Accelerating DNA basecalling of Nanopore reads on FPGAs

Genomics has revolutionized our understanding of evolution, hereditary diseases, and more. The advent of long-read DNA sequencers i.e. Oxford Nanopore Technologies' innovations, has opened many new research potentials in genomics. These sequencers produce significantly longer DNA reads, facilitating novel applications. However, this...

Tydi-Chisel: Collaborative and Interface-Driven Data-Streaming Accelerator Design

In spite of progress on hardware design languages, the design of high-performance hardware accelerators forces many design decisions specializing the interfaces of these accelerators in ways that complicate the understanding of the design and hinder modularity and collaboration. In response to this challenge, Tydi has been presented as an open...

Zero-serialization, Zero-copy memory pooling in compute clusters: Disaggregated memory made accessible

With the rise of the new interconnect standards CXL and previously OpenCAPI, has come a great deal of possibilities to step away from the classical approach where CPUs are in charge of moving data between external devices and local memory. Specifically, OpenCAPI allows for attached devices to directly interface with the host memory bus in a near...

A Toolchain for Streaming Dataflow Accelerator Designs for Big Data Analytics: Defining an IR for Composable Typed Streaming Dataflow Designs

Tydi is an open specification for streaming dataflow designs in digital circuits, allowing designers to express how composite and variable-length data structures are transferred over streams using clear, data-centric types. This provides a higher-level method for defining interfaces between components as opposed to existing bit- and byte-based...

Tydi-lang: a language for typed streaming hardware: A manual for future Tydi-lang compiler developers

Transferring composite data structures with variable-length fields often requires designing non-trivial protocols that are not compatible between hardware designs. When each project designs its own data format and protocols the ability to collaborate between hardware developers is diminished, which is an issue especially in the open-source...

Enabling High Performance Posit Arithmetic Applications Using Hardware Acceleration

The demand for higher precision arithmetic is increasing due to the rapid development of new computing paradigms. The novel posit number representation system, as introduced by John L. Gustafson, claims to be able to provide more accurate answers to mathematical problems with equal or less number of bits compared to the well-established IEEE 754...

An FPGA-based Snappy Decompressor-Filter

New interfaces to interconnect CPUs and accelerators at memory-class bandwidth pose new opportunities and challenges for the design of accelerators. This thesis studies one such accelerator, a decompressor for Parquet files compressed with the Snappy library. Our design targets reconfigurable logic (FPGAs) attached via the open coherent...

Multi-way Hash Join Based on FPGAs

The multi-way hash join is one of the commonly used and time-consuming database operations. Many algorithms have been developed to accelerate this operation, some of which use accelerators such as field programmable gate arrays (FPGAs). However, most of the previous work was focused on computation-intensive operations such as (de)compression,...

Acceleration of the Chan-Vese model for 3D segmentation of tumors in CT scans using GPUs

Segmentation and annotation of tumors in CT scans of the brain is a cumbersome time-consuming task for medical experts. Carefully annotated data can be used to build training data sets for machine learning frameworks, with the ultimate goal to fully automate this process. This thesis focuses on acceleration of the annotation process by...

Acceleration of read alignment with coherent attached FPGA coprocessors

With the advent of Next Generation Sequencing (NGS), the cost of sequencing human DNA has decreased significantly over the past decade. This decrease in cost has attracted a great deal of attention from medical research and is now transitioning to clinical practice. Precision medicine, tailored to a persons's genetic profile, is becoming a...

Evaluation of different storage systems for Apache Spark and Apache Hadoop

Big Data systems have been used for multiple years to solve problems that require scale. A framework takes care of scalability and resiliency issues, and allows the user to focus on relevant computation, in the form of map and reduce functions. In these Big Data systems, we currently see a shift from the traditional use of the Hard Disk Drive ...