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Working with lakeFS Data Locally

lakeFS is a scalable data version control system designed to scale to billions of objects. The larger the data, the less feasible it becomes to consume it from a single machine. lakeFS addresses this challenge by enabling efficient management of large-scale data stored remotely. In addition to its capability to manage large datasets, lakeFS offers the flexibility to perform partial checkouts when necessary for working with specific portions of the data locally.

This page explains lakectl local, a command that lets you clone specific portions of lakeFS’ data to your local environment, and to keep remote and local locations in sync.

Use cases

Local development of ML models

The development of machine learning models is a dynamic and iterative process, including experimentation with various data versions, transformations, algorithms, and hyperparameters. To optimize this iterative workflow, experiments must be conducted with speed, ease of tracking, and reproducibility in mind. Localizing the model data during development enhances the development process. It accelerates the development process by enabling interactive and offline development and reducing data access latency.

The local availability of data is required to seamlessly integrate data version control systems and source control systems like Git. This integration is vital for achieving model reproducibility, allowing for a more efficient and collaborative model development environment.

Data Locality for Optimized GPU Utilization

Training Deep Learning models requires expensive GPUs. In the context of running such programs, the goal is to optimize GPU usage and prevent them from sitting idle. Many deep learning tasks involve accessing images, and in some cases, the same images are accessed multiple times. Localizing the data can eliminate redundant round trip times to access remote storage, resulting in cost savings.

lakectl local: The way to work with lakeFS data locally

The local command of lakeFS’ CLI lakectl enables working with lakeFS data locally. It allows cloning lakeFS data into a directory on any machine, syncing local directories with remote lakeFS locations, and to seamlessly integrate lakeFS with Git.

Here are the available lakectl local commands:

Command What it does Notes  
init Connects between a local directory and a lakeFS remote URI to enable data sync To undo a directory init, delete the .lakefs_ref.yaml file created in the initialized directory  
clone Clones lakeFS data from a path into an empty local directory and initializes the directory A directory can only track a single lakeFS remote location. i.e., you cannot clone data into an already initialized directory  
list Lists directories that are synced with lakeFS It is recommended to follow any init or clone command with a list command to verify its success  
status Shows remote and local changes to the directory and the remote location it tracks    
commit Commits changes from local directory to the lakeFS branch it tracks Uncommitted changes to directories connected to lakeFS remote locations will not reflect in lakeFS until after doing lakectl local commit.  
pull Fetches latest changes from a lakeFS remote location into a connected local directory    
checkout Syncs a local directory with the state of a lakeFS ref    

Note: The data size you work with locally should be reasonable for smooth operation on a local machine.

Example: Using lakectl local in tandem with Git

We are going to develop an ML model that predicts whether an image is an Alpaca or not. Our goal is to improve the input for the model. The code for the model is versioned by Git while the model dataset is versioned by lakeFS. We will be using lakectl local to tie code versions to data versions to achieve model reproducibility.

Setup

To get start with, we have initialized a Git repo called is_alpaca that includes the model code: Git repo

We also created a lakeFS repository and uploaded the is_alpaca train dataset by Kaggel into it: lakeFS repo

Create an Isolated Environment for Experiments

Our goal is to improve the model predictions. To meet our goal, we will experiment with editing the training dataset. We will run our experiments in isolation to not change anything until after we are certain the data is improved and ready.

Let’s create a new lakeFS branch called experiment-1. Our is_alpaca dataset is accessible on that branch, and we will interact with the data from that branch only. experiment-1-branch

On the code side, we will create a Git branch also called experiment-1 to not pollute our main branch with a dataset which is under tuning.

Clone lakeFS Data into a Local Git Repository

Inspecting the train.py script, we can see that it expects an input on the input directory.

