NOTE: these routines by default take unbatched sample as input so the
>>> # user can customize their batching routines here
>>>
>>> batch = batched(local_batch_size, collation_fn=lambda
                    list_samples : torch.vstack(list_samples))
>>> pipeline_prebatch_wld = {
        Split.train: [shuffle(n_samples[Split.train],
                              rng=random.Random(seed_rng_shfl)), batch],
        Split.val : batch,
        Split.test : batch
    }
>>>
>>> # the user can optionally specify the kwargs for WebDataset and
>>> # WebLoader
>>>
>>> kwargs_wds = {
>>>     split : {'shardshuffle' : split == Split.train,
>>>              'nodesplitter' : wds.split_by_node,
>>>              'seed' : seed_rng_shfl}
>>>     for split in Split
>>>     }
>>>
>>> kwargs_wld = {
>>>     split : {"num_workers": 2} for split in Split
>>>     }
>>>
>>> invoke_wds = {
>>>     split: [("with_epoch", {"nbatches" : 5})] for split in Split
>>>     }
>>>
>>> invoke_wld = {
>>>     split: [("with_epoch", {"nbatches" : 5}] for split in Split
>>>     }
>>>
>>> # construct the data module
>>> data_module = WebDataModule(suffix_keys_wds,
                                dirs_of_tar_files,
                                prefix_tars_wds=tar_file_prefix,
                                pipeline_wds=pipeline_wds,
                                pipeline_prebatch_wld=pipeline_prebatch_wld,
                                kwargs_wds=kwargs_wds,
                                kwargs_wld=kwargs_wld,
                                invoke_wds=invoke_wds,
                                invoke_wld=invoke_wld,
                                )

__init__

def __init__(
    suffix_keys_wds: Union[str, Iterable[str]],
    dirs_tars_wds: Dict[Split, str],
    prefix_tars_wds: str = "wdshards",
    pipeline_wds: Optional[Dict[Split, Union[Iterable[Iterable[Any]],
                                             Iterable[Any]]]] = None,
    pipeline_prebatch_wld: Optional[Dict[Split, Union[Iterable[Iterable[Any]],
                                                      Iterable[Any]]]] = None,
    kwargs_wds: Optional[Dict[Split, Dict[str, Any]]] = None,
    kwargs_wld: Optional[Dict[Split, Dict[str, Any]]] = None,
    invoke_wds: Optional[Dict[Split, List[Tuple[str, Dict[str, Any]]]]] = None,
    invoke_wld: Optional[Dict[Split, List[Tuple[str, Dict[str,
                                                          Any]]]]] = None)

Constructor.

Arguments:

• suffix_keys_wds - a set of keys each corresponding to a data object in the webdataset tar file dictionary. The data objects of these keys will be extracted and tupled for each sample in the tar files
• dirs_tars_wds - input dictionary: Split -> tar file directory that contains the webdataset tar files for each split Kwargs:
• prefix_tars_wds - name prefix of the input webdataset tar files. The input tar files are globbed by "{dirs_tars_wds[split]}/{prefix_tars_wds}-*.tar"
• pipeline_wds - a dictionary of webdatast composable, i.e., functor that maps a iterator to another iterator that transforms the data sample yield from the dataset object, for different splits, or an iterable to such a sequence of such iterators. For example, this can be used to transform the sample in the worker before sending it to the main process of the dataloader
• pipeline_prebatch_wld - a dictionary of webloader composable, i.e., functor that maps a iterator to another iterator that transforms the data sample yield from the WebLoader object, for different splits, or an iterable to a seuqnence of such iterators. For example, this can be used for batching the samples. NOTE: this is applied before batching is yield from the WebLoader
• kwargs_wds - kwargs for the WebDataset.init() kwargs_wld : kwargs for the WebLoader.init(), e.g., num_workers, of each split
• invoke_wds - a dictionary of WebDataset methods to be called upon WebDataset construction. These methods must return the WebDataset object itself. Examples are .with_length() and .with_epoch(). These methods will be applied towards the end of returning the WebDataset object, i.e., after the pipline_wds have been applied. The inner list of tuples each has its first element as the method name and the second element as the corresponding method's kwargs.
• invoke_wld - a dictionary of WebLoader methods to be called upon WebLoader construction. These methods must return the WebLoader object itself. Examples are .with_length() and .with_epoch(). These methods will be applied towards the end of returning the WebLoader object, i.e., after the pipelin_prebatch_wld have been applied. The inner list of tuples each has its first element as the method name and the second element as the corresponding method's kwargs.

prepare_data

def prepare_data() -> None

This is called only by the main process by the Lightning workflow.

Do not rely on this data module object's state update here as there is no way to communicate the state update to other subprocesses. Is a no-op.

setup

def setup(stage: str) -> None

This is called on all Lightning-managed nodes in a multi-node training session.

