Experiment Manager

Experiment Manager#

ATOMMIC’s Experiment Manager leverages PyTorch Lightning for model checkpointing, TensorBoard Logging and Weights and Biases logging. The Experiment Manager is included by default in all ATOMMIC example scripts.

To use the experiment manager simply call exp_manager and pass in the PyTorch Lightning Trainer.

exp_dir = exp_manager(trainer, cfg.get("exp_manager", None))

And is configurable via YAML with Hydra.

exp_manager:
    exp_dir: /path/to/my/experiments
    name: my_experiment_name
    create_tensorboard_logger: True
    create_checkpoint_callback: True

Optionally, launch TensorBoard to view the training results in ./atommic_experiments (by default).

tensorboard --bind_all --logdir atommic_experiments

If create_checkpoint_callback is set to True, then ATOMMIC automatically creates checkpoints during training using PyTorch Lightning’s ModelCheckpoint. We can configure the ModelCheckpoint via YAML or CLI.

exp_manager:
    ...
    # configure the PyTorch Lightning ModelCheckpoint using checkpoint_call_back_params
    # any ModelCheckpoint argument can be set here

    # save the best checkpoints based on this metric
    checkpoint_callback_params.monitor=val_loss

    # choose how many total checkpoints to save
    checkpoint_callback_params.save_top_k=5

Resume Training#

We can auto-resume training as well by configuring the exp_manager. Being able to auto-resume is important when doing long training runs that are premptible or may be shut down before the training procedure has completed. To auto-resume training, set the following via YAML or CLI:

exp_manager:
    ...
    # resume training if checkpoints already exist
    resume_if_exists: True

    # to start training with no existing checkpoints
    resume_ignore_no_checkpoint: True

    # by default experiments will be versioned by datetime
    # we can set our own version with
    exp_manager.version: my_experiment_version

Experiment Loggers#

Alongside Tensorboard, ATOMMIC also supports Weights and Biases. To use this logger, simply set the following via YAML or ExpManagerConfig.

Weights and Biases (WandB)#

exp_manager:
    ...
    create_checkpoint_callback: True
    create_wandb_logger: True
    wandb_logger_kwargs:
        name: ${name}
        project: ${project}
        entity: ${entity}
        <Add any other arguments supported by WandB logger here>

Exponential Moving Average#

ATOMMIC supports using exponential moving average (EMA) for model parameters. This can be useful for improving model generalization and stability. To use EMA, simply set the following via YAML or ExpManagerConfig.

exp_manager:
    ...
    # use exponential moving average for model parameters
    ema:
        enabled: True  # False by default
        decay: 0.999  # decay rate
        cpu_offload: False  # If EMA parameters should be offloaded to CPU to save GPU memory
        every_n_steps: 1  # How often to update EMA weights
        validate_original_weights: False  # Whether to use original weights for validation calculation or EMA weights

Support for Preemption#

ATOMMIC adds support for a callback upon preemption while running the models on clusters. The callback takes care of saving the current state of training via the .ckpt file followed by a graceful exit from the run. The checkpoint saved upon preemption has the *last.ckpt suffix and replaces the previously saved last checkpoints. This feature is useful to increase utilization on clusters. The PreemptionCallback is enabled by default. To disable it simply add create_preemption_callback: False under exp_manager in the config YAML file.

Hydra Multi-Run with ATOMMIC#

When training neural networks, it is common to perform hyper parameter search in order to improve the performance of a model on some validation data. However, it can be tedious to manually prepare a grid of experiments and management of all checkpoints and their metrics. In order to simplify such tasks, ATOMMIC integrates with Hydra Multi-Run support in order to provide a unified way to run a set of experiments all from the config.

There are certain limitations to this framework, which we list below:

All experiments are assumed to be run on a single GPU, and multi GPU for single run (model parallel models are not

supported as of now).

ATOMMIC Multi-Run supports only grid search over a set of hyper-parameters, but we will eventually add support for

advanced hyper parameter search strategies.

ATOMMIC Multi-Run only supports running on one or more GPUs and will not work if no GPU devices are present.

Config Setup#

In order to enable ATOMMIC Multi-Run, we first update our YAML configs with some information to let Hydra know we expect to run multiple experiments from this one config -

# Required for Hydra launch of hyperparameter search via multirun
defaults:
  - override hydra/launcher: atommic_launcher

# Hydra arguments necessary for hyperparameter optimization
hydra:
  # Helper arguments to ensure all hyper parameter runs are from the directory that launches the script.
  sweep:
    dir: "."
    subdir: "."

