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Running pipelines

To run a pipeline, you can use either dvc repro or dvc exp run. Either will run the pipeline, and dvc exp run will save the results as an experiment (and has other experiment-related features like modifying parameters from the command line):

$ dvc exp run --set-param featurize.ngrams=3

Reproducing experiment 'funny-dado'
'data/data.xml.dvc' didn't change, skipping
Stage 'prepare' didn't change, skipping
Running stage 'featurize':
> python src/featurization.py data/prepared data/features
Updating lock file 'dvc.lock'

Running stage 'train':
> python src/train.py data/features model.pkl
Updating lock file 'dvc.lock'

Running stage 'evaluate':
> python src/evaluate.py model.pkl data/features
Updating lock file 'dvc.lock'

Ran experiment(s): funny-dado
Experiment results have been applied to your workspace.

Stage outputs are deleted from the workspace before executing the stage commands that produce them (unless persist: true is used in dvc.yaml).

DAG

DVC runs the DAG stages sequentially, in the order defined by the dependencies and outputs. Consider this example dvc.yaml:

stages:
  prepare:
    cmd: python src/prepare.py data/data.xml
    deps:
      - data/data.xml
      - src/prepare.py
    params:
      - prepare.seed
      - prepare.split
    outs:
      - data/prepared
  featurize:
    cmd: python src/featurization.py data/prepared data/features
    deps:
      - data/prepared
      - src/featurization.py
    params:
      - featurize.max_features
      - featurize.ngrams
    outs:
      - data/features

The prepare stage will always precede the featurize stage because data/prepared is an output of prepare and a dependency of featurize.

Caching Stages

DVC will try to avoid recomputing stages that have been run before. If you run a stage without changing its commands, dependencies, or parameters, DVC will skip that stage:

Stage 'prepare' didn't change, skipping

DVC will also recover the outputs from previous runs using the run cache.

Stage 'prepare' is cached - skipping run, checking out outputs

If you want a stage to run every time, you can use always changed in dvc.yaml:

stages:
  pull_latest:
    cmd: python pull_latest.py
    deps:
      - pull_latest.py
    outs:
      - latest_results.csv
    always_changed: true

Pull Missing Data

By default, DVC expects that all data to run the pipeline is available locally. Any missing data will be considered deleted and may cause the pipeline to fail. --pull will download missing dependencies (and will download the cached outputs of previous runs saved in the run cache), so you don't need to pull all data for your project before running the pipeline. --allow-missing will skip stages with no other changes than missing data. You can combine the --pull and --allow-missing flags to run a pipeline while only pulling the data that is actually needed to run the changed stages.

Given the pipeline used in example-get-started-experiments:

$ dvc dag
    +--------------------+
    | data/pool_data.dvc |
    +--------------------+
               *
               *
               *
        +------------+
        | data_split |
        +------------+
         **        **
       **            **
      *                **
+-------+                *
| train |              **
+-------+            **
         **        **
           **    **
             *  *
         +----------+
         | evaluate |
         +----------+

If we are in a machine where all the data is missing:

$ dvc status
Not in cache:
  (use "dvc fetch <file>..." to download files)
        models/model.pkl
        data/pool_data/
        data/test_data/
        data/train_data/

We can modify the evaluate stage and DVC will only pull the necessary data to run that stage (models/model.pkl data/test_data/) while skipping the rest of the stages:

$ dvc exp run --pull --allow-missing --set-param evaluate.n_samples_to_save=20
Reproducing experiment 'hefty-tils'
'data/pool_data.dvc' didn't change, skipping
Stage 'data_split' didn't change, skipping
Stage 'train' didn't change, skipping
Running stage 'evaluate':
...

Verify Pipeline Status

In scenarios like CI jobs, you may want to check that the pipeline is up to date without pulling or running anything. dvc repro --dry will check which pipeline stages to run without actually running them. However, if data is missing, --dry will fail because DVC does not know whether that data simply needs to be pulled or is missing for some other reason. To check which stages to run and ignore any missing data, use dvc repro --dry --allow-missing.

This command will succeed if nothing has changed:

In the example below, data is missing because nothing has been pulled, but otherwise the pipeline is up to date.

$ dvc status
data_split:
        changed deps:
                deleted:            data/pool_data
        changed outs:
                not in cache:       data/test_data
                not in cache:       data/train_data
train:
        changed deps:
                deleted:            data/train_data
        changed outs:
                not in cache:       models/model.pkl
evaluate:
        changed deps:
                deleted:            data/test_data
                deleted:            models/model.pkl
data/pool_data.dvc:
        changed outs:
                not in cache:       data/pool_data
$ dvc repro --allow-missing --dry
'data/pool_data.dvc' didn't change, skipping
Stage 'data_split' didn't change, skipping
Stage 'train' didn't change, skipping
Stage 'evaluate' didn't change, skipping

If anything is not up to date, the command will fail:

In the example below, the data_split parameter in params.yaml was modified, so the pipeline is not up to date.

$ dvc status
data_split:
        changed deps:
                deleted:            data/pool_data
                params.yaml:
                        modified:           data_split
        changed outs:
                not in cache:       data/test_data
                not in cache:       data/train_data
train:
        changed deps:
                deleted:            data/train_data
        changed outs:
                not in cache:       models/model.pkl
evaluate:
        changed deps:
                deleted:            data/test_data
                deleted:            models/model.pkl
data/pool_data.dvc:
        changed outs:
                not in cache:       data/pool_data
$ dvc repro --allow-missing --dry
'data/pool_data.dvc' didn't change, skipping
ERROR: failed to reproduce 'data_split': [Errno 2] No such file or directory: '.../example-get-started-experiments/data/pool_data'

To ensure any missing data exists, you can also check that all data exists on the remote. The command below will succeed (set the exit code to 0) if all data is found in the remote. Otherwise, it will fail (set the exit code to 1).

$ dvc data status --not-in-remote --json | grep -v not_in_remote
true

Debugging Stages

If you are using advanced features to interpolate values for your pipeline, like templating or Hydra composition, you can get the interpolated values by running dvc repro -vv or dvc exp run -vv, which will include information like:

2023-05-18 07:38:43,955 TRACE: Hydra composition enabled.
Contents dumped to params.yaml: {'model': {'batch_size':
512, 'latent_dim': 8, 'lr': 0.01, 'duration': '00:00:30:00',
'max_epochs': 2}, 'data_path': 'fra.txt', 'num_samples':
100000, 'seed': 423}
2023-05-18 07:38:44,027 TRACE: Context during resolution of
stage download: {'model': {'batch_size': 512, 'latent_dim':
8, 'lr': 0.01, 'duration': '00:00:30:00', 'max_epochs': 2},
'data_path': 'fra.txt', 'num_samples': 100000, 'seed': 423}
2023-05-18 07:38:44,073 TRACE: Context during resolution of
stage train: {'model': {'batch_size': 512, 'latent_dim': 8,
'lr': 0.01, 'duration': '00:00:30:00', 'max_epochs': 2},
'data_path': 'fra.txt', 'num_samples': 100000, 'seed': 423}
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