#!/usr/bin/env python
import tensorflow as tf

input_location = './input'
model_location = './models/is_alpaca.h5'

def get_ds(subset):
    return tf.keras.utils.image_dataset_from_directory(
        input_location, validation_split=0.2, subset=subset,
        seed=123, image_size=(244, 244), batch_size=32)

train_ds = get_ds("training")
val_ds = get_ds("validation")

model = tf.keras.Sequential([
    tf.keras.layers.Rescaling(1./255),
    tf.keras.layers.Conv2D(32, 3, activation='relu'),
    tf.keras.layers.MaxPooling2D(),
    tf.keras.layers.Conv2D(32, 3, activation='relu'),
    tf.keras.layers.MaxPooling2D(),
    tf.keras.layers.Conv2D(32, 3, activation='relu'),
    tf.keras.layers.MaxPooling2D(),
    tf.keras.layers.Flatten(),
    tf.keras.layers.Dense(128, activation='relu'),
    tf.keras.layers.Dense(2)])

# Fit and save
loss_fn = tf.keras.losses.SparseCategoricalCrossentropy(from_logits=True)
model.compile(optimizer='adam', loss=loss_fn, metrics=['accuracy'])
model.fit(train_ds, validation_data=val_ds, epochs=3)
model.save(model_location)

This means that to be able to locally develop our model and experiment with it we need to have the is_alpaca dataset managed by lakeFS available locally on that path. To do that, we will use the lakectl local clone command from our local Git repository root:

lakectl local clone lakefs://is-alpaca/experiment-1/dataset/train/ input

This command will do a diff between out local input directory (that did not exist until now) and the provided lakeFS path and identify that there are files to be downloaded from lakeFS.

Successfully cloned lakefs://is-alpaca/experiment-1/dataset/train/ to ~/ml_models/is_alpaca/input

Clone Summary:

Downloaded: 250
Uploaded: 0
Removed: 0

Running lakectl local list from our Git repository root will show that the input directory is now in sync with a lakeFS prefix (Remote URI), and what lakeFS version of the data (Synced Commit) the is it tracking:

 is_alpaca % lakectl local list                 
+-----------+------------------------------------------------+------------------------------------------------------------------+
| DIRECTORY | REMOTE URI                                     | SYNCED COMMIT                                                    |
+-----------+------------------------------------------------+------------------------------------------------------------------+
| input     | lakefs://is-alpaca/experiment-1/dataset/train/ | 589f87704418c6bac80c5a6fc1b52c245af347b9ad1ea8d06597e4437fae4ca3 |
+-----------+------------------------------------------------+------------------------------------------------------------------+

Tie Code Version and Data Version

Now let’s tell Git to stage the dataset we’ve added and inspect our Git branch status:

is_alpaca % git add input/
is_alpaca % git status 
On branch experiment-1
Changes to be committed:
  (use "git restore --staged <file>..." to unstage)
	new file:   input/.lakefs_ref.yaml

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
	modified:   .gitignore

We can see that the .gitignore file changed, and that the files we cloned from lakeFS into the input directory are not tracked by git. This is intentional - remember that lakeFS is the one managing the data. But wait, what is this special input/.lakefs_ref.yaml file that Git does track?

is_alpaca % cat input/.lakefs_ref.yaml

src: lakefs://is-alpaca/experiment-1/dataset/train/s
at_head: 589f87704418c6bac80c5a6fc1b52c245af347b9ad1ea8d06597e4437fae4ca3

This file includes the lakeFS version of the data that the Git repository is currently pointing to.

Let’s commit the changes to Git with:

git commit -m "added is_alpaca dataset" 

By committing to Git, we tie the current code version of the model to the dataset version in lakeFS as it appears in input/.lakefs_ref.yaml.

Experiment and Version Results

We ran the train script on the cloned input, and it generated a model. Now, let’s use the model to predict whether an axolotl is an alpaca.

A reminder - this is how an axolotl looks like - not like an alpaca!

axolotl

Here are the (surprising) results:

is_alpaca % ./predict.py ~/axolotl1.jpeg
{'alpaca': 0.32112, 'not alpaca': 0.07260383}

We expected the model to provide a more concise prediction, so let’s try to improve it. To do that, we will add additional images of axolotls to the model input directory:

is_alpaca % cp ~/axolotls_images/* input/not_alpaca

To inspect what changes we made to out dataset we will use lakectl local status.

is_alpaca % lakectl local status input 
diff 'local:///ml_models/is_alpaca/input' <--> 'lakefs://is-alpaca/589f87704418c6bac80c5a6fc1b52c245af347b9ad1ea8d06597e4437fae4ca3/dataset/train/'...
diff 'lakefs://is-alpaca/589f87704418c6bac80c5a6fc1b52c245af347b9ad1ea8d06597e4437fae4ca3/dataset/train/' <--> 'lakefs://is-alpaca/experiment-1/dataset/train/'...

