Customer story

Dompé Cuts Drug Discovery Workloads from Months to Minutes with MariaDB

Dompé built its Exscalate drug design platform on a MariaDB database cluster that compares trillions of chemical structures, turning workloads that once took months into minutes.

About Dompé

Dompé Farmaceutici is a global bio-pharmaceutical company with a 130-year history of medical innovation. Operating with over 800 employees worldwide, eight production lines, and reporting €776 million in revenue in 2022, the company maintains research and development hubs in Boston and the San Francisco Bay Area.

The Challenge

To accelerate its drug discovery process, Dompé developed Exscalate, an intelligent supercomputing platform for drug design. However, Dompé faced significant bottlenecks in storing and managing the colossal datasets required for this platform. The company needed to process incredibly fast results across a library of trillions of potential chemical structures. Traditional and non-traditional databases failed to meet the stringent size, performance, scalability, and redundancy requirements necessary for the project.

“The co-design approach allowed us to create an extremely high-performance system, developing specific hardware and software components and configurations tailored to our use case… we achieved a 10-fold improvement in the overall efficiency of Dompé’s TCS system.”

Anna Fava

Former Senior Software Engineer, Dompé Farmaceutici S.p.A.

The Solution

Partnering with E4 Computer Engineering and MariaDB, Dompé implemented a highly customized, high-performance computing infrastructure tailored to support Exscalate’s massive workloads.

The custom infrastructure features:

Storage Cluster (4 Nodes): MinIO SW Managed S3 Storage Layer combined with a GPU Chemical Cartridge. Powered by Intel Xeon CPUs (18 Cores, 2.6 GHz), 768 GB RAM, and massive PCI-e NVMe data disks (12.8 TB each).
Database Cluster (3 Nodes): MariaDB ColumnStore DB engine with NVMesh RAM swap. Configured with 1536 GB DDR4 ECC RAM and PCI-e NVMe disks (15.3 TB each) capable of comparing over 2×10^13 molecules instantly.
Management Node: MariaDB MaxScale proxy engine for agile traffic routing.
High-Speed Network: Mellanox NVIDIA redundant switches providing 200 Gb/s per connection.

This hardware foundation supports the Tangible Chemical Space (TCS), the world’s largest virtual ligand library, alongside target databases and molecular docking simulators.

Read the full success story which first published in E4 Computer Engineering, “Exscalate Tangible Chemical Space: Harnessing technology to accelerate the discovery of new drugs.”