TileDB VS ClickHouse

- single cell genomics: in collaboration with the Chan-Zuckerberg Initiative, we recently released TileDB-SOMA for single cell data, with APIs for both Python and R built around a common storage specification: https://tiledb.com/blog/tiledb-101-single-cell

With TileDB, all data — tables, genomics, images, videos, location, time-series — across multiple domains is captured as multi-dimensional arrays. TileDB Cloud implements a totally serverless infrastructure and delivers access control, easier data and code sharing and distributed computing at global scale, eliminating cluster management, minimizing TCO and promoting scientific collaboration and reproducibility.

Website: https://tiledb.com

GitHub: https://github.com/TileDB-Inc/TileDB

Stavros from TileDB here (Founder and CEO). I thought of requesting some feedback from the community on this blog. It was only natural for a multi-dimensional array database like TileDB to offer vector (i.e., 1D array) search capabilities. But the team managed to do it very well and the results surprised us. We are just getting started in this domain and a lot of new algorithms and features are coming up, but the sooner we get feedback the better.

TileDB-Vector-Search Github repo: https://github.com/TileDB-Inc/TileDB-Vector-Search

TileDB-Embedded (core array engine) Github repo: https://github.com/TileDB-Inc/TileDB

TileDB 101: Vector Search (blog to get kickstarted): https://tiledb.com/blog/tiledb-101-vector-search/

TileDB, Inc. | Full-Time | REMOTE | USA | Greece | https://tiledb.com

TileDB is the database for complex data, allowing data scientists, researchers, and analysts to access, analyze, and share any data with any tool at global scale. We have just launched a vector search library leveraging TileDB and TileDB Cloud for powerful local search and seamless scaling to multi-modal organizational datasets and batched computation: https://tiledb.com/blog/why-tiledb-as-a-vector-database

With TileDB, all data — tables, genomics, images, videos, location, time-series — across multiple domains is captured as multi-dimensional arrays. Our vector search library and other offerings are designed to empower these datasets with extreme interoperability via numerous APIs and tool integrations across the data science ecosystem, eliminating the hassles and inefficiencies of data conversion. TileDB Cloud implements a totally serverless infrastructure and delivers access control, easier data and code sharing and distributed computing at global scale, eliminating cluster management, minimizing TCO and promoting scientific collaboration and reproducibility.

TileDB, Inc. | Full-Time | REMOTE | USA | Greece | https://tiledb.com

TileDB transforms the lives of analytics professionals and data scientists with a universal database, allowing them to access, analyze, and share any data with any tool at global scale. TileDB unifies the way we think about data, delivering superior performance and foundational data management capabilities. All data — tables, genomics, images, videos, location, time-series — across multiple domains is captured as multi-dimensional arrays. TileDB offers extreme interoperability via numerous APIs and tool integrations across the data science ecosystem, eliminating the hassles and inefficiencies of data conversion. TileDB Cloud implements a totally serverless infrastructure and delivers access control, easier data and code sharing and distributed computing at global scale, eliminating cluster management, minimizing TCO and promoting scientific collaboration and reproducibility.

TileDB, Inc. was spun out of MIT and Intel Labs in May 2017 and is backed by Two Bear Capital, Nexus Venture Partners, Uncorrelated Ventures, Intel Capital and Big Pi.

Recent HN article: https://news.ycombinator.com/item?id=23896131

Website: https://tiledb.com

GitHub: https://github.com/TileDB-Inc/TileDB

Docs: https://docs.tiledb.com

Blog: https://tiledb.com/blog

Our headquarters are located in Cambridge, MA and we have a subsidiary in Athens, Greece. We offer the ability to work remotely. If you are located outside of the USA and Greece we have options to accommodate this, don't hesitate to apply!

We have several open positions aimed at increasing TileDB’s feature set, growth and adoption. You will have the opportunity to work on innovative technology that creates impact on challenging and exciting problems in Genomics, Geospatial, Time Series, and more. Immediate features on the roadmap for TileDB Cloud include, advanced distributed computations, advanced computation pushdown, improved multi-cloud deployments and more.

We are actively seeking:

- Senior Golang Engineer

- Senior Python Engineer

- Site Reliability Engineer

- React Frontend Engineer

Apply today at https://tiledb.workable.com !

Interesting. Have you come across TileDB before?

https://tiledb.com/

Hi folks, Stavros from TileDB here. Here are my two cents on tabular data. TileDB (Embedded) is a very serious competitor to Parquet, the only other sane choice IMO when it comes to storing large volumes of tabular data (especially when combined with Arrow). Admittedly, we haven’t been advertising TileDB’s tabular capabilities, but that’s only because we were busy with much more challenging applications, such as genomics (population and single-cell), LiDAR, imaging and other very convoluted (from a data format perspective) domains.

Similar to Parquet:

* TileDB is columnar and comes with a lot of compressors, checksum and encryption filters.

* TileDB is built in C++ with multi-threading and vectorization in mind

* TileDB integrates with Arrow, using zero-copy techniques

* TileDB has numerous optimized APIs (C, C++, C#, Python, R, Java, Go)

* TileDB pushes compute down to storage, similar to what Arrow does

Better than Parquet:

* TileDB is multi-dimensional, allowing rapid multi-column conditions

* TileDB builds versioning and time-traveling into the format (no need for Delta Lake, Iceberg, etc)

* TileDB allows for lock-free parallel writes / parallel reads with ACID properties (no need for Delta Lake, Iceberg, etc)

* TileDB can handle more than tables, for example n-dimensional dense arrays (e.g., for imaging, video, etc)

Useful links:

* Github repo (https://github.com/TileDB-Inc/TileDB)

* TileDB Embedded overview (https://tiledb.com/products/tiledb-embedded/)

* Docs (https://docs.tiledb.com/)

* Webinar on why arrays as a universal data model (https://tiledb.com/blog/why-arrays-as-a-universal-data-model)

Happy to hear everyone’s thoughts.

