Working with S3¶

This is a simple guide that demonstrates how to use TileDB on S3-compatible backends. We will first explain how to set up an AWS account and configure TileDB for AWS S3, and then show how to set up and use minio locally.

After setting up TileDB to work with AWS S3 or minio, your TileDB programs will function properly without any API change! All you need to do is, instead of using local file system paths when creating/accessing groups, arrays, key-value stores, and VFS files, use URIs that start with s3://. For instance, if you wish to create (and subsequently write/read) an array on S3, you use URI s3://<your-bucket>/<your-array-name> for the array name.

AWS¶

First, we need to set up an AWS account and generate access keys.

Create a new AWS account.
Visit the AWS console and sign in.
On the AWS console, click on the Services drop-down menu and select Storage->S3. You can create S3 buckets there.
On the AWS console, click on the Services drop-down menu and select Security, Identity & Compliance->IAM.
Click on Users from the left-hand side menu, and then click on the Add User button. Provide the email or username of the user you wish to add, select the Programmatic Access checkbox and click on Next: Permissions.
Click on the Attach existing policies directly button, search for the S3-related policies and add the policy of your choice (e.g., full-access, read-only, etc.). Click on Next and then Create User.
Upon successful creation, the next page will show the user along with two keys: Access key ID and Secret access key. Write down both these keys.

8a. Export these keys to your environment from a console:

Linux / macOS

export AWS_ACCESS_KEY_ID=<your-access-key-id>
export AWS_SECRET_ACCESS_KEY=<your-secret-access-key>

Windows (PS)

$env:AWS_ACCESS_KEY_ID = "<your-access-key-id>"
$env:AWS_SECRET_ACCESS_KEY = "<your-secret-access-key>"

Windows (cmd.exe)

set AWS_ACCESS_KEY_ID=<your-access-key-id>
set AWS_SECRET_ACCESS_KEY=<your-secret-access-key>

8b. Or, set the following keys in a configuration object:

TileDB AWS S3 access settings¶
Parameter	Default Value
`"vfs.s3.aws_access_key_id"`	`""`
`"vfs.s3.aws_secret_access_key"`	`""`

Now you are ready to start writing TileDB programs! When creating a TileDB context or a VFS object, you need to set up a configuration object with the following parameters for AWS S3 (supposing that your S3 buckets are on region us-east- - you can set an arbitrary region).

TileDB AWS S3 config settings¶
Parameter	Value
`"vfs.s3.scheme"`	`"https"`
`"vfs.s3.region"`	`"us-east-1"`
`"vfs.s3.endpoint_override"`	`""`
`"vfs.s3.use_virtual_addressing"`	`"true"`

Note

The above configuration parameters are currently set as shown in TileDB by default. However, we suggest to always check whether the default values are the desired ones for your application.

GCS¶

Warning

TileDB GCS support is experimental. Our test suite passes and we have done limited experiments with large arrays; however, we have not used GCS extensively and recommend thoroughly testing writes up to the largest expected object sizes.

TileDB supports the Google Cloud Storage S3 compatibility mode. GCS S3 compatibility does not support multipart uploads, therefore we have added a configuration option to disable multipart uploads and use single PutObject requests instead. Uploads in this mode may be slower than comparable operations using AWS S3. Currently, vfs.s3.multipart_part_size should be set to a value larger than the expected file size, up to available memory or backend limits (the maximum object size for GCS is 5 TB).

TileDB GCS config settings¶
Parameter	Value
`"vfs.s3.region"`	`"(region must be configured!)"`
`"vfs.s3.use_multipart_upload"`	`"false"`
`"vfs.s3.multipart_part_size"`	`5000000000000`
`"vfs.s3.max_parallel_ops"`	`1`

minio¶

minio is a lightweight S3-compliant object-store. Although it has many nice features, here we focus only on local deployment, which is very useful if you wish to quickly test your TileDB-S3 programs locally. See the minio quickstart guide for installation instructions. Here is what we do to run minio on port 9999:

$ mkdir -p /tmp/minio-data
$ docker run -e MINIO_ACCESS_KEY=minio -e MINIO_SECRET_KEY=miniosecretkey \
      -d -p 9999:9000 minio/minio server /tmp/minio-data
$ export AWS_ACCESS_KEY_ID=minio
$ export AWS_SECRET_ACCESS_KEY=miniosecretkey

Once you get minio server running, you need to set the S3 configurations as follows (below, <port> stands for the port on which you are running the minio server, equal to 9999 if you run the minio docker as shown above):

TileDB minio S3 config settings¶
Parameter	Value
`"vfs.s3.scheme"`	`"http"`
`"vfs.s3.region"`	`""`
`"vfs.s3.endpoint_override"`	`"localhost:<port>"`
`"vfs.s3.use_virtual_addressing"`	`"false"`

Physical Organization on S3¶

So far we explained that a TileDB array, key-value store or group are stored as directories in local storage. There is no directory concept on S3 and other similar object stores. However, S3 uses character / in the object URIs which allows the same conceptual organization as a directory hierarchy in local storage. At a physical level, TileDB stores on S3 all the files it would create locally as objects. For instance, for array s3://bucket/path/to/array, TileDB creates array schema object s3://bucket/path/to/array/__array_schema.tdb, fragment metadata object s3://bucket/path/to/array/<fragment>/__fragment_metadata.tdb, and similarly all the other files/objects. Since there is no notion of a “directory” on S3, nothing special is persisted on S3 for directories, e.g., s3://bucket/path/to/array/<fragment>/ does not exist as an object.

The AWS S3 CLI allows you to sync (i.e., download) the S3 objects having a common URI prefix to local storage, organizing them into a directory hierarchy based on the use of / in the object URIs. This makes it very easy to clone TileDB arrays, key-value stores or entire groups locally from S3. For instance, given an array my_array you created and wrote on an S3 bucket my_bucket, you can clone it locally to an array my_local_array with the following command from your console:

$ aws s3 sync s3://my_bucket/my_array my_local_array

After downloading an array locally, your TileDB program will function properly by changing the array name from s3://my_bucket/my_array to my_local_array, without any other modification.

S3 performance¶

TileDB writes the various fragment files as append-only objects using the multi-part upload API of the AWS C++ SDK. In addition to enabling appends, this API renders the TileDB writes to S3 particularly amenable to optimizations via parallelization. Since TileDB updates arrays only by writing (appending to) new files (i.e., it never updates a file in-place), TileDB does not need to download entire objects, update them, and re-upload them to S3. This leads to excellent write performance.

TileDB reads utilize the range GET request API of the AWS SDK, which retrieves only the requested (contiguous) bytes from a file/object, rather than downloading the entire file from the cloud. This results in extremely fast subarray reads, especially because of the array tiling. Recall that a tile (which groups cell values that are stored contiguously in the file) is the atomic unit of IO. The range GET API enables reading each tile from S3 in a single request. Finally, TileDB performs all reads in parallel using multiple threads, which is a tunable configuration parameter.

See Introduction to Performance for more information on TileDB performance and how to optimize it.