╔════════╦════════╦════════════════════════════╗
║ SOURCE ║ CHANGE ║ PATH                       ║
╠════════╬════════╬════════════════════════════╣
║ local  ║ added  ║ not_alpaca/axolotl2.jpeg ║
║ local  ║ added  ║ not_alpaca/axolotl3.png  ║
║ local  ║ added  ║ not_alpaca/axolotl4.jpeg ║
╚════════╩════════╩════════════════════════════╝

At this point, the dataset changes are not yet tracked by lakeFS. We will validate that by looking at the uncommitted changes area of our experiment branch and verifying it is empty.

To commit these changes to lakeFS we will use lakectl local commit:

is_alpaca % lakectl local commit input -m "add images of axolotls to the training dataset"

Getting branch: experiment-1

diff 'local:///ml_models/is_alpaca/input' <--> 'lakefs://is-alpaca/589f87704418c6bac80c5a6fc1b52c245af347b9ad1ea8d06597e4437fae4ca3/dataset/train/'...
upload not_alpaca/axolotl3.png              ... done! [5.04KB in 679ms]
upload not_alpaca/axolotl2.jpeg             ... done! [38.31KB in 685ms]
upload not_alpaca/axolotl4.jpeg             ... done! [7.70KB in 718ms]

Sync Summary:

Downloaded: 0
Uploaded: 3
Removed: 0

Finished syncing changes. Perform commit on branch...
Commit for branch "experiment-1" completed.

ID: 0b376f01b925a075851bbaffacf104a80de04a43ed7e56054bf54c42d2c8cce6
Message: add images of axolotls to the training dataset
Timestamp: 2024-02-08 17:41:20 +0200 IST
Parents: 589f87704418c6bac80c5a6fc1b52c245af347b9ad1ea8d06597e4437fae4ca3

Looking at the lakeFS UI we can see that the lakeFS commit includes metadata that tells us what was the code version of the linked Git repository at the time of the commit. git metadata in lakeFS

Inspecting the Git repository, we can see that the input/.lakefs_ref.yaml is pointing to the latest lakeFS commit 0b376f01b925a075851bbaffacf104a80de04a43ed7e56054bf54c42d2c8cce6.

We will now re-train our model with the modified dataset and give a try to predict whether an axolotl is an alpaca:

is_alpaca % ./predict.py ~/axolotl1.jpeg
{'alpaca': 0.12443, 'not alpaca': 0.47260383}

Results are indeed more accurate.

Sync a Local Directory with lakeFS

Now that we think that the latest version of our model generates reliable predictions, let’s validate it against a test dataset rather than against a single picture. We will use the test dataset provided by Kaggel. Let’s create a local testDataset directory in our git repository and populate it with the test dataset.

Now, we will use lakectl local init to sync the testDataset directory with our lakeFS repository:

is_alpaca % lakectl local init lakefs://is-alpaca/main/dataset/test/ testDataset 
Location added to /is_alpaca/.gitignore
Successfully linked local directory '/is_alpaca/testDataset' with remote 'lakefs://is-alpaca/main/dataset/test/'

And validate that the directory was linked successfully:

is_alpaca % lakectl local list                                                           
+-------------+-------------------------------------------------+------------------------------------------------------------------+
| DIRECTORY   | REMOTE URI                                      | SYNCED COMMIT                                                    |
+-------------+-------------------------------------------------+------------------------------------------------------------------+
| input       | lakefs://is-alpaca/main/dataset/train/          | 0b376f01b925a075851bbaffacf104a80de04a43ed7e56054bf54c42d2c8cce6 |
| testDataset | lakefs://is-alpaca/main/dataset/test/           | 0b376f01b925a075851bbaffacf104a80de04a43ed7e56054bf54c42d2c8cce6 |
+-------------+-------------------------------------------------+------------------------------------------------------------------+

Now we will tell Git to track the testDataset directory with git add testDataset, and as we saw earlier Git will only track the testDataset/.lakefs_ref.yaml for that directory rather than its content.