It could be worth checking out TileDB: https://github.com/TileDB-Inc/TileDB The entire system, down to the data format itself, is optimized around storing multi-dimensional arrays. It also supports timestamps and real numbers as dimensions, which could be handy given your example data. [Full disclosure: I currently work for TileDB.]

TileDB, Inc. | Full-Time | REMOTE | USA | Greece | https://tiledb.com

TileDB, Inc. is the company behind TileDB, the first universal data engine. TileDB allows analytics professionals and data scientists to access, analyze, and share complex data sets with any tool at extreme scale. TileDB overcomes the constraints of columnar tables, flat files, and SQL-only tools, handling all data with a multi-dimensional array engine and extreme interoperability across the data science ecosystem. TileDB Cloud is a totally serverless offering of TileDB, which delivers access control and enables distributed computing at planet-scale, eliminating all cluster management and minimizing cost. TileDB, Inc. was spun out of MIT and Intel Labs in May 2017 and closed a $15M Series A in July 2020, following a previous $4M Seed Round.

Recent HN article: https://news.ycombinator.com/item?id=23896131

Website: https://tiledb.com

GitHub: https://github.com/TileDB-Inc/TileDB

Docs: https://docs.tiledb.com

Blog: https://tiledb.com/blog

Our headquarters are located in Cambridge, MA and we have a subsidiary in Athens, Greece. We offer the ability to work remotely, but the candidates must reside either in the US or in Greece. US candidates must be US citizens, whereas Greek candidates must be Greek or EU citizens.

We have several open positions aimed at increasing TileDB’s feature set, growth and adoption. You will have the opportunity to work on innovative technology that creates impact on challenging and exciting problems in Genomics, Geospatial, Time Series, and more. A few features on the roadmap include enhancing our TileDB Cloud offering, optimizing our serverless framework, improving integration with JupyterLab, and expanding our marketplace functionality.

We are primarily seeking:

- Senior Golang Engineer

Apply today at https://tiledb.workable.com !

Yes, we are working on it! :) Taking some of the learnings from current experimental JSON Object datatype, we are now working on what will become the production-ready implementation. Details here: https://github.com/ClickHouse/ClickHouse/issues/54864

Variant datatype is already available as experimental in 24.1, Dynamic datatype is WIP (PR almost ready), and JSON datatype is next up. Check out the latest comment on that issue with how the Dynamic datatype will work: https://github.com/ClickHouse/ClickHouse/issues/54864#issuec...

In our repository, I've set up a few hard limits: each translation unit cannot spend more than a certain amount of memory for compilation and a certain amount of CPU time, and the compiled binary has to be not larger than a certain size.

When these limits are reached, the CI stops working, and we have to remove the bloat: https://github.com/ClickHouse/ClickHouse/issues/61121

Although these limits are too generous as of today: for example, the maximum CPU time to compile a translation unit is set to 1000 seconds, and the memory limit is 5 GB, which is ridiculously high.

I have a project dedicated to this topic: https://github.com/ClickHouse/ClickBench

It is important to explain the limitations of a benchmark, provide a methodology, and make it reproducible. It also has to be simple enough, otherwise it will not be realistic to include a large number of participants.

I'm also collecting all database benchmarks I could find: https://github.com/ClickHouse/ClickHouse/issues/22398

ClickHouse: A fast open-source column-oriented database management system. ClickHouse is designed for real-time analytics on large datasets and excels in high-speed data insertion and querying, making it ideal for real-time monitoring and reporting.

Today we're going to create an UDF (User-defined Function) in Golang that can be run inside Clickhouse query, this function will parse uuid v1 and return timestamp of it since Clickhouse doesn't have this function for now. Inspired from the python version with TabSeparated delimiter (since it's easiest to parse), UDF in Clickhouse will read line by line (each row is each line, and each text separated with tab is each column/cell value):

For the third, examples here might be analytics plugins in specialized databases like Clickhouse, data-transformations in places like your ETL pipeline using Airflow or Fivetran, or special integrations in your authentication workflow with Auth0 hooks and rules.

Online analytical processing (OLAP) databases like Apache Druid, Apache Pinot, and ClickHouse shine in addressing user-initiated analytical queries. You might write a query to analyze historical data to find the most-clicked products over the past month efficiently using OLAP databases. When contrasting with streaming databases, they may not be optimized for incremental computation, leading to challenges in maintaining the freshness of results. The query in the streaming database focuses on recent data, making it suitable for continuous monitoring. Using streaming databases, you can run queries like finding the top 10 sold products where the “top 10 product list” might change in real-time.

Proton is a lightweight streaming processing "add-on" for ClickHouse, and we are making these delta parts as standalone as possible. Meanwhile contributing back to the ClickHouse community can also help a lot.

Please check this PR from the proton team: https://github.com/ClickHouse/ClickHouse/pull/54870

curl https://clickhouse.com/ | sh

But I continue to find garbage in some of our CI scripts.

Here is an example: https://github.com/ClickHouse/ClickHouse/pull/58794/files

The right way is to:

- always pin versions of all packages;