Arguments:

• stage - "fit", "test" or "predict"

train_dataloader

def train_dataloader() -> wds.WebLoader

Webdataset for the training data.

val_dataloader

def val_dataloader() -> wds.WebLoader

Webdataset for the validation data.

test_dataloader

def test_dataloader() -> wds.WebLoader

Webdataset for the test data.

predict_dataloader

def predict_dataloader() -> wds.WebLoader

Alias for :func:test_dataloader.

PickledDataWDS Objects

class PickledDataWDS(WebDataModule)

A LightningDataModule to process pickled data into webdataset tar files.

PickledDataWDS is a LightningDataModule to process pickled data into webdataset tar files and setup dataset and dataloader. This inherits the webdataset setup from its parent module WebDataModule. This data module takes a directory of pickled data files, data filename prefixes for train/val/test splits, data filename suffixes and prepare webdataset tar files by globbing the specific pickle data files {dir_pickles}/{name_subset[split]}.{suffix_pickles} and outputing to webdataset tar file with the dict structure: NOTE: this assumes only one pickled file is processed for each sample. In its setup() function, it creates the webdataset object chaining up the input pipeline_wds workflow. In its train/val/test_dataloader(), it creates the WebLoader object chaining up the pipeline_prebatch_wld workflow.

    {"__key__" : name.replace(".", "-"),
     suffix_pickles : pickled.dumps(data) }

Examples:

---

1. create the data module with a directory of pickle files and the file name prefix thereof for different splits to used by Lightning.Trainer.fit()

>>> from bionemo.core.data.datamodule import Split, PickledDataWDS

>>> dir_pickles = "/path/to/my/pickles/dir"

>>> # the following will use `sample1.mydata.pt` and `sample2.mydata.pt` as the
>>> # training dataset and `sample4.mydata.pt` and `sample5.mydata.pt` as the
>>> # validation dataset

>>> suffix_pickles = "mydata.pt"

>>> names_subset = {
>>>     Split.train: [sample1, sample2],
>>>     Split.val: [sample4, sample5],
>>> }

>>> # the following setting will attempt to create at least 5 tar files in
>>> # `/path/to/output/tars/dir/myshards-00000{0-5}.tar`

>>> n_tars_wds = 5
>>> prefix_tars_wds = "myshards"
>>> output_dir_tar_files = {
        Split.train : "/path/to/output/tars/dir-train",
        Split.val : "/path/to/output/tars/dir-val",
        Split.test : "/path/to/output/tars/dir-test",
    }

>>> # user can optionally customize the data processing routines and kwargs used
>>> # in the WebDataset and WebLoader (see the examples in `WebDataModule`)

>>> pipeline_wds = { Split.train: ... }

>>> pipeline_prebatch_wld = { Split.train: ... }

>>> kwargs_wds = { Split.train: ..., Split.val: ... }

>>> kwargs_wld = { Split.train: ..., Split.val: ... }

>>> invoke_wds = { Split.train: ..., Split.val: ... }

>>> invoke_wld = { Split.train: ..., Split.val: ... }

>>> # create the data module
>>> data_module = PickledDataWDS(
>>>     dir_pickles,
>>>     names_subset,
>>>     suffix_pickles, # `WebDataModule` args
>>>     output_dir_tar_files, # `WebDataModule` args
>>>     n_tars_wds=n_tars_wds,
>>>     prefix_tars_wds=prefix_tars_wds, # `WebDataModule` kwargs
>>>     pipeline_wds=pipeline_wds, # `WebDataModule` kwargs
>>>     pipeline_prebatch_wld=pipelines_wdl_batch, # `WebDataModule` kwargs
>>>     kwargs_wds=kwargs_wds, # `WebDataModule` kwargs
>>>     kwargs_wld=kwargs_wld, # `WebDataModule` kwargs
>>>     invoke_wds=invoke_wds, # `WebDataModule` kwargs
>>>     invoke_wld=invoke_wld, # `WebDataModule` kwargs
>>> )

__init__

def __init__(dir_pickles: str,
             names_subset: Dict[Split, List[str]],
             *args,
             n_tars_wds: Optional[int] = None,
             **kwargs) -> None

Constructor.

Arguments:

• dir_pickles - input directory of pickled data files
• names_subset - list of filename prefix of the data samples to be loaded in the dataset and dataloader for each of the split
• *args - arguments passed to the parent WebDataModule
• n_tars_wds - attempt to create at least this number of webdataset shards
• **kwargs - arguments passed to the parent WebDataModule

prepare_data

def prepare_data() -> None

This is called only by the main process by the Lightning workflow.

Do not rely on this data module object's state update here as there is no way to communicate the state update to other subprocesses. The nesting pickles_to_tars function goes through the data name prefixes in the different splits, read the corresponding pickled file and output a webdataset tar archive with the dict structure: {"key" : name.replace(".", "-"), suffix_pickles : pickled.dumps(data) }.