  # Define all the hyper parameters here
  sweeper:
    params:
      # Place all the parameters you wish to search over here (corresponding to the rest of the config)
      # NOTE: Make sure that there are no spaces between the commas that separate the config params !
      model.optim.lr: 0.001,0.0001
      model.encoder.dim: 32,64,96,128
      model.decoder.dropout: 0.0,0.1,0.2

  # Arguments to the process launcher
  launcher:
    num_gpus: -1  # Number of gpus to use. Each run works on a single GPU.
    jobs_per_gpu: 1  # If each GPU has large memory, you can run multiple jobs on the same GPU for faster results (until OOM).

Next, we will setup the config for Experiment Manager. When we perform hyper parameter search, each run may take some time to complete. We want to therefore avoid the case where a run ends (say due to OOM or timeout on the machine) and we need to redo all experiments. We therefore setup the experiment manager config such that every experiment has a unique “key”, whose value corresponds to a single resumable experiment.

Let us see how to setup such a unique “key” via the experiment name. Simply attach all the hyper parameter arguments to the experiment name as shown below -

exp_manager:
  exp_dir: null  # Can be set by the user.

  # Add a unique name for all hyper parameter arguments to allow continued training.
  # NOTE: It is necessary to add all hyperparameter arguments to the name !
  # This ensures successful restoration of model runs in case HP search crashes.
  name: ${name}-lr-${model.optim.lr}-adim-${model.adapter.dim}-sd-${model.adapter.adapter_strategy.stochastic_depth}

  ...
  checkpoint_callback_params:
    ...
    save_top_k: 1  # Dont save too many .ckpt files during HP search
    always_save_atommic: True # saves the checkpoints as atommic files for fast checking of results later
  ...

  # We highly recommend use of any experiment tracking took to gather all the experiments in one location
  create_wandb_logger: True
  wandb_logger_kwargs:
    project: "<Add some project name here>"

  # HP Search may crash due to various reasons, best to attempt continuation in order to
  # resume from where the last failure case occured.
  resume_if_exists: true
  resume_ignore_no_checkpoint: true

Running a Multi-Run config#

Once the config has been updated, we can now run it just like any normal Hydra script – with one special flag (-m) !

atommic run -c BC -m

Tips and Tricks#

Preserving disk space for large number of experiments

Some models may have a large number of parameters, and it may be very expensive to save a large number of checkpoints on physical storage drives. For example, if you use Adam optimizer, each PyTorch Lightning “.ckpt” file will actually be 3x the size of just the model parameters - per ckpt file ! This can be exhorbitant if you have multiple runs.

In the above config, we explicitly set save_top_k: 1 and always_save_atommic: True - what this does is limit the number of ckpt files to just 1, and also save a ATOMMIC file (which will contain just the model parameters without optimizer state) and can be restored immediately for further work.

We can further reduce the storage space by utilizing some utility functions of ATOMMIC to automatically delete either ckpt or ATOMMIC files after a training run has finished. This is sufficient in case you are collecting results in some experiment tracking tool and can simply rerun the best config after the search is finished.

# Import `clean_exp_ckpt` along with exp_manager
from atommic.utils.exp_manager import clean_exp_ckpt, exp_manager

@hydra_runner(...)
def main(cfg):
    ...

    # Keep track of the experiment directory
    exp_log_dir = exp_manager(trainer, cfg.get("exp_manager", None))

    ... add any training code here as needed ...

    # Add following line to end of the training script
    # Remove PTL ckpt file, and potentially also remove .atommic file to conserve storage space.
    clean_exp_ckpt(exp_log_dir, remove_ckpt=True, remove_atommic=False)

Debugging Multi-Run Scripts

When running hydra scripts, you may sometimes face config issues which crash the program. In ATOMMIC Multi-Run, a crash in any one run will not crash the entire program, we will simply take note of it and move onto the next job. Once all jobs are completed, we then raise the error in the order that it occurred (it will crash the program with the first error’s stack trace).

In order to debug Muti-Run, we suggest to comment out the full hyper parameter config set inside sweep.params and instead run just a single experiment with the config - which would immediately raise the error.

Experiment name cannot be parsed by Hydra

Sometimes our hyper parameters include PyTorch Lightning trainer arguments - such as number of steps, number of epochs whether to use gradient accumulation or not etc. When we attempt to add these as keys to the experiment manager’s name. Hydra may complain that trainer.xyz cannot be resolved.

A simple solution is to finalize the hydra config before you call exp_manager() as follows -

@hydra_runner(...)
def main(cfg):
    # Make any changes as necessary to the config
    cfg.xyz.abc = uvw

    # Finalize the config
    cfg = OmegaConf.resolve(cfg)

    # Carry on as normal by calling trainer and exp_manager
    trainer = pl.Trainer(**cfg.trainer)
    exp_log_dir = exp_manager(trainer, cfg.get("exp_manager", None))
    ...