To see the difference between our local testDataset directory and its lakeFS location lakefs://is-alpaca/main/dataset/test/ we will use lakectl local status:

is_alpaca % lakectl local status testDataset 

diff 'local:///ml_models/is_alpaca/testDataset' <--> 'lakefs://is-alpaca/0b376f01b925a075851bbaffacf104a80de04a43ed7e56054bf54c42d2c8cce6/dataset/test/'...
diff 'lakefs://is-alpaca/0b376f01b925a075851bbaffacf104a80de04a43ed7e56054bf54c42d2c8cce6/dataset/test/' <--> 'lakefs://is-alpaca/main/dataset/test/'...

╔════════╦════════╦════════════════════════════════╗
║ SOURCE ║ CHANGE ║ PATH                           ║
╠════════╬════════╬════════════════════════════════╣
║ local  ║ added  ║ alpaca/alpaca (1).jpg          ║
║ local  ║ added  ║ alpaca/alpaca (10).jpg         ║
    .        .                  .
    .        .                  .
    .        .                  .local  ║ added  ║ not_alpaca/not_alpaca (9).jpg  ║
╚════════╩════════╩════════════════════════════════╝

We can see that multiple files were locally added to the synced directory.

To apply these changes to lakeFS we will commit them:

is_alpaca % lakectl local commit testDataset -m "add is_alpaca test dataset to lakeFS" 

Getting branch: experiment-1

diff 'local:///ml_models/is_alpaca/testDataset' <--> 'lakefs://is-alpaca/0b376f01b925a075851bbaffacf104a80de04a43ed7e56054bf54c42d2c8cce6/dataset/test/'...
upload alpaca/alpaca (23).jpg            ... done! [113.81KB in 1.241s]
upload alpaca/alpaca (26).jpg            ... done! [102.74KB in 1.4s]
          .                                             .
          .                                             .
upload not_alpaca/not_alpaca (42).jpg    ... done! [886.93KB in 14.336s]

Sync Summary:

Downloaded: 0
Uploaded: 77
Removed: 0

Finished syncing changes. Perform commit on branch...
Commit for branch "experiment-1" completed.

ID: c8be7f4f5c13dd2e489ae85e6f747230bfde8e50f9cd9b6af20b2baebfb576cf
Message: add is_alpaca test dataset to lakeFS
Timestamp: 2024-02-10 12:31:53 +0200 IST
Parents: 0b376f01b925a075851bbaffacf104a80de04a43ed7e56054bf54c42d2c8cce6

Looking at the lakFS UI we see that our test data is now available at lakeFS: test_dataset

Finally, we will Git commit the local changes to link between the Git and lakeFS repositories state.

Note: While syncing a local directory with a lakeF prefix, it is recommended to first commit the data to lakeFS and then do a Git commit that will include the changes done to the .lakefs_ref.yaml for the synced directory. Reasoning is that only after committing the data to lakeFS, the .lakefs_ref.yaml file points to a lakeFS commit that includes the added content from the directory.

Reproduce Model Results

What if we wanted to re-run the model that predicted that an axolotl is more likely to be an alpaca? This question translates into the question: “How do I roll back my code and data to the time before we optimized the train dataset?” Which translates to: “What was the Git commit ID at this point?”

Searching our Git log we find this commit:

commit 5403ec29903942b692aabef404598b8dd3577f8a

    added is_alpaca dataset

So, all we have to do now is git checkout 5403ec29903942b692aabef404598b8dd3577f8a and we are good to reproduce the model results!

Checkout our article about ML Data Version Control and Reproducibility at Scale to get another example for how lakeFS and Git work seamlessly together.