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Migrate Vector Data from PostgreSQL to MyScale

Update (2023-10-17): Check out our new blog post Comparing MyScale with Postgres and OpenSearch: An Exploration into Integrated Vector Databases (opens new window) for a comprehensive comparison between MyScale and PostgreSQL.

The rapid growth of AI and ML applications, particularly those involving large-scale data analysis, has increased demand for vector databases that can efficiently store, index, and query vector embeddings. Therefore, vector databases like MyScale, Pinecone, and Qdrant continue to be developed and expanded to meet these requirements.

At the same time, traditional databases continue to improve their vector data storage and retrieval capabilities. For instance, the well-known relational database PostgreSQL and its pgvector extension (opens new window) provide similar functionality, albeit less effectively than a well-optimized vector database.

There are significant differences in performance, accuracy, and other aspects when using a general-purpose database like PostgreSQL. These differences can lead to bottlenecks in performance and data scale. To address these issues, upgrading to a more efficient vector database like MyScale is recommended.

What sets MyScale apart from other specialized vector databases is its ability to provide full SQL support without compromising on high performance. This makes the migration process from PostgreSQL to MyScale much smoother and simpler.

To add value to this statement, let’s consider a use case where we have vector data stored in a PostgreSQL database but have performance and data scale bottlenecks. Therefore, as a solution, we have decided to upgrade to MyScale.

# Migrate Data From PostgreSQL to MyScale

A core part of upgrading to MyScale from PostgreSQL is to migrate the data from the old to the new database. Let's look at how this is done.

Note:

To demonstrate how to migrate data from PostgreSQL to MyScale, we must set up both databases even though our use case notes that we already have vector data in a PostgreSQL database.

Before we begin, it's important to note that we will use the following environments and datasets:

# Environments

Database Tier DB Version Extension Version
PostgreSQL on Supabase (opens new window) Free (up to 500MB database space) 15.1 pgvector 4.0
MyScale (opens new window) Development (up to 5 million 768-dimensional vectors) 0.10.0.0

# Dataset

We used the first 1M rows (1,000,448 rows exactly) from the LAION-400-MILLION OPEN DATASET (opens new window) for this exercise to demonstrate a scenario where the data scale continues to increase after migration.

Note:

This dataset has 400 million entries, each consisting of a 512-dimensional vector.

# Load the Data into PostgreSQL

If you already know about PostgreSQL and pgvector, you can skip ahead to the migration process by clicking here.

The first step is to load the data into a PostgreSQL database by working through the following step-by-step guide:

# Create PostgreSQL Database and Set Environment Variables

Create a PostgreSQL instance with pgvector in Supabase as follows:

  • Navigate to the Supabase website (opens new window) and log in.
  • Create an organization and name it.
  • Wait for the organization and its database to be created.
  • Enable the pgvector extension.

The following GIF describes this process further.

Create PostgreSQL using Supabase

Once the PostgreSQL database has been created and pgvector enabled, the next step is to configure the following three environment variables to establish the connection to PostgreSQL using psql:

export PGHOST=db.qwbcctzfbpmzmvdnqfmj.supabase.co
export PGUSER=postgres
export PGPASSWORD='********'

Additionally, run the following script to increase the memory and request duration limits, making sure any SQL queries we run are not interrupted:

$ psql -c "SET maintenance_work_mem='300MB';"
SET
$ psql -c "SET work_mem='350MB';"
SET
$ psql -c "SET statement_timeout=4800000;"
SET
$ psql -c "ALTER ROLE postgres SET statement_timeout=4800000;";
ALTER ROLE

# Create a PostgreSQL Data Table

Execute the following SQL statement to create a PostgreSQL data table. Ensure both the vector columns (text_embedding and image_embedding) are of type vector(512).

Note:

The vector columns must be consistent with our data's vector dimensions.

$ psql -c "CREATE TABLE laion_dataset (
    id serial,
    url character varying(2048) null,
    caption character varying(2048) null,
    similarity float null,
    image_embedding vector(512) not null,
    text_embedding vector(512) not null,
    constraint laion_dataset_not_null_pkey primary key (id)
);"

# Insert the Data Into the PostgreSQL Table

Insert the data in batches of 500K rows.

Note:

We have only inserted the first set of 500K rows to test how successfully the data was inserted before adding the rest.

$ wget https://myscale-datasets.s3.ap-southeast-1.amazonaws.com/laion_dataset.sql.tar.gz
$ tar -zxvf laion_dataset.sql.tar.gz
$ cd laion_dataset
$ psql < laion_dataset_id_lt500K.sql
INSERT 0 1000
INSERT 0 1000
INSERT 0 1000
INSERT 0 1000
INSERT 0 1000
...

# Build an ANN Index

The next step is to create an index that uses Approximate Nearest Neighbor search (ANN).

Note:

Set the lists parameter to 1000 as the expected number of rows in the data table is 1M rows. (https://github.com/pgvector/pgvector#indexing (opens new window))

$ psql -c "CREATE INDEX ON laion_dataset 
  USING ivfflat (image_embedding vector_cosine_ops) 
  WITH (lists = 1000);";
CREATE INDEX

# Run a SQL Query

The last step is to test that everything works by executing the following SQL statement:

$ psql -c "SET ivfflat.probes = 100;
  SELECT id, url, caption, image_embedding <=> (SELECT image_embedding FROM laion_dataset WHERE id=14358) AS dist 
  FROM laion_dataset WHERE id!=14358 ORDER BY dist ASC LIMIT 10;"

If your result set looks like ours, we can proceed.

id url caption dist
134746 Pretty Ragdoll cat on white background Royalty Free Stock Image 0.0749262628626345
195973 cat sitting in front and looking at camera isolated on white background Stock Photo 0.0929287358264965
83158 Abyssinian Cat Pictures 0.105731256045087
432425 Russian blue kitten Stock Images 0.108455925228164
99628 Norwegian Forest Cat on white background. Show champion black and white Norwegian Forest Cat, on white background royalty free stock image 0.111603095925331
478216 himalayan cat: Cat isolated over white background 0.115501832572401
281881 Sealpoint Ragdoll lying on white background Stock Images 0.121348724151614
497148 Frightened black kitten standing in front of white background 0.127657010206311
490374 Lying russian blue cat Stock Photo 0.129595023570348
401134 Maine coon cat on pastel pink Stock Image 0.130214431419139

# Insert the Rest of the Data

Add the rest of the data to the PostgreSQL table. This is important to validate the performance of pgvector at scale.

$ psql < laion_dataset_id_ge500K_lt1m.sql
INSERT 0 1000
INSERT 0 1000
INSERT 0 1000
INSERT 0 1000
...
ERROR: cannot execute INSERT in a read-only transaction
ERROR: cannot execute INSERT in a read-only transaction

As you can see from this script's output (and the following image), inserting the rest of the data returns errors. Supabase sets the PostgreSQL instance to read-only mode, preventing storage consumption beyond its free tier limits.

overflowed supabase store size

Note:

Only 500K rows have been inserted into the PostgreSQL table and not 1M rows.

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# Migrate to MyScale

Let's now migrate the data to MyScale by following the step-by-step guide described below:

Note:

Not only is MyScale an high-performant integrated vector database, but benchmarking reports that MyScale can outperform other specialized vector databases with respect to search performance, accuracy, and resource utilization. MyScale's proprietary vector indexing algorithm, Multi-Scale Tree Graph (MSTG), utilizes local NVMe SSD as a cache disk, significantly increasing the supported index scale when compared to in-memory situations.

# Create a MyScale Cluster

The first step is to create and launch a new MyScale cluster.

The following image describes this process further:

creating myscale cluster

# Create a Data Table

Once the cluster is running, execute the following SQL script to create a new database table:

CREATE TABLE laion_dataset
(
    `id` Int64,
    `url` String,
    `caption` String,
    `similarity` Nullable(Float32),
    `image_embedding` Array(Float32),
     CONSTRAINT check_length CHECK length(image_embedding) = 512,
    `text_embedding` Array(Float32),
     CONSTRAINT check_length CHECK length(text_embedding) = 512
)
ENGINE = MergeTree
ORDER BY id;

# Migrating Data from PostgreSQL

When you have created the database table, use the PostgreSQL() table engine (opens new window) to migrate the data from PostgreSQL easily.

INSERT INTO default.laion_dataset 
SELECT id, url, caption, similarity, image_embedding, text_embedding 
FROM PostgreSQL('db.qwbcctzfbpmzmvdnqfmj.supabase.co:5432',
    'postgres', 'laion_dataset',
    'postgres', '************') 
SETTINGS min_insert_block_size_rows=65505;

Note:

The setting min_insert_block_size_rows is added to limit the number of rows inserted per batch, preventing excessive memory usage.

# Confirm the Total Number of Rows Inserted

Use the SELECT count(*) statement to confirm whether all the data has migrated to MyScale from the PostgreSQL table.

SELECT count(*) FROM default.laion_dataset;

The following result set shows the migration is successful because this query returns 500K (500000) rows.

count()
500000

# Build Database Table Index

The next step is to build an index with the index type MSTG and metric_type (distance calculation method) as cosine.

ALTER TABLE default.laion_dataset 
ADD VECTOR INDEX laion_dataset_vector_idx image_embedding 
TYPE MSTG('metric_type=cosine');

Once this ALTER TABLE statement has finished executing, the next step is to check the index's status. Run the following script and if the status returns as Built, the index was successfully created.

SELECT database, table, type, status FROM system.vector_indices;
database table type status
default laion_dataset MSTG Built

# Execute an ANN Query

Run the following script to execute an ANN query using the MSTG index we have just created.

SELECT id, url, caption, 
distance('alpha=4')(image_embedding, 
    (SELECT image_embedding FROM laion_dataset WHERE id=14358) 
) AS dist 
FROM default.laion_dataset where id!=14358 ORDER BY dist ASC LIMIT 10;

If the following result table is consistent with the results from the PostgreSQL query, our data migration is successful.

id url caption dist
134746 Pretty Ragdoll cat on white background Royalty Free Stock Image 0.0749262628626345
195973 cat sitting in front and looking at camera isolated on white background 0.0929287358264965
83158 Abyssinian Cat Pictures 0.105731256045087
432425 Russian blue kitten Stock Images 0.108455925228164
99628 Norwegian Forest Cat on white background. Show champion black and white... 0.111603095925331
478216 himalayan cat: Cat isolated over white background 0.115501832572401
281881 Sealpoint Ragdoll lying on white background Stock Images 0.121348724151614
497148 Frightened black kitten standing in front of white background 0.127657010206311
490374 Lying russian blue cat Stock Photo 0.129595023570348
401134 Maine coon cat on pastel pink Stock Image 0.130214431419139
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# Insert the Rest of the Data Into the MyScale table

Let's add the rest of the data to the MyScale table.

# Import Data from CSV/Parquet

The good news is that we can import the data directly from the Amazon S3 bucket using the following MyScale method:

INSERT INTO laion_dataset 
SELECT * FROM s3(
'https://myscale-datasets.s3.ap-southeast-1.amazonaws.com/laion-1m-pic-vector.csv',
'CSV', 
'id Int64, url String, caption String, similarity Nullable(Float32), image_embedding Array(Float32), text_embedding Array(Float32)')  
WHERE id >= 500000 SETTINGS min_insert_block_size_rows=65505;

This automates the data insertion process, reducing the time spent manually adding the rows in 500K batches.

# Confirm the Total Number of Rows Inserted

Once again, run the following SELECT count(*) statement to confirm whether all the data from the S3 bucket has been imported into MyScale.

SELECT count(*) FROM default.laion_dataset;

The following result set shows that the correct number of rows have been imported.

count()
1000448

Note:

The free pod of MyScale can store a total of 5M 768-dimensional vectors.

# Execute an ANN Query

We can use the same SQL query as we used above to perform queries on a dataset of 1M rows.

To refresh your memory, here is the SQL statement again:

SELECT id, url, caption, distance('alpha=4')(image_embedding,
    (SELECT image_embedding FROM laion_dataset WHERE id=14358)) AS dist 
FROM default.laion_dataset WHERE id!=14358 ORDER BY dist ASC LIMIT 10;

Here is the query result set, including the newly-added data:

id url caption dist
134746 Pretty Ragdoll cat on white background Royalty Free Stock Image 0.07492614
195973 cat sitting in front and looking at camera isolated on white background Stock Photo 0.09292877
693487 Russian Blue cat, mysterious cat, friendly cat, Frances Simpson, cat breeds, cats breed 0.09316337
574275 Mixed-breed cat, Felis catus, 6 months old Royalty Free Stock Photo 0.09820753
83158 Abyssinian Cat Pictures 0.10573125
797777 Male Cat Names For Orange Cats 0.10775411
432425 Russian blue kitten Stock Images 0.10845572
99628 Norwegian Forest Cat on white background. Show champion black and white... 0.1116029
864554 Rear view of a Maine Coon kitten sitting, looking up, 4 months old, isolated on white 0.11200631
478216 himalayan cat: Cat isolated over white background 0.11550176

# In Conclusion

This discussion describes how migrating vector data from PostgreSQL to MyScale is straightforward. And even as we increase the data volume in MyScale by migrating data from PostgreSQL and importing new data, MyScale continues to exhibit reliable performance irrespective of the size of the dataset. The colloquial phrase: The bigger, the better, rings true in this regard. MyScale's performance remains reliable even when querying super-large datasets.

Therefore, if your business experiences data scale or performance bottlenecks, we strongly recommend migrating your data to MyScale using the steps outlined in this article.

Migrate Data From PostgreSQL to MyScale
Environments
Dataset
Load the Data into PostgreSQL
Create PostgreSQL Database and Set Environment Variables
Create a PostgreSQL Data Table
Insert the Data Into the PostgreSQL Table
Build an ANN Index
Run a SQL Query
Insert the Rest of the Data
Migrate to MyScale
Create a MyScale Cluster
Create a Data Table
Migrating Data from PostgreSQL
Confirm the Total Number of Rows Inserted
Build Database Table Index
Execute an ANN Query
Insert the Rest of the Data Into the MyScale table
Import Data from CSV/Parquet
Confirm the Total Number of Rows Inserted
Execute an ANN Query
In Conclusion
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