ExpManagerConfig#

class atommic.utils.exp_manager.ExpManagerConfig(explicit_log_dir: Optional[str] = None, exp_dir: Optional[str] = None, name: Optional[str] = None, version: Optional[str] = None, use_datetime_version: Optional[bool] = True, resume_if_exists: Optional[bool] = False, resume_past_end: Optional[bool] = False, resume_ignore_no_checkpoint: Optional[bool] = False, resume_from_checkpoint: Optional[str] = None, create_tensorboard_logger: Optional[bool] = True, summary_writer_kwargs: Optional[Dict[Any, Any]] = None, create_wandb_logger: Optional[bool] = False, wandb_logger_kwargs: Optional[Dict[Any, Any]] = None, create_checkpoint_callback: Optional[bool] = True, checkpoint_callback_params: Optional[CallbackParams] = CallbackParams(filepath=None, dirpath=None, filename=None, monitor='val_loss', verbose=True, save_last=True, save_top_k=3, save_weights_only=False, mode='min', auto_insert_metric_name=True, every_n_epochs=1, every_n_train_steps=None, train_time_interval=None, prefix=None, postfix='.atommic', save_best_model=False, always_save_atommic=False, save_atommic_on_train_end=True, model_parallel_size=None, save_on_train_epoch_end=False), create_early_stopping_callback: Optional[bool] = False, early_stopping_callback_params: Optional[EarlyStoppingParams] = EarlyStoppingParams(monitor='val_loss', mode='min', min_delta=0.001, patience=10, verbose=True, strict=True, check_finite=True, stopping_threshold=None, divergence_threshold=None, check_on_train_epoch_end=None, log_rank_zero_only=False), create_preemption_callback: Optional[bool] = True, files_to_copy: Optional[List[str]] = None, log_step_timing: Optional[bool] = True, step_timing_kwargs: Optional[StepTimingParams] = StepTimingParams(reduction='mean', sync_cuda=False, buffer_size=1), log_local_rank_0_only: Optional[bool] = False, log_global_rank_0_only: Optional[bool] = False, disable_validation_on_resume: Optional[bool] = True, ema: Optional[EMAParams] = EMAParams(enable=False, decay=0.999, cpu_offload=False, validate_original_weights=False, every_n_steps=1), max_time_per_run: Optional[str] = None, seconds_to_sleep: float = 5)[source]#

Bases: object

Configuration for the experiment manager.

explicit_log_dir: Optional[str] = None#

exp_dir: Optional[str] = None#

name: Optional[str] = None#

version: Optional[str] = None#

use_datetime_version: Optional[bool] = True#

resume_if_exists: Optional[bool] = False#

resume_past_end: Optional[bool] = False#

resume_ignore_no_checkpoint: Optional[bool] = False#

resume_from_checkpoint: Optional[str] = None#

create_tensorboard_logger: Optional[bool] = True#

summary_writer_kwargs: Optional[Dict[Any, Any]] = None#

create_wandb_logger: Optional[bool] = False#

wandb_logger_kwargs: Optional[Dict[Any, Any]] = None#

create_checkpoint_callback: Optional[bool] = True#

checkpoint_callback_params: Optional[CallbackParams] = CallbackParams(filepath=None, dirpath=None, filename=None, monitor='val_loss', verbose=True, save_last=True, save_top_k=3, save_weights_only=False, mode='min', auto_insert_metric_name=True, every_n_epochs=1, every_n_train_steps=None, train_time_interval=None, prefix=None, postfix='.atommic', save_best_model=False, always_save_atommic=False, save_atommic_on_train_end=True, model_parallel_size=None, save_on_train_epoch_end=False)#

create_early_stopping_callback: Optional[bool] = False#

early_stopping_callback_params: Optional[EarlyStoppingParams] = EarlyStoppingParams(monitor='val_loss', mode='min', min_delta=0.001, patience=10, verbose=True, strict=True, check_finite=True, stopping_threshold=None, divergence_threshold=None, check_on_train_epoch_end=None, log_rank_zero_only=False)#

create_preemption_callback: Optional[bool] = True#

files_to_copy: Optional[List[str]] = None#

log_step_timing: Optional[bool] = True#

step_timing_kwargs: Optional[StepTimingParams] = StepTimingParams(reduction='mean', sync_cuda=False, buffer_size=1)#

log_local_rank_0_only: Optional[bool] = False#

log_global_rank_0_only: Optional[bool] = False#

disable_validation_on_resume: Optional[bool] = True#

ema: Optional[EMAParams] = EMAParams(enable=False, decay=0.999, cpu_offload=False, validate_original_weights=False, every_n_steps=1)#

max_time_per_run: Optional[str] = None#

seconds_to_sleep: